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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Nguyen, Duy;

    Many chemical reactions occurring at aqueous interfaces show different kinetics and thermodynamics than the same reactions occurring in the bulk. The nature of these chemical reactions is central in understanding environmental, industrial, and biological processes; but remains incompletely understood due to its complexity and experimental difficulties in tuning and characterizing reactions at aqueous interfaces. In this dissertation, different experimental approaches are utilized to generate large, well-characterized aqueous interfaces for kinetic studies of chemical reactions. Chapter 1 introduces deviations of chemistry at aqueous interfaces that can alter physiochemical properties of chemical processes. In chapter 2, I study mechanistic rate accelerations of organic reactions at the organic-water interface and find that free OH groups of interfacial water molecules play an essential role in catalysis. In chapter 3, I revisit the effects of electric fields at the air-water interface of water microdroplets on directly converting water into hydrogen peroxide which is thermodynamically unfavorable in solution. Contrast to previous reports, no hydrogen peroxide production is observed in water microdroplets when tuning the electric fields at droplet surfaces. In chapter 4, I discuss claims of spontaneous hydrogen peroxide formation at the air-water interface and pinpoint potential experiments that can help to clarify them. Chapter 5 is the conclusion of the work presented in this dissertation.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ eScholarship - Unive...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ eScholarship - Unive...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sebens, Charles T.;

    Problems of self-interaction arise in both classical and quantum field theories. To understand how such problems are to be addressed in a quantum theory of the Dirac and electromagnetic fields (quantum electrodynamics), we can start by analyzing a classical theory of these fields. In such a classical field theory, the electron has a spread-out distribution of charge that avoids some of the problems of self-interaction facing point charge models. However, there remains the problem that the electron will experience self-repulsion. This self-repulsion cannot be eliminated within classical field theory without also losing Coulomb interactions between distinct particles. But, electron self-repulsion can be eliminated from quantum electrodynamics in the Coulomb gauge by fully normal-ordering the Coulomb term in the Hamiltonian. After normal-ordering, the Coulomb term contains pieces describing attraction and repulsion between distinct particles and also pieces describing particle creation and annihilation, but no pieces describing self-repulsion.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Caltech Authorsarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Caltech Authorsarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Cha, Biblia;

    Korean Americans experience many untreated mental health needs, and a significant percentage prefer to seek help from clergy for mental health issues. There is limited scholarship on Korean Americans’ social network characteristics and how they are related to church-goers’ intentions to seek professional mental health services and clergy’s intentions to refer to professional mental health services. Survey data was collected from 163 Korean American church-goers and 77 Korean American clergy in Los Angeles and Orange Counties between December 2020 and October 2021 to investigate if network size, network tie density, and network tie closeness are associated with Korean American church-goers’ intentions to seek professional mental health services and Korean American clergy’s intentions to refer to professional mental health services. Three possible mediators along these pathways were examined: 1) perceived availability of instrumental support; 2) perceived availability of emotional support; and 3) perceived social norms. The third study based on 21 semi-structured interviews conducted with Korean American clergy in Los Angeles and Orange Counties between December 2020 and November 2021 examined clergy’s perceptions and experience of providing mental health referrals to congregants, and what factors they consider in the decision-making process. Findings indicate that for Korean American church-goers, family and friend networks are important contexts for both perceived social norms and intentions related to seeking professional mental health services. Clergy are shaped by multiple social contexts in their referral decision-making process, including family and church networks, as well as friend networks mostly comprised of fellow clergy. The relationship between network characteristics and perceived availability of both instrumental and social support vary for church-goers and clergy by network. Finally, the qualitative study indicates that Korean American clergy mental health referrals are driven by specific factors, including their occupational context. Findings suggest clergy can act as both gateway providers and advocates for professional mental health services, and that more Korean American clergy are willing to make referrals than previously shown in the literature. Future studies can investigate mechanisms of network-specific social support and alter characteristics for pathways to professional mental health services or referrals.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ eScholarship - Unive...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Rozas Krause, Valentina J.;

    Memorials and the Cult of Apology examines how contemporary memorials have come to embody more than memory. It begins with a simple observation of the growing demand for apologies across the globe and the related proliferation of memorials that aim to atone for past injustices. In effect, apologies are being materialized into memorials, a phenomenon of global importance, which presents a major shift in national self-representation. In the broadest terms, my research is an intervention into the cultural history of the built environment. As the first scholarly work to address memorials as apologies, my dissertation builds an empirical and theoretical understanding of multiple aspects of apology and memorialization, of their material forms, the actors involved, and the diverse effects built apologies produce. It uses five representative case studies located in Berlin, Buenos Aires, and San Francisco, to develop this argument. Since memorialization is an inherently interdisciplinary topic, my work incorporates methods, readings, and theories from a vast array of humanistic disciplines, particularly postcolonial theory, Holocaust and human rights scholarship, and debates about justice, recognition, reparation, and morality. My archival and field research combines methods drawn from architectural history and the humanities ¬–close reading, literary interpretation, and storytelling–, which I apply to the formal analysis of built memorials and their urban contexts. This formal analysis is complemented with ethnographic interviews with designers, experts and site visitors, as well as participant observation of both commemorative events and what has been called ‘apology activism.’

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ eScholarship - Unive...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Wang, Manhua; Parikh, Ravi; Jeon, Myounghoon;

    Ensuring a safe transition between the automation system and human operators is critical in conditionally automated vehicles. During the automation-to-human transition process, hazard avoidance plays an important role after human drivers regain the vehicle control. This study applies the multilevel Hidden Markov Model to understand the hazard avoidance processes in response to static road hazards as continuous processes. The three-state model—Approaching, Negotiating, and Recovering—had the best model fitness, compared to the four-state and five-state models. The trained model reaches an average of 66% accuracy rate on predicting hazard avoidance states on the testing data. The prediction performance reveals the possibility to use the hazard avoidance pattern to recognize driving behaviors. We further propose several improvements at the end to generalize our models into other scenarios, including the potential to model hazard avoidance as a basic driving skill across different levels of automation conditions. Published online version

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Khodabandeh, Hadi;

    Spanners are fundamental graph structures that preserve lengths of shortest paths in an input graph $G$, up to some multiplicative distortion.Given an edge-weighted graph $G = (V,E)$, a subgraph $H = (V, E_H)$ is a $t$-spanner of $G$, for $t\ge 1$, if for every $u,v \in V$, the distance between $u$ and $v$ in $H$ is at most $t$ times their distance than in $G$.In this thesis, we study the existing literature on offline and online spanners, and we introduce some new results on online spanners in metric spaces. Suppose that we are given a sequence of points $(s_1, \ldots, s_n)$, where the points are presented one-by-one, i.e., point $s_i$ is presented at the step~$i$, and $S_i = \{s_1, \ldots , s_i\}$ for $i=1,\ldots , n$.The objective of an online algorithm is to maintain a geometric $t$-spanner $G_i$ for $S_i$ for all $i$. The algorithm is allowed to add edges to the spanner when a new point arrives, however, it is not allowed to remove any edge from the spanner. The performance of an online algorithm is measured by its competitive ratio, which is the supremum, over all sequences of points, of the ratio between the weight of the spanner constructed by the algorithm and the minimum weight of a $t$-spanner on $S_n$. Here the weight of a spanner is the sum of all its edge weights.Under the $L_2$-norm in $\mathbb{R}^d$ for arbitrary constant $d\in \mathbb{N}$,we present an online algorithm for $(1+\eps)$-spanner with competitive ratio $O_d(\eps^{-d} \log n)$, improving the previous bound of $O_d(\eps^{-(d+1)}\log n)$. Moreover, the spanner maintained by the algorithm has $O_d(\eps^{1-d}\log \eps^{-1})\cdot n$ edges, almost matching the (offline) optimal bound of $O_d(\eps^{1-d})\cdot n$. In the plane, a tighter analysis of the same algorithm provides an almost quadratic improvement of the competitive ratio to $O(\eps^{-3/2}\log\eps^{-1}\log n)$, by comparing the online spanner with an instance-optimal spanner directly, bypassing the comparison to an MST (i.e., lightness). As a counterpart, we design a sequence of points that yields a $\Omega_d(\eps^{-d})$ lower bound for the competitive ratio for online $(1+\eps)$-spanner algorithms in $\mathbb{R}^d$ under the $L_1$-norm.Then we turn our attention to online spanners in general metrics.Note that, it is not possible to obtain a spanner with stretch less than 3 with a subquadratic number of edges, even in the offline settings, for general metrics. We analyze an online version of the celebrated greedy spanner algorithm, dubbed \emph{ordered greedy}. With stretch factor $t = (2k-1)(1+\eps)$ for $k\ge 2$ and $\eps\in(0,1)$, we show that it maintains a spanner with $O(\eps^{-1}\log\frac{k}{\eps}) \cdot n^{1+\frac{1}{k}}$ edges and $O(\eps^{-1}n^{\frac{1}{k}}\log^2 n)$ lightness for a sequence of $n$ points in a metric space. We show that these bounds cannot be significantly improved, by introducing an instance that achieves an $\Omega(\frac{1}{k}\cdot n^{1/k})$ competitive ratio on both sparsity and lightness. Furthermore, we establish the trade-off among stretch, number of edges and lightness for points in ultrametrics, showing that one can maintain a $(2+\eps)$-spanner for ultrametrics with $O(n\cdot\eps^{-1}\log\eps^{-1})$ edges and $O(\eps^{-2})$ lightness.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ eScholarship - Unive...arrow_drop_down
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    Authors: Nguyen, Minh;

    While named entity recognition (NER) from speech has been around as long as NER from written text has, the accuracy of NER from speech has generally been much lower than that of NER from text. The rise in popularity of spoken dialog systems such as Siri or Alexa highlights the need for more accurate NER from speech because NER is a core component for understanding what users said in dialogs. Deployed spoken dialog systems receive user input in the form of automatic speech recognition (ASR) transcripts, and simply applying NER model trained on written text to ASR transcripts often leads to low accuracy because compared to written text, ASR transcripts lack important cues such as punctuation and capitalization. Besides, errors in ASR transcripts also make NER from speech challenging. We propose two models that exploit dialog context and speech pattern clues to extract named entities more accurately from open-domain dialogs in spoken dialog systems. Our results show the benefit of modeling dialog context and speech patterns in two settings: a standard setting with random partition of data and a more realistic but also more difficult setting where many named entities encountered during deployment are unseen during training.

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    Authors: Prodanov, Timofey;

    Segmental duplications or low-copy repeats (LCRs) are long segments of duplicated DNA that cover more than 5% of the human genome and overlap more than 600 protein-coding genes. Copy number and sequence variants in over 150 such duplicated genes (e.g. SMN1/2, STRC, NCF1) are associated with risk for rare and complex human diseases. Paralogous sequence variants (PSVs) are short differences between homologous sequences within duplicated loci. It has been shown that many PSVs are not fixed in the population, which reduces their potential to differentiate paralogous regions. Moreover, segmental duplications exhibit extensive copy number variation, and are characterized by poor read mappability even for long-read data. All these factors lead to diminished accuracy of existing bioinformatical tools for short- and long-read data in duplicated regions. This dissertation presents three novel computational methods that solve classical bioinformatical problems (read mapping, variant calling and copy number variation detection) in LCR regions. In contrast to existing tools, three proposed methods examine PSV genotypes in order to distinguish sets of reliable and unreliable PSVs, and use reliable PSVs to achieve higher accuracy than state-of-the-art methods in the field.First, we describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping within LCR regions. It iteratively genotypes PSVs and leverages reliable PSVs to distinguish between candidate read locations. This allows for high accuracy variant calling in segmental duplications using long reads. Next, we present the first toolkit for LCR regions, Parascopy. Parascopy uses short-read whole-genome sequencing to estimate total copy number as well as paralog-specific copy number for duplicated genes. Parascopy analyzes reads mapped to different repeat copies and utilizes multiple samples to mitigate sequencing bias and identify reliable PSVs. Accurate copy number estimation facilitates discovery of pathogenic copy number changes in duplicated genes. A novel variant caller, ParascopyVC, builds upon copy number variation detection and uses short-read data to call pooled and locus-specific variants within segmental duplications. ParascopyVC uses population allele frequencies and pooled genotypes to select informative PSVs. Finally, the tool uses informative PSVs to identify additional locus-specific variants, enabling the discovery of novel disease-causing variants in duplicated genes.

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    Authors: RAZMA, CONNOR JOHN;

    Influenza affects millions worldwide each year with responses varying from individual to individual. Influenza can be broken down into several subtypes, specifically H1N1, H3N2, Yamagata, and Victoria. One way to measure the immune response to influenza is to measure a person’s antibody response to influenza. To measure how many antibodies are present in a sample, a hemagglutination inhibition assay (HAI) is used. DNA methylation is an epigenetic mechanism used to regulate gene expression in cells. Its mechanism of action is the addition of a methyl group to cytosine at a cytosine-guanine pair. DNA methylation has been shown to change in response to stimuli such as viral or bacterial infections. DNA methylation can be measured by bisulfite sequencing. In this study, data was taken from patients who had the flu vaccination. Their antibody data was measured using the HAI assay by the University of Georgia and their methylation data was measured using reduced representation bisulfite sequencing by the Pellegrini and Reed labs at UCLA. Using various statistical learning algorithms, we were able to find methylated sites that were good predictors of vaccine response. Elastic net regression proved to be a particularly good predictor of vaccine response, and after further analysis, it was revealed that the best prediction happened with relatively few methylated sites being used in prediction. Some of these significant sites seem to be involved in regulating immune response and membrane function. Further work will be done to determine the prediction accuracy of these algorithms with just these sites. Ideally, after this future work and other experiments, these methylated sites can be used as biomarkers to predict response to flu vaccination.

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    Authors: Luo, Chenyao;

    The two-dimensional flow over the cylinder is simulated using Ansys Fluent and analyzed using spectral proper orthogonal decomposition (SPOD). The SPOD eigenvalues and eigenvectors are used to get the Strouhal numbers ($St$) and eigenmodes. Circular and square cylinder flows are analyzed at three different Reynolds numbers ($Re$) of 60, 100, and 150. Elliptical cylinder flows are analyzed at $Re$ = 150 with different aspect ratios of 0.25, 0.5, and 4. The $St$ of circular cylinder flow is close to literature data and the ones of square and elliptical cylinder flow have greater differences from literature data. The $St$ is larger at larger $Re$. The modes show symmetric structures at $St$ and 3$St$ and anti-symmetric structures at 2$St$ for all cases. Elliptical cylinder cases are simulated again in a larger domain. The case with AR = 0.25 shows a secondary vortex street structure at the far wake. A secondary frequency at 0.07781 is observed and the modes at that frequency have Karman vortex street structures at the far wake.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Nguyen, Duy;

    Many chemical reactions occurring at aqueous interfaces show different kinetics and thermodynamics than the same reactions occurring in the bulk. The nature of these chemical reactions is central in understanding environmental, industrial, and biological processes; but remains incompletely understood due to its complexity and experimental difficulties in tuning and characterizing reactions at aqueous interfaces. In this dissertation, different experimental approaches are utilized to generate large, well-characterized aqueous interfaces for kinetic studies of chemical reactions. Chapter 1 introduces deviations of chemistry at aqueous interfaces that can alter physiochemical properties of chemical processes. In chapter 2, I study mechanistic rate accelerations of organic reactions at the organic-water interface and find that free OH groups of interfacial water molecules play an essential role in catalysis. In chapter 3, I revisit the effects of electric fields at the air-water interface of water microdroplets on directly converting water into hydrogen peroxide which is thermodynamically unfavorable in solution. Contrast to previous reports, no hydrogen peroxide production is observed in water microdroplets when tuning the electric fields at droplet surfaces. In chapter 4, I discuss claims of spontaneous hydrogen peroxide formation at the air-water interface and pinpoint potential experiments that can help to clarify them. Chapter 5 is the conclusion of the work presented in this dissertation.

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    Authors: Sebens, Charles T.;

    Problems of self-interaction arise in both classical and quantum field theories. To understand how such problems are to be addressed in a quantum theory of the Dirac and electromagnetic fields (quantum electrodynamics), we can start by analyzing a classical theory of these fields. In such a classical field theory, the electron has a spread-out distribution of charge that avoids some of the problems of self-interaction facing point charge models. However, there remains the problem that the electron will experience self-repulsion. This self-repulsion cannot be eliminated within classical field theory without also losing Coulomb interactions between distinct particles. But, electron self-repulsion can be eliminated from quantum electrodynamics in the Coulomb gauge by fully normal-ordering the Coulomb term in the Hamiltonian. After normal-ordering, the Coulomb term contains pieces describing attraction and repulsion between distinct particles and also pieces describing particle creation and annihilation, but no pieces describing self-repulsion.

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    Authors: Cha, Biblia;

    Korean Americans experience many untreated mental health needs, and a significant percentage prefer to seek help from clergy for mental health issues. There is limited scholarship on Korean Americans’ social network characteristics and how they are related to church-goers’ intentions to seek professional mental health services and clergy’s intentions to refer to professional mental health services. Survey data was collected from 163 Korean American church-goers and 77 Korean American clergy in Los Angeles and Orange Counties between December 2020 and October 2021 to investigate if network size, network tie density, and network tie closeness are associated with Korean American church-goers’ intentions to seek professional mental health services and Korean American clergy’s intentions to refer to professional mental health services. Three possible mediators along these pathways were examined: 1) perceived availability of instrumental support; 2) perceived availability of emotional support; and 3) perceived social norms. The third study based on 21 semi-structured interviews conducted with Korean American clergy in Los Angeles and Orange Counties between December 2020 and November 2021 examined clergy’s perceptions and experience of providing mental health referrals to congregants, and what factors they consider in the decision-making process. Findings indicate that for Korean American church-goers, family and friend networks are important contexts for both perceived social norms and intentions related to seeking professional mental health services. Clergy are shaped by multiple social contexts in their referral decision-making process, including family and church networks, as well as friend networks mostly comprised of fellow clergy. The relationship between network characteristics and perceived availability of both instrumental and social support vary for church-goers and clergy by network. Finally, the qualitative study indicates that Korean American clergy mental health referrals are driven by specific factors, including their occupational context. Findings suggest clergy can act as both gateway providers and advocates for professional mental health services, and that more Korean American clergy are willing to make referrals than previously shown in the literature. Future studies can investigate mechanisms of network-specific social support and alter characteristics for pathways to professional mental health services or referrals.

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    Authors: Rozas Krause, Valentina J.;

    Memorials and the Cult of Apology examines how contemporary memorials have come to embody more than memory. It begins with a simple observation of the growing demand for apologies across the globe and the related proliferation of memorials that aim to atone for past injustices. In effect, apologies are being materialized into memorials, a phenomenon of global importance, which presents a major shift in national self-representation. In the broadest terms, my research is an intervention into the cultural history of the built environment. As the first scholarly work to address memorials as apologies, my dissertation builds an empirical and theoretical understanding of multiple aspects of apology and memorialization, of their material forms, the actors involved, and the diverse effects built apologies produce. It uses five representative case studies located in Berlin, Buenos Aires, and San Francisco, to develop this argument. Since memorialization is an inherently interdisciplinary topic, my work incorporates methods, readings, and theories from a vast array of humanistic disciplines, particularly postcolonial theory, Holocaust and human rights scholarship, and debates about justice, recognition, reparation, and morality. My archival and field research combines methods drawn from architectural history and the humanities ¬–close reading, literary interpretation, and storytelling–, which I apply to the formal analysis of built memorials and their urban contexts. This formal analysis is complemented with ethnographic interviews with designers, experts and site visitors, as well as participant observation of both commemorative events and what has been called ‘apology activism.’

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    Authors: Wang, Manhua; Parikh, Ravi; Jeon, Myounghoon;

    Ensuring a safe transition between the automation system and human operators is critical in conditionally automated vehicles. During the automation-to-human transition process, hazard avoidance plays an important role after human drivers regain the vehicle control. This study applies the multilevel Hidden Markov Model to understand the hazard avoidance processes in response to static road hazards as continuous processes. The three-state model—Approaching, Negotiating, and Recovering—had the best model fitness, compared to the four-state and five-state models. The trained model reaches an average of 66% accuracy rate on predicting hazard avoidance states on the testing data. The prediction performance reveals the possibility to use the hazard avoidance pattern to recognize driving behaviors. We further propose several improvements at the end to generalize our models into other scenarios, including the potential to model hazard avoidance as a basic driving skill across different levels of automation conditions. Published online version

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    Authors: Khodabandeh, Hadi;

    Spanners are fundamental graph structures that preserve lengths of shortest paths in an input graph $G$, up to some multiplicative distortion.Given an edge-weighted graph $G = (V,E)$, a subgraph $H = (V, E_H)$ is a $t$-spanner of $G$, for $t\ge 1$, if for every $u,v \in V$, the distance between $u$ and $v$ in $H$ is at most $t$ times their distance than in $G$.In this thesis, we study the existing literature on offline and online spanners, and we introduce some new results on online spanners in metric spaces. Suppose that we are given a sequence of points $(s_1, \ldots, s_n)$, where the points are presented one-by-one, i.e., point $s_i$ is presented at the step~$i$, and $S_i = \{s_1, \ldots , s_i\}$ for $i=1,\ldots , n$.The objective of an online algorithm is to maintain a geometric $t$-spanner $G_i$ for $S_i$ for all $i$. The algorithm is allowed to add edges to the spanner when a new point arrives, however, it is not allowed to remove any edge from the spanner. The performance of an online algorithm is measured by its competitive ratio, which is the supremum, over all sequences of points, of the ratio between the weight of the spanner constructed by the algorithm and the minimum weight of a $t$-spanner on $S_n$. Here the weight of a spanner is the sum of all its edge weights.Under the $L_2$-norm in $\mathbb{R}^d$ for arbitrary constant $d\in \mathbb{N}$,we present an online algorithm for $(1+\eps)$-spanner with competitive ratio $O_d(\eps^{-d} \log n)$, improving the previous bound of $O_d(\eps^{-(d+1)}\log n)$. Moreover, the spanner maintained by the algorithm has $O_d(\eps^{1-d}\log \eps^{-1})\cdot n$ edges, almost matching the (offline) optimal bound of $O_d(\eps^{1-d})\cdot n$. In the plane, a tighter analysis of the same algorithm provides an almost quadratic improvement of the competitive ratio to $O(\eps^{-3/2}\log\eps^{-1}\log n)$, by comparing the online spanner with an instance-optimal spanner directly, bypassing the comparison to an MST (i.e., lightness). As a counterpart, we design a sequence of points that yields a $\Omega_d(\eps^{-d})$ lower bound for the competitive ratio for online $(1+\eps)$-spanner algorithms in $\mathbb{R}^d$ under the $L_1$-norm.Then we turn our attention to online spanners in general metrics.Note that, it is not possible to obtain a spanner with stretch less than 3 with a subquadratic number of edges, even in the offline settings, for general metrics. We analyze an online version of the celebrated greedy spanner algorithm, dubbed \emph{ordered greedy}. With stretch factor $t = (2k-1)(1+\eps)$ for $k\ge 2$ and $\eps\in(0,1)$, we show that it maintains a spanner with $O(\eps^{-1}\log\frac{k}{\eps}) \cdot n^{1+\frac{1}{k}}$ edges and $O(\eps^{-1}n^{\frac{1}{k}}\log^2 n)$ lightness for a sequence of $n$ points in a metric space. We show that these bounds cannot be significantly improved, by introducing an instance that achieves an $\Omega(\frac{1}{k}\cdot n^{1/k})$ competitive ratio on both sparsity and lightness. Furthermore, we establish the trade-off among stretch, number of edges and lightness for points in ultrametrics, showing that one can maintain a $(2+\eps)$-spanner for ultrametrics with $O(n\cdot\eps^{-1}\log\eps^{-1})$ edges and $O(\eps^{-2})$ lightness.

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    Authors: Nguyen, Minh;

    While named entity recognition (NER) from speech has been around as long as NER from written text has, the accuracy of NER from speech has generally been much lower than that of NER from text. The rise in popularity of spoken dialog systems such as Siri or Alexa highlights the need for more accurate NER from speech because NER is a core component for understanding what users said in dialogs. Deployed spoken dialog systems receive user input in the form of automatic speech recognition (ASR) transcripts, and simply applying NER model trained on written text to ASR transcripts often leads to low accuracy because compared to written text, ASR transcripts lack important cues such as punctuation and capitalization. Besides, errors in ASR transcripts also make NER from speech challenging. We propose two models that exploit dialog context and speech pattern clues to extract named entities more accurately from open-domain dialogs in spoken dialog systems. Our results show the benefit of modeling dialog context and speech patterns in two settings: a standard setting with random partition of data and a more realistic but also more difficult setting where many named entities encountered during deployment are unseen during training.

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    Authors: Prodanov, Timofey;

    Segmental duplications or low-copy repeats (LCRs) are long segments of duplicated DNA that cover more than 5% of the human genome and overlap more than 600 protein-coding genes. Copy number and sequence variants in over 150 such duplicated genes (e.g. SMN1/2, STRC, NCF1) are associated with risk for rare and complex human diseases. Paralogous sequence variants (PSVs) are short differences between homologous sequences within duplicated loci. It has been shown that many PSVs are not fixed in the population, which reduces their potential to differentiate paralogous regions. Moreover, segmental duplications exhibit extensive copy number variation, and are characterized by poor read mappability even for long-read data. All these factors lead to diminished accuracy of existing bioinformatical tools for short- and long-read data in duplicated regions. This dissertation presents three novel computational methods that solve classical bioinformatical problems (read mapping, variant calling and copy number variation detection) in LCR regions. In contrast to existing tools, three proposed methods examine PSV genotypes in order to distinguish sets of reliable and unreliable PSVs, and use reliable PSVs to achieve higher accuracy than state-of-the-art methods in the field.First, we describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping within LCR regions. It iteratively genotypes PSVs and leverages reliable PSVs to distinguish between candidate read locations. This allows for high accuracy variant calling in segmental duplications using long reads. Next, we present the first toolkit for LCR regions, Parascopy. Parascopy uses short-read whole-genome sequencing to estimate total copy number as well as paralog-specific copy number for duplicated genes. Parascopy analyzes reads mapped to different repeat copies and utilizes multiple samples to mitigate sequencing bias and identify reliable PSVs. Accurate copy number estimation facilitates discovery of pathogenic copy number changes in duplicated genes. A novel variant caller, ParascopyVC, builds upon copy number variation detection and uses short-read data to call pooled and locus-specific variants within segmental duplications. ParascopyVC uses population allele frequencies and pooled genotypes to select informative PSVs. Finally, the tool uses informative PSVs to identify additional locus-specific variants, enabling the discovery of novel disease-causing variants in duplicated genes.

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    Authors: RAZMA, CONNOR JOHN;

    Influenza affects millions worldwide each year with responses varying from individual to individual. Influenza can be broken down into several subtypes, specifically H1N1, H3N2, Yamagata, and Victoria. One way to measure the immune response to influenza is to measure a person’s antibody response to influenza. To measure how many antibodies are present in a sample, a hemagglutination inhibition assay (HAI) is used. DNA methylation is an epigenetic mechanism used to regulate gene expression in cells. Its mechanism of action is the addition of a methyl group to cytosine at a cytosine-guanine pair. DNA methylation has been shown to change in response to stimuli such as viral or bacterial infections. DNA methylation can be measured by bisulfite sequencing. In this study, data was taken from patients who had the flu vaccination. Their antibody data was measured using the HAI assay by the University of Georgia and their methylation data was measured using reduced representation bisulfite sequencing by the Pellegrini and Reed labs at UCLA. Using various statistical learning algorithms, we were able to find methylated sites that were good predictors of vaccine response. Elastic net regression proved to be a particularly good predictor of vaccine response, and after further analysis, it was revealed that the best prediction happened with relatively few methylated sites being used in prediction. Some of these significant sites seem to be involved in regulating immune response and membrane function. Further work will be done to determine the prediction accuracy of these algorithms with just these sites. Ideally, after this future work and other experiments, these methylated sites can be used as biomarkers to predict response to flu vaccination.

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    Authors: Luo, Chenyao;

    The two-dimensional flow over the cylinder is simulated using Ansys Fluent and analyzed using spectral proper orthogonal decomposition (SPOD). The SPOD eigenvalues and eigenvectors are used to get the Strouhal numbers ($St$) and eigenmodes. Circular and square cylinder flows are analyzed at three different Reynolds numbers ($Re$) of 60, 100, and 150. Elliptical cylinder flows are analyzed at $Re$ = 150 with different aspect ratios of 0.25, 0.5, and 4. The $St$ of circular cylinder flow is close to literature data and the ones of square and elliptical cylinder flow have greater differences from literature data. The $St$ is larger at larger $Re$. The modes show symmetric structures at $St$ and 3$St$ and anti-symmetric structures at 2$St$ for all cases. Elliptical cylinder cases are simulated again in a larger domain. The case with AR = 0.25 shows a secondary vortex street structure at the far wake. A secondary frequency at 0.07781 is observed and the modes at that frequency have Karman vortex street structures at the far wake.

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