VictorJuiz/thesis huggingface dataset:
Gamma Strength from Quasi-Continuum Lifetimes using 56Fe(p,p')

A new experimental method is presented to normalize the Gamma Strength Function (GSF) using proton-γ coincidences from 56 Fe(p,p’γ) with an excitation dependent variation of the Doppler Shift Attenuation Method where lifetimes of quasi-continuum states delay low-lying γ-ray transitions by an amount inversely proportional to the GSF magnitude. The E-∆E scintillator array Phoswich Wall measures proton energies which designate initial nuclear excitation energy. The γ-ray tracking spectrometer GRETINA measures signature γ-ray transitions which designate the fed low-lying level. Doppler shift indicates γ-ray cascade time if comparable to the nuclear stopping time. Results provide the first 56 Fe GSF normalization.

Advisor: Bernstein, Lee A
Van Bibber, Karl A
Scenes, For Two-Channel Fixed Media

This paper is an account of the creative process that resulted in the dissertation for a PhD in music composition, Scenes, a two-channel fixed-media composition of electroacoustic music. The commentary is provided as a supplement to the music composition that forms the primary work carried out for the dissertation./nThe practice of studio composition demands from the composer both the conception and realization of a musical work. The effect of interdisciplinary practice necessitated by these demands informs both technical and aesthetic approaches. Software tools written by the composer with a specific goal of realizing an aesthetic intent provide an insight into the discovery of musical language. Conceived to serve the music, the defining features of the toolset outline the nature of the musical problem that the technology was designed to solve./nThe composition of Scenes is a combination of imagined behaviors, embodied improvisation, and experimentation with tools. Discussion of the novel tools generated for the piece illustrate the aesthetics of Scenes. The first, trajectories, provides kinetic spatialization effects to static sounds. The second, utterance, transforms composer’s vocal improvisations into electroacoustic sound. The tools presented here are not mere sound processing devices, readily available for a particular effect in the music of others. Rather, they are a manifestation of the act of music making, of composition, capable of transforming their author’s ideas based on the lessons learned from their conception and implementation.

Advisor: Melford, Myra
Monitoring Forest Policy from Space

Satellite imagery is an increasingly valuable data source in agricultural and resource economics. It offers credible, consistent, and globally comparable information on landscape-scale changes to the environment; and the supply of the information is accelerating with innovations in satellite technology. This dissertation presents the critical value of satellite imagery for environmental policy evaluation, focusing specifically on deforestation. Tropical deforestation may account for as much as one tenth of net global greenhouse gas emissions each year. Any viable effort to mitigate the impact of climate change must address deforestation. The effective design of forest policy is dependent on reliable impact analysis. Satellites offer a method of direct observation of forest cover loss, rather than incomplete or biased estimates. The dissertation first presents an algorithm to convert raw satellite imagery into a new and novel data source on tropical deforestation. Next, the data are used to explain the counter-intuitive outcomes from a 2012 conservation policy in Indonesia, relying on the spatial detail afforded by the new data. Finally, a set of empirical results describe the relationship of deforestation to interest rates, commodity prices, and other economic variables, using the temporal detail afforded by the new data. Together, these case studies demonstrate the effective use of a new data source in direct and credible policy analysis for natural resource economics.

Advisor: Auffhammer, Maximilian
FCC Ti

Investigation of FCC Ti in TEM Foils Formed Under Three Separate Conditions/nby/nRachel E. Traylor/nDoctor of Philosophy in Materials Science and Engineering/nUniversity of California, Berkeley/nProfessor Andrew M. Minor, Chair/nA hexagonal-close packed (HCP) to face-centered cubic (FCC) phase transition has been observed in freestanding alpha-titanium thin foils under three separate conditions: Type I – upon focused ion beam (FIB) irradiation, Type II – during in situ heating in a transmission electron microscope (TEM), and Type III – during in situ TEM straining. FCC Ti has not been anticipated based on the equilibrium phase diagram, however, all FCC Ti phases were found to be stable after formation under ambient conditions. Investigations into the chemical nature of these anomalous FCC Ti phases have revealed that FIB-induced FCC Ti is actually a form of titanium hydride while thermally-induced is more closely related to oxygen contamination. Strain-induced FCC Ti is neither a hydride nor an oxide and readily undergoes FCC deformation twinning under an applied load. In situ TEM experimentation coupled with high-resolution nanobeam diffraction of titanium foils has suggested that this anomalous phase transformation is facilitated by HCP a-type dislocation nucleation, dissociation into partials, and propagation. For different reasons (primarily due to hydrogen, oxygen, and aluminum solutes for the type I, II, and III FCC investigations, respectively) it was suspected that HCP (not FCC) deformation twinning was suppressed in all samples where an HCP to FCC transformation was initiated. In addition, all TEM samples containing FCC Ti precipitates experienced stresses along the <0001>HCP in some form. Therefore, it is proposed that the series of transformations observed in the strain induced FCC Ti; HCP-to-FCC, and FCC-to-FCC twin help accommodate strains along the <0001>HCP when deformation twinning and (c+a) dislocation slip are not available.

Advisor: Minor, Andrew M
The Molecular Mechanisms of Mechanosensitive Neural Stem Cell Differentiation

Until recently, adult mammals were not believed to maintain active neurogenesis into adulthood, and brains were thought to be fully formed and most-mitotic by the end of adolescence. However, it has recently been appreciated that continuous neurogenesis in mammals occurs in the subventricular and subgranular zones of the brain, and the ongoing process of neurogenesis has ramifications for mammalian learning, memory formation, and diseases such as Alzheimer's. They also serve as a potential reservoir for transplantation or stimulation therapies, where stem cells can repopulate and repair areas of the central nervous system damaged by disease or injury. However, in order to harness the potential of these cells and to understand the processes of learning and memory in mammals, we must first understand the deep molecular identities and pathways that govern stem cell fate specification and behavior. A growing body of literature has identified many factors that influence neural stem cell (NSC) differentiation, which includes soluble signals such as sonic hedgehog or VEGF or cell-cell signals such as Notch and ephrins. However, in addition to biochemical cues, mechanical properties of the stem cell niche such as substrate stiffness have also been found to contribute strongly to NSC fate specification./nA panel of studies were undertaken in order to determine the biological relevance of substrate stffness in NSC differentiation. We used atomic force microscopy to probe the natural stiffness variations and heterogeneities in the brain matrix, and then used these measurements to guide the synthesis of a dynamic, mechanically tunable hydrogel that allows for dynamic control of substrate stiffness. With this study, we identify a candidate molecular, YAP, that transduces information about extracellular elastic modulus to fate specification pathways within the cell – specifically, β-catenin. We then expand our model into a three-dimensional platform, and identify another signaling pathway critical for neurogenesis – CD44, a hyaluronan receptor molecule./nThese discoveries improve our understanding of basic NSC mechanobiology, and reveal new target pathways for modulation in generating in vitro culture platforms or engineering NSCs for transplantation or stimulation therapies.

Advisor: Schaffer, David V
Kumar, Sanjay
Performance Approaches to Semantics in Human Language

Over the course of human history, prominent hypotheses for the source of human behavioral uniqueness have included freedom from metaphysical necessity, rational intention, and strong social altruism. However, when applied to questions concerning the evolution and current use of human language, these hypotheses generate more problems than they solve. These include everything from the statistical improbability of "hopeful monster" mutations to the unstable strategy of altruism without reciprocity. Adopting a performative view of human language removes these problematic dependencies, and explains aspects of language like phatic speech, fossils, and register, that require special pleading by one or more of the popular hypotheses./nThis thesis provides two pieces of computational evidence for a performative view of human language. First, it shows that the possibility space of human language is much smaller than expected for a rule based but otherwise semantically unrestricted communication system. Second, it shows that the semantic information contained in an entire speech act is poorly predicted by the semantic information of its individual parts, as might be expected for a compositional system designed for efficient communication./nTo conduct this second analysis, a novel method was developed based on the distributional theory of semantics for measuring the information content of human speech. Briefly, it is a measure of the distance between the distribution of terms in a language and the conditional probability of their appearance within a context of interest. This same method shows promise for testing other hypotheses about the nature and origin of language that involve an informational component.

Advisor: Deacon, Terrence
Simultaneous Coding of Microscopic and Macroscopic Features of Touch in Mouse Somatosensory Cortex

The cerebral cortex is thought to generate sensory experience and facilitate broadly integrative processing used in attention, decision making, and learning. A major goal in neuroscience is to understand how neurons in cortex interact to represent sensory change in the world. Rodents use whiskers to actively palpate their surroundings and gather tactile information. While it is known that rodents can discriminate different textures using whisker input, how the whisker system encodes local spatial features, like shape, is not well understood./nFor many perceptual tasks rodents must pay attention to whisker input in order to extract relevant sensory information. Neural oscillations (gamma) may indicate attentive brain states, and Chapter 2 explores how sensory experience may shape the brain’s ability to generate these rhythms. Superficial layers of primary somatosensory cortex (S1) showed a profound reduction in recurrent inhibition after sensory deprivation, as well as a sharp reduction in spontaneous and evoked gamma oscillations. These findings suggest cortical rhythms change with sensory experience in a recurrent inhibition-dependent manner./nHow the whisker system encodes spatial features, like shape is unknown. In Chapter 3 we describe an experiment designed to study basic elements of shape encoding, using a set of tactile gratings. We trained mice to discriminate smooth surfaces from rough surfaces composed of raised gratings or sandpaper. High-speed whisker imaging revealed that stick-slip micromotions clustered on discrete grating ridges, evoking spatially and temporally precise spikes in S1. At the same time, slip-responsive neurons also responded to whisker contact and texture, forming an overlapping population of tactile feature responses. Mean firing rate was higher on rough surfaces due to stick-slip-evoked spikes, and by weighting individual units we could accurately predict rough vs. smooth trials from neural activity alone. Surprisingly, 20% of neurons showed selectivity among rough textures, including tuning for specific gratings. Thus, S1 neurons simultaneously coded microscopic and macroscopic features of touch during active palpation of tactile gratings.

Advisor: Feldman, Daniel E
Human Cytomegalovirus and Small RNAs

With a genome size of 230–240 kb, human cytomegalovirus (HCMV) has the largest genome in the human herpes virus family. Once the hosts are infected with HCMV, HCMV remains latent throughout the lifetime, but the latent infection can be reactivated when the host is immunocompromised. The infection symptom is mild or subclinical diseases in immunocompetent adults, but HCMV infection leads to severe, life-threatening complications in people who are immunocompromised, including AIDS patients and transplant recipients. While there’s no vaccine available for HCMV infection, understanding the nature of HCMV replication, latency, and transmission is crucial for preventing and curing the disease./nHere we discussed the relationship between various small RNAs and HCMV. In the first part of the study, we examined one viral encoded micro RNA, HCMV-mir-UL22A*, and its influence on HCMV viral infection. We investigated the mechanism of blunt-end HCMV-mir-UL22A* inhibition of HCMV viral replication. The rapid and long lasting suppression of viral replication by blunt-end HCMV-mir-UL22A* suggests blunt-end HCMV-mir-UL22A* a promising antiviral agent. Furthermore, we studied the stagger-end HCMV-mir-UL22A* in regulating host innate immune response. Stagger-end HCMV-mir-UL22A* targets innate immune sensors and facilitate HCMV evade host innate immune response during viral infection. Blunt-end HCMV-mir-UL22A* showed potential for treating CMV infection, while stagger-end HCMV-mir-UL22A* helped us understand HCMV viral innate immune evasion strategy./nIn the second part of the study, we focused on applying RNA based precise gene editing technology to treat HCMV infection. Curing CMV infection requires disruption of the viral genome by novel gene editing technology. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system is a gene editing tool for the site-specific cleavage of DNA. We adapted CRISPR/Cas9 system in CMV infected cells. CRISPR/Cas9 could suppress HCMV and MCMV infection in vitro in cell model. Our study suggests CRISPR/Cas9 can potentially be applied to treat CMV infection.

Advisor: Liu, Fenyong
Contribution of the Exit Mechanism Extrusion in Chlamydia trachomatis Pathogenesis

Chlamydia trachomatis is an obligate intracellular bacterium that is a public health burden worldwide. The precise strategies that intracellular pathogens use to exit host cells have a direct impact on their ability to disseminate within a host, transmit to new hosts, and manipulate immune responses. Chlamydia exits the host cell by two distinct strategies, lysis and extrusion. Lysis is a sequential rupture of vacuole, nuclear and plasma membranes, culminating in the release of free infectious bacteria. Extrusion is a packaged release of Chlamydia that begins with invagination of the chlamydial inclusion, followed by the pinching of the cell plasma membrane, resulting in a double membrane compartment containing Chlamydia, chlamydial inclusion, host cell cytoplasm, and host plasma membrane./nHost cytokinesis proteins are required for the pinching of the chlamydial inclusion just prior to extrusion, but deeper mechanistic understanding of the host requirements that govern the final severing of the extrusion from the host cell have yet to be elucidated. Abscission, the final stage of cytokinesis that severs two daughter cells, is governed largely by the ESCRT-III family of proteins, which also participate in virus budding. Here, we define a role for host abscission proteins in the release of extrusion from the host cell./nThe defining characteristics of extrusions, and advantages gained by Chlamydia within this unique double-membrane structure are not well understood. Results presented here define extrusions as mostly devoid of host organelles, and containing phosphatidylserine on the outer surface of the extrusion membrane. Results further demonstrate that extrusion is highly conserved across Chlamydiae. Extrusions also served as transient, intracellular-like niches for enhanced Chlamydia survival outside the host cell. In addition to enhanced extracellular survival, extrusions are phagocytosed by primary bone marrow-derived macrophages, after which they provide a protective microenvironment for Chlamydia. Extrusion-derived Chlamydia staved off macrophage-based killing, and culminated in the release of infectious EB. Based on these findings, we propose a model in which extrusions serve as ‘trojan horses’ for Chlamydia, by exploiting macrophages as vehicles for dissemination, immune evasion, and potentially transmission.

Advisor: Stephens, Richard
Hybiske, Kevin
Nonlinear Silicon Photonics: Phase-Matching and Dispersion Engineering

Nonlinear silicon photonics offers on-chip wavelength converters and light emitters based on nonlinear optical effects such as self-phase modulation, four-wave mixing, supercontinuum generation, and stimulated Raman scattering. However, the efficient second harmonic generation has not been demonstrated by silicon-based optical components since group IV materials are centrosymmetric crystals in which the second-order nonlinearity is absent. To solve the problem, we proposed “bimodal phase-matching” for second harmonic generation. A plasmonic particle emits second harmonic radiation, which can be controlled by the shape of the particle. Hence, the plasmonic particle was designed to match the radiation pattern with the higher mode of the waveguide at the wavelength of the second harmonic emission. Besides, the fundamental mode of the waveguide at fundamental wavelength was also matched with the higher order mode of the waveguide at the wavelength of second harmonic. This concept was confirmed by observing built up second harmonic light in suspended silicon nitride waveguides./nAnother challenge in silicon photonics is the demonstration of optical components operating at mid-infrared wavelength. Although mid-infrared silicon photonics is a promising technology for spectroscopy and ultrafast optical telecommunications, the absorption in the buried oxide layer and the dispersion of the waveguide restrict the performance of the mid-infrared optical devices on a silicon chip. Here, we demonstrated mid-infrared supercontinuum generation from a suspended silicon waveguide. The device improved the transmission in the mid-infrared range because the oxide layer was etched and the waveguide was suspended. Furthermore, the waveguide was engineered to have a flat dispersion in the anomalous regime. We fabricated suspended silicon waveguides and measured octave-spanning supercontinuum spectra in the mid-infrared range from the waveguide. The mid-infrared light converter on a silicon chip will pave the way for next generation communication devices and new sensing devices.

Advisor: Zhang, Xiang
Galaxies in the Young Universe: Structures, Masses, and Composition of Star-Forming Galaxies at z~1.5-3

Understanding the physical processes governing galaxy growth and evolution remains an outstanding challenge in astronomy. Constraining these processes requires observations at multiple epochs, but despite exquisite observations of galaxies in the local universe, relatively little is known about galaxies at early times. In the last decade, large photometric surveys have revealed many details about galaxies across the past 10 billion years. However, fully understanding galaxies in the early universe and how they connect to today's galaxy population requires observations of their physical properties through spectroscopy as well as photometry. Recent instrumentation advances have now paved the way for spectroscopic surveys of large samples of distant galaxies, which provide key insights into the earlier phases of galaxy evolution./nIn this dissertation, I use detailed photometric and spectroscopic observations and simulations to investigate the dust content, masses, and kinematic structures of star-forming galaxies at z~1.5-3, near the peak of cosmic star formation. I present results using Hubble Space Telescope (HST) grism observations of an unbiased sample of galaxies at z~1.5 from the 3D-HST survey to measure the relation between nebular and stellar dust attenuation. These constraints on the dust content of distant galaxies enable accurate measurements of star formation rates, and help to characterize the dust distribution in early galaxies./nI also investigate the internal kinematics of galaxies at z~1.5-3 using moderate-resolution near-infrared spectra from the MOSDEF survey with Keck/MOSFIRE together with high spatial-resolution HST imaging. I develop a set of models to measure and interpret kinematics from spectra taken with galaxy-slit misalignments, including galaxies without spatially-resolved spectra. I then use these models to derive independent, dynamical estimates of the galaxy masses, and to constrain the amount of support from ordered versus random motions for hundreds of galaxies with Mstar ~ 10^9 - 10^11.5 Msun. Additionally, I explore the correlation of kinematic structure with other properties and constrain how the dark matter fraction in star-forming galaxies changes over time./nFinally, I use mock observations of galaxies from the high-resolution MassiveFIRE cosmological simulation suite to determine how well intrinsic galaxy sizes and stellar masses are recovered from observations. I also explore the impact of random viewing angles on observed galaxy properties, which has implications for the interpretation of the scatter in galaxy scaling relations.

Advisor: Kriek, Mariska