VictorJuiz/thesis huggingface dataset:
Organic field-effect transistor sensors for the selective, in situ detection of chemical and biological analytes [electronic resource]

Organic field-effect transistors (OFETs) are unique platforms for the detection of chemical and biomolecular species. However, in order to define sensitivity for a particular molecule of interest, integration of a receptor group into the device's architecture is necessary. Unfortunately, the direct chemical modification of the organic semiconductor to incorporate specific recognition sites has been demonstrated to diminish the electronic performance of OFETs. To address this issue, we developed a novel OFET sensor platform capable of stable operation in an aqueous environment that permits the selective detection of user-defined analytes. Sensitivity for the targeted analyte is conferred by virtue of an ordered array of gold nanoparticles (AuNPs) decorating the OFET's surface that is deposited through a block-copolymer templating process. This highly versatile platform is compatible with a large, previously existing library of thiolated receptor groups that can functionalize the AuNPs through the well-known gold-thiol (Au--S) linkage. As a proof-of-concept demonstration of chemical detection, we used this platform to demonstrate the highly selective detection of toxic mercury(II) ion in water. We then expanded the sensing capabilities of the AuNP-decorated OFET platform for biodetection applications by demonstrating the selective and highly sensitive detection of thrombin. Using thrombin detection as a model system, we built a comprehensive picture of biodetection with OFETs by performing a thorough and empirical investigation of the effects of varying the pH of the buffer, the average center-to-center distance between the receptor sites, and the ionic strength of the buffer. During this comprehensive investigation, we elucidated that electrostatic screening, caused by operation of the OFET sensors in highly ionic media (mimicking the physiological environment), restricted our ability to observe charge-based detection events. We therefore adapted a traditional enzyme-linked immunosorbent assay (ELISA) to be compatible with electronic readout using an OFET. Using this assay, we demonstrated the multiplexed detection of a panel of three biomarkers in serum at clinically relevant concentrations in order to build a predictive screening tool for preeclampsia, a potentially fatal pregnancy disorder. To take advantage of the full potential offered by these biosensors, we fabricated an inkjet printed OFET sensor capable of detecting the preeclampsia biomarkers in undiluted buffer, revealing that inexpensive, potentially disposable OFET biosensors for point-of-care applications could be a possibility in the near future.

Keywords: Chemical Engineering.
Advisor: Bao Zhenan primary advisor. Thesis advisor
Bent Stacey advisor. Thesis advisor
Dunn Alexander Robert advisor. Thesis advisor
Our Budget is Our Vision: An Analysis of the Clarity and Transparency of the Budgetary Process in San Francisco Unified School District (SFUSD)

Objective: In this study, I investigated the clarity and transparency of the school budgetary process in the San Francisco Unified School District (SFUSD). SFUSD practices school site based budgeting through the involvement of “school site councils” in the budgetary process, comprised of school administrators, teachers, and parents. Method: I surveyed 44 school site council members (Administrators, Parents, Teachers, Staff, and Volunteers) across elementary schools in SFUSD. Participants answered questions regarding their understanding of budgets, the SFUSD budget guide, and the budget-making process. Additionally, I conducted a textual analysis of the school budget documents, assessing their clarity of formatting and content. Results: The participant’s results showed that almost all participants felt they were a “valuable” part of the budgetary process. However, parents and teachers in particular reported lower awareness of available resources in SFUSD, lower general knowledge of the funding process, and lower technical skills. Most parents and teachers did not know about the SFUSD budget guide and indicated they had questions regarding budget-writing (acronyms, funding categories, formatting, etc.). The budgets themselves were unclear without exposure to the SFUSD budget guide. Conclusions: Parents and teachers are invested in the budgetary process and can be more impactful if given additional training, especially around the general funding process and technical skills. In order to make sure training is effective, SFUSD would benefit from stronger, more direct communication between the district and school site council members (eg. parents and teachers). Streamlined communication can improve the clarity and transparency with regards to (1) financial literacy (2) existing guides and workshops and (3) budget details.

Keywords:  Graduate School of Education
School Site Budgeting
School Site Council
Participatory Budgeting
Budgetary Process
Community Engagement
Budget Clarity
Budget Transparency
Stanford University
Graduate School of Education
Thesis
Advisor: Hakuta Kenji
Willinsky John
Moorhead Laura
Oxysterols reveal novel Smoothened regulatory mechanisms in vertebrate Hedgehog signaling [electronic resource]

The Hedgehog pathway is a highly conserved signaling cascade that coordinates embryonic development. Loss of function and aberrant activation of Hedgehog signaling have also been implicated in a variety of pathologies. The membrane protein Smoothened is a central signal transducer in this pathway, but how it is regulated is a longstanding mystery. It has been proposed that Smoothened has an endogenous small molecule ligand that could be regulated by the upstream regulator, Patched. Oxysterols are a class of endogenous cholesterol metabolites that can activate Hedgehog signaling, but their mechanism of action was a mystery. I focused on 20(S)-hydroxycholesterol (20(S)-OHC), the most potent activator out of the panel of oxysterols initially tested. Through pharmacological and biochemical analysis, I found that oxysterols target Smoothened through a site that is distinct from the one most other Smoothened drugs occupy. I went on to map the oxysterol binding site to the extracellular Smoothened cysteine rich domain (CRD). These studies revealed that the Smoothened CRD represents a crucial regulatory module of Smoothened in the context of endogenous signaling through Patched. Through the work presented here, I developed novel chemical tools that have allowed me to identify the mechanism by which oxysterols activate Hedgehog signaling through Smoothened. Most importantly, however, this work has revealed a conserved role for the Smoothened CRD in the regulation of Hedgehog signaling. It remains to be determined whether the Smoothened CRD directly receives a signal from Patched, or whether it plays a more indirect role in regulating signaling levels. Understanding this has important implications for the broader question of how Smoothened is regulated by Patched.

Keywords: Biochemistry.
Advisor: Rohatgi Rajat primary advisor. Thesis advisor
Harbury Pehr advisor. Thesis advisor
Pfeffer Suzanne advisor. Thesis advisor
Parallel measurement of dynamic changes in translation rates in individuals cells [electronic resource] : translational control in cell cycle

The concentration of proteins is regulated by signaling mechanisms that change mRNA levels, the rate of protein degradation or the rate of protein translation. In mammalian cells, overall protein abundance is predominantly controlled at the level of translation; therefore, understanding the translational control is crucial to understand the regulation of protein abundance, a fundamental building block of life. Translational control in metazoan is often very rapid and dynamic process: upon numerous signaling inputs such as nutrients, growth factors, and various stresses, cells quickly convey these signals through downstream signaling pathways to modulate mRNA translation either in sequence specific or nonspecific manner. Nevertheless, it has been challenging to directly monitor mRNA translation in living cells due to the lack of proper methods. In this thesis, we developed a reporter system to measure real-time changes of translation rates in individual cells by conjugating translation translational regulatory motifs to sequence encoding a fluorescent protein and a controllable destabilization domain. Application of the method showed that individual cells undergo marked fluctuations in the translation rate of mRNAs with 5' terminal oligopyrimidine (TOP) motifs that regulate the synthesis of ribosomal proteins. Furthermore, we show that small and medium reductions in amino acid levels signal through different mTOR complex 1 (mTORC1)-mediated non-4EBP and 4EBP signaling pathways, respectively, while large reductions caused an eIF2A-mediated suppression of general translation. We also investigated cell-cycle dependent translational control of TOP mRNAs using our translation reporter system in combination with live cell-cycle reporter. Cells were first aligned by cell-cycle transition points either between G0 and G1 or between G1 and S using Geminin and CDK sensors respectively and relative changes of TOP mRNA translation across the transition points were measured. This study not only showed that TOP mRNA translation were up-regulated during G1, but also showed that the TOP translation peaked in early S phase and decreased toward the late cell cycle phase. Given that TOP mRNA translation directly controls the synthesis of ribosomes and translation machineries, our finding suggested the important regulatory mechanism of cell-size control during cell-cycle progression. In summary, we developed the real-time translation reporter working at the single-cell levels, and have revealed a number of novel translational behaviors, including the fluctuation in the translation rate of TOP mRNA and the possible regulatory mechanism of cell-size control through the up-regulation of TOP mRNA translation.

Keywords: Chemical and Systems Biology.
Advisor: Meyer Tobias primary advisor. Thesis advisor
Elias Joshua advisor. Thesis advisor
Ferrell James Ellsworth advisor. Thesis advisor
Sarnow P. (Peter) advisor. Thesis advisor
Paramagnetic interactions in nuclear magnetic resonance spectroscopy of geologic materials [electronic resource]

This thesis documents the findings and results of our work toward the application of solid-state Nuclear Magnetic Resonance (NMR) spectroscopy to geological materials containing paramagnetic species. Commonly encountered and geologically important paramagnetic species include ions of most of the transition metals and the rare earth elements that have unpaired electrons and will be magnetized in the presence of an external magnetic field. Interactions between the magnetic moments of the paramagnetic ion and the NMR nucleus have important implications for the NMR experiment. Early studies, especially those conducted in the first decade after the wide acceptance of Magic-Angle Spinning NMR (MAS-NMR), pointed out that even modest concentrations of a paramagnetic ion in natural minerals, such as a few % Fe in a feldspar, could cause signal loss and low signal to noise, peak broadening, and "smearing" of the intensity from the isotropic peak to the spinning sidebands with resultant loss of information about chemical shift anisotropy. This early work prompted most solid-state NMR spectroscopists studying geological materials to work almost solely on synthetic non-paramagnetic materials. However, in this work, the argument is advanced that in many cases, valuable structural information can be obtained for paramagnetic geological materials, especially information concerning short-range ordering in solid solutions that cannot be determined using more traditional long-range diffraction techniques. The first two studies presented herein document the presence of distinct paramagnetically shifted NMR resonances in the 27Al and 29Si NMR spectra of two Dora Maira pyrope garnets and in the 31P NMR spectra of a suite of REE3+-bearing synthetic monazite (LaPO4) and xenotime (YPO4). By comparing the number of these peaks and their positions and intensities to the known crystal structures of these materials, peak assignments can be made to specific geometric configurations of the NMR-active atom and the paramagnetic species. Higher quality data for REE3+-beearing synthetic monazite and xenotime are presented later using homogeneous flux-grown material. Peaks related to 31P having more than one neighboring paramagnetic REE3+ are observed and their relative intensities provide evidence of random distributions of cation species in these solid solutions. Additionally, a study is presented on Fe- and Al-bearing MgSiO3 perovskite, an important lower mantle phase. The magnitude of 27Al and 29Si NMR signal loss compared to the concentration of Fe in these materials provides strong evidence of short-range ordering of charge-balancing Fe3+ and Al3+.

Keywords: Geological and Environmental Sciences.
Advisor: Stebbins Jonathan Farwell primary advisor. Thesis advisor
Brown G. E. (Gordon E.)
Mao Wendy (Wendy Li-wen) advisor. Thesis advisor
Particle accelerator on a wafer [electronic resource] : demonstration of electron acceleration and diagnostics with microstructures

Particle accelerators are synonymous with massive scientific instruments reserved for national laboratories, universities, or other large research facilities. At the same time, they are also an essential tool for the advancement of science and technology, playing a key role in multiple fields from high-energy physics to radiation oncology. In some ways, the size and inaccessibility of the particle accelerator today is very much akin to the computer in the 1940s or the laser in the 1960s. While particle accelerators firmly remain an expensive and specialized instrument, both the computer and the laser have evolved into compact, affordable, everyday devices which permeate all aspects of the modern world. In this thesis, we present an approach to particle acceleration, which could move particle accelerators along a similar path to commercialization as the computer and the laser. To achieve this, we leverage the semiconductor manufacturing techniques developed by the computer industry to fabricate dielectric accelerator structures, which are then powered by the latest in laser technology. We've named our approach the Dielectric Laser-driven Accelerator (DLA).

Keywords: Applied Physics.
Advisor: Byer R. L. (Robert L.)
Raubenheimer Tor O. advisor. Thesis advisor
Ruth Ronald D. advisor. Thesis advisor
Path to Fluency: Motivation in Puerto Rican Students to Develop their English Language Skills

The role of the English language in Puerto Rico has been a controversial topic for the past few decades. Even though English is taught in schools as a second language and is one of the official languages in the island, many people are not learning English. Many scholars claim that people are not learning English due to differing attitudes towards the language; however, most of this research presented by these scholars has been performed on adults. This study therefore looks into the different motivations that elementary Puerto Rican students have when learning English in schools. One hundred and five students were given a survey that asked about their different uses and exposure to English. I primarily addressed the following question in the course of this study: what motivates students to exert effort and seek opportunities to develop their English skills? Research results show that students’ efforts towards learning English in the classroom and the extent to which they use the language outside of the classroom are predictable by different motivations, such as motivations coming from external forces, motivations towards seeing English as an important instrument for their future, and the value they place in learning English. The exposure to English in students’ families was also highly correlated to how much effort students exert in learning English in the classroom.

Keywords: English learning
Puerto Rico
motivation
language motivation
effort
second language
English in Puerto Rico
Thesis
Advisor: Valdes Guadalupe
Stipek Deborah
Paths toward lower cost, high efficiency thin film solar cells [electronic resource]

The cost of modern high efficiency wafer-based solar cells is driven in part by poor materials utilization of the absorber materials. Solar cells made from thin film absorbers attached to inexpensive support substrates potentially offer reduced materials costs compared to wafer-based devices; however, conventional processes for producing thin film absorber layers on amorphous or polycrystalline substrates result in amorphous or polycrystalline films, which, due to a high degree of crystalline imperfection, suffer from reduced carrier lifetime due to Shockley-Read-Hall recombination. Here, I present work I have done on ion-beam-assisted deposition, environmentally-assisted cracking induced epitaxial liftoff, and laser liftoff of epitaxial GaAs thin films, as potential pathways for the scalable production of absorber materials for lower cost, high efficiency thin film solar cells. Additionally, I discuss multiple concepts in X-ray diffraction and Reflected High Energy Electron Diffraction that are used extensively throughout this work to investigate the atomic structure of thin films.

Keywords: Materials Science and Engineering.
Advisor: Clemens Bruce A.
Salleo Alberto
McGehee Michael
Patterns of the earth [electronic resource] : writing geography in early medieval China

This study explores the first flourishing of geographical writing in China during the early medieval period (ca. 200--600 CE). It examines the reasons for the initial emergence of geographical writing, its development of new spatial conceptualizations, and the cultural work that it accomplished. The dissertation argues that dramatic shifts in the political, demographic, and religious landscape of this distinctive period of imperial fragmentation inspired a re-evaluation of classical geographic notions of a monolithic China at the center of the world. Since this once substantial body of texts has now been lost, I rely primarily upon the sole extant comprehensive geography from the period, Li Daoyuan's Shuijing zhu (Commentary on the Classic of Waterways), as well as other fragmentary remnants of other texts and retrospective accounts from the seventh century, to piece together the evidence. I also employ Geographic Information Systems (GIS) in a spatial analysis of these texts. My findings reveal an emic spatial representation of China that runs contrary to the official orthodoxy of a court-centered, Sino-centric imperial geography. These sources manifest a culturally subversive spatial model that prioritized environmental over political geography, emphasized regional over imperial cohesiveness, and displaced China from the center of the world.

Keywords: History.
Advisor: Lewis Mark primary advisor. Thesis advisor
Dien Albert E. advisor. Thesis advisor
Sommer Matthew Harvey
Wigen Kären
Peeling back the label [electronic resource] : studies of educational opportunity among students learning English

This dissertation examines the educational opportunities and resulting outcomes of the fastest growing official subgroup of students in U.S. schools, students learning English. Using quantitative methodologies, longitudinal data from a large, urban school district in California, and drawing upon sociological theory on educational stratification, immigration, language, race and ethnicity, and labeling, the dissertation is comprised of three main analyses. The first analysis examines the reclassification patterns of Latino English learner students, identifying not only the median amount of time it takes to reclassify but, importantly, what proportion of students reclassify by the end of elementary, middle, and high school, and how these reclassification patterns differ based on students' instructional environment (English immersion, transitional bilingual, maintenance bilingual, and dual immersion). The second analysis examines English learner students' access to core content in middle school both descriptively and quasi-experimentally. The third analysis turns to look at the long-term effects of classification as an English learner on achievement. In summary, this dissertation addresses an issue of enormous importance in education today: the highly inequitable outcomes of students learning English. The dissertation explores key aspects of the educational opportunities afforded to English learners, the causal outcomes of those opportunities, and, importantly, the malleable factors that can improve the opportunities and outcomes of students learning English.

Keywords: Education.
Advisor: Reardon Sean F. primary advisor. Thesis advisor
Carnoy Martin advisor. Thesis advisor
Goldenberg Claude
Hakuta Kenji advisor. Thesis advisor
Jiménez Tomás R. (Tomás Roberto)
Peer effects within homeowner adoption of solar-PV panels [electronic resource] : a case-control study of three Northern California cities

What motivates homeowners to install solar-photovoltaic (PV) panels on their roofs? In particular, how significant is it if a homeowner knows another homeowner who's already done it? In this case-control study of PV adopters and non-adopters from San Francisco, San Jose, and Fresno, I collected economic, environmental, and social information from nearly 200 homeowners in order to answer these questions. Outside of PV adoption, I found PV adopters to behave no more environmentally than do PV non-adopters. With regards to economic considerations, PV adoption is best predicted by whether the homeowner's expected PV electricity rate is less than his current PG& E electricity average rate. Concerning social influences, a homeowner who knows one more PV adopter than does the average homeowner has a probability of PV adoption that is two- to three-times that of the average homeowner. Driving this peer effect is an amplification of the environmental benefits of PV panels, not the acquisition of new or improved information. Policies that leverage this peer effect may serve as effective complements to traditional subsidization policies.

Advisor: Granovetter Mark S. primary advisor. Thesis advisor
McAdam Doug primary advisor. Thesis advisor
Reardon Sean F. advisor. Thesis advisor
Pension Obligations: A Threat to Fiscal Stability?

Using state pension data from 2001-2011, this paper explores the relationship between unfunded liabilities and demographic, fiscal, and political variables. Many have blamed the current decline in pension funding on poor market returns during the Great Recession and the “.com” bubble before that. Others claim that pension funds are just poorly managed. While the latter may be true, I show that investment returns cannot fully account for the change in funding ratio. In fact the mean compound return over this time period stands in stark contrast to the decline in the mean funding ratio. I argue that political and legal factors are responsible for inadequate contributions to pension funds. Furthermore, I show that pension funding is correlated with state debt and many categories of state spending.

Keywords:  Department of Economics
public pensions
unfunded liabilities
state government
politics
debt
finance
investment
Stanford Department of Economics
Thesis
Advisor: Boskin Michael