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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: Chater, John Matthew;

    Pomegranate (Punica granatum L.) is an ancient deciduous fruit tree crop in the family Lythraceae. Pomegranate juice is a highly valued beverage, long believed by many of the world’s cultures to possess medicinal properties. Recently the juice has been demonstrated to contain large quantities of polyphenolic compounds with powerful antioxidant properties. Commercial pomegranate planting area has increased substantially in the western hemisphere due to increased consumer interest. Low nursery inventory has caused many farmers to propagate their own trees and limited availability of only a few cultivars is believed to have contributed to the lack of diversity in the market. ‘Wonderful,’ the industry standard, has been propagated in the U.S. for decades and dominates the market, leading to the present-day monoculture. The USDA-ARS pomegranate germplasm collection conserves approximately 280 cultivars, many of which have not been evaluated for commercial production. In this dissertation, 14 preselected pomegranate cultivars from the USDA collection were evaluated: 1) to develop protocols that optimize propagation of pomegranate for nurseries and growers; 2) in new field trials planted specifically to determine establishment rates, productivity and eco-physiological performance of different cultivars in inland versus coastal environments; and 3) to establish dates of fruit maturity, identify unique cultivars with consumer-friendly traits, and to select candidates that meet or exceed juice quality parameters of Wonderful. The overall goal of this research was to identify promising pomegranate cultivars with the potential to be developed for commercial production in coastal and inland areas of southern and central California. Propagation experiments determined that some pomegranate cultivars were difficult to root. Establishment rates and precocity were significantly different among cultivars and between sites, with the inland planting producing more fruit than the coastal site. Juice quality for 14 cultivars was chemically analyzed with spectrophotometry, refractometry, titration, nuclear magnetic resonance, ion and liquid chromatography to identify candidate cultivars meeting or exceeding Wonderful juice quality specifications. This research was the first of its kind to establish experimental field trials of pomegranate germplasm in California to quantify and provide phenotypic, eco-physiological and horticultural data for growers, breeders, and the food and beverage industries.

    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/
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    Authors: Tcacenco, Andrei;

    My research looks at Soviet republics outside the Russian Federation such as the Ukrainian and Moldavian SSRs, and takes a more localized approach to understanding the state’s campaigns to produce a moral Soviet citizen during the Late Socialist period of Soviet history. I look at how interactions between Soviet citizens in the periphery and Central Party organs resulted in a dynamic, negotiated understanding of socialist morality and concepts of the New Socialist Person in new discursive spaces of home entertainment, especially television and radio. Soviet citizens utilized mass media to spark debates about the meaning of Soviet identity, nationalism and morality, and sometimes to express outright hostility toward the Soviet state. The appropriation of official Soviet language in the periphery led to the creation of new, unpredictable meanings in Soviet discourse. I show that some former Soviet citizens often viewed their national identity as a form of resistance to the Soviet state, while others saw little contradiction between their national and Soviet identities. This paradox is central to my project, as I aim to explore the fluidity, ambiguity, and variation of national and Soviet identity. Ultimately, I argue that the conversations and arguments surrounding morality led to the collapse of the Soviet Union by December 1991.

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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: Li, Sihuan;

    Extremely large scale scientific simulation applications have been very important in many scientific domains including cosmology, climate, fluid dynamics, chemistry and so on. It has been shown that running the simulations at a larger scale can bring more discoveries. On one hand, with the increasing scale of those applications, the saturated I/O bandwidth can slow down the execution of the simulation significantly because of the huge amount of data needed to be dumped to the storage system. On the other hand, soft errors striking the simulations are not negligible considering the great number of components in the supercomputer and a single scientific execution spending days to finish. Therefore, it is meaningful to reduce the I/O time and harden the resilience of those large scale simulations. Though hardware solutions like designing new storage systems or error resilient computing devices have great generality, it usually takes longer development time and much more effort than software solutions. This thesis seeks software solutions by designing efficient and resilient lossy compressors for large scale scientific simulations.To improve the overall simulation performance, we propose a better lossy compressor which has a much higher compression ratio to reduce the I/O time significantly. More specifically, we focus on particle based scientific simulations. As we know, greater compression ratios imply less data to be written to the storage system which in turn, reduces I/O time. The state-of-art lossy compressor takes the advantage of spatial smoothness to achieve high compression ratios. However, particle based simulations have very limited smoothness in space which leads to inadequate compression ratios. In contrast, we propose to exploit smoothness in time for lossy compression and design an optimized compression model based on the existing lossy compressor. Results show our optimized compression model achieves much better compression ratios and significantly reduces I/O time at large scale.To improve the resilience of the simulation applications equipped with lossy compression, we design soft error resilient schemes for lossy compressors. First, we provide an algorithm-scope protection for one widely used lossy compressor named SZ. Then, we provide an application-scope protection that can be applied to all error-bounded lossy compressors. The algorithm-scope protection can only cover soft errors happening during the execution of the lossy compression itself while the application-scope protection can cover soft errors during simulation, lossy compression and even data writing. Both the algorithm- scope and the application-scope protections can provide significantly better resilience but keep the performance overhead low.

    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/
  • 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: Xu, Jialin;

    Protein Tyrosine Phosphatases (PTPs) are drug target candidates due to their role in cell signaling and involvement in the pathologies of various diseases. Difficulty in developing orthosteric inhibitors of PTPs has raised interest in the development of allosteric inhibitors. Previous studies have identified an allosteric mechanism in receptor-type protein tyrosine phosphatase α (RPTPα), yet the mechanism requires further characterization for future development of small molecule therapeutics. In this study, through comparing RPTPα and the closely related RPTPε, we achieved the identification and in vitro validation of a segment of RPTPα (residues 261-330) responsible for its allosteric effect. It lays the groundwork for identification of amino acid residues participating in the establishment of allostery, which is a step in fully elucidating the allosteric mechanism.

    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: Cole, William TS; Fellers, Raymond S; Viant, Mark R; Saykally, Richard J;

    Hydrogen bonds in solid and liquid water are formed and broken via librational vibrations, hence characterizing the details of these motions is vital to understanding these important dynamics. Here we report the measurement and assignment of 875 transitions comprising 6 subbands originating from out-of-plane librational transitions of the water pentamer-d10 near 512 cm-1. The precisely measured (ca. 1 ppm) transitions reveal bifurcation splittings of ∼1884 MHz, a ∼4000× enhancement over ground state splittings and 100× greater than predicted by theory. The pentamer is thus the third water cluster to display greatly enhanced bifurcation tunneling upon single quantum excitation of librational vibrations. From the intensity pattern of the observed transitions, the mechanism of bifurcation is established by comparison with theoretical predictions.

    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/ eScholarship - Unive...arrow_drop_down
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: McLaughlin, Katherine Rumjahn;

    Respondent-driven sampling (RDS) is a network sampling methodology used worldwide to sample key populations at high risk for HIV/AIDS who often practice stigmatized/illegal behaviors and are not typically reachable by conventional sampling techniques. In RDS, study participants recruit their peers to enroll, resulting in a sampling mechanism that is unknown to researchers. Current estimators for RDS data require many assumptions about the sampling process, including that recruiters choose people from their network uniformly at random to participate in the study. However, this is likely not true in practice. We believe that people recruit based on observable covariates, such as age, frequency of interaction, geography, socioeconomic status, or social capital.To model preferential recruitment, I develop a sequential two-sided rational-choice framework, referred to as the RCPR model. At each wave of recruitment, each recruiter has a utility for selecting each peer, and symmetrically each peer has a utility for being recruited by each recruiter. Each person also has utilities for selecting themself (not recruiting or not participating). People in the network behave in a way that maximizes their utility given the constraints of the network and the restrictions on recruitment. Although a person's utility is not observed, it can be modeled as a linear combination of observable nodal or dyadic covariates plus unobserved pair-specific heterogeneities. This framework allows generative probabilistic network models to be created for the RDS recruitment process. The models can incorporate observable characteristics of the population and have interpretable parameters. It greatly increases the sophistication of the modeling of the RDS sampling mechanism. Inference can be made about the preference coefficients by maximizing the likelihood of the observed recruitment chain given the observed covariates. As the likelihood is computationally intractable, I develop a Bayesian framework where inference is made feasible by approximating the posterior distribution of the preference coefficients via a Markov chain Monte Carlo algorithm. Each update step samples new values of the preference coefficients and utilities via Metropolis-Hastings, subject to constraints. New prevalence estimates can be calculated be generating many recruitment chains from the population using the RCPR coefficients, then directly obtaining the first-order and second-order inclusion probabilities. This framework allows the incorporation of covariates we think effect recruitment into the sample weights.

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao eScholarship - Unive...arrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao eScholarship - Unive...arrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
  • 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: Lybrand, Eric;

    This thesis explores the topic of quantization in the context of data science and digital signal processing. It is already well-known that quantization plays a critical role in signal processing given the ubiquity of digital devices. Applications of quantization to data science have only recently started emerging. Perhaps the most important application is that of quantizing neural networks. Below, we consider quantization in three particular contexts. The first chapter considers the problem of quantizing a pre-trained neural network with a data-driven approach. I propose a novel algorithm for quantizing the weights of a hidden unit in a given layer using a greedy path following algorithm which is equivalent to running a dynamical system. I prove that this dynamical system is stable when quantizing a single layer neural network, or equivalently the first layer of a multi-layer network, when the training data are Gaussian. I then give bounds on the generalization error of the learned quantization and describe how these bounds may be tightened when the feature data lay in a low-dimensional subspace. In the second chapter, I generalize a 2016 result proven by Saab, Wang, and Yilmaz for recovering sparse vectors to the setting of low-rank matrices. Specifically, I show that low-rank matrices may be robustly recovered from \(\Sigma\Delta\) quantized subgaussian linear measurements. Using these techniques I show that the reconstruction error associated with our methods decays polynomially with the oversampling factor, and that one can leverage this result to obtain root-exponential accuracy by optimizing over the choice of quantization scheme. Additionally, if a random encoding of the quantized measurements is used then the reconstruction bound exhibits a near-optimal exponential rate-distortion trade-off. In the third chapter, I generalize work done by Iwen, Krahmer, Krause-Solberg, and Maly in 2018 to prove that signal recovery is possible when given \(\Sigma\Delta\) quantized linear measurements of signals from a manifold where the manifold is only approximately known through a Geometric Multi-Resolution Analysis. In addition to proving error bounds that outperform those in the Memoryless Scalar Quantization approach taken in the aforementioned work, we also extend the ensemble of linear measurements beyond the Gaussian case.

    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: holm, Adam;

    How do people process feedback that violates their expectations? To address this question, our study uses an auditory delayed match-to-sample task with a novel half-congruent, half-incongruent presentation of response feedback. We hypothesized that feedback-related surprise would have effects on event-related potential (ERP) amplitude and latency in a “dose-dependent” manner (largest effect on the easiest trials, smallest effect on the hardest). The resulting waveform was identified as the feedback-related negativity (FRN). While our hypothesis was not confirmed, the results were noteworthy. Despite the feedback’s visual nature, the scalp tomography was highly auditory. This suggests that the FRN may be partially generated in the auditory cortex. To the best of our knowledge, this is a new finding within the FRN literature.

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    Authors: Leung, Allen;

    Biological processes resulting in observable cell state changes, such as synaptic plasticity inneuronal dendritic spines and muscular hypertrophy in skeletal muscles, share common characteristics. Both are influenced by calcium signaling, metabolic networks, mitochondria, and protein kinase activation. This research presents computational models of these processes, offering insights into synaptic plasticity and the skeletal muscle response to exercise. The first model is a spatial representation of mitochondrial ATP generation during calcium signaling in neurons, emphasizing the role of mitochondrial ER contact sites in increasing calcium levels in the mitochondria, thus enhancing mitochondrial potential. This model underscores the importance of subcellular geometry, metabolic consumption rates, and transport processes in ATP production, in addition to enzymatic activity. The second model is a compartmental model exploring the role of signaling frequency in protein kinase activation in dendritic spines. This model analyzes the interaction between the canonical neuronal signaling cascade, the AMP-Activated Protein Kinase (AMPK) cascade, and the insulin signaling cascade in conditions of high neurotransmitter stimulation rates, which activate calcium signaling and consume significant cellular energy. The final model, a logic-based representation of skeletal muscle signaling in response to resistance, endurance, and sprint exercise, investigates potential mechanisms of exercise-induced changes in mitochondrial morphology. Together, these models deepen our understanding of the dynamic interplay between signaling and metabolism in synaptic plasticity and exercise physiology, laying the groundwork for further investigation and potential development of therapeutic strategies for neurological disorders and improvements in exercise efficiency.

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    Authors: Li, Jun; Zhao, Patrick X.;

    Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

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    Frontiers in Plant Science
    2016 . Peer-reviewed
    Data sources: Frontiers
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      Frontiers in Plant Science
      2016 . Peer-reviewed
      Data sources: Frontiers
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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: Chater, John Matthew;

    Pomegranate (Punica granatum L.) is an ancient deciduous fruit tree crop in the family Lythraceae. Pomegranate juice is a highly valued beverage, long believed by many of the world’s cultures to possess medicinal properties. Recently the juice has been demonstrated to contain large quantities of polyphenolic compounds with powerful antioxidant properties. Commercial pomegranate planting area has increased substantially in the western hemisphere due to increased consumer interest. Low nursery inventory has caused many farmers to propagate their own trees and limited availability of only a few cultivars is believed to have contributed to the lack of diversity in the market. ‘Wonderful,’ the industry standard, has been propagated in the U.S. for decades and dominates the market, leading to the present-day monoculture. The USDA-ARS pomegranate germplasm collection conserves approximately 280 cultivars, many of which have not been evaluated for commercial production. In this dissertation, 14 preselected pomegranate cultivars from the USDA collection were evaluated: 1) to develop protocols that optimize propagation of pomegranate for nurseries and growers; 2) in new field trials planted specifically to determine establishment rates, productivity and eco-physiological performance of different cultivars in inland versus coastal environments; and 3) to establish dates of fruit maturity, identify unique cultivars with consumer-friendly traits, and to select candidates that meet or exceed juice quality parameters of Wonderful. The overall goal of this research was to identify promising pomegranate cultivars with the potential to be developed for commercial production in coastal and inland areas of southern and central California. Propagation experiments determined that some pomegranate cultivars were difficult to root. Establishment rates and precocity were significantly different among cultivars and between sites, with the inland planting producing more fruit than the coastal site. Juice quality for 14 cultivars was chemically analyzed with spectrophotometry, refractometry, titration, nuclear magnetic resonance, ion and liquid chromatography to identify candidate cultivars meeting or exceeding Wonderful juice quality specifications. This research was the first of its kind to establish experimental field trials of pomegranate germplasm in California to quantify and provide phenotypic, eco-physiological and horticultural data for growers, breeders, and the food and beverage industries.

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    Authors: Tcacenco, Andrei;

    My research looks at Soviet republics outside the Russian Federation such as the Ukrainian and Moldavian SSRs, and takes a more localized approach to understanding the state’s campaigns to produce a moral Soviet citizen during the Late Socialist period of Soviet history. I look at how interactions between Soviet citizens in the periphery and Central Party organs resulted in a dynamic, negotiated understanding of socialist morality and concepts of the New Socialist Person in new discursive spaces of home entertainment, especially television and radio. Soviet citizens utilized mass media to spark debates about the meaning of Soviet identity, nationalism and morality, and sometimes to express outright hostility toward the Soviet state. The appropriation of official Soviet language in the periphery led to the creation of new, unpredictable meanings in Soviet discourse. I show that some former Soviet citizens often viewed their national identity as a form of resistance to the Soviet state, while others saw little contradiction between their national and Soviet identities. This paradox is central to my project, as I aim to explore the fluidity, ambiguity, and variation of national and Soviet identity. Ultimately, I argue that the conversations and arguments surrounding morality led to the collapse of the Soviet Union by December 1991.

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    Authors: Li, Sihuan;

    Extremely large scale scientific simulation applications have been very important in many scientific domains including cosmology, climate, fluid dynamics, chemistry and so on. It has been shown that running the simulations at a larger scale can bring more discoveries. On one hand, with the increasing scale of those applications, the saturated I/O bandwidth can slow down the execution of the simulation significantly because of the huge amount of data needed to be dumped to the storage system. On the other hand, soft errors striking the simulations are not negligible considering the great number of components in the supercomputer and a single scientific execution spending days to finish. Therefore, it is meaningful to reduce the I/O time and harden the resilience of those large scale simulations. Though hardware solutions like designing new storage systems or error resilient computing devices have great generality, it usually takes longer development time and much more effort than software solutions. This thesis seeks software solutions by designing efficient and resilient lossy compressors for large scale scientific simulations.To improve the overall simulation performance, we propose a better lossy compressor which has a much higher compression ratio to reduce the I/O time significantly. More specifically, we focus on particle based scientific simulations. As we know, greater compression ratios imply less data to be written to the storage system which in turn, reduces I/O time. The state-of-art lossy compressor takes the advantage of spatial smoothness to achieve high compression ratios. However, particle based simulations have very limited smoothness in space which leads to inadequate compression ratios. In contrast, we propose to exploit smoothness in time for lossy compression and design an optimized compression model based on the existing lossy compressor. Results show our optimized compression model achieves much better compression ratios and significantly reduces I/O time at large scale.To improve the resilience of the simulation applications equipped with lossy compression, we design soft error resilient schemes for lossy compressors. First, we provide an algorithm-scope protection for one widely used lossy compressor named SZ. Then, we provide an application-scope protection that can be applied to all error-bounded lossy compressors. The algorithm-scope protection can only cover soft errors happening during the execution of the lossy compression itself while the application-scope protection can cover soft errors during simulation, lossy compression and even data writing. Both the algorithm- scope and the application-scope protections can provide significantly better resilience but keep the performance overhead low.

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    Authors: Xu, Jialin;

    Protein Tyrosine Phosphatases (PTPs) are drug target candidates due to their role in cell signaling and involvement in the pathologies of various diseases. Difficulty in developing orthosteric inhibitors of PTPs has raised interest in the development of allosteric inhibitors. Previous studies have identified an allosteric mechanism in receptor-type protein tyrosine phosphatase α (RPTPα), yet the mechanism requires further characterization for future development of small molecule therapeutics. In this study, through comparing RPTPα and the closely related RPTPε, we achieved the identification and in vitro validation of a segment of RPTPα (residues 261-330) responsible for its allosteric effect. It lays the groundwork for identification of amino acid residues participating in the establishment of allostery, which is a step in fully elucidating the allosteric mechanism.

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    Authors: Cole, William TS; Fellers, Raymond S; Viant, Mark R; Saykally, Richard J;

    Hydrogen bonds in solid and liquid water are formed and broken via librational vibrations, hence characterizing the details of these motions is vital to understanding these important dynamics. Here we report the measurement and assignment of 875 transitions comprising 6 subbands originating from out-of-plane librational transitions of the water pentamer-d10 near 512 cm-1. The precisely measured (ca. 1 ppm) transitions reveal bifurcation splittings of ∼1884 MHz, a ∼4000× enhancement over ground state splittings and 100× greater than predicted by theory. The pentamer is thus the third water cluster to display greatly enhanced bifurcation tunneling upon single quantum excitation of librational vibrations. From the intensity pattern of the observed transitions, the mechanism of bifurcation is established by comparison with theoretical predictions.

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    Authors: McLaughlin, Katherine Rumjahn;

    Respondent-driven sampling (RDS) is a network sampling methodology used worldwide to sample key populations at high risk for HIV/AIDS who often practice stigmatized/illegal behaviors and are not typically reachable by conventional sampling techniques. In RDS, study participants recruit their peers to enroll, resulting in a sampling mechanism that is unknown to researchers. Current estimators for RDS data require many assumptions about the sampling process, including that recruiters choose people from their network uniformly at random to participate in the study. However, this is likely not true in practice. We believe that people recruit based on observable covariates, such as age, frequency of interaction, geography, socioeconomic status, or social capital.To model preferential recruitment, I develop a sequential two-sided rational-choice framework, referred to as the RCPR model. At each wave of recruitment, each recruiter has a utility for selecting each peer, and symmetrically each peer has a utility for being recruited by each recruiter. Each person also has utilities for selecting themself (not recruiting or not participating). People in the network behave in a way that maximizes their utility given the constraints of the network and the restrictions on recruitment. Although a person's utility is not observed, it can be modeled as a linear combination of observable nodal or dyadic covariates plus unobserved pair-specific heterogeneities. This framework allows generative probabilistic network models to be created for the RDS recruitment process. The models can incorporate observable characteristics of the population and have interpretable parameters. It greatly increases the sophistication of the modeling of the RDS sampling mechanism. Inference can be made about the preference coefficients by maximizing the likelihood of the observed recruitment chain given the observed covariates. As the likelihood is computationally intractable, I develop a Bayesian framework where inference is made feasible by approximating the posterior distribution of the preference coefficients via a Markov chain Monte Carlo algorithm. Each update step samples new values of the preference coefficients and utilities via Metropolis-Hastings, subject to constraints. New prevalence estimates can be calculated be generating many recruitment chains from the population using the RCPR coefficients, then directly obtaining the first-order and second-order inclusion probabilities. This framework allows the incorporation of covariates we think effect recruitment into the sample weights.

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    Authors: Lybrand, Eric;

    This thesis explores the topic of quantization in the context of data science and digital signal processing. It is already well-known that quantization plays a critical role in signal processing given the ubiquity of digital devices. Applications of quantization to data science have only recently started emerging. Perhaps the most important application is that of quantizing neural networks. Below, we consider quantization in three particular contexts. The first chapter considers the problem of quantizing a pre-trained neural network with a data-driven approach. I propose a novel algorithm for quantizing the weights of a hidden unit in a given layer using a greedy path following algorithm which is equivalent to running a dynamical system. I prove that this dynamical system is stable when quantizing a single layer neural network, or equivalently the first layer of a multi-layer network, when the training data are Gaussian. I then give bounds on the generalization error of the learned quantization and describe how these bounds may be tightened when the feature data lay in a low-dimensional subspace. In the second chapter, I generalize a 2016 result proven by Saab, Wang, and Yilmaz for recovering sparse vectors to the setting of low-rank matrices. Specifically, I show that low-rank matrices may be robustly recovered from \(\Sigma\Delta\) quantized subgaussian linear measurements. Using these techniques I show that the reconstruction error associated with our methods decays polynomially with the oversampling factor, and that one can leverage this result to obtain root-exponential accuracy by optimizing over the choice of quantization scheme. Additionally, if a random encoding of the quantized measurements is used then the reconstruction bound exhibits a near-optimal exponential rate-distortion trade-off. In the third chapter, I generalize work done by Iwen, Krahmer, Krause-Solberg, and Maly in 2018 to prove that signal recovery is possible when given \(\Sigma\Delta\) quantized linear measurements of signals from a manifold where the manifold is only approximately known through a Geometric Multi-Resolution Analysis. In addition to proving error bounds that outperform those in the Memoryless Scalar Quantization approach taken in the aforementioned work, we also extend the ensemble of linear measurements beyond the Gaussian case.

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    Authors: holm, Adam;

    How do people process feedback that violates their expectations? To address this question, our study uses an auditory delayed match-to-sample task with a novel half-congruent, half-incongruent presentation of response feedback. We hypothesized that feedback-related surprise would have effects on event-related potential (ERP) amplitude and latency in a “dose-dependent” manner (largest effect on the easiest trials, smallest effect on the hardest). The resulting waveform was identified as the feedback-related negativity (FRN). While our hypothesis was not confirmed, the results were noteworthy. Despite the feedback’s visual nature, the scalp tomography was highly auditory. This suggests that the FRN may be partially generated in the auditory cortex. To the best of our knowledge, this is a new finding within the FRN literature.

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    Authors: Leung, Allen;

    Biological processes resulting in observable cell state changes, such as synaptic plasticity inneuronal dendritic spines and muscular hypertrophy in skeletal muscles, share common characteristics. Both are influenced by calcium signaling, metabolic networks, mitochondria, and protein kinase activation. This research presents computational models of these processes, offering insights into synaptic plasticity and the skeletal muscle response to exercise. The first model is a spatial representation of mitochondrial ATP generation during calcium signaling in neurons, emphasizing the role of mitochondrial ER contact sites in increasing calcium levels in the mitochondria, thus enhancing mitochondrial potential. This model underscores the importance of subcellular geometry, metabolic consumption rates, and transport processes in ATP production, in addition to enzymatic activity. The second model is a compartmental model exploring the role of signaling frequency in protein kinase activation in dendritic spines. This model analyzes the interaction between the canonical neuronal signaling cascade, the AMP-Activated Protein Kinase (AMPK) cascade, and the insulin signaling cascade in conditions of high neurotransmitter stimulation rates, which activate calcium signaling and consume significant cellular energy. The final model, a logic-based representation of skeletal muscle signaling in response to resistance, endurance, and sprint exercise, investigates potential mechanisms of exercise-induced changes in mitochondrial morphology. Together, these models deepen our understanding of the dynamic interplay between signaling and metabolism in synaptic plasticity and exercise physiology, laying the groundwork for further investigation and potential development of therapeutic strategies for neurological disorders and improvements in exercise efficiency.

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    Authors: Li, Jun; Zhao, Patrick X.;

    Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

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    Frontiers in Plant Science
    2016 . Peer-reviewed
    Data sources: Frontiers
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      Frontiers in Plant Science
      2016 . Peer-reviewed
      Data sources: Frontiers