VictorJuiz/thesis huggingface dataset:
Drivers of spatial and temporal variation in nectarivorous microbial communities [electronic resource]
Keywords: Biology.

Earlier ecologists such as C. Linnaeus (1781), Dawin (1859) and Humboldt (1845) began the monumental task of cataloging the temporal and geographic variation of earth's biodiversity. Concurrently early mycologists such as Augustin de Candolle (1820), Miles Joseph Berkely (1963), Bass Becking (1934) and Bisby (1943) questioned whether microbes exhibited geographic and temporal variations. As recently as 10 years ago, contemporary researchers were involved in heated debate about whether microbes exhibit biogeographical patterns. Molecular techniques have revealed that microbes unequivocally exhibit biogeographical patterns. My thesis offers insight into the processes shaping biogeographical patterns in one type of microbial community and examines the effects that anthropogenic changes are having on microbial community structure (Chapters 3 and 4). I use yeast that live in the nectar of flowers and on their pollinator vectors as a model system to examine microbial biogeography. We show that these nectarivorous microbes significantly affect nectar quality (Chapter 5), and previous research indicates that changes in nectar quality in turn affects pollinator behavior. In addition nectar yeast distribution and community structure is shaped by pollinator behavior, as these yeast are dependent on pollinators to be transferred among food sources (Chapter 3, 4). I found that in multiple cases, yeast abundance and community composition were most strongly influenced by pollinator behavior and not by any of the environmental factors tested (Chapter 2 and 3). However, pollinators were strongly influenced by environmental factors in particular the amount of treecover, floral density and habitat type (Chapter 2, 3 and 4). As a whole we used this thesis to explore many of the processes involved in microbial biogeography such as dispersal limitation, environmental conditions, habitat chemistry, and competition. We found that although all of these factors play a role in shaping the structure of yeast communities, dispersal limitation seemed to be the most important factor and yeast communities on pollinators were highly mutable (Chapter 4), most likely contributing to the magnitude of dispersal effects. In addition these studies examine the spatial and temporal scales that are most important in determining microbial species' abundance and distribution.
Dynamic asset allocation using adaptive particle filters [electronic resource]
Keywords: Management Science and Engineering.

Asset allocation is one of the most important problems in practical investment management and also plays a central role in financial economics. This study is devoted to an econometric treatment of asset allocation problems. We propose a very general procedure for dynamic asset allocation by using adaptive particle filters. It represents an advance over the traditional asset allocation because it incorporates jumps in mean returns and volatilities when using historical data. An advantage of our procedure is that it is very general and independent from any specific utilities. The empirical study shows our procedure indeed outperforms traditionally methods. The theoretical contribution of our paper is that we propose a general methodology which can accommodate lots of asset allocation problems. The methodology is easy to implement and simple to apply many models which are popular in returns modelling and asset allocation. It also inherits all the advantages of many variants of particle filtering approach. In fact, we provide a powerful tool for the researchers in finance area to solve the problems mentioned above. The empirical contribution is that we first apply our approach to the double-jump model. Based on S& P 500 data from 1996 to 2011, we find variations in posterior distributions of parameters. Our algorithm can quickly adapt to the new information and update the values. Next, we apply our framework to Log and Power utility. In general, we observe the same pattern for both cases: higher cumulative excess returns and larger CER for SVCJ model than SV model with same framework, higher cumulative excess returns and larger CER for our sequential strategy than others with same model.
A dynamic attenuator for computed tomography [electronic resource]
Keywords: Electrical Engineering.

The utilization of x-ray computed tomography (CT) has increased dramatically in recent decades. While extremely useful, a major drawback of CT scans is their use of ionizing radiation. Today, one quarter of the radiation dose received by the U.S. population can be attributed to CT scans. We present the use of a dynamic attenuator which is capable of personalizing the radiation usage in the scan. This attenuator is inspired by a stationary-source, inverse geometry CT scanner, which is an architecture with several advantages but which is also very complex. The dynamic attenuator consists of a series of movable wedges which together produce a time-varying, piecewise-linear thickness profile. In simulations, this attenuator reduces dose by 30% in nontargeted scans and 50% in targeted scans without increasing peak noise. On many datasets, this attenuator can also achieve order-of-magnitude dynamic range reductions, which may aid in the adoption of photon-counting detectors, a separate technology which may provide additional dose reductions. We show that most of these dose reduction benefits can be achieved using a real-time control algorithm to position the wedges dynamically during the scan. Additionally, we have developed a framework for optimizing the control of a broad range of dynamic attenuators. A prototype system suggests that the level of artifacts produced by the wedge transitions is within the range of tens of Hounsfield units, although further refinements are expected to reduce artifacts. Based on these positive results, we believe that this dynamic, piecewise-linear attenuator is a practical and effective option for CT.
Dynamic portfolio execution [electronic resource]
Keywords: Management Science and Engineering.

As financial markets have become increasingly complex, the need to understand price dynamics at the microstructure level has become vital for market participants. Over the past decade, highly sophisticated ``high-frequency'' trading firms have emerged and have come to dominate equity markets and other asset classes, controlling anywhere between 50\%-90\% of the average traded volume on any given day. These sophisticated players utilize price and supply/demand dynamics in limit order markets to make trading decisions and provide liquidity at the micro-second level. In this environment, the optimal management of execution costs and control of price impact is of central importance to market participants, including portfolio managers for pension and mutual funds, hedge funds, market markers, etc. This thesis analyzes the optimal execution problem of a portfolio manager trading multiple assets in a limit order book environment. In addition to the consideration of liquidity and risk of each individual asset, we have to consider cross-asset interactions in these two dimensions, which are challenging to address. Focusing on the market microstructure, we develop a tractable order book model to capture the supply/demand dynamics in a multi-asset setting. The results suggest that cross-asset risk and liquidity considerations are of critical importance in constructing the optimal execution policies. Even when the goal is to trade a single asset, its optimal execution may involve transitory trades in other assets. In general, optimally managing the risk of the portfolio during the execution process influences the synchronization of trading in different assets. Moreover, correlations in the liquidity across assets lead to complex patterns in the optimal execution policies. In particular, we highlight cases where aggregate costs can be reduced by temporarily overshooting one's target portfolio.
Dynamics of payoff and stimulus effects on decisions under time pressure [electronic resource] : combined behavioral, EEG and model-based analysis
Keywords: Electrical Engineering.

It is well established that prior knowledge about payoff can bias decisions toward higher-paying alternatives. However, little is known about how payoff information affects the neural mechanism underlying these biased choices in humans. We address this question by recording electroencephalography (EEG) signals from 13 participants while they performed a two-alternative forced-choice task. On each trial, the participant judged whether a rectangle was shifted to the right or to the left of the fixation point and responded by squeezing the right- or left-hand dynamometer. Participants were cued about the payoff of each choice before stimulus onset and had to respond correctly before a short deadline (375-475 ms) to obtain the payoff. We show that payoff information influences participants' choices and response times: the frequency and speed of choices toward the higher-paying alternative increases. Moreover, we show that payoff bias is represented in the lateralized readiness potential (LRP), a response-related brain potential reflecting the preparation of motor activity in a specific hand. The representation of payoff bias in LRP has two components: a static component that shifts the LRP baseline toward the higher-paying alternative for hundreds of milliseconds before stimulus onset; and a dynamic component that causes an abrupt rise in LRP toward the higher-paying alternative after stimulus onset (but before stimulus information influences the decision). These components seem to reflect different processes; while the static component is not predictive of participants' choices or response times, the dynamic component predicts both. We also provide evidence showing that the static and dynamic LRP components propagate down to the muscles and can generate isometric forces measurable by dynamometers. Finally, drawing on both the LRP and motor responses, we present a new model for the effects of payoff information on the decision-making process. This model is based on a competition between a fast- guess process that is informed solely by payoff information and an evidence accumulation process that is informed by the sensory stimulus.
Dynamics of photo-excited bismuth [electronic resource]
Keywords: Applied Physics.

The dynamics of photo-excited semi-metallic bismuth are determined by the strong interactions between the electronic and lattice degrees of freedom. In this thesis, I present results from ultrafast optical and x-ray experiments that explore the nonequilibrium behavior of photo-excited bismuth and help elucidate the coupling between these degrees of freedom. First of all, there has been sustained interest in the coupling between the photo-excited carriers and the zone-center longitudinal (A1g) optical phonon, as it relates directly to the magnitude of the Peierls distortion. Therefore, I have used optical pump-probe method to study the inverse Peierls distortion by directly looking at the A1g phonons under high carrier photo-excitation. In addition, the mechanism of ultrafast-excitation of A1g and Eg (transverse optical) phonon modes has been widely studied but not yet fully understood. Older models, including Impulsive Stimulated Raman Scattering (ISRS) the Displacive Excitation of Coherent Phonons (DECP) cannot perfectly explain the discrepancy of the data between spontaneous and time-resolved Raman scattering. We show that elements of both models are responsible for the excitation mechanism and attribute the weak coupling to the coherent Eg mode as due to the fragile Eg electronic coherence, and in the process of figuring out a novel way of probing extremely fast electron decoherence rates. Optical experiments are primarily sensitive to zone-center excitations. To further understand the non-zero momentum phonon behavior of photo-excited Bi as well as the ultrafast melting process, I have utilized time resolved x-ray diffuse scattering using different X-ray sources, including synchrotron generation and X-ray free electron lasers (FEL). I have observed thermally activated phonons whose lifetime is consistent with the thermal transport characteristic time. This time scale also dictates the epitaxial regrowth following laser induced melting. Non-equillibrium phonons, which live for hundreds of ps have also been observed, similar to our earlier observation in polar semiconductors. With better time resolution (~100 fs) from the Linac Coherent Light Source (LCLS), we were able to produce and observe large momentum squeezed phonons. Experimental results were consistent with simulation from first principle calculations throughout the Brillouin Zone (BZ). Ultrafast melting measurements with 100 fs resolution show results consistent with observations from earlier ultrafast electron diffraction. Moreover, they also show for the first time the highly anisotropic phonon softening, which lives for up to 1 ps, before the melting happens.
The dynamics of translation initiation and elongation [electronic resource]
Keywords: Applied Physics.

Translation is the final step that converts genetic information into proteins composed of amino acids using the ribosome-- a complex molecular machine that coordinates the kinetics, chemistry, and mechanics necessary to synthesize a polypeptide. Translation is highly dynamic with processes taking place on the microseconds to minutes timescales. Among the different techniques employed to probe the dynamics of translation, single-molecule fluorescence occupies a unique position, being able to track heterogeneous compositional and conformational changes occurring within tens of milliseconds to minutes. Leveraging several fluorescent signals, we probed the dynamics of translation initiation. Instead of a linear pathway, we observed several different pathways all leading to the formation of an elongation competent ribosome complex, with the flux through each modulated by initiation factors, tRNAs, and mRNA sequence. Next, we tracked how the aminoglycoside family of antibiotics inhibits ribosome and tRNA dynamics during peptide synthesis (elongation), concluding that their potency as bactericides stems from kinetically inhibiting elongation. Finally, we transitioned from model systems into observing elongation dynamics on a biologically functional protein stall sequence, SecM. Our results suggest that stalling the ribosome requires several precisely-timed peptide-ribosome interactions and that ribosomes stall in a distribution of locations on the SecM sequence. These results demonstrate the power of single-molecule fluorescence to monitor global translation dynamics, as well as highlighting the importance of the temporal dimension in forming a coherent and global mechanism for translation.
"E Ho'omau!" a study of Hawai'i teachers navigating change through generative praxis [electronic resource]
Keywords: Education.

This study aims to make visible the practices of a group of teachers who are part of a community shift in Hawai'i, described here as the "Hawaiian Indigenous Movement for Education and Native Intelligence" (HIMENI). Revitalization of indigenous knowledge systems and practices has grown over the past thirty years in Hawai'i. The aims and outcomes that HIMENI teachers pursue are rooted in Hawaiian worldviews, and are aligned with Hawaiian cultural values; in some cases they differ greatly from the aims of conventional schooling. Study participants were enrolled in an inservice teacher education program and came from diverse schools across the state. During the five-year span of the ethnographic study, eight themes emerged, revealing a values-based conceptual framework that was coherently guiding HIMENI teachers across various learning contexts to strengthen the alignment between their principles and teaching practices. As they led their students through encounters with locally- and globally-valued knowledge, the eight themes helped them navigate change and build new teaching knowledge generatively—through embodied, contextualized knowledge that flowed in conversation with theory to shape practice. The HIMENI teachers' practices and pedagogies show clearly what "generative praxis" can look like, and what it can accomplish; a pedagogical model for generative praxis is proposed. HIMENI teachers cultivate generative praxis through their professional work, and also nurture its growth among their K-12 students. Analysis of the conceptual framework illuminates parallels between locally-recognized concepts and broadly-recognized constructs from the learning sciences that inform teacher practice, such as ecological models of context, embodied cognition, communities of practice, adaptive expertise and design thinking. Generative praxis is also aligned with enduring learning theories such those proposed by Vygotsky, Dewey, Bruner etc. Taken as a whole, the set of practices and processes used by this group of HIMENI teachers may be seen as an instantiation of "generative praxis"—an orientation to knowledge that powerfully promotes context-adaptive, dynamic knowledge development for teachers and learners alike. Standing alongside "content knowledge" and "pedagogical content knowledge"—two widely-recognized categories of knowledge for teaching—generative praxis gives us a new term to describe a third essential knowledge base for teaching: contextualized, iterative knowing-in-action. The teaching profession must acknowledge and cultivate generative praxis (by any name) if teacher educators and teachers are to successfully navigate the rapidly diversifying languages, cultures, knowledge(s) and routes of access to knowledge that are part of US contexts for learning in the 21st century.
Early-life failures in digital logic circuits [electronic resource]
Keywords: Electrical Engineering.

Manufacturing tests detect defective integrated circuits (ICs) before they are shipped to customers. Early-life failures (ELF, also referred to as infant mortality failures) are caused by defective ICs that pass manufacturing tests but fail early in the field, much earlier than expected product lifetime. Such failures can hurt the reputation of IC suppliers, and can have consequences ranging from annoying computer crashes, loss of data and services, to financial and productivity losses, or even loss of human life. Major ELF causes include defects in transistor gate dielectrics and inter-metal dielectrics (IMD). Burn-in is traditionally used for ELF screening, where ICs are stressed at elevated voltage and temperature to accelerate defects so that they get detected during manufacturing tests. Burn-in accounts for a significant portion of manufacturing test costs, and there are serious concerns about its potentially reduced effectiveness in advanced technologies. Hence, low-cost burn-in alternatives are necessary. In this dissertation, we make the following contributions: 1. Using test chips over several IC technologies, we derive and experimentally demonstrate a new ELF signature for defects in transistor gate dielectrics: the presence of a gate-dielectric ELF transistor (i.e., a transistor with gate-dielectric defect that may result in ELF) inside a logic gate results in changes in delay of that logic gate over time before functional failures appear. This signature is distinct from gradual delay degradation effects exhibited by several circuit aging mechanisms. 2. We experimentally demonstrate that the ELF signature for IMD defects in advanced IC technologies (e.g., 28nm) is similar to that of transistor gate dielectrics. 3. We experimentally demonstrate that the derived ELF signature can be successfully detected using an on-chip clock control technique. 4. Using an industrial design with 8 processor cores supporting 64 hardware threads, we demonstrate the practicality of automatically generating special test patterns to detect ELF-induced changes in delays. Our results may be used to provide early indications of ELF-induced impending circuit failures during manufacturing tests, or during normal system operation for robust systems with built-in support for on-line self-test, diagnostics, and self-repair.
Ecology of a threatened shorebird in an altered habitat: Bristle-thighed Curlews (Numenius tahitiensis) on Palmyra Atoll
Keywords: Stanford Biology Department
Palmyra Atoll
Bristle-thighed Curlews
Numenius tahitiensis
habitat selection
Thesis

Palmyra Atoll, USA has remained mostly uninhabited since construction and abandonment of a US naval base during World War II. However, the effects of Navy modifications made to the land and lagoons have persisted, affecting the extent, physical conditions, and benthic habitat quality of Palmyra’s lagoon sand flats. Sand flats provide critical non-breeding habitat for Bristle-thighed Curlews (Numenius tahitiensis) and the atoll hosts one of the largest wintering populations of curlews of any central Pacific island. N. tahitiensis are listed as “vulnerable” by the IUCN due to loss of non-breeding winter foraging grounds and predation by introduced mammals. Thus, Palmyra – an uninhabited island recently devoid of invasive predators – provides an appropriate setting for studying how land alterations have changed the availability of preferred lagoon flat habitat for curlews. Using camera trapping, observations of focal individuals, and quantification of prey availability and sediment characteristics to monitor curlew habitat selection across a gradient of different levels of historical anthropogenic impact, I found that curlew habitat preferences were not determined by the degree of Navy impact on lagoon flat habitat. Curlew abundance was most strongly correlated with availability of prey, such as spionid polychaetes (Malacoceros spp.), and coarse sediment composition. These findings provide new ecological information on a shorebird species of conservation concern and have implications, such as habitat loss, for land management at Palmyra Atoll and other curlew wintering grounds.
The effect of electrolyte gating on several solid state systems [electronic resource]
Keywords: Physics.

Recently, electrolyte gating has become a popular technique in studying the carrier density dependent physical properties in solid state materials, due to its capability of producing large carrier density modulation. The mechanism of conductance control by electrolyte gating has been widely accepted to be an electric double layer (EDL) capacitor model, which was originally proposed by Helmholtz in the 19th century to describe the electrolyte-electrode interface. However, this EDL picture is known for a number of imperfections. In this thesis, we take two transition metal oxide materials, namely the perovskite SrTiO$_3$ and rutile TiO$_2$, as examples, to show that the imperfections of EDL picture could manifest themselves in the physical properties one observes, and therefore should be included in drawing physical conclusions on electrolyte gated materials. Specifically, we show that electrolyte gated SrTiO$_3$ (001) shows two distinct electromagnetic transport regimes, which is consistent with a percolation picture, and suggests that the charge distribution in the EDL can be disordered. We also show that electrolyte gating effect on TiO$_2$ rutile is facet dependent, and strongly correlated with the TiO$_2$ surface energies. Gating cycles on TiO$_2$ rutile (101) shows large electrolyte dependent hysteresis, which is a signature of specific adsorption and ion-surface interactions. We further show that oxygen vacancy formation is more likely to be the origin of conductance in electrolyte gated TiO$_2$ rutile, and possibly SrTiO$_3$ as well. Electrochemical process could play a significant role even at low gate voltages. We finally study the electrolyte gating effect in the environment of oxygen, and propose it as a potential technique in detecting oxygen vacancy formation in electrolyte gated oxides. A number of other incomplete projects related to electrolyte gating will also be presented.