VictorJuiz/thesis huggingface dataset:
Abiotic and biotic factors affecting light brown apple moth, Epiphyas postvittana, in California

With the increase of globalization, the introduction of exotic species into new regions has become a worldwide threat for biodiversity and agricultural production. However, invasiveness of alien species depends on the extent to which abiotic and biotic factors affect the impact of exotic species in a new region. The Light Brown Apple Moth (LBAM), Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae), is a leafroller native to southeastern Australia that was discovered in California in 2006. At the time of its discovery, little was known about how abiotic and biotic factors might limit its distribution and impact in California and North America. I therefore measured high and low temperature tolerance of LBAM in laboratory studies and found that it exhibited only moderate tolerance of extreme temperatures, which may limit its potential distribution in California and North America. I also monitored LBAM populations in the field and measured parasitism rates over a four year study period to determine the influence of of biotic resistance and to provide baseline population data for use in management decisions. I found that LBAM populations were cyclic or decreasing, had strongly overlapping generations and produced three generations annually in San Francisco and and four in Santa Cruz. The parasitoid assemblage of LBAM in California consisted of many species and parasitism rates were unusually high, but provided no evidence of an ability to regulate LBAM populations. I also found that low density LBAM populations did not exhibit demographic Allee effects, but instead populations of all sizes exhibited strong negative density dependence./nI also studied life history parameters of Meteorus ictericus, the most abundant parasitoid of LBAM in California, and found that it has a number of traits that could account for its dominance in the parasitoid assemblage. It was able to attack and develop in a wide range of host larval instars, had a preference for late larval instars, a female only lifestyle, a low generation time ratio in relation to LBAM, and similar temperature maxima and minima for development. However, M. ictericus exhibited an unusually low lifetime fecundity, which could pose an important constraint on its potential to suppress LBAM populations./nOverall, the results of these studies have provided valuable insights that can be used to better understand the potential geographic distribution of LBAM, and to better inform management decisions. In addition, I suggest that the high level of resistance from resident parasitoids on LBAM in California, in combination with other pest management strategies, could prevent the widespread losses from agricultural crops that were originally anticipated in the United States.

Advisor: Mills, Nicholas J
Some new methods for Hamilton-Jacobi type nonlinear partial differential equations

I present two recent research directions in this dissertation. The first direction is on the study of the Nonlinear Adjoint Method for Hamilton-Jacobi equations, which was introduced recently by Evans [27]. The main feature of this new method consists of the introduction of an additional equation to derive new information about the solutions of the regularized Hamilton-Jacobi equations. More specifically, we linearize the regularized/nHamilton-Jacobi equations first and then introduce the corresponding adjoint equations. Looking at the behavior of the solutions of the adjoint equations and using integration by/nparts techniques, we can prove new estimates, which could not be obtained by previous techniques./nWe use the Nonlinear Adjoint Method to study the eikonal-like Hamilton-Jacobi equations [79], and Aubry-Mather theory in the non convex settings [10]. The latter one is based on joint work with Filippo Cagnetti and Diogo Gomes. We are able to relax the/nconvexity conditions of the Hamiltonians in both situations and achieve some new results./nThe second direction, based on joint work with Hiroyoshi Mitake [69, 68], concerns the study of the properties of viscosity solutions of weakly coupled systems of Hamilton-Jacobi equations. In particular, we are interested in cell problems, large time behavior, and homogenization results of the solutions, which have not been studied much in the literature./nWe obtain homogenization results for weakly coupled systems of Hamilton-Jacobi equations with fast switching rates and analyze rigorously the initial layers appearing naturally in the systems. Moreover, some properties of the effective Hamiltonian are also derived./nFinally, we study the large time behavior of the solutions of weakly coupled systems of Hamilton-Jacobi equations and prove the results under some specific conditions. The general case is still open up to now.

Advisor: Evans, Lawrence C
From scenes to spikes: understanding vision from the outside in

The human genome (containing around 1E10 bits of information) is unlikely to fully specify the connectivity between neurons in our brains -- such a ``wiring diagram" requires around 1E14 bits. Physiological evidence suggests that the genome instead specifies plasticity rules through which the brain self-organizes in response to experience. As systems neuroscientists, we seek to understand those rules and, by extension, our brains. In this thesis, I will use this approach to study the primary visual cortex (V1) -- the brain region that receives visual inputs from the eyes, via a relay station called the lateral geniculate nucleus. I first study the statistical structure of natural images, which provide the visual experience that shapes V1. Then, I introduce a biophysically motivated model for visual cortex, which adapts to natural image statistics in order to efficiently encode them -- in this case, the neural plasticity rules can be shown to optimize this ``efficient" representation. I then demonstrate that this model can account for several features of V1 physiology, including the features to which V1 neurons respond (``receptive fields"), and the developmental trends in the sparseness of V1 activity. I will conclude that efficient coding models can be implemented within the constraints imposed by the neural substrate, and that efficient coding principles may yield a parsimonious systems-level understanding of visual cortex.

Advisor: DeWeese, Michael R
Thermo-regulation in Pseudomonas syringae: Phenotypes and Genetics

Pseudomonas syringae is an important member of the phyllosphere microbial community and has been studied for many decades both as a model saprophyte, residing epiphytically, and a pathogen, living in the plant apoplast. While much is known about the traits that contribute to P. syringae's success as a phyllosphere microbe, one area that is not well understood, is the contribution of temperature dependent gene regulation, or thermo-regulation, to P. syringae's epiphytic colonization and survival strategies./nFlagellar-mediated motility is a trait conserved among plant-associated Pseudomonads. In P. syringae, motility contributes both to epiphytic colonization and survival, as well as pathogenicity by allowing cells to invade into the leaf interior. We have found that multiple forms of flagellar-mediated motility, including swarming and swimming motility, are thermo-repressed at around 30 °C. Repression of swarming results from reduced expression of both flagellar genes, including flagellin, encoded by fliC, as well genes involved in regulation and biosynthesis of syringafactin, the major surfactant produced by P. syringae B728a. Thermo-regulation of the flagellum is context dependent, being influenced by the nutrient status of the agar, which together with temperature contribute to a heterogeneous swimming phenotype at elevated temperatures. The heterogeneous swimming phenotype may represent a so-called "bet-hedging" strategy, which may be an important strategy for colonization of the leaf surface under varying and unpredictable weather conditions./nInvestigation into the molecular determinants of thermo-regulation revealed several regulators, which are all conserved across the Pseudomonas genus, potentially indicating these are conserved thermo-regulators with in this important group of organisms. flgM as well as fleN were both involved in thermo-regulation of the flagellum. Additionally, fleN appeared to be important for the heterogeneous swimming phenotype, as mutations in Spontaneous Hot Swimming (SHS) mutants, which swim at elevated temperatures with a cool, diffuse swimming phenotype, commonly mapped to this gene, as determined by genome resequencing. Two separate loci, an acyl-CoA dehydrogenase and a nudix hydrolase, together contributed to thermo-regulation of genes involved in the regulation and synthesis of syringafactin. Interestingly, mutations that contributed to thermo-regulation of the flagellum did not affect thermo-regulation of syringafactin, while mutations affecting thermo-regulation of syringafactin did not affect thermo-regulation of the flagellum, indicating that thermo-regulation of these two traits are independently controlled.

Advisor: Lindow, Steven E
Algebraic Structures in Modular q-hypergeometric Series

We will discuss several questions related to q-hypergeometric series and modular functions. Nahm's conjecture is an attempt to answer the question of when a certain q-hypergeometric series can have modularity. With this conjecture as motivation, we will consider a few closely related algebraic objects such as Bloch groups, Y-systems, T-systems, Q-systems, the dilogarithm function and its variants.

Advisor: Borcherds, Richard E.
Searches for Exotic Radio Sources and Intelligent Life on Other Worlds

Here I describe several experiments that explore some of the rarest and most intriguing phenomena in the sky: short duration radio transients and possible electromagnetic emission from advanced extraterrestrial technology. Motivated by new discoveries and new technologies, we have performed, and are performing, some of the most thorough searches for these sources ever attempted. Our experiments include a "fly's eye" search for bright radio pulses at the Allen Telescope Array, commensal searches for extraterrestrial intelligence at the Arecibo Observatory, a targeted search of extrasolar planets for narrow-band radio emission using the Green Bank Telescope and an ongoing effort to discover pulsars in orbit around SgrA*. Although our experiments explore very different physics, they share common tools and techniques, notably a need for high performance digital signal processing. The experiments described here are prime examples of the synergy that exists between science and technology. Aided by dramatic advances in computing technology and the use of commodity components, we have enabled the processing of heretofore unheard of quantities of observational data. By taking advantage of a reusable design paradigm in which instruments do not have to be built from scratch, we have been able to develop new instruments quickly and efficiently. Our experiments are exploring wavelengths and signal types never before searched with high sensitivity, presenting the exciting chance for serendipitous discovery of unexpected phenomena. With an optimistic spirit, we venture into unexplored territory and expect the unexpected./nThis thesis is structured as follows: Chapter 1 presents an introduction to the scientific motivations for our experiments and the tools with which we conduct them, Chapter 2 describes our Fly's Eye Search for short duration radio transients at the Allen Telescope Array, Chapter 3 discusses our ongoing SETI experiments at radio and optical wavelengths and our plans for the future, Chapter 4 describes a 1.1-1.9 GHz search for narrow-band emission from planet candidates identified by the Kepler mission and Chapter 5 details our ongoing search for pulsars near Sgr A*.

Advisor: Bower, Geoffrey C.
Werthimer, Daniel J.
An evaluation of diarrheagenic Escherichia coli survival after ingestion by Tetrahymena sp. and Helicobacter pylori's fate after ingestion by Tetrahymena sp. and Acanthamoeba polyphaga

Diarrheagenic pathotypes of Escherichia coli are responsible for a substantial number of childhood deaths each year, and Helicobacter pylori causes gastric diseases in both children and adults worldwide. Free-living protozoa have been implicated in the survival and transport of pathogens in the environment, but the relationship between non-Shiga toxin-producing E. coli or H. pylori and free-living ciliated protozoa has not been characterized. Likewise, there is a paucity of research regarding the ability of these pathogenic bacteria to survive phagocytosis by amoebae./nA literature review revealed two articles demonstrating survival of E. coli O157:H7 or an environmental isolate of E. coli in Acanthamoeba and one article reporting survival of H. pylori in Acanthamoeba. There have been several reports of E. coli O157:H7 or genetically modified laboratory strains surviving digestion by the ciliate, Tetrahymena, and no investigations on the resistance of H. pylori to digestion by this protozoan./nTherefore, for the present study, six diarrheagenic serotypes of E. coli and an isolate of H. pylori were evaluated for their susceptibility to digestion by Tetrahymena. Escherichia coli and H. pylori were fed separately to Tetrahymena strain MB125, and the ciliate's egested products were examined for viable pathogens. Viability was assessed by the BacLightTM LIVE/DEADTM assay, by a cell elongation method, and by colony counts. Three H. pylori strains were used: one expressing the green fluorescent protein, an ATCC strain originating from a clinical isolate, and a fresh clinical isolate of H. pylori, and each was fed separately to Acanthamoeba polyphaga. Viability of H. pylori in Acanthamoeba was assessed with: the BacLightTM LIVE/DEADTM assay, fluorescent in situ hybridization, and quantification of amplified gene products unique to H. pylori over time, determined by a real time polymerase chain reaction test./nAll six pathogenic E. coli serotypes survived digestion by Tetrahymena and emerged as viable cells in fecal pellets, whereas H. pylori was digested. Growth of E. coli on agar plates indicated that the bacteria were able to replicate after passage through the ciliate. Transmission electron micrographs of E. coli cells as intact rods versus degraded H. pylori cells corroborated these results. Scanning electron microscopy revealed a net-like matrix around intact E. coli cells in fecal pellets. Helicobacter pylori did not survive phagocytosis by Acanthamoeba./nThese results suggest a possible role for Tetrahymena and its egested fecal pellets in the survival and dissemination of diarrheagenic E. coliin the environment. This bacterial-protozoan association may increase opportunities for transmission of these bacterial pathogens to mammalian hosts including humans.

Advisor: Spear, Robert C
Riley, Lee W
Effectiveness of Strain Solutions for Next-Generation MOSFETs

The conventional planar bulk MOSFET is difficult to scale down to sub-20nm gate length, due to the worsening performance variability and short channel effects. Thin body transistors, including Multiple-Gate (FinFET & Tri-Gate FET) and Fully Depleted SOI (FD-SOI) MOSFETs are anticipated to replace the current transistor architecture, and will be used in future CMOS technology nodes. Strained Silicon technology is widely used today to boost planar bulk transistor performance. Thus it's technically important to examine the strain-induced performance enhancement in these thin body transistors, for nanometer scale channel length. A comprehensive study on impact of channel stress on ultra-thin-body FD-SOI MOSFETs is presented. It's found that strain-induced mobility enhancement diminishes with Silicon body thickness scaling below 5nm for electrons, but not for holes. Strain-induced carrier transport enhancement is maintained with gate-length scaling. By applying forward back biasing (FBB) through the ultra-thin Buried Oxide layer, both carrier mobilities and their responses to strain get enhanced. For Multiple-gate FETs, the impact of performance enhancement through various types of stressors (including CESL, SiGe Source/Drain, Strained SOI and Metal Gate Last process) is studied, for different fin crystalline orientations and aspect ratios, to provide guidance for 3-D transistor design optimization.

Advisor: King Liu, Tsu-Jae
Cap-and-Trade Modeling and Analysis: Congested Electricity Market Equilibrium

This dissertation presents an equilibrium framework for analyzing the impact of cap-and-trade regulation on transmission-constrained electricity market. The cap-and-trade regulation of greenhouse gas emissions has gained momentum in the past decade. The impact of the regulation and its efficacy in the electric power industry depend on interactions of demand elasticity, transmission network, market structure, and strategic behavior of firms. I develop an equilibrium model of an oligopoly electricity market in conjunction with a market for tradable emissions permits to study the implications of such interactions. My goal is to identify inefficiencies that may arise from policy design elements and to avoid any unintended adverse consequences on the electric power sector./nI demonstrate this modeling framework with three case studies examining the impact of carbon cap-and-trade regulation. In the first case study, I study equilibrium results under various scenarios of resource ownership and emission targets using a 24-bus IEEE electric transmission system. The second and third case studies apply the equilibrium model to a realistic electricity market, Western Electricity Coordinating Council (WECC) 225-bus system with a detailed representation of the California market./nIn the first and second case studies, I examine oligopoly in electricity with perfect competition in the permit market. I find that under a stringent emission cap and a high degree of concentration of non-polluting firms, the electricity market is subject to potential abuses of market power. Also, market power can occur in the procurement of non-polluting energy through the permit market when non-polluting resources are geographically concentrated in a transmission-constrained market./nIn the third case study, I relax the competitive market structure assumption of the permit market by allowing oligopolistic competition in the market through a conjectural variation approach. A short-term equilibrium analysis of the joint markets in the presence of market power reveals that strategic permit trading can play a vital role in determining economic outcomes in the electricity market. In particular, I find that a firm with more efficient technologies can employ strategic withholding of permits, which allows for its increase in output share in the electricity market at the expense of other less efficient firms. In addition, strategic permit trading can influence patterns of transmission congestion./nThese results illustrate that market structure and transmission congestion can have a significant impact on the market performance and environmental outcome of the regulation while the interactions of such factors can lead to unintended consequences. The proposed approach is proven useful as a tool for market monitoring purposes in the short run from the perspective of a system operator, whose responsibility has become indirectly intertwined with emission trading regulation.

Advisor: Oren, Shmuel S
Carrier Transport and Related Effects in Detectors of the Cryogenic Dark Matter Search

The Cryogenic Dark Matter Search (CDMS) is searching for weakly-interacting massive particles (WIMPS), which could explain the dark matter problem in cosmology and particle physics./nBy simultaneously measuring signals from deposited charge and the energy in non-equilibrium phonons created by particle interactions in intrinsic germanium crystals at a temperature of 40 mK, a signature response for each event is produced. This response, combined with phonon pulse-shape information, allows CDMS to actively discriminate candidate WIMP interactions with nuclei from electromagnetic radioactive background which interacts with electrons./nThe challenges associated with these techniques are unique. Carrier scattering is dominated by the spontaneous emission of Luke-Neganov phonons due to zero-point fluctuations of the lattice ions. Drift fields are maintained at only a few V/cm, else these emitted phonons would dominate the phonons of the original interaction. The dominant systematic issues with CDMS detectors are due to the effects of space charge accumulation. It has been an open question how space charge accrues, and by which of several potential recombination and ionization processes./nIn this work, we have simulated the transport of electrons and holes in germanium under CDMS conditions. We have implemented both a traditional Monte Carlo technique based on carrier energy, followed later by a novel Monte Carlo algorithm with scattering rates defined and sampled by vector momentum. This vector-based method provides for a full anisotropic simulation of carrier transport including free-flight acceleration with an anisotropic mass, and anisotropic scattering rates./nWith knowledge of steady state carrier dynamics as a function of applied field, the results of our Monte Carlo simulations allow us to make a wide variety of predictions for energy dependent processes for both electrons and holes. Such processes include carrier capture by charged impurities, neutral impurities, static dipoles, and capture forming ``anion'' (D-/A+) states. We also generate predictions for impact ionization of shallow impurities and of impact ``neutralization'' of D-/A+ states. We use measurements of carrier capture performed on CDMS detectors to validate a plausible model for electron and hole capture due to neutral shallow impurities and their charged D-/A+ states. This model, along with carrier drift and diffusion parameters from Monte Carlo simulation, can be used as the foundation for simulations of space charge evolution in CDMS detectors, simultaneously solving continuity equations with Poisson's equation.

Advisor: Sadoulet, Bernard
The Development of Infant Detection of Inauthentic Emotion

Appreciating authentic and inauthentic emotional communication is central to the formation of trusting and intimate interpersonal relationships. However, when infants are able to discriminate and respond to inauthentic emotion has not been investigated. The present set of studies was designed to investigate infant sensitivity to three specific cues of inauthenticity: the contextual congruency of the emotion, the degree of exaggeration of the emotion, and the clarity with which the emotion is communicated. In each experiment, 16- and 19-month-old infants were presented with an emotional communication in which an inauthentic cue was present or absent. Infant behavioral responding to the emotional context was observed and coded. In all three experiments, 19-month-old infants, but not 16-month-old infants, detected inauthentic emotional communication and differentially responded to the environment accordingly. These findings demonstrate that infants do not simply take all emotional communication at face value and are sensitive to features of emotional contexts beyond what is expressively communicated by the adult. Possible developmental mechanisms that may account for the observed developmental shift in infant emotional development are proposed, and implications for the present findings on future research in emotion and emotional development are highlighted.

Advisor: Campos, Joseph J