VictorJuiz/thesis huggingface dataset:
Seeding survival: The value of school gardens in under-resourced communities in Cape Town

Amid the growing effort in environmental education to foster links between children and nature, school gardens are one focus of increasing attention. Research on school gardens suggests positive outcomes for students in academic achievement, personal development, health and nutrition, community development, and environmental attitudes. Although the World Bank categorizes South Africa as an upper-middle income country, the country remains plagued by stark disparities in quality of life, health and education. Because of the aforementioned benefits, under-resourced areas of South Africa would seem to benefit from school garden programs, yet evidence from research and practice indicate that school gardens may be expensive and challenging to maintain. This tension raises a question: are school gardens worth the financial and human resources required to create and maintain them? This study addresses this tension by asking: in what ways do teachers, principals and caretakers in under-resourced schools in Cape Town value school gardens? The data were collected through interviews with 44 teachers, principals, and caretakers from 7 schools. Findings suggest that interviewees valued the following, in decreasing order of salience: teaching students skills to grow food, immediate and long-term nutrition, academic achievement, and environmental education-related outcomes. Participants also suggested that school gardens are one of the only places for students to gain certain experiences and skills. The data constellated around one theme: the garden spoke to the importance of greater self-sufficiency for all involved. In this way, the school gardens, helped conceptions of environmental education to converge with everyday living. These findings call attention to the diverse values held by school communities and provide insight into the future implementation, design, and framing of school gardens in South Africa and beyond.

Keywords: school garden
environmental education
nutrition
garden-based learning
youth development
self-sufficiency
Cape Town
Thesis
Advisor: Ardoin Nicole M
Seismic collapse risk assessment of buildings [electronic resource] : effects of intensity measure selection and computational approach

Life safety and collapse prevention have always been primary goals of earthquake engineering. Although the collapse risk of structures has not been explicitly quantified until recently, interest in doing so has risen significantly. A primary reason for this is the advent of performance-based earthquake engineering, which considers uncertainties in the seismic hazard and structural response and seeks to engineer structures that will achieve a desired level of performance in terms of expected monetary losses, downtime and casualties. Collapse risk assessment of a structure involves combining information about the seismic hazard at the site with the behavior of the structure. Typically an intensity measure (IM) is used to describe the level of ground motion shaking and quantify the seismic hazard. The behavior of the structure is then characterized through nonlinear response history analysis by subjecting the structure to many different ground motions at various intensity levels. A collapse fragility curve, which describes how the probability of collapse increases as a function of the ground motion intensity, is constructed based on analysis results and combined with the seismic hazard curve to compute the mean annual frequency of collapse. This dissertation focuses on evaluating the effects of IM selection and computational approach on the computed collapse risk, and contributions are made in the following areas: (1) quantifying the uncertainty in the collapse risk estimate due to the number of ground motions used in structural analysis; (2) characterizing the ability of different IMs to efficiently predict structural collapse and provide reliable estimates of the collapse risk; (3) explaining why certain IMs perform better than others with respect to the previous point; and (4) because the spectral acceleration averaged over a period range has been identified as a promising IM for collapse risk assessment, providing recommendations on the period ranges that maximize the efficiency of this IM as a function of structural properties.

Advisor: Miranda Eduardo (Miranda Mijares) primary advisor. Thesis advisor
Baker Jack W. advisor. Thesis advisor
Lignos Dimitrios
Seismic hazard analysis using the ambient seismic field [electronic resource]

With the recent occurrence of unexpectedly large earthquakes, seismic hazard analysis is now at a critical point, for which ground motion prediction is a key element. Traditionally, ground motion intensity is predicted using the empirical ground motion prediction equations, relations developed from observed ground motion measurements. There is a clear shortage of data for large events at short distances, and seismologists increasingly turn to physics based approaches to simulate ground shaking. Ground motion prediction is commonly divided into three main components: source characterization, wave propagation through a three-dimensional crustal structure, and non-linear site response. Each of these represents a challenging research endeavor, with significant source of uncertainty. In this thesis, I develop the foundation for using ambient-noise seismology to predict ground motion, and apply the methods I build to data in California and Japan. The cross-correlation of the ambient noise recorded simultaneously at two seismic stations has similar properties to the Green's function between the two stations. In this thesis, I develop techniques for robust estimation of reliable Green's functions. Once stable Green's functions are obtained, I use a newly established surface-wave eigen problem solver to correct the surface impulse response for source depth and mechanism to construct a virtual earthquake. I validate the virtual earthquake seismograms against data from nearby moderate earthquakes and demonstrate that strong basin amplification occurs at the same locations in both data sets. I expand the virtual point sources to extended ruptures and characterize the Los Angeles sedimentary basin amplification sensitivity to M7+ scenarios on the San Andreas Fault. In Japan, I use the ambient seismic field Green's functions to characterize basin resonance, identify virtual sources that have for strong shaking potential and recover detailed and complex wave propagation effects due to the basin structure that affect seismic amplification in central Tokyo. This thesis demonstrates the powerful opportunities that weak signals like the ambient seismic field bring to seismic hazard analysis, and gives rise to new research questions that will contribute to improve our understanding of the seismic hazard in populated areas.

Keywords: Prieto, Germán A., 1979-
Geophysics.
Advisor: Beroza Gregory C. (Gregory Christian) primary advisor. Thesis advisor
Dunham Eric advisor. Thesis advisor
The semantics of syntactic choice an analysis of English emotion verbs [electronic resource]

Psychological verbs ('`psych-verbs'') such as admire, amaze, fear, and frighten, have long been known to exhibit marked syntactic behavior in many languages. This behavior has inspired numerous analyses which assume that there is a unified explanation for the observed patterns. In this dissertation, I focus on the more problematic class of psych-verbs, the so-called Object-Experiencer (Obj-Exp) verbs (e.g. amaze, depress, frighten, fascinate) and argue, as some others have, that the explanation for their unusual character is primarily semantic in nature, and can be traced back to the ways in which humans conceptualize psychological events and processes. It is commonly argued that the special behavior of these verbs obtains only in their stative and/or more controversially non-agentive readings. Through qualitative and quantitative analyses of the semantic properties of Obj-Exp verbs and their arguments, I explore a controversial topic in previous research: the interaction of stativity and passivization among different subclasses of Obj-Exp verbs in English. Analysis of corpus data shows that eventive and stative uses are available to all Obj-Exp verbs in both the active and passive. I show that the choice between active and passive uses is particularly sensitive to the causal role of the stimulus and the nature of the emotion denoted by the verb; together these determine the linguistic construal of the situation as either a causative process or an attitudinal state. Additionally, I examine the variable (un-)acceptability of English Obj-Exp verbs in agentive contexts, and offer experimental and corpus data showing that a given verb's acceptability in an agentive context directly correlates with the tendency for its emotion to be iv associated with a controllable antecedent. These facts argue against analyzing differences in agentivity among psych-verbs at the level of lexical semantic structure, and instead suggest treating agentivity as an inference arising from the total integration of semantic, syntactic, and contextual information in the clause. Overall, the findings of these linguistic studies align well with recent theories developed in the psychological literature on emotion.

Keywords: Linguistics.
Advisor: Levin Beth primary advisor. Thesis advisor
Bresnan Joan advisor. Thesis advisor
Wasow Thomas advisor. Thesis advisor
Sensing conformational dynamics of single trapped proteins in solution [electronic resource]

Proteins are macromolecular nanomachines that perform a wide variety of essential functions in living organisms. Distinct types of proteins in the cell serve as molecular sensors and signalers, sunlight-harvesting antennas and transducers, molecular motors for transport and metabolic energy storage, and oxidizers and reducers of physiological metal ions, to name a few. To achieve these complex functions, proteins are not static building blocks, but instead adopt multiple conformations in distinct functional states. These functions are inherently dynamic, meaning that methods capable of resolving dynamic behavior are necessary to fully elucidate protein function. Many bulk fluorescence methods have been used to study proteins by averaging together the signals from many copies of the same protein. However, such methods fail to capture distributions in protein conformations (e.g. mixtures of active and inactive states) and unsynchronized dynamics among these conformations (e.g. transition rates from inactive to active states under various conditions). Single-molecule fluorescence spectroscopy of proteins, on the other hand, allows direct observation of distributions and dynamics by watching only one protein at a time. In particular, a special device known as the Anti-Brownian ELectrokinetic (ABEL) trap can hold single fluorescently labeled proteins in solution for several seconds of spectroscopic observation without surface attachment, encapsulation, or the use of large beads. The ABEL trap combines fluorescence-based position estimation obtained by scanning a laser spot with the application of electrokinetic feedback forces to counter the Brownian motion of single proteins, one at a time. In this Dissertation I will describe my use of the ABEL trap technique to study dynamics of a variety of biomolecules, with emphasis on two proteins: the [beta]2-adrenergic receptor ([beta]2AR), an essential cellular signaling protein, and the peridinin-chlorophyll-protein (PCP), a sunlight-harvesting pigment-protein complex found in algae. In [beta]2AR, I observed a shift in protein conformation and in time scales of protein dynamics upon binding of an activating drug. In PCP, I observed two distinct classes of conformational change, indicating light-induced conformational flexibility, which may play a physiological role. Ongoing projects include resolving conformational substeps in FoF1 ATP synthase and measuring electron transfer kinetics of the multicopper oxidase Fet3p.

Keywords: Physics.
Advisor: Burchat P. (Patricia) primary advisor. Thesis advisor
Moerner W. E. (William Esco)
Das Rhiju
Kobilka Brian K. advisor. Thesis advisor
Serine integrases for non-viral gene & [and] cell therapy [electronic resource]

The "integrase" enzyme of the bacterial virus phiC31 mediates the unidirectional fusion of the phiC31 and host-bacterium genomes. This recombination reaction occurs between two specific DNA sequences (att-sites), and can be performed by the enzyme without accessory factors in a wide variety of cellular environments, including human cells. Although its primary application to date in eukaryotes has been in organisms where the native phiC31 integrase (C31-int) att-sites have been pre-introduced, C31-int can also function on certain endogenous sequences (pseudosites) in animal genomes, albeit with significantly reduced activity. The ability of C31-int to perform pseudosite integration has made it the focus of several whole-animal and tissue-culture gene-therapy studies over the past decade, as there is currently no means to safely maintain the therapeutic DNA that is delivered for gene-therapy. The focus of my graduate work has been to assist these efforts to apply C31-int for gene-therapy. Specifically, I have sought to increase our basic scientific understanding of DNA recognition by C31-int through deletion and chimera studies (Chapters 2-3), and I have also attempted to improve the implementation of C31-int applications in mammals through my contributions to applied C31-int projects (Chapters 4-6). The results from my deletion and chimera studies have helped to clarify that C31-int employs DNA binding domains that are largely modular and have also helped to lay the groundwork for a potential means to derive serine integrases with novel specificities. The results from my contributions to applied C31-int projects have made it possible to reverse the wild-type reaction in mammalian cells (Chapter 4), to produce high-quality mouse induced-pluripotent-stem cells (iPSC) with C31-int (Chapter 5), and to genetically engineer mouse iPSCs (Chapter 6). Although C31-int will still require significant engineering before it is suitable for use in human gene therapy, and although additional work will be required to fully realize the potential of our iPSC-production and -engineering scheme in human cells, my experience with C31-int and related enzymes that I describe in this dissertation has left me optimistic that these are not unreasonable goals.

Keywords: Genetics.
Advisor: Calos Michele P. primary advisor. Thesis advisor
Wu Joseph Ching-Ming
Cherry Joe Michael advisor. Thesis advisor
Pringle John R.
Show me your listening position [electronic resource] : embodied silence and speech in a second grade class of language-minority students

Previous scholarship identifies silence as one of the most pervasive yet least analyzed communicative behaviors in U.S. classrooms. Most studies of classroom interaction focus solely on verbal communication. In contrast, this study examines the silences that accompany the speech of language-minority students as well as the circumstances that contribute to silence or create space for talk. Its findings demonstrate that although silence is commonly thought of as an absence of speech, in this class silence had a palpable presence. The findings identify and categorize different silence types and subtypes, which accomplished different kinds of interactive and sociocultural work. Finally, the study illustrates how listening for silence can reveal insights about talk as well as how participants attend to knowledge and learning.

Keywords: Education.
Advisor: McDermott Ray (Raymond Patrick)
Valdés Guadalupe primary advisor. Thesis advisor
Goldenberg Claude
Inoue Miyako
Signal processing and pattern recognition for nocturnal polysomnography sleep studies [electronic resource]

In this dissertation, I show how signal estimation and classification techniques, combined with visual interaction and receiver operating characteristics (ROC) studies, a commonly used statistical analysis method, can be used to investigate polysomnography (PSG) based sleep studies (and measures) from large, diverse populations for genetic, medical, and clinically relevant purposes. I do this by considering four problems currently faced by the sleep research community and developing the signal processing, classification, optimization, and visualization measures needed for each. These problems include: (1) improving diagnostic criteria for narcolepsy using clinical and PSG measures; (2) selecting electroencephalogram (EEG) power spectral density phenotypes for genome wide association (GWAS) (3) dependably detecting and classifying periodic leg movements (PLM) in sleep; (4) measuring rapid eye movements in patients with post traumatic stress disorder and major depressive disorder. ROC theory was extended and a combinatorial, iteratively bounded search method presented and used to optimize diagnostic testing (both parameter cutpoints and configuration) in a tool we called softROC. The Stanford EEG Viewer (SEV), a MATLAB toolbox, is developed to graphically analyze individual sleep studies and automate analysis of collections of sleep studies. The SEV provided the framework necessary to develop and optimize a new PLM classification algorithm, which implements a novel two pass, variable threshold calculation base on the current noise floor calculation. This algorithm was validated using human scored PLM data from a healthy cohort and a cohort with known sleep disorders. Time locked analysis of PLM with respiratory events illuminated the prevalence of PLM apart from respiratory events. I provide empirical evidence for improving PLM measures that are currently being put into clinical practice. Lastly, several eye movement algorithms are evaluated and a new tracking approach is developed which uses a wavelet denoised signal estimate of movement using two ocular channels (horizontal and vertical). Eye movements are characterized by activity and position and examined progressively by sleep cycle and elapsed sleep in combat veterans across four consecutive sleep studies.

Keywords: Electrical Engineering.
Advisor: Mignot Emmanuel
Shenoy Krishna V. (Krishna Vaughn) advisor. Thesis advisor
Widrow Bernard
Woodward Steven (Steven H.) advisor. Thesis advisor
Signal transduction in cardiovascular biology [electronic resource]

The cardiovascular system provides blood circulation throughout the body and is essential for our survival. The major components of the circuitry—the heart, the valves, and the vasculature—require precise signaling events for their prenatal morphogenesis and postnatal homeostasis. Here, we describe the role of cell signaling in cardiovascular biology. In the arterial system, VEGF/Vegfr-2 signaling is essential for vascular remodeling. A pulse of VEGF/Vegfr-2 signaling in the vascular adventitia within hours after vascular injury activates Sca1+ tissue stem cells to differentiate into adventitial and neointimal cells, forming the neointima that occludes the vessel. In the myocardium, calcineurin/NFAT signaling controls cardiac fiber orientation and the expression of dystrophin, a-dystrobrevin, and utrophin—components of the dystrophin glycoprotein complex frequently found abnormal in patients with Duchenne, Becker, or other muscular dystrophies. Deletion of calcineurin in the myocardium results in cardiomyopathy, a phenotype similar to that observed in Duchenne muscular dystrophy patients. In the secondary heart field, calcineurin/NFATc1 signaling is required for semilunar valve morphogenesis. Conditional ablation of calcineurin or NFATc1 causes regression of heart valve primordium, leading to complete absence of the aortic and pulmonic valves, severe valve regurgitation, and perinatal lethality. These studies demonstrate novel functions and molecular mechanisms of cell signaling in three facets of cardiovascular biology.

Advisor: Axelrod Jeffrey (Jeffrey David)
Graves Edward (Edward Elliot)
Koong Albert
Lipsick Joseph Steven
Silicon photonics for optical interconnects, sensing and electron acceleration [electronic resource]

Silicon photonics has been extensively studied in recent years due to its compatibility with electronics and its potential for a wide range of applications. As three applications of this tremendous potential, we attempt to implement silicon photonic devices on standard silicon wafers with CMOS compatible technology that is well suited for optical interconnects, optical sensing and laser electron acceleration applications. We have demonstrated low loss silicon waveguides from standard silicon wafers, eliminating the need for silicon-on-insulator (SOI) wafers. The fabricated silicon waveguides show low propagation loss and oval shape, which have comparable loss to existing low loss SOI channel waveguides (2-3 dB/cm). This silicon photonic technology can be further expanded to fabricate multi-layered photonic devices for 3D photonics. Our fabrication methods simplify integration of photonics and electronics and show promise for the implementation of optical interconnects in standard silicon wafers. In addition to applications in optical interconnects targeted to solve the interconnect bottleneck, our silicon photonic technology can be applied to integrated optical sensors for temperature, chemical and biological signals. By using the air cladding method, we have demonstrated waveguide Bragg reflectors that generate asymmetric Fano resonances. Sensitive to changes in refractive index, these Bragg reflectors can measure environmental changes by two mechanisms: spectral shifts and spectral shape changes. We have demonstrated integrated temperature sensors based on the spectral shifts with sensitivity of 77pm/oC, comparable to the theoretical limit of the devices. Another important application of my silicon photonics research is a cost-effective, integrated laser driven electron accelerator (SLAC-on-a-chip) used as an X-ray source. We have designed and fabricated dielectric laser electron accelerators that achieve large accelerating gradients and that can be fabricated using standard silicon wafers and high-aspect-ratio processing technology. Finite-difference-time-domain (FDTD) simulations show that the silicon buried gratings can increase the accelerating factors to more than double those of reported quartz grating accelerators; consequently, silicon buried gratings only require 40% of the input laser fluence to achieve the same accelerating gradient. With a 100fs pulse laser, our silicon buried gratings can achieve a maximum gradient of 1.1 GV/m, indicating that the buried-grating accelerators have potential for numerous electron-accelerator applications.

Keywords: Electrical Engineering.
Advisor: Solgaard Olav primary advisor. Thesis advisor
Howe Roger Thomas advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor