Search results

Title: Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae).
Creator: Young, Andrew Donovan, Lemmon, Alan R, Skevington, Jeffrey H, Mengual, Ximo, Ståhls, Gunilla, Reemer, Menno, Jordaens, Kurt, Kelso, Scott, Lemmon, Emily Moriarty, Hauser, Martin...
Show moreYoung, Andrew Donovan, Lemmon, Alan R, Skevington, Jeffrey H, Mengual, Ximo, Ståhls, Gunilla, Reemer, Menno, Jordaens, Kurt, Kelso, Scott, Lemmon, Emily Moriarty, Hauser, Martin, De Meyer, Marc, Misof, Bernhard, Wiegmann, Brian M
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Abstract/Description: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse...
Show moreAnchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.
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Date Issued: 2016-06-29
Identifier: FSU_pmch_27357120, 10.1186/s12862-016-0714-0, PMC4928351, 27357120, 27357120, 10.1186/s12862-016-0714-0
Format: Citation

Title: A Landmark-Free Method for Three-Dimensional Shape Analysis.
Creator: Pomidor, Benjamin J., Makedonska, Jana, Slice, Dennis E.
Abstract/Description: Background The tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts....
Show moreBackground The tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts. This is especially true of those investigating smooth or featureless surfaces. Methods In this paper, we present a new method to perform this transformation for data obtained from high-resolution scanning technology. This method uses surface scans, instead of landmarks, to calculate a shape difference metric analogous to Procrustes distance and perform superimposition. This is accomplished by building upon and extending the Iterative Closest Point algorithm. We also explore some new ways this data can be used; for example, we can calculate an averaged surface directly and visualize point-wise shape information over this surface. Finally, we briefly demonstrate this method on a set of primate skulls and compare the results of the new methodology with traditional geometric morphometric analysis.
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Date Issued: 2016-03-08
Identifier: FSU_libsubv1_wos_000371991300024, 10.1371/journal.pone.0150368
Format: Citation

Title: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life.
Creator: Hamilton, Chris A, Lemmon, Alan R, Lemmon, Emily Moriarty, Bond, Jason E
Abstract/Description: Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds...
Show moreDespite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
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Date Issued: 2016-10-13
Identifier: FSU_pmch_27733110, 10.1186/s12862-016-0769-y, PMC5062932, 27733110, 27733110, 10.1186/s12862-016-0769-y
Format: Citation

Title: A MULTISCALE IMPLEMENTATION BASED ON ADAPTIVE MESH REFINEMENT FOR THE NONLOCAL PERIDYNAMICS MODEL IN ONE DIMENSION.
Creator: Xu, Feifei, Gunzburger, Max, Burkardt, John, Du, Qiang
Abstract/Description: Peridynamics models for solid mechanics feature a horizon parameter (5 that specifies the maximum extent of nonlocal interactions. In this paper, a multiscale implementation of peridynamics models is proposed. In regions in which the displacement field is smooth, grid sizes are large relative to delta, leading to a local behavior of the models, whereas in regions containing defects, e.g., cracks, delta is larger than the grid size. Discontinuous (continuous) Galerkin finite element...
Show morePeridynamics models for solid mechanics feature a horizon parameter (5 that specifies the maximum extent of nonlocal interactions. In this paper, a multiscale implementation of peridynamics models is proposed. In regions in which the displacement field is smooth, grid sizes are large relative to delta, leading to a local behavior of the models, whereas in regions containing defects, e.g., cracks, delta is larger than the grid size. Discontinuous (continuous) Galerkin finite element discretizations are used in regions where defects do (do not) occur. Moreover, in regions where no defects occur, the multiscale implementation seamlessly transitions to the use of a standard finite element discretization of a corresponding PDE model. Here, we demonstrate the multiscale implementation in a simple one-dimensional setting. An adaptive strategy is incorporated to detect discontinuities and effect grid refinement, resulting in a highly accurate and efficient implementation of peridynamics.
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Date Issued: 2016
Identifier: FSU_libsubv1_wos_000373366500014, 10.1137/15M1010300
Format: Citation

Title: Anchored Enrichment Dataset For True Flies (order Diptera) Reveals Insights Into The Phylogeny Of Flower Flies (family Syrphidae).
Creator: Young, Andrew Donovan, Lemmon, Alan R., Skevington, Jeffrey H., Mengual, Ximo, Stahls, Gunilla, Reemer, Menno, Jordaens, Kurt, Kelso, Scott, Lemmon, Emily Moriarty, Hauser,...
Show moreYoung, Andrew Donovan, Lemmon, Alan R., Skevington, Jeffrey H., Mengual, Ximo, Stahls, Gunilla, Reemer, Menno, Jordaens, Kurt, Kelso, Scott, Lemmon, Emily Moriarty, Hauser, Martin, De Meyer, Marc, Misof, Bernhard, Wiegmann, Brian M.
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Abstract/Description: Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly...
Show moreBackground: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. Results: We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Conclusions: Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.
Show less
Date Issued: 2016-06-29
Identifier: FSU_libsubv1_wos_000378675500003, 10.1186/s12862-016-0714-0
Format: Citation

Title: Estimating daily air temperatures over the Tibetan Plateau by dynamically integrating MODIS LST data.
Creator: Zhang, Hongbo, Zhang, Fan, Ye, Ming, Che, Tao, Zhang, Guoqing
Abstract/Description: Recently, remotely sensed land surface temperature (LST) data have been used to estimate air temperatures because of the sparseness of station measurements in remote mountainous areas. Due to the availability and accuracy of Moderate Resolution Imaging Spectroradiometer (MODIS) LST data, the use of a single term or a fixed combination of terms (e.g., Terra/Aqua night and Terra/Aqua day), as used in previous estimation methods, provides only limited practical application. Furthermore, the...
Show moreRecently, remotely sensed land surface temperature (LST) data have been used to estimate air temperatures because of the sparseness of station measurements in remote mountainous areas. Due to the availability and accuracy of Moderate Resolution Imaging Spectroradiometer (MODIS) LST data, the use of a single term or a fixed combination of terms (e.g., Terra/Aqua night and Terra/Aqua day), as used in previous estimation methods, provides only limited practical application. Furthermore, the estimation accuracy may be affected by different combinations and variable data quality among the MODIS LST terms and models. This study presents a method that dynamically integrates the available LST terms to estimate the daily mean air temperature and simultaneously considers model selection, data quality, and estimation accuracy. The results indicate that the differences in model performance are related to the combinations of LST terms and their data quality. The spatially averaged cloud cover of similar to 14% for the developed product between 2003 and 2010 is much lower than the 35-54% for single LST terms. The average cross-validation root-mean-square difference values are approximately 2 degrees C. This study identifies the best LST combinations and statistical models and provides an efficient method for daily air temperature estimation with low cloud blockage over the Tibetan Plateau (TP). The developed data set and the method proposed in this study can help alleviate the problem of sparse air temperature data over the TP.
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Date Issued: 2016-10
Identifier: FSU_libsubv1_wos_000386976100033, 10.1002/2016JD025154
Format: Citation

Title: Evaluating marginal likelihood with thermodynamic integration method and comparison with several other numerical methods.
Creator: Liu, Peigui, Elshall, Ahmed S., Ye, Ming, Beerli, Peter, Zeng, Xiankui, Lu, Dan, Tao, Yuezan
Abstract/Description: Evaluating marginal likelihood is the most critical and computationally expensive task, when conducting Bayesian model averaging to quantify parametric and model uncertainties. The evaluation is commonly done by using Laplace approximations to evaluate semianalytical expressions of the marginal likelihood or by using Monte Carlo (MC) methods to evaluate arithmetic or harmonic mean of a joint likelihood function. This study introduces a new MC method, i.e., thermodynamic integration, which has...
Show moreEvaluating marginal likelihood is the most critical and computationally expensive task, when conducting Bayesian model averaging to quantify parametric and model uncertainties. The evaluation is commonly done by using Laplace approximations to evaluate semianalytical expressions of the marginal likelihood or by using Monte Carlo (MC) methods to evaluate arithmetic or harmonic mean of a joint likelihood function. This study introduces a new MC method, i.e., thermodynamic integration, which has not been attempted in environmental modeling. Instead of using samples only from prior parameter space (as in arithmetic mean evaluation) or posterior parameter space (as in harmonic mean evaluation), the thermodynamic integration method uses samples generated gradually from the prior to posterior parameter space. This is done through a path sampling that conducts Markov chain Monte Carlo simulation with different power coefficient values applied to the joint likelihood function. The thermodynamic integration method is evaluated using three analytical functions by comparing the method with two variants of the Laplace approximation method and three MC methods, including the nested sampling method that is recently introduced into environmental modeling. The thermodynamic integration method outperforms the other methods in terms of their accuracy, convergence, and consistency. The thermodynamic integration method is also applied to a synthetic case of groundwater modeling with four alternative models. The application shows that model probabilities obtained using the thermodynamic integration method improves predictive performance of Bayesian model averaging. The thermodynamic integration method is mathematically rigorous, and its MC implementation is computationally general for a wide range of environmental problems.
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Date Issued: 2016-02
Identifier: FSU_libsubv1_wos_000373117300008, 10.1002/2014WR016718
Format: Citation

Title: Extending the density functional embedding theory to finite temperature and an efficient iterative method for solving for embedding potentials.
Creator: Huang, Chen
Abstract/Description: A key element in the density functional embedding theory (DFET) is the embedding potential. We discuss two major issues related to the embedding potential: (1) its non-uniqueness and (2) the numerical difficulty for solving for it, especially for the spin-polarized systems. To resolve the first issue, we extend DFET to finite temperature: all quantities, such as the subsystem densities and the total system's density, are calculated at a finite temperature. This is a physical extension since...
Show moreA key element in the density functional embedding theory (DFET) is the embedding potential. We discuss two major issues related to the embedding potential: (1) its non-uniqueness and (2) the numerical difficulty for solving for it, especially for the spin-polarized systems. To resolve the first issue, we extend DFET to finite temperature: all quantities, such as the subsystem densities and the total system's density, are calculated at a finite temperature. This is a physical extension since materials work at finite temperatures. We show that the embedding potential is strictly unique at T > 0. To resolve the second issue, we introduce an efficient iterative embedding potential solver. We discuss how to relax the magnetic moments in subsystems and how to equilibrate the chemical potentials across subsystems. The solver is robust and efficient for several non-trivial examples, in all of which good quality spin-polarized embedding potentials were obtained. We also demonstrate the solver on an extended periodic system: iron body-centered cubic (110) surface, which is related to the modeling of the heterogeneous catalysis involving iron, such as the Fischer-Tropsch and the Haber processes. This work would make it efficient and accurate to perform embedding simulations of some challenging material problems, such as the heterogeneous catalysis and the defects of complicated spin configurations in electronic materials. (C) 2016 AIP Publishing LLC.
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Date Issued: 2016-03-28
Identifier: FSU_libsubv1_wos_000373644400009, 10.1063/1.4944464
Format: Citation

Title: A Measure-Theoretic Algorithm for Estimating Bottom Friction in a Coastal Inlet: Case Study of Bay St. Louis during Hurricane Gustav (2008).
Creator: Graham, Lindley, Butler, Troy, Walsh, Scott, Dawson, Clint, Westerink, Joannes J.
Abstract/Description: The majority of structural damage and loss of life during a hurricane is due to storm surge, thus it is important for communities in hurricane-prone regions to understand their risk due to surge. Storm surge in particular is largely influenced by coastal features such as topography/bathymetry and bottom roughness. Bottom roughness determines how much resistance there is to the flow. Manning’s formula can be used to model the bottom stress with the Manning’s n coefficient, a spatially...
Show moreThe majority of structural damage and loss of life during a hurricane is due to storm surge, thus it is important for communities in hurricane-prone regions to understand their risk due to surge. Storm surge in particular is largely influenced by coastal features such as topography/bathymetry and bottom roughness. Bottom roughness determines how much resistance there is to the flow. Manning’s formula can be used to model the bottom stress with the Manning’s n coefficient, a spatially dependent field. Given a storm surge model and a set of model outputs, an inverse problem may be solved to determine probable Manning’s n fields to use for predictive simulations. The inverse problem is formulated and solved in a measure-theoretic framework using the state-ofthe-art Advanced Circulation (ADCIRC) storm surge model. The use of measure theory requires minimal assumptions and involves the direct inversion of the physics-based map from model inputs to output data determined by the ADCIRC model. Thus, key geometric relationships in this map are preserved and exploited. By using a recently available subdomain implementation of ADCIRC that significantly reduces the computational cost of forward model solves, the authors demonstrate the method on a case study using data obtained from an ADCIRC hindcast study of Hurricane Gustav (2008) to quantify uncertainties in Manning’s n within Bay St. Louis. However, the methodology is general and could be applied to any inverse problem that involves a map from model input to output quantities of interest.
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Date Issued: 2017-02-21
Identifier: FSU_libsubv1_scholarship_submission_1487883656, 10.1175/MWR-D-16-0149.1
Format: Citation

Title: A Measure-theoretic Algorithm For Estimating Bottom Friction In A Coastal Inlet: Case Study Of Bay St. Louis During Hurricane Gustav (2008).
Creator: Graham, Lindley, Butler, Troy, Walsh, Scott, Dawson, Clint, Westerink, Joannes J.
Abstract/Description: The majority of structural damage and loss of life during a hurricane is due to storm surge, thus it is important for communities in hurricane-prone regions to understand their risk due to surge. Storm surge in particular is largely influenced by coastal features such as topography/ bathymetry and bottom roughness. Bottom roughness determines how much resistance there is to the flow. Manning's formula can be used to model the bottom stress with the Manning's n coefficient, a spatially...
Show moreThe majority of structural damage and loss of life during a hurricane is due to storm surge, thus it is important for communities in hurricane-prone regions to understand their risk due to surge. Storm surge in particular is largely influenced by coastal features such as topography/ bathymetry and bottom roughness. Bottom roughness determines how much resistance there is to the flow. Manning's formula can be used to model the bottom stress with the Manning's n coefficient, a spatially dependent field. Given a storm surge model and a set of model outputs, an inverse problem may be solved to determine probable Manning's n fields to use for predictive simulations. The inverse problem is formulated and solved in a measure-theoretic framework using the state-ofthe- art Advanced Circulation (ADCIRC) storm surge model. The use of measure theory requires minimal assumptions and involves the direct inversion of the physics-based map from model inputs to output data determined by the ADCIRC model. Thus, key geometric relationships in this map are preserved and exploited. By using a recently available subdomain implementation of ADCIRC that significantly reduces the computational cost of forward model solves, the authors demonstrate the method on a case study using data obtained from anADCIRC hindcast study of HurricaneGustav (2008) to quantify uncertainties in Manning's n within Bay St. Louis. However, the methodology is general and could be applied to any inverse problem that involves a map from model input to output quantities of interest.
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Date Issued: 2017-03
Identifier: FSU_libsubv1_wos_000399327900006, 10.1175/MWR-D-16-0149.1
Format: Citation

Title: Inter- And Intra-observer Agreement Of Bi-rads-based Subjective Visual Estimation Of Amount Of Fibroglandular Breast Tissue With Magnetic Resonance Imaging.
Creator: Wengert, G. J., Helbich, T. H., Woitek, R., Kapetas, P., Clauser, P., Baltzer, P. A., Vogl, W.-D., Weber, M., Meyer-Baese, A., Pinker, Katja
Abstract/Description: To evaluate the inter-/intra-observer agreement of BI-RADS-based subjective visual estimation of the amount of fibroglandular tissue (FGT) with magnetic resonance imaging (MRI), and to investigate whether FGT assessment benefits from an automated, observer-independent, quantitative MRI measurement by comparing both approaches. Eighty women with no imaging abnormalities (BI-RADS 1 and 2) were included in this institutional review board (IRB)-approved prospective study. All women underwent un...
Show moreTo evaluate the inter-/intra-observer agreement of BI-RADS-based subjective visual estimation of the amount of fibroglandular tissue (FGT) with magnetic resonance imaging (MRI), and to investigate whether FGT assessment benefits from an automated, observer-independent, quantitative MRI measurement by comparing both approaches. Eighty women with no imaging abnormalities (BI-RADS 1 and 2) were included in this institutional review board (IRB)-approved prospective study. All women underwent un-enhanced breast MRI. Four radiologists independently assessed FGT with MRI by subjective visual estimation according to BI-RADS. Automated observer-independent quantitative measurement of FGT with MRI was performed using a previously described measurement system. Inter-/intra-observer agreements of qualitative and quantitative FGT measurements were assessed using Cohen's kappa (k). Inexperienced readers achieved moderate inter-/intra-observer agreement and experienced readers a substantial inter- and perfect intra-observer agreement for subjective visual estimation of FGT. Practice and experience reduced observer-dependency. Automated observer-independent quantitative measurement of FGT was successfully performed and revealed only fair to moderate agreement (k = 0.209-0.497) with subjective visual estimations of FGT. Subjective visual estimation of FGT with MRI shows moderate intra-/inter-observer agreement, which can be improved by practice and experience. Automated observer-independent quantitative measurements of FGT are necessary to allow a standardized risk evaluation. aEuro cent Subjective FGT estimation with MRI shows moderate intra-/inter-observer agreement in inexperienced readers. aEuro cent Inter-observer agreement can be improved by practice and experience. aEuro cent Automated observer-independent quantitative measurements can provide reliable and standardized assessment of FGT with MRI.
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Date Issued: 2016-11
Identifier: FSU_libsubv1_wos_000385248600016, 10.1007/s00330-016-4274-x
Format: Citation

Title: Hyperspherical Sparse Approximation Techniques for High-Dimensional Discontinuity Detection.
Creator: Zhang, Guannan, Webster, Clayton G., Gunzburger, Max, Burkardt, John
Abstract/Description: This work proposes a hyperspherical sparse approximation framework for detecting jump discontinuities in functions in high-dimensional spaces. The need for a novel approach results from the theoretical and computational inefficiencies of well-known approaches, such as adaptive sparse grids, for discontinuity detection. Our approach constructs the hyperspherical coordinate representation of the discontinuity surface of a function. Then sparse approximations of the transformed function are...
Show moreThis work proposes a hyperspherical sparse approximation framework for detecting jump discontinuities in functions in high-dimensional spaces. The need for a novel approach results from the theoretical and computational inefficiencies of well-known approaches, such as adaptive sparse grids, for discontinuity detection. Our approach constructs the hyperspherical coordinate representation of the discontinuity surface of a function. Then sparse approximations of the transformed function are built in the hyperspherical coordinate system, with values at each point estimated by solving a one-dimensional discontinuity detection problem. Due to the smoothness of the hypersurface, the new technique can identify jump discontinuities with significantly reduced computational cost, compared to existing methods. Several approaches are used to approximate the transformed discontinuity surface in the hyperspherical system, including adaptive sparse grid and radial basis function interpolation, discrete least squares projection, and compressed sensing approximation. Moreover, hierarchical acceleration techniques are also incorporated to further reduce the overall complexity. Rigorous complexity analyses of the new methods are provided, as are several numerical examples that illustrate the effectiveness of our approach.
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Date Issued: 2016
Identifier: FSU_libsubv1_wos_000381097400005, 10.1137/16M1071699
Format: Citation

Title: A Landmark-Free Method for Three-Dimensional Shape Analysis.
Creator: Slice, Dennis, Pomidor, Benjamin J.
Abstract/Description: Background The tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts....
Show moreBackground The tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts. This is especially true of those investigating smooth or featureless surfaces. Methods In this paper, we present a new method to perform this transformation for data obtained from high-resolution scanning technology. This method uses surface scans, instead of landmarks, to calculate a shape difference metric analogous to Procrustes distance and perform superimposition. This is accomplished by building upon and extending the Iterative Closest Point algorithm. We also explore some new ways this data can be used; for example, we can calculate an averaged surface directly and visualize point-wise shape information over this surface. Finally, we briefly demonstrate this method on a set of primate skulls and compare the results of the new methodology with traditional geometric morphometric analysis.
Show less
Date Issued: 2016-03-08
Identifier: FSU_libsubv1_scholarship_submission_1475156153, 10.1371/journal.pone.0150368
Format: Citation

Title: No Double Detonations But Core Carbon Ignitions In High-resolution, Grid-based Simulations Of Binary White Dwarf Mergers.
Creator: Fenn, D., Plewa, T., Gawryszczak, A.
Abstract/Description: We study the violent phase of the merger of massive binary white dwarf systems. Our aim is to characterize the conditions for explosive burning to occur, and identify a possible explosion mechanism of Type Ia supernovae. The primary components of our model systems are carbon-oxygen (C/O) white dwarfs, while the secondaries are made either of C/O or of pure helium. We account for tidal effects in the initial conditions in a self-consistent way, and consider initially well-separated systems...
Show moreWe study the violent phase of the merger of massive binary white dwarf systems. Our aim is to characterize the conditions for explosive burning to occur, and identify a possible explosion mechanism of Type Ia supernovae. The primary components of our model systems are carbon-oxygen (C/O) white dwarfs, while the secondaries are made either of C/O or of pure helium. We account for tidal effects in the initial conditions in a self-consistent way, and consider initially well-separated systems with slow inspiral rates. We study the merger evolution using an adaptive mesh refinement, reactive, Eulerian code in three dimensions, assuming symmetry across the orbital plane. We use a corotating reference frame to minimize the effects of numerical diffusion, and solve for self-gravity using a multigrid approach. We find a novel detonation mechanism in C/O mergers with massive primaries. Here, the detonation occurs in the primary's core and relies on the combined action of tidal heating, accretion heating, and self-heating due to nuclear burning. The exploding structure is compositionally stratified, with a reverse shock formed at the surface of the dense ejecta. The existence of such a shock has not been reported elsewhere. The explosion energy (1.6 x 10(51) erg) and Ni-56 mass (0.86 M-circle dot) are consistent with an SN Ia at the bright end of the luminosity distribution, with an approximated decline rate of Delta m(15)(B) approximate to 0.99. Our study does not support double-detonation scenarios in the case of a system with a 0.6 M-circle dot helium secondary and a 0.9 M-circle dot primary. Although the accreted helium detonates, it fails to ignite carbon at the base of the boundary layer or in the primary's core.
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Date Issued: 2016-11-01
Identifier: FSU_libsubv1_wos_000384676000015, 10.1093/mnras/stw1831
Format: Citation

Title: A New Process Sensitivity Index To Identify Important System Processes Under Process Model And Parametric Uncertainty.
Creator: Dai, Heng, Ye, Ming, Walker, Anthony P., Chen, Xingyuan
Abstract/Description: A hydrological model consists of multiple process level submodels, and each submodel represents a process key to the operation of the simulated system. Global sensitivity analysis methods have been widely used to identify important processes for system model development and improvement. The existing methods of global sensitivity analysis only consider parametric uncertainty, and are not capable of handling model uncertainty caused by multiple process models that arise from competing...
Show moreA hydrological model consists of multiple process level submodels, and each submodel represents a process key to the operation of the simulated system. Global sensitivity analysis methods have been widely used to identify important processes for system model development and improvement. The existing methods of global sensitivity analysis only consider parametric uncertainty, and are not capable of handling model uncertainty caused by multiple process models that arise from competing hypotheses about one or more processes. To address this problem, this study develops a new method to probe model output sensitivity to competing process models by integrating model averaging methods with variance-based global sensitivity analysis. A process sensitivity index is derived as a single summary measure of relative process importance, and the index includes variance in model outputs caused by uncertainty in both process models and their parameters. For demonstration, the new index is used to assign importance to the processes of recharge and geology in a synthetic study of groundwater reactive transport modeling. The recharge process is simulated by two models that convert precipitation to recharge, and the geology process is simulated by two models of hydraulic conductivity. Each process model has its own random parameters. The new process sensitivity index is mathematically general, and can be applied to a wide range of problems in hydrology and beyond. Plain Language Summary If we have only one model, we always know how to identify the important factors of the models. However, if there are multiple models, it is not always clear how to identify the important factors. The factors important to one model may not be important to another model. It is necessary to develop a method that can identify important factors not for a single model but for multiple models. This study aims at resolving this problem by developing a mathematically rigorous method to provide a single summary measure for identifying important factors in the face of competing models. This is called multi-model process sensitivity analysis, and the mathematical measure is called process sensitivity index. The new index is demonstrated using a numerical example of groundwater reactive transport modeling with two recharge models and two geology models. The multimodel process sensitivity analysis has a wide range of applications in hydrologic and environmental modeling.
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Date Issued: 2017-04
Identifier: FSU_libsubv1_wos_000403682600053, 10.1002/2016WR019715
Format: Citation

Title: Multiparametric [F-18]Fluorodeoxyglucose/[F-18]Fluoromisonidazole Positron Emission Tomography/Magnetic Resonance Imaging of Locally Advanced Cervical Cancer for the Non-Invasive Detection of Tumor Heterogeneity: A Pilot Study.
Creator: Pinker, Katja, Andrzejewski, Piotr, Baltzer, Pascal, Polanec, Stephan H., Sturdza, Alina, Georg, Dietmar, Helbich, Thomas H., Karanikas, Georgios, Grimm, Christoph, Polterauer,...
Show morePinker, Katja, Andrzejewski, Piotr, Baltzer, Pascal, Polanec, Stephan H., Sturdza, Alina, Georg, Dietmar, Helbich, Thomas H., Karanikas, Georgios, Grimm, Christoph, Polterauer, Stephan, Poetter, Richard, Wadsak, Wolfgang, Mitterhauser, Markus, Georg, Petra
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Abstract/Description: Objectives To investigate fused multiparametric positron emission tomography/magnetic resonance imaging (MP PET/MRI) at 3T in patients with locally advanced cervical cancer, using high-resolution T2-weighted, contrast-enhanced MRI (CE-MRI), diffusion-weighted imaging (DWI), and the radiotracers [F-18]fluorodeoxyglucose ([F-18]FDG) and [F-18]fluoromisonidazol ([F-18]FMISO) for the non-invasive detection of tumor heterogeneity for an improved planning of chemo-radiation therapy (CRT). Materials...
Show moreObjectives To investigate fused multiparametric positron emission tomography/magnetic resonance imaging (MP PET/MRI) at 3T in patients with locally advanced cervical cancer, using high-resolution T2-weighted, contrast-enhanced MRI (CE-MRI), diffusion-weighted imaging (DWI), and the radiotracers [F-18]fluorodeoxyglucose ([F-18]FDG) and [F-18]fluoromisonidazol ([F-18]FMISO) for the non-invasive detection of tumor heterogeneity for an improved planning of chemo-radiation therapy (CRT). Materials and Methods Sixteen patients with locally advanced cervix were enrolled in this IRB approved and were examined with fused MP [F-18]FDG/[F-18]FMISO PET/MRI and in eleven patients complete data sets were acquired. MP PET/MRI was assessed for tumor volume, enhancement (EH)-kinetics, diffusivity, and [F-18]FDG/[F-18]FMISO-avidity. Descriptive statistics and voxel-by-voxel analysis of MRI and PET parameters were performed. Correlations were assessed using multiple correlation analysis. Results All tumors displayed imaging parameters concordant with cervix cancer, i.e. type II/III EH-kinetics, restricted diffusivity (median ADC 0.80x10(-3)mm(2)/sec), [F-18]FDG-(median SUV(max)16.2) and [F-18]FMISO-avidity (median SUV(max)3.1). In all patients, [F-18]FMISO PET identified the hypoxic tumor subvolume, which was independent of tumor volume. A voxel-by-voxel analysis revealed only weak correlations between the MRI and PET parameters (0.05-0.22), indicating that each individual parameter yields independent information and the presence of tumor heterogeneity. Conclusion
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Date Issued: 2016-05-11
Identifier: FSU_libsubv1_wos_000376587300065, 10.1371/journal.pone.0155333
Format: Citation

Title: Bayesian Calibration Of Groundwater Models With Input Data Uncertainty.
Creator: Xu, Tianfang, Valocchi, Albert J., Ye, Ming, Liang, Feng, Lin, Yu-Feng
Abstract/Description: Effective water resources management typically relies on numerical models to analyze groundwater flow and solute transport processes. Groundwater models are often subject to input data uncertainty, as some inputs (such as recharge and well pumping rates) are estimated and subject to uncertainty. Current practices of groundwater model calibration often overlook uncertainties in input data; this can lead to biased parameter estimates and compromised predictions. Through a synthetic case study...
Show moreEffective water resources management typically relies on numerical models to analyze groundwater flow and solute transport processes. Groundwater models are often subject to input data uncertainty, as some inputs (such as recharge and well pumping rates) are estimated and subject to uncertainty. Current practices of groundwater model calibration often overlook uncertainties in input data; this can lead to biased parameter estimates and compromised predictions. Through a synthetic case study of surface-ground water interaction under changing pumping conditions and land use, we investigate the impacts of uncertain pumping and recharge rates on model calibration and uncertainty analysis. We then present a Bayesian framework of model calibration to handle uncertain input of groundwater models. The framework implements a marginalizing step to account for input data uncertainty when evaluating likelihood. It was found that not accounting for input uncertainty may lead to biased, overconfident parameter estimates because parameters could be over-adjusted to compensate for possible input data errors. Parameter compensation can have deleterious impacts when the calibrated model is used to make forecast under a scenario that is different from calibration conditions. By marginalizing input data uncertainty, the Bayesian calibration approach effectively alleviates parameter compensation and gives more accurate predictions in the synthetic case study. The marginalizing Bayesian method also decomposes prediction uncertainty into uncertainties contributed by parameters, input data, and measurements. The results underscore the need to account for input uncertainty to better inform postmodeling decision making.
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Date Issued: 2017-04
Identifier: FSU_libsubv1_wos_000403682600039, 10.1002/2016WR019512
Format: Citation

Title: On the origin of high ionic conductivity in Na-doped SrSiO3.
Creator: Chien, Po-Hsiu, Jee, Youngseok, Huang, Chen, Dervisoglu, Riza, Hung, Ivan, Gan, Zhehong, Huang, Kevin, Hu, Yan-Yan
Abstract/Description: Understanding the local structure and ion dynamics is at the heart of ion conductor research. This paper reports on high-resolution solid-state Si-29, Na-23, and O-17 NMR investigation of the structure, chemical composition, and ion dynamics of a newly discovered fast ion conductor, Na-doped SrSiO3, which exhibited a much higher ionic conductivity than most of current oxide ion conductors. Quantitative analyses reveal that with a small dose (10 mol% Na doping, phase separation occurs, leading...
Show moreUnderstanding the local structure and ion dynamics is at the heart of ion conductor research. This paper reports on high-resolution solid-state Si-29, Na-23, and O-17 NMR investigation of the structure, chemical composition, and ion dynamics of a newly discovered fast ion conductor, Na-doped SrSiO3, which exhibited a much higher ionic conductivity than most of current oxide ion conductors. Quantitative analyses reveal that with a small dose (<10 mol%) of Na, the doped Na integrates into the SrSiO3 structure to form NaxSr1-xSiO3-0.5x, and with >10 mol% Na doping, phase separation occurs, leading to the formation of an amorphous phase beta-Na2Si2O5 and a crystalline Sr-rich phase. Variable-temperature Na-23 and O-17 magic-angle-spinning NMR up to 618 degrees C have shown significant changes in Na ion dynamics at high temperatures but little oxide ion motion, suggesting that Na ions are responsible for the observed high ionic conductivity. In addition, beta-Na2Si2O5 starts to crystallize at temperatures higher than 480 degrees C with prolonged heating, resulting in reduction in Na+ motion, and thus degradation of ionic conductivity. This study has contributed critical evidence to the understanding of ionic conduction in Na-doped SrSiO3 and demonstrated that multinuclear high-resolution and high-temperature solid-state NMR is a uniquely useful tool for investigating ion conductors at their operating conditions.
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Date Issued: 2016
Identifier: FSU_libsubv1_wos_000377262200023, 10.1039/c5sc04270d
Format: Citation

Title: OPTIMAL MODEL MANAGEMENT FOR MULTIFIDELITY MONTE CARLO ESTIMATION.
Creator: Peherstorfer, Benjamin, Willcox, Karen, Gunzburger, Max
Abstract/Description: This work presents an optimal model management strategy that exploits multifidelity surrogate models to accelerate the estimation of statistics of outputs of computationally expensive high-fidelity models. Existing acceleration methods typically exploit a multilevel hierarchy of surrogate models that follow a known rate of error decay and computational costs; however, a general collection of surrogate models, which may include projection-based reduced models, data-fit models, support vector...
Show moreThis work presents an optimal model management strategy that exploits multifidelity surrogate models to accelerate the estimation of statistics of outputs of computationally expensive high-fidelity models. Existing acceleration methods typically exploit a multilevel hierarchy of surrogate models that follow a known rate of error decay and computational costs; however, a general collection of surrogate models, which may include projection-based reduced models, data-fit models, support vector machines, and simplified-physics models, does not necessarily give rise to such a hierarchy. Our multifidelity approach provides a framework to combine an arbitrary number of surrogate models of any type. Instead of relying on error and cost rates, an optimization problem balances the number of model evaluations across the high-fidelity and surrogate models with respect to error and costs. We show that a unique analytic solution of the model management optimization problem exists under mild conditions on the models. Our multifidelity method makes occasional recourse to the high-fidelity model; in doing so it provides an unbiased estimator of the statistics of the high-fidelity model, even in the absence of error bounds and error estimators for the surrogate models. Numerical experiments with linear and nonlinear examples show that speedups by orders of magnitude are obtained compared to Monte Carlo estimation that invokes a single model only.
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Date Issued: 2016
Identifier: FSU_libsubv1_wos_000387347700070, 10.1137/15M1046472
Format: Citation

Title: Visualizing phylogenetic tree landscapes.
Creator: Wilgenbusch, James C, Huang, Wen, Gallivan, Kyle A
Abstract/Description: Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential...
Show moreGenomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D projections significantly increase the fit between the tree-to-tree distances and can facilitate the interpretation of the relationship among phylogenetic trees. We demonstrate that the choice of dimensionality reduction method can significantly influence the spatial relationship among a large set of competing phylogenetic trees. We highlight the importance of selecting a dimensionality reduction method to visualize large multi-locus phylogenetic landscapes and demonstrate that 3D projections of mitochondrial tree landscapes better capture the relationship among the trees being compared.
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Date Issued: 2017-02-02
Identifier: FSU_pmch_28153045, 10.1186/s12859-017-1479-1, PMC5290614, 28153045, 28153045, 10.1186/s12859-017-1479-1
Format: Citation

Title: Selection To Increase Expression, Not Sequence Diversity, Precedes Gene Family Origin and Expansion in Rattlesnake Venom.
Creator: Margres, Mark J, Bigelow, Alyssa T, Lemmon, Emily Moriarty, Lemmon, Alan R, Rokyta, Darin R
Abstract/Description: Gene duplication is the primary mechanism leading to new genes and phenotypic novelty, but the proximate evolutionary processes underlying gene family origin, maintenance, and expansion are poorly understood. Although sub- and neofunctionalization provide clear long-term advantages, selection does not act with foresight, and unless a redundant gene copy provides an immediate fitness advantage, the copy will most likely be lost. Many models for the evolution of genes immediately following...
Show moreGene duplication is the primary mechanism leading to new genes and phenotypic novelty, but the proximate evolutionary processes underlying gene family origin, maintenance, and expansion are poorly understood. Although sub- and neofunctionalization provide clear long-term advantages, selection does not act with foresight, and unless a redundant gene copy provides an immediate fitness advantage, the copy will most likely be lost. Many models for the evolution of genes immediately following duplication have been proposed, but the robustness and applicability of these models is unclear because of the lack of data at the population level. We used qPCR, protein expression data, genome sequencing, and hybrid enrichment to test three competing models that differ in whether selection favoring the spread of duplicates acts primarily on expression level or sequence diversity for specific toxin-encoding loci in the eastern diamondback rattlesnake (). We sampled 178 individuals and identified significant inter- and intrapopulation variation in copy number, demonstrated that copy number was significantly and positively correlated with protein expression, and found little to no sequence variation across paralogs in all populations. Collectively, these results demonstrate that selection for increased expression, not sequence diversity, was the proximate evolutionary process underlying gene family origin and expansion, providing data needed to resolve the debate over which evolutionary processes govern the fates of gene copies immediately following duplication.
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Date Issued: 2017-07-01
Identifier: FSU_pmch_28476866, 10.1534/genetics.117.202655, PMC5500151, 28476866, 28476866, genetics.117.202655
Format: Citation

Title: Resolving Cypriniformes relationships using an anchored enrichment approach.
Creator: Stout, Carla C, Tan, Milton, Lemmon, Alan R, Lemmon, Emily Moriarty, Armbruster, Jonathan W
Abstract/Description: Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288...
Show moreCypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.
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Date Issued: 2016-11-09
Identifier: FSU_pmch_27829363, 10.1186/s12862-016-0819-5, PMC5103605, 27829363, 27829363, 10.1186/s12862-016-0819-5
Format: Citation

Title: Diversification in wild populations of the model organism: A genome-wide phylogeographic investigation..
Creator: Manthey, Joseph D, Tollis, Marc, Lemmon, Alan R, Moriarty Lemmon, Emily, Boissinot, Stéphane
Abstract/Description: The green anole () is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of evolutionary history in association with morphological,...
Show moreThe green anole () is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito-nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade-southern Florida restricted to the Everglades region-while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long-term population sizes in southern phylogeographic groups, indicate that diversification in occurred northward from southern Florida.
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Date Issued: 2016-10-17
Identifier: FSU_pmch_27891220, 10.1002/ece3.2547, PMC5108263, 27891220, 27891220, ECE32547
Format: Citation

Title: Diversification In Wild Populations Of The Model Organism Anolis Carolinensis: A Genome-wide Phylogeographic Investigation.
Creator: Manthey, Joseph D., Tollis, Marc, Lemmon, Alan R., Lemmon, Emily Moriarty, Boissinot, Stephane
Abstract/Description: The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary...
Show moreThe green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito-nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade-southern Florida restricted to the Everglades region-while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long-term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.
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Date Issued: 2016-11
Identifier: FSU_libsubv1_wos_000387664500017, 10.1002/ece3.2547
Format: Citation

Title: A Landmark-Free Method for Three-Dimensional Shape Analysis.
Creator: Pomidor, Benjamin J, Makedonska, Jana, Slice, Dennis E
Abstract/Description: The tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts. This is...
Show moreThe tools and techniques used in morphometrics have always aimed to transform the physical shape of an object into a concise set of numerical data for mathematical analysis. The advent of landmark-based morphometrics opened new avenues of research, but these methods are not without drawbacks. The time investment required of trained individuals to accurately landmark a data set is significant, and the reliance on readily-identifiable physical features can hamper research efforts. This is especially true of those investigating smooth or featureless surfaces. In this paper, we present a new method to perform this transformation for data obtained from high-resolution scanning technology. This method uses surface scans, instead of landmarks, to calculate a shape difference metric analogous to Procrustes distance and perform superimposition. This is accomplished by building upon and extending the Iterative Closest Point algorithm. We also explore some new ways this data can be used; for example, we can calculate an averaged surface directly and visualize point-wise shape information over this surface. Finally, we briefly demonstrate this method on a set of primate skulls and compare the results of the new methodology with traditional geometric morphometric analysis.
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Date Issued: 2016-03-08
Identifier: FSU_pmch_26953573, 10.1371/journal.pone.0150368, PMC4783062, 26953573, 26953573, PONE-D-15-18418
Format: Citation

Title: Detonability Of White Dwarf Plasma: Turbulence Models At Low Densities.
Creator: Fenn, D., Plewa, T.
Abstract/Description: We study the conditions required to produce self-sustained detonations in turbulent, carbon-oxygen degenerate plasma at low densities. We perform a series of three-dimensional hydrodynamic simulations of turbulence driven with various degrees of compressibility. The average conditions in the simulations are representative of models of merging binary white dwarfs. We find that material with very short ignition times is abundant in case turbulence is driven compressively. This material forms...
Show moreWe study the conditions required to produce self-sustained detonations in turbulent, carbon-oxygen degenerate plasma at low densities. We perform a series of three-dimensional hydrodynamic simulations of turbulence driven with various degrees of compressibility. The average conditions in the simulations are representative of models of merging binary white dwarfs. We find that material with very short ignition times is abundant in case turbulence is driven compressively. This material forms contiguous structures that persist overmany ignition times, and that we identify as prospective detonation kernels. Detailed analysis of prospective kernels reveals that these objects are centrally condensed and their shape is characterized by low curvature, supportive of self-sustained detonations. The key characteristic of the newly proposed detonation mechanism is thus high degree of compressibility of turbulent drive. The simulated detonation kernels have sizes notably smaller than the spatial resolution of any white dwarf merger simulation performed to date. The resolution required to resolve kernels is 0.1 km. Our results indicate a high probability of detonations in such well-resolved simulations of carbon-oxygen white dwarf mergers. These simulations will likely produce detonations in systems of lower total mass, thus broadening the population of white dwarf binaries capable of producing Type Ia supernovae. Consequently, we expect a downward revision of the lower limit of the total merger mass that is capable of producing a prompt detonation. We review application of the new detonation mechanism to various explosion scenarios of single, Chandrasekhar-mass white dwarfs.
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Date Issued: 2017-06
Identifier: FSU_libsubv1_wos_000399429600007, 10.1093/mnras/stx524
Format: Citation

Title: Viremia and Clinical Presentation in Nicaraguan Patients Infected With Zika Virus, Chikungunya Virus, and Dengue Virus.
Creator: Waggoner, Jesse J, Gresh, Lionel, Vargas, Maria Jose, Ballesteros, Gabriela, Tellez, Yolanda, Soda, K James, Sahoo, Malaya K, Nuñez, Andrea, Balmaseda, Angel, Harris, Eva,...
Show moreWaggoner, Jesse J, Gresh, Lionel, Vargas, Maria Jose, Ballesteros, Gabriela, Tellez, Yolanda, Soda, K James, Sahoo, Malaya K, Nuñez, Andrea, Balmaseda, Angel, Harris, Eva, Pinsky, Benjamin A
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Abstract/Description: Zika virus (ZIKV), chikungunya virus (CHIKV), and dengue virus (DENV) cocirculate in Nicaragua. In this study, we sought to compare the quantified viremia and clinical presentation of patients infected with 1 or more of these viruses. Acute-phase serum samples from 346 patients with a suspected arboviral illness were tested using a multiplex real-time reverse-transcription polymerase chain reaction for ZIKV, CHIKV, and DENV. Viremia was quantitated for each detected virus, and clinical...
Show more Zika virus (ZIKV), chikungunya virus (CHIKV), and dengue virus (DENV) cocirculate in Nicaragua. In this study, we sought to compare the quantified viremia and clinical presentation of patients infected with 1 or more of these viruses. Acute-phase serum samples from 346 patients with a suspected arboviral illness were tested using a multiplex real-time reverse-transcription polymerase chain reaction for ZIKV, CHIKV, and DENV. Viremia was quantitated for each detected virus, and clinical information from request forms submitted with each sample was recorded. A total of 263 patients tested positive for 1 or more viruses: 192 patients tested positive for a single virus (monoinfections) and 71 patients tested positive for 2 or all 3 viruses (coinfections). Quantifiable viremia was lower in ZIKV infections compared with CHIKV or DENV (mean 4.70 vs 6.42 and 5.84 log copies/mL serum, respectively; P < .001 for both comparisons), and for each virus, mean viremia was significantly lower in coinfections than in monoinfections. Compared with patients with CHIKV or DENV, ZIKV patients were more likely to have a rash (P < .001) and less likely to be febrile (P < .05) or require hospitalization (P < .001). Among all patients, hospitalized cases had higher viremia than those who did not require hospitalization (7.1 vs 4.1 log10 copies/mL serum, respectively; P < .001). ZIKV, CHIKV, and DENV result in similar clinical presentations, and coinfections may be relatively common. Our findings illustrate the need for accurate, multiplex diagnostics for patient care and epidemiologic surveillance.
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Date Issued: 2016-12-15
Identifier: FSU_pmch_27578819, 10.1093/cid/ciw589, PMC5146717, 27578819, 27578819, ciw589
Format: Citation

Title: Regional Quasi-Three-Dimensional Unsaturated-Saturated Water Flow Model Based on a Vertical-Horizontal Splitting Concept.
Creator: Zhu, Yan, Shi, Liangsheng, Wu, Jingwei, Ye, Ming, Cui, Lihong, Yang, Jinzhong
Abstract/Description: Due to the high nonlinearity of the three-dimensional (3-D) unsaturated-saturated water flow equation, using a fully 3-D numerical model is computationally expensive for large scale applications. A new unsaturated-saturated water flow model is developed in this paper based on the vertical/horizontal splitting (VHS) concept to split the 3-D unsaturated-saturated Richards' equation into a two-dimensional (2-D) horizontal equation and a one-dimensional (1-D) vertical equation. The horizontal...
Show moreDue to the high nonlinearity of the three-dimensional (3-D) unsaturated-saturated water flow equation, using a fully 3-D numerical model is computationally expensive for large scale applications. A new unsaturated-saturated water flow model is developed in this paper based on the vertical/horizontal splitting (VHS) concept to split the 3-D unsaturated-saturated Richards' equation into a two-dimensional (2-D) horizontal equation and a one-dimensional (1-D) vertical equation. The horizontal plane of average head gradient in the triangular prism element is derived to split the 3-D equation into the 2-D equation. The lateral flow in the horizontal plane of average head gradient represented by the 2-D equation is then calculated by the water balance method. The 1-D vertical equation is discretized by the finite difference method. The two equations are solved simultaneously by coupling them into a unified nonlinear system with a single matrix. Three synthetic cases are used to evaluate the developed model code by comparing the modeling results with those of Hydrus1D, SWMS2D and FEFLOW. We further apply the model to regional-scale modeling to simulate groundwater table fluctuations for assessing the model applicability in complex conditions. The proposed modeling method is found to be accurate with respect to measurements.
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Date Issued: 2016-05
Identifier: FSU_libsubv1_wos_000377984300026, 10.3390/w8050195
Format: Citation

Title: Quantification of mixing in vesicle suspensions using numerical simulations in two dimensions.
Creator: Kabacaoğlu, G, Quaife, B, Biros, G
Abstract/Description: We study mixing in Stokesian vesicle suspensions in two dimensions on a cylindrical Couette apparatus using numerical simulations. The vesicle flow simulation is done using a boundary integral method, and the advection-diffusion equation for the mixing of the solute is solved using a pseudo-spectral scheme. We study the effect of the area fraction, the viscosity contrast between the inside (the vesicles) and the outside (the bulk) fluid, the initial condition of the solute, and the mixing...
Show moreWe study mixing in Stokesian vesicle suspensions in two dimensions on a cylindrical Couette apparatus using numerical simulations. The vesicle flow simulation is done using a boundary integral method, and the advection-diffusion equation for the mixing of the solute is solved using a pseudo-spectral scheme. We study the effect of the area fraction, the viscosity contrast between the inside (the vesicles) and the outside (the bulk) fluid, the initial condition of the solute, and the mixing metric. We compare mixing in the suspension with mixing in the Couette apparatus without vesicles. On the one hand, the presence of vesicles in most cases slightly suppresses mixing. This is because the solute can be only diffused across the vesicle interface and not advected. On the other hand, there exist spatial distributions of the solute for which the unperturbed Couette flow completely fails to mix whereas the presence of vesicles enables mixing. We derive a simple condition that relates the velocity and solute and can be used to characterize the cases in which the presence of vesicles promotes mixing.
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Date Issued: 2017-02-01
Identifier: FSU_pmch_28344432, 10.1063/1.4975154, PMC5321511, 28344432, 28344432, 1.4975154
Format: Citation

Title: Multidimensional Models Of Type Ia Supernova Nebular Spectra: Strong Emission Lines From Stripped Companion Gas Rule Out Classic Single-degenerate Systems.
Creator: Botyanszki, Janos, Kasen, Daniel, Plewa, Tomasz
Abstract/Description: The classic single-degenerate model for the progenitors of Type Ia supernova (SN Ia) predicts that the supernova ejecta should be enriched with solar-like abundance material stripped from the companion star. Spectroscopic observations of normal SNe. Ia at late times, however, have not resulted in definite detection of hydrogen. In this Letter, we study line formation in SNe Ia at nebular times using non-LTE spectral modeling. We present, for the first time, multidimensional radiative transfer...
Show moreThe classic single-degenerate model for the progenitors of Type Ia supernova (SN Ia) predicts that the supernova ejecta should be enriched with solar-like abundance material stripped from the companion star. Spectroscopic observations of normal SNe. Ia at late times, however, have not resulted in definite detection of hydrogen. In this Letter, we study line formation in SNe Ia at nebular times using non-LTE spectral modeling. We present, for the first time, multidimensional radiative transfer calculations of SNe Ia with stripped material mixed in the ejecta core, based on hydrodynamical simulations of ejecta-companion interaction. We find that interaction models with main-sequence companions produce significant Ha emission at late times, ruling out these types of binaries being viable progenitors of SNe Ia. We also predict significant He I line emission at optical and near-infrared wavelengths for both hydrogen-rich or helium-rich material, providing an additional observational probe of stripped ejecta. We produce models with reduced stripped masses and find a more stringent mass limit of M-st less than or similar to 1 x 10(-4) M-circle dot of stripped companion material for SN 2011fe.
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Date Issued: 2018-01-01
Identifier: FSU_libsubv1_wos_000418932600003, 10.3847/2041-8213/aaa07b
Format: Citation

Title: Daily Air Temperature Estimation On Glacier Surfaces In The Tibetan Plateau Using Modis Lst Data.
Creator: Zhang, Hongbo, Zhang, Fan, Zhang, Guoqing, Ma, Yaoming, Yang, Kun, Ye, Ming
Abstract/Description: The MODerate resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) data have been widely used for air temperature estimation in mountainous regions where station observations are sparse. However, the performance of MODIS LST in high-elevation glacierized areas remains unclear. This study investigates air temperature estimation in glacierized areas based on ground observations at four glaciers across the Tibetan Plateau. Before being used to estimate the air temperature,...
Show moreThe MODerate resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) data have been widely used for air temperature estimation in mountainous regions where station observations are sparse. However, the performance of MODIS LST in high-elevation glacierized areas remains unclear. This study investigates air temperature estimation in glacierized areas based on ground observations at four glaciers across the Tibetan Plateau. Before being used to estimate the air temperature, MODIS LST data are evaluated at two of the glaciers, which indicates that MODIS night-time LST is more reliable than MODIS daytime LST data. Then, linear models based on each of the individual MODIS LST products from two platforms (Terra and Aqua) and two overpasses (nighttime and daytime) are built to estimate daily mean, minimum and maximum air temperatures in glacierized areas. Regional glacier surface (RGS) models (mean /-mean-square differences: 3.3, 3.0 and 4.8 degrees C for daily mean, minimum and maximum air temperatures, respectively) show higher accuracy than local non-glacier surface models (mean root-mean-square differences: 4.2, 4.7 and 5.7 degrees C). In addition, the RGS models based on MODIS night-time LST perform better to estimate daily mean, minimum and maximum air temperatures than using temperature lapse rate derived from local stations.
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Date Issued: 2018-02
Identifier: FSU_libsubv1_wos_000426960600012, 10.1017/jog.2018.6
Format: Citation

Title: How High Energy Fluxes May Affect Rayleigh-taylor Instability Growth In Young Supernova Remnants.
Creator: Kuranz, C. C., Park, H.-S., Huntington, C. M., Miles, A. R., Remington, B. A., Plewa, T., Trantham, M. R., Robey, H. F., Shvarts, D., Shimony, A., Raman, K., MacLaren, S., Wan,...
Show moreKuranz, C. C., Park, H.-S., Huntington, C. M., Miles, A. R., Remington, B. A., Plewa, T., Trantham, M. R., Robey, H. F., Shvarts, D., Shimony, A., Raman, K., MacLaren, S., Wan, W. C., Doss, F. W., Kline, J., Flippo, K. A., Malamud, G., Handy, T. A., Prisbrey, S., Krauland, C. M., Klein, S. R., Harding, E. C., Wallace, R., Grosskopf, M. J., Marion, D. C., Kalantar, D., Giraldez, E., Drake, R. P.
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Abstract/Description: Energy-transport effects can alter the structure that develops as a supernova evolves into a supernova remnant. The Rayleigh-Taylor instability is thought to produce structure at the interface between the stellar ejecta and the circumstellar matter, based on simple models and hydrodynamic simulations. Here we report experimental results from the National Ignition Facility to explore how large energy fluxes, which are present in supernovae, affect this structure. We observed a reduction in...
Show moreEnergy-transport effects can alter the structure that develops as a supernova evolves into a supernova remnant. The Rayleigh-Taylor instability is thought to produce structure at the interface between the stellar ejecta and the circumstellar matter, based on simple models and hydrodynamic simulations. Here we report experimental results from the National Ignition Facility to explore how large energy fluxes, which are present in supernovae, affect this structure. We observed a reduction in Rayleigh-Taylor growth. In analyzing the comparison with supernova SN1993J, a Type II supernova, we found that the energy fluxes produced by heat conduction appear to be larger than the radiative energy fluxes, and large enough to have dramatic consequences. No reported astrophysical simulations have included radiation and heat conduction self-consistently in modeling supernova remnants and these dynamics should be noted in the understanding of young supernova remnants.
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Date Issued: 2018-04-19
Identifier: FSU_libsubv1_wos_000430389100016, 10.1038/s41467-018-03548-7
Format: Citation

Title: Phylogenomics Uncovers Early Hybridization And Adaptive Loci Shaping The Radiation Of Lake Tanganyika Cichlid Fishes.
Creator: Irisarri, Iker, Singh, Pooja, Koblmuller, Stephan, Torres-Dowdall, Julian, Henning, Frederico, Franchini, Paolo, Fischer, Christoph, Lemmon, Alan R., Lemmon, Emily Moriarty,...
Show moreIrisarri, Iker, Singh, Pooja, Koblmuller, Stephan, Torres-Dowdall, Julian, Henning, Frederico, Franchini, Paolo, Fischer, Christoph, Lemmon, Alan R., Lemmon, Emily Moriarty, Thallinger, Gerhard G., Sturmbauer, Christian, Meyer, Axel
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Abstract/Description: Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using...
Show moreLake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species' dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.
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Date Issued: 2018-08-08
Identifier: FSU_libsubv1_wos_000440982800001, 10.1038/s41467-018-05479-9
Format: Citation

Title: Fixed Point Theorems For A Class Of Nonlinear Sum-type Operators And Application In A Fractional Differential Equation.
Creator: Wang, Hui, Zhang, Lingling, Wang, Xiaoqiang
Abstract/Description: In this paper, we consider the fixed point for a class of nonlinear sum-type operators 'A +B+ C' on an ordered Banach space, where A, B are two mixed monotone operators, C is an increasing operator. Without assuming the existence of upper-lower solutions or compactness or continuity conditions, we prove the unique existence of a positive fixed point and also construct two iterative schemes to approximate it. As applications, we research a nonlinear fractional differential equation with multi...
Show moreIn this paper, we consider the fixed point for a class of nonlinear sum-type operators 'A +B+ C' on an ordered Banach space, where A, B are two mixed monotone operators, C is an increasing operator. Without assuming the existence of upper-lower solutions or compactness or continuity conditions, we prove the unique existence of a positive fixed point and also construct two iterative schemes to approximate it. As applications, we research a nonlinear fractional differential equation with multi-point fractional boundary conditions. By using the obtained fixed point theorems of sum-type operator, we get the sufficient conditions which guarantee the existence and uniqueness of positive solutions. At last, a specific example is provided to illustrate our result.
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Date Issued: 2018-09-18
Identifier: FSU_libsubv1_wos_000446257800001, 10.1186/s13661-018-1059-y
Format: Citation

Title: Multi-stage Optimization Of A Deep Model: A Case Study On Ground Motion Modeling.
Creator: Tahmassebi, Amirhessam, Gandomi, Amir H., Fong, Simon, Meyer-Baese, Anke, Foo, Simon Y.
Abstract/Description: In this study, a multi-stage optimization procedure is proposed to develop deep neural network models which results in a powerful deep learning pipeline called intelligent deep learning (iDeepLe). The proposed pipeline is then evaluated by a challenging real-world problem, the modeling of the spectral acceleration experienced by a particle during earthquakes. This approach has three main stages to optimize the deep model topology, the hyper-parameters, and its performance, respectively. This...
Show moreIn this study, a multi-stage optimization procedure is proposed to develop deep neural network models which results in a powerful deep learning pipeline called intelligent deep learning (iDeepLe). The proposed pipeline is then evaluated by a challenging real-world problem, the modeling of the spectral acceleration experienced by a particle during earthquakes. This approach has three main stages to optimize the deep model topology, the hyper-parameters, and its performance, respectively. This pipeline optimizes the deep model via adaptive learning rate optimization algorithms for both accuracy and complexity in multiple stages, while simultaneously solving the unknown parameters of the regression model. Among the seven adaptive learning rate optimization algorithms, Nadam optimization algorithm has shown the best performance results in the current study. The proposed approach is shown to be a suitable tool to generate solid models for this complex real-world system. The results also show that the parallel pipeline of iDeepLe has the capacity to handle big data problems as well.
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Date Issued: 2018-09-19
Identifier: FSU_libsubv1_wos_000445164300050, 10.1371/journal.pone.0203829
Format: Citation

Title: Survey Of Multifidelity Methods In Uncertainty Propagation, Inference, And Optimization.
Creator: Peherstorfer, Benjamin, Willcox, Karen, Gunzburger, Max
Abstract/Description: In many situations across computational science and engineering, multiple computational models are available that describe a system of interest. These different models have varying evaluation costs and varying fidelities. Typically, a computationally expensive high-fidelity model describes the system with the accuracy required by the current application at hand, while lower-fidelity models are less accurate but computationally cheaper than the high-fidelity model. Outer-loop applications,...
Show moreIn many situations across computational science and engineering, multiple computational models are available that describe a system of interest. These different models have varying evaluation costs and varying fidelities. Typically, a computationally expensive high-fidelity model describes the system with the accuracy required by the current application at hand, while lower-fidelity models are less accurate but computationally cheaper than the high-fidelity model. Outer-loop applications, such as optimization, inference, and uncertainty quantification, require multiple model evaluations at many different inputs, which often leads to computational demands that exceed available resources if only the high-fidelity model is used. This work surveys multifidelity methods that accelerate the solution of outer-loop applications by combining high-fidelity and low-fidelity model evaluations, where the low-fidelity evaluations arise from an explicit low-fidelity model (e.g., a simplified physics approximation, a reduced model, a data-fit surrogate) that approximates the same output quantity as the high-fidelity model. The overall premise of these multifidelity methods is that, low-fidelity models are leveraged for speedup while the high-fidelity model is kept in the loop to establish accuracy and/or convergence guarantees. We categorize multifidelity methods according to three classes of strategies: adaptation, fusion, and filtering. The paper reviews multifidelity methods in the outer-loop contexts of uncertainty propagation, inference, and Optimization.
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Date Issued: 2018-09-01
Identifier: FSU_libsubv1_wos_000441079500002, 10.1137/16M1082469
Format: Citation

Title: Characterization of Dengue Virus Infections Among Febrile Children Clinically Diagnosed With a Non-Dengue Illness, Managua, Nicaragua.
Creator: Waggoner, Jesse J, Gresh, Lionel, Mohamed-Hadley, Alisha, Balmaseda, Angel, Soda, K James, Abeynayake, Janaki, Sahoo, Malaya K, Liu, Yuanyuan, Kuan, Guillermina, Harris, Eva,...
Show moreWaggoner, Jesse J, Gresh, Lionel, Mohamed-Hadley, Alisha, Balmaseda, Angel, Soda, K James, Abeynayake, Janaki, Sahoo, Malaya K, Liu, Yuanyuan, Kuan, Guillermina, Harris, Eva, Pinsky, Benjamin A
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Abstract/Description: We sought to characterize dengue virus (DENV) infections among febrile children enrolled in a pediatric cohort study who were clinically diagnosed with a non-dengue illness ("C cases"). DENV infections were detected and viral load quantitated by real-time reverse transcription-polymerase chain reaction in C cases presenting between January 2007 and January 2013. One hundred forty-one of 2892 C cases (4.88%) tested positive for DENV. Of all febrile cases in the study, DENV-positive C cases...
Show moreWe sought to characterize dengue virus (DENV) infections among febrile children enrolled in a pediatric cohort study who were clinically diagnosed with a non-dengue illness ("C cases"). DENV infections were detected and viral load quantitated by real-time reverse transcription-polymerase chain reaction in C cases presenting between January 2007 and January 2013. One hundred forty-one of 2892 C cases (4.88%) tested positive for DENV. Of all febrile cases in the study, DENV-positive C cases accounted for an estimated 52.0% of patients with DENV viremia at presentation. Compared with previously detected, symptomatic dengue cases, DENV-positive C cases were significantly less likely to develop long-lasting humoral immune responses to DENV, as measured in healthy annual serum samples (79.7% vs 47.8%; P < .001). Humoral immunity was associated with viral load at presentation: 40 of 43 patients (93.0%) with a viral load ≥7.0 log10 copies/mL serum developed the expected rise in anti-DENV antibodies in annual samples versus 13 of 68 (19.1%) patients with a viral load below this level (P < .001). Antibody responses to DENV-positive C cases differ from responses to classic symptomatic dengue. These findings have important implications for DENV transmission modeling, immunology, and epidemiologic surveillance.
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Date Issued: 2017-06-15
Identifier: FSU_pmch_28863466, 10.1093/infdis/jix195, PMC5853235, 28863466, 28863466, 3747427
Format: Citation

Title: Cell-cell communication enhances bacterial chemotaxis toward external attractants.
Creator: Long, Zhicheng, Quaife, Bryan, Salman, Hanna, Oltvai, Zoltán N
Abstract/Description: Bacteria are able to coordinate their movement, growth and biochemical activities through cell-cell communication. While the biophysical mechanism of bacterial chemotaxis has been well understood in individual cells, the role of communication in the chemotaxis of bacterial populations is not clear. Here we report experimental evidence for cell-cell communication that significantly enhances the chemotactic migration of bacterial populations, a finding that we further substantiate using...
Show moreBacteria are able to coordinate their movement, growth and biochemical activities through cell-cell communication. While the biophysical mechanism of bacterial chemotaxis has been well understood in individual cells, the role of communication in the chemotaxis of bacterial populations is not clear. Here we report experimental evidence for cell-cell communication that significantly enhances the chemotactic migration of bacterial populations, a finding that we further substantiate using numerical simulations. Using a microfluidic approach, we find that E. coli cells respond to the gradient of chemoattractant not only by biasing their own random-walk swimming pattern through the well-understood intracellular chemotaxis signaling, but also by actively secreting a chemical signal into the extracellular medium, possibly through a hitherto unknown communication signal transduction pathway. This extracellular signaling molecule is a strong chemoattractant that attracts distant cells to the food source. The observed behavior may represent a common evolved solution to accelerate the function of biochemical networks of interacting cells.
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Date Issued: 2017-10-09
Identifier: FSU_pmch_28993669, 10.1038/s41598-017-13183-9, PMC5634484, 28993669, 28993669, 10.1038/s41598-017-13183-9
Format: Citation

Title: Dynamical Graph Theory Networks Methods for the Analysis of Sparse Functional Connectivity Networks and for Determining Pinning Observability in Brain Networks.
Creator: Meyer-Bäse, Anke, Roberts, Rodney G, Illan, Ignacio A, Meyer-Bäse, Uwe, Lobbes, Marc, Stadlbauer, Andreas, Pinker-Domenig, Katja
Abstract/Description: Neuroimaging in combination with graph theory has been successful in analyzing the functional connectome. However almost all analysis are performed based on static graph theory. The derived quantitative graph measures can only describe a snap shot of the disease over time. Neurodegenerative disease evolution is poorly understood and treatment strategies are consequently only of limited efficiency. Fusing modern dynamic graph network theory techniques and modeling strategies at different time...
Show moreNeuroimaging in combination with graph theory has been successful in analyzing the functional connectome. However almost all analysis are performed based on static graph theory. The derived quantitative graph measures can only describe a snap shot of the disease over time. Neurodegenerative disease evolution is poorly understood and treatment strategies are consequently only of limited efficiency. Fusing modern dynamic graph network theory techniques and modeling strategies at different time scales with pinning observability of complex brain networks will lay the foundation for a transformational paradigm in neurodegnerative diseases research regarding disease evolution at the patient level, treatment response evaluation and revealing some central mechanism in a network that drives alterations in these diseases. We model and analyze brain networks as two-time scale sparse dynamic graph networks with hubs (clusters) representing the fast sub-system and the interconnections between hubs the slow sub-system. Alterations in brain function as seen in dementia can be dynamically modeled by determining the clusters in which disturbance inputs have entered and the impact they have on the large-scale dementia dynamic system. Observing a small fraction of specific nodes in dementia networks such that the others can be recovered is accomplished by the novel concept of pinning observability. In addition, how to control this complex network seems to be crucial in understanding the progressive abnormal neural circuits in many neurodegenerative diseases. Detecting the controlling regions in the networks, which serve as key nodes to control the aberrant dynamics of the networks to a desired state and thus influence the progressive abnormal behavior, will have a huge impact in understanding and developing therapeutic solutions and also will provide useful information about the trajectory of the disease. In this paper, we present the theoretical framework and derive the necessary conditions for (1) area aggregation and time-scale modeling in brain networks and for (2) pinning observability of nodes in dynamic graph networks. Simulation examples are given to illustrate the theoretical concepts.
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Date Issued: 2017-10-05
Identifier: FSU_pmch_29051730, 10.3389/fncom.2017.00087, PMC5633615, 29051730, 29051730
Format: Citation

Title: Parameter Identification Techniques Applied To An Environmental Pollution Model.
Creator: Wang, Yuepeng, Cheng, Yue, Navon, I. Michael, Guan, Yuanhong
Abstract/Description: The retrieval of parameters related to an environmental model is explored. We address computational challenges occurring due to a significant numerical difference of up to two orders of magnitude between the two model parameters we aim to retrieve. First, the corresponding optimization problem is poorly scaled, causing minimization algorithms to perform poorly (see Gill et al.,practical optimization, AP,1981,401pp). This issue is addressed by proper rescaling. Difficulties also arise from the...
Show moreThe retrieval of parameters related to an environmental model is explored. We address computational challenges occurring due to a significant numerical difference of up to two orders of magnitude between the two model parameters we aim to retrieve. First, the corresponding optimization problem is poorly scaled, causing minimization algorithms to perform poorly (see Gill et al.,practical optimization, AP,1981,401pp). This issue is addressed by proper rescaling. Difficulties also arise from the presence of strong nonlinearity and ill-posedness which means that the parameters do not converge to a single deterministic set of values, but rather there exists a range of parameter combinations that produce the same model behavior. We address these computational issues by the addition of a regularization term in the cost function. All these computational approaches are addressed in the framework of variational adjoint data assimilation. The used observational data are derived from numerical simulation results located at only two spatial points. The effect of different initial guess values of parameters on retrieval results is also considered. As indicated by results of numerical experiments, the method presented in this paper achieves a near perfect parameter identification, and overcomes the indefiniteness that may occur in inversion process even in the case of noisy input data.
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Date Issued: 2018-04-01
Identifier: FSU_libsubv1_wos_000438846500024, 10.3934/jimo.2017077
Format: Citation

Title: A Heavy Tailed Expectation Maximization Hidden Markov Random Field Model with Applications to Segmentation of MRI.
Creator: Castillo-Barnes, Diego, Peis, Ignacio, Martínez-Murcia, Francisco J, Segovia, Fermín, Illán, Ignacio A, Górriz, Juan M, Ramírez, Javier, Salas-Gonzalez, Diego
Abstract/Description: A wide range of segmentation approaches assumes that intensity histograms extracted from magnetic resonance images (MRI) have a distribution for each brain tissue that can be modeled by a Gaussian distribution or a mixture of them. Nevertheless, intensity histograms of White Matter and Gray Matter are not symmetric and they exhibit heavy tails. In this work, we present a hidden Markov random field model with expectation maximization (EM-HMRF) modeling the components using the α-stable...
Show moreA wide range of segmentation approaches assumes that intensity histograms extracted from magnetic resonance images (MRI) have a distribution for each brain tissue that can be modeled by a Gaussian distribution or a mixture of them. Nevertheless, intensity histograms of White Matter and Gray Matter are not symmetric and they exhibit heavy tails. In this work, we present a hidden Markov random field model with expectation maximization (EM-HMRF) modeling the components using the α-stable distribution. The proposed model is a generalization of the widely used EM-HMRF algorithm with Gaussian distributions. We test the α-stable EM-HMRF model in synthetic data and brain MRI data. The proposed methodology presents two main advantages: Firstly, it is more robust to outliers. Secondly, we obtain similar results than using Gaussian when the Gaussian assumption holds. This approach is able to model the spatial dependence between neighboring voxels in tomographic brain MRI.
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Date Issued: 2017-11-21
Identifier: FSU_pmch_29209194, 10.3389/fninf.2017.00066, PMC5702363, 29209194, 29209194
Format: Citation

Title: A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment.
Creator: Maddison, Wayne P, Evans, Samuel C, Hamilton, Chris A, Bond, Jason E, Lemmon, Alan R, Lemmon, Emily Moriarty
Abstract/Description: We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results,...
Show moreWe present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines sister), Salticoida, Amycoida, Saltafresia, and Simonida. The agoriines, previously difficult to place beyond subfamily, are finally placed confidently within the saltafresians as relatives of the chrysillines and hasariines. Relationships among the baviines, astioids, marpissoids, and saltafresians remain uncertain, though our analyses tentatively conclude the first three form a clade together. Deep relationships, among the seven subfamilies, appear to be largely resolved, with spartaeines, lyssomanines, and asemoneines forming a clade. In most analyses, (representing the onomastines) is strongly supported as sister to the hisponines plus salticines. Overall, the much-improved resolution of many deep relationships despite a relatively sparse taxon sample suggests AHE is a promising technique for salticid phylogenetics.
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Date Issued: 2017-09-04
Identifier: FSU_pmch_29134008, 10.3897/zookeys.695.13852, PMC5673835, 29134008, 29134008
Format: Citation

Title: Functional Brain Imaging Synthesis Based on Image Decomposition and Kernel Modeling: Application to Neurodegenerative Diseases..
Creator: Martinez-Murcia, Francisco J, Górriz, Juan M, Ramírez, Javier, Illán, Ignacio A, Segovia, Fermín, Castillo-Barnes, Diego, Salas-Gonzalez, Diego
Abstract/Description: The rise of neuroimaging in research and clinical practice, together with the development of new machine learning techniques has strongly encouraged the Computer Aided Diagnosis (CAD) of different diseases and disorders. However, these algorithms are often tested in proprietary datasets to which the access is limited and, therefore, a direct comparison between CAD procedures is not possible. Furthermore, the sample size is often small for developing accurate machine learning methods. Multi...
Show moreThe rise of neuroimaging in research and clinical practice, together with the development of new machine learning techniques has strongly encouraged the Computer Aided Diagnosis (CAD) of different diseases and disorders. However, these algorithms are often tested in proprietary datasets to which the access is limited and, therefore, a direct comparison between CAD procedures is not possible. Furthermore, the sample size is often small for developing accurate machine learning methods. Multi-center initiatives are currently a very useful, although limited, tool in the recruitment of large populations and standardization of CAD evaluation. Conversely, we propose a brain image synthesis procedure intended to generate a new image set that share characteristics with an original one. Our system focuses on nuclear imaging modalities such as PET or SPECT brain images. We analyze the dataset by applying PCA to the original dataset, and then model the distribution of samples in the projected eigenbrain space using a Probability Density Function (PDF) estimator. Once the model has been built, we can generate new coordinates on the eigenbrain space belonging to the same class, which can be then projected back to the image space. The system has been evaluated on different functional neuroimaging datasets assessing the: resemblance of the synthetic images with the original ones, the differences between them, their generalization ability and the independence of the synthetic dataset with respect to the original. The synthetic images maintain the differences between groups found at the original dataset, with no significant differences when comparing them to real-world samples. Furthermore, they featured a similar performance and generalization capability to that of the original dataset. These results prove that these images are suitable for standardizing the evaluation of CAD pipelines, and providing data augmentation in machine learning systems -e.g. in deep learning-, or even to train future professionals at medical school.
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Date Issued: 2017-11-14
Identifier: FSU_pmch_29184492, 10.3389/fninf.2017.00065, PMC5694626, 29184492, 29184492
Format: Citation

Title: How high energy fluxes may affect Rayleigh-Taylor instability growth in young supernova remnants.
Creator: Kuranz, C C, Park, H-S, Huntington, C M, Miles, A R, Remington, B A, Plewa, T, Trantham, M R, Robey, H F, Shvarts, D, Shimony, A, Raman, K, MacLaren, S, Wan, W C, Doss, F W,...
Show moreKuranz, C C, Park, H-S, Huntington, C M, Miles, A R, Remington, B A, Plewa, T, Trantham, M R, Robey, H F, Shvarts, D, Shimony, A, Raman, K, MacLaren, S, Wan, W C, Doss, F W, Kline, J, Flippo, K A, Malamud, G, Handy, T A, Prisbrey, S, Krauland, C M, Klein, S R, Harding, E C, Wallace, R, Grosskopf, M J, Marion, D C, Kalantar, D, Giraldez, E, Drake, R P
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Abstract/Description: Energy-transport effects can alter the structure that develops as a supernova evolves into a supernova remnant. The Rayleigh-Taylor instability is thought to produce structure at the interface between the stellar ejecta and the circumstellar matter, based on simple models and hydrodynamic simulations. Here we report experimental results from the National Ignition Facility to explore how large energy fluxes, which are present in supernovae, affect this structure. We observed a reduction in...
Show moreEnergy-transport effects can alter the structure that develops as a supernova evolves into a supernova remnant. The Rayleigh-Taylor instability is thought to produce structure at the interface between the stellar ejecta and the circumstellar matter, based on simple models and hydrodynamic simulations. Here we report experimental results from the National Ignition Facility to explore how large energy fluxes, which are present in supernovae, affect this structure. We observed a reduction in Rayleigh-Taylor growth. In analyzing the comparison with supernova SN1993J, a Type II supernova, we found that the energy fluxes produced by heat conduction appear to be larger than the radiative energy fluxes, and large enough to have dramatic consequences. No reported astrophysical simulations have included radiation and heat conduction self-consistently in modeling supernova remnants and these dynamics should be noted in the understanding of young supernova remnants.
Show less
Date Issued: 2018-04-19
Identifier: FSU_pmch_29674695, 10.1038/s41467-018-03548-7, PMC5908785, 29674695, 29674695, 10.1038/s41467-018-03548-7
Format: Citation

Title: The Application of Dynamic Models to the Exploration of -AR Overactivation as a Cause of Heart Failure.
Creator: Wang, Xiaoyun, Zhao, Min, Wang, Xiaoqiang, Li, Shuping, Cao, Ning, Liu, Huirong
Abstract/Description: High titer of -adrenoreceptor autoantibodies (-AA) has been reported to appear in heart failure patients. It induces sustained -adrenergic receptor (-AR) activation which leads to heart failure (HF), but the mechanism is as yet unclear. In order to investigate the mechanisms causing -AR non-desensitization, we studied the beating frequency of the neonatal rat cardiomyocytes (NRCMs) under different conditions (an injection of isoprenaline (ISO) for one group and -AA for the other) and...
Show moreHigh titer of -adrenoreceptor autoantibodies (-AA) has been reported to appear in heart failure patients. It induces sustained -adrenergic receptor (-AR) activation which leads to heart failure (HF), but the mechanism is as yet unclear. In order to investigate the mechanisms causing -AR non-desensitization, we studied the beating frequency of the neonatal rat cardiomyocytes (NRCMs) under different conditions (an injection of isoprenaline (ISO) for one group and -AA for the other) and established three dynamic models in order to best describe the true relationships shown in medical experiments; one model used a control group of healthy rats; then in HF rats one focused on conformation changes in -AR; the other examined interaction between -AR and -adrenergic receptors (-AR). Comparing the experimental data and corresponding Akaike information criterion (AIC) values, we concluded that the interaction model was the most likely mechanism. We used mathematical methods to explore the mechanism for the development of heart failure and to find potential targets for prevention and treatment. The aim of the paper was to provide a strong theoretical basis for the clinical development of personalized treatment programs. We also carried out sensitivity analysis of the initial concentration -AA and found that they had a noticeable effect on the fitting results.
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Date Issued: 2018-07-30
Identifier: FSU_pmch_30154911, 10.1155/2018/1613290, PMC6091447, 30154911, 30154911
Format: Citation

Title: Multi-stage optimization of a deep model: A case study on ground motion modeling..
Creator: Tahmassebi, Amirhessam, Gandomi, Amir H, Fong, Simon, Meyer-Baese, Anke, Foo, Simon Y
Abstract/Description: In this study, a multi-stage optimization procedure is proposed to develop deep neural network models which results in a powerful deep learning pipeline called intelligent deep learning (iDeepLe). The proposed pipeline is then evaluated by a challenging real-world problem, the modeling of the spectral acceleration experienced by a particle during earthquakes. This approach has three main stages to optimize the deep model topology, the hyper-parameters, and its performance, respectively. This...
Show moreIn this study, a multi-stage optimization procedure is proposed to develop deep neural network models which results in a powerful deep learning pipeline called intelligent deep learning (iDeepLe). The proposed pipeline is then evaluated by a challenging real-world problem, the modeling of the spectral acceleration experienced by a particle during earthquakes. This approach has three main stages to optimize the deep model topology, the hyper-parameters, and its performance, respectively. This pipeline optimizes the deep model via adaptive learning rate optimization algorithms for both accuracy and complexity in multiple stages, while simultaneously solving the unknown parameters of the regression model. Among the seven adaptive learning rate optimization algorithms, Nadam optimization algorithm has shown the best performance results in the current study. The proposed approach is shown to be a suitable tool to generate solid models for this complex real-world system. The results also show that the parallel pipeline of iDeepLe has the capacity to handle big data problems as well.
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Date Issued: 2018-09-19
Identifier: FSU_pmch_30231077, 10.1371/journal.pone.0203829, PMC6145533, 30231077, 30231077, PONE-D-18-08965
Format: Citation

Title: On the origin of high ionic conductivity in Na-doped SrSiO.
Creator: Chien, Po-Hsiu, Jee, Youngseok, Huang, Chen, Dervişoğlu, Riza, Hung, Ivan, Gan, Zhehong, Huang, Kevin, Hu, Yan-Yan
Abstract/Description: Understanding the local structure and ion dynamics is at the heart of ion conductor research. This paper reports on high-resolution solid-state Si, Na, and O NMR investigation of the structure, chemical composition, and ion dynamics of a newly discovered fast ion conductor, Na-doped SrSiO, which exhibited a much higher ionic conductivity than most of current oxide ion conductors. Quantitative analyses reveal that with a small dose (10 mol% Na doping, phase separation occurs, leading to the...
Show moreUnderstanding the local structure and ion dynamics is at the heart of ion conductor research. This paper reports on high-resolution solid-state Si, Na, and O NMR investigation of the structure, chemical composition, and ion dynamics of a newly discovered fast ion conductor, Na-doped SrSiO, which exhibited a much higher ionic conductivity than most of current oxide ion conductors. Quantitative analyses reveal that with a small dose (<10 mol%) of Na, the doped Na integrates into the SrSiO structure to form Na Sr SiO , and with >10 mol% Na doping, phase separation occurs, leading to the formation of an amorphous phase β-NaSiO and a crystalline Sr-rich phase. Variable-temperature Na and O magic-angle-spinning NMR up to 618 °C have shown significant changes in Na ion dynamics at high temperatures but little oxide ion motion, suggesting that Na ions are responsible for the observed high ionic conductivity. In addition, β-NaSiO starts to crystallize at temperatures higher than 480 °C with prolonged heating, resulting in reduction in Na motion, and thus degradation of ionic conductivity. This study has contributed critical evidence to the understanding of ionic conduction in Na-doped SrSiO and demonstrated that multinuclear high-resolution and high-temperature solid-state NMR is a uniquely useful tool for investigating ion conductors at their operating conditions.
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Date Issued: 2016-06-01
Identifier: FSU_pmch_29997858, 10.1039/c5sc04270d, PMC6008723, 29997858, 29997858, c5sc04270d
Format: Citation

Title: Phylogenomic evidence overturns current conceptions of social evolution in wasps (Vespidae).
Creator: Piekarski, P K, Carpenter, J M, Lemmon, A R, Moriarty Lemmon, E, Sharanowski, B J
Abstract/Description: The hypothesis that eusociality originated once in Vespidae has shaped interpretation of social evolution for decades and has driven the supposition that preimaginal morphophysiological differences between castes were absent at the outset of eusociality. Many researchers also consider casteless nest-sharing an antecedent to eusociality. Together, these ideas endorse a stepwise progression of social evolution in wasps (solitary → casteless nest-sharing → eusociality with rudimentary behavioral...
Show moreThe hypothesis that eusociality originated once in Vespidae has shaped interpretation of social evolution for decades and has driven the supposition that preimaginal morphophysiological differences between castes were absent at the outset of eusociality. Many researchers also consider casteless nest-sharing an antecedent to eusociality. Together, these ideas endorse a stepwise progression of social evolution in wasps (solitary → casteless nest-sharing → eusociality with rudimentary behavioral castes → eusociality with preimaginal caste-biasing → morphologically differentiated castes). Here we infer the phylogeny of Vespidae using sequence data generated via anchored hybrid enrichment from 378 loci across 136 vespid species and perform ancestral state reconstructions to test whether rudimentary and monomorphic castes characterized the initial stages of eusocial evolution. Our results reject the single origin of eusociality hypothesis, contest the supposition that eusociality emerged from a casteless nest-sharing ancestor, and suggest that eusociality in Polistinae + Vespinae began with castes having morphological differences. An abrupt appearance of castes with ontogenetically established morphophysiological differences conflicts with the current conception of stepwise social evolution and suggests that the climb up the ladder of sociality does not occur through sequential mutation. Phenotypic plasticity and standing genetic variation could explain how cooperative brood care evolved in concert with nest-sharing and how morphologically dissimilar castes arose without a rudimentary intermediate. Furthermore, preimaginal caste-biasing at the outset of eusociality implicates a subsocial route to eusociality in Polistinae + Vespinae, emphasizing the role of mother-daughter interactions and subfertility (i.e. the cost component of kin selection) in the origin of workers.
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Date Issued: 2018-06-19
Identifier: FSU_pmch_29924339, 10.1093/molbev/msy124, PMC6107056, 29924339, 29924339, 5040136
Format: Citation

Title: Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes.
Creator: Irisarri, Iker, Singh, Pooja, Koblmüller, Stephan, Torres-Dowdall, Julián, Henning, Frederico, Franchini, Paolo, Fischer, Christoph, Lemmon, Alan R, Lemmon, Emily Moriarty,...
Show moreIrisarri, Iker, Singh, Pooja, Koblmüller, Stephan, Torres-Dowdall, Julián, Henning, Frederico, Franchini, Paolo, Fischer, Christoph, Lemmon, Alan R, Lemmon, Emily Moriarty, Thallinger, Gerhard G, Sturmbauer, Christian, Meyer, Axel
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Abstract/Description: Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using...
Show moreLake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species' dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.
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Date Issued: 2018-08-08
Identifier: FSU_pmch_30089797, 10.1038/s41467-018-05479-9, PMC6082878, 30089797, 30089797, 10.1038/s41467-018-05479-9
Format: Citation

Title: A Domain Decomposition Non-Intrusive Reduced Order Model for Turbulent Flows.
Creator: Navon, Ionel, Xiao, Dunhui, Heaney, Claire E., Fang, Fangxin, Mottet, Laetitia, Hu, R., Bistrian, Diana Alina, Aristodemou, Elsa, Pain, Christopher
Abstract/Description: In this paper, a new Domain Decomposition Non-Intrusive Reduced Order Model (DDNIROM) is developed for turbulent flows. The method works by partitioning the computational domain into a number of subdomains in such a way that the summation of weights associated with the finite element nodes within each subdomain is approximately equal, and the communication between subdomains is minimised. With suitably chosen weights, it is expected that there will be approximately equal accuracy associated...
Show moreIn this paper, a new Domain Decomposition Non-Intrusive Reduced Order Model (DDNIROM) is developed for turbulent flows. The method works by partitioning the computational domain into a number of subdomains in such a way that the summation of weights associated with the finite element nodes within each subdomain is approximately equal, and the communication between subdomains is minimised. With suitably chosen weights, it is expected that there will be approximately equal accuracy associated with each subdomain. This accuracy is maximised by allowing the partitioning to occur through areas of the domain that have relatively little flow activity, which, in this case, is characterised by the pointwise maximum Reynolds stresses. A Gaussian Process Regression (GPR) machine learning method is used to construct a set of local approximation functions (hypersurfaces) for each subdomain. Each local hypersurface represents not only the fluid dynamics over the subdomain it belongs to, but also the interactions of the flow dynamics with the surrounding subdomains. Thus, in this way, the surrounding subdomains may be viewed as providing boundary conditions for the current subdomain. We consider a specific example of turbulent air flow within an urban neighbourhood at a test site in London and demonstrate the effectiveness of the proposed DDNIROM.
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Date Issued: 2019-02-14
Identifier: FSU_libsubv1_scholarship_submission_1567612701_cbbb5a0f, 10.1016/j.compßuid.2019.02.012
Format: Citation

Department of Biological Science (10)	+ -
Department of Electrical and Computer Engineering (3)	+ -
National High Magnetic Field Laboratory (2)	+ -
Department of Chemistry and Biochemistry (2)	+ -
Department of Mathematics (1)	+ -

Animals (6)	+ -
Phylogeny (5)	+ -
Evolution, Molecular (4)	+ -
Sequence Analysis, DNA (4)	+ -
Humans (3)	+ -

Male (3)	+ -
Species Specificity (3)	+ -
Dengue/virology (2)	+ -
Female (2)	+ -
Genome (2)	+ -
Genomics/methods (2)	+ -
Likelihood Functions (2)	+ -
Sequence Alignment (2)	+ -
Adaptation, Biological/radiation effects (1)	+ -
Adult (1)	+ -
Africa, Eastern (1)	+ -
Algorithms (1)	+ -
Antibodies, Viral/blood (1)	+ -
Antibody Formation/immunology (1)	+ -
Base Pairing/genetics (1)	+ -
Biodiversity (1)	+ -
Biological Evolution (1)	+ -
Case-Control Studies (1)	+ -
Chikungunya Fever/complications (1)	+ -
Chikungunya Fever/physiopathology (1)	+ -
Chikungunya Fever/virology (1)	+ -
Child (1)	+ -
Child, Preschool (1)	+ -
Cichlids/classification (1)	+ -
Cichlids/genetics (1)	+ -

text (54)	+ -
journal article (38)	+ -

Lemmon, Emily Moriarty (9)	+ -
Lemmon, Alan R (7)	+ -
Ye, Ming (6)	+ -
Gunzburger, Max (4)	+ -
Huang, Chen (3)	+ -

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