WorldWideScience

Sample records for scalable interactive phylogenetic

  1. Orthology prediction at scalable resolution by phylogenetic tree analysis

    NARCIS (Netherlands)

    Heijden, R.T.J.M. van der; Snel, B.; Noort, V. van; Huynen, M.A.

    2007-01-01

    BACKGROUND: Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic

  2. Orthology prediction at scalable resolution by phylogenetic tree analysis

    Directory of Open Access Journals (Sweden)

    Huynen Martijn A

    2007-03-01

    Full Text Available Abstract Background Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups. Results We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable. Conclusion The "levels of orthology" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from the LOFT website http://www.cmbi.ru.nl/LOFT.

  3. A scalable pairwise class interaction framework for multidimensional classification

    DEFF Research Database (Denmark)

    Arias, Jacinto; Gámez, Jose A.; Nielsen, Thomas Dyhre

    2016-01-01

    We present a general framework for multidimensional classification that cap- tures the pairwise interactions between class variables. The pairwise class inter- actions are encoded using a collection of base classifiers (Phase 1), for which the class predictions are combined in a Markov random field...... inference methods in the second phase. We describe the basic framework and its main properties, as well as strategies for ensuring the scalability of the framework. We include a detailed experimental evaluation based on a range of publicly available databases. Here we analyze the overall performance...

  4. A scalable method for computing quadruplet wave-wave interactions

    Science.gov (United States)

    Van Vledder, Gerbrant

    2017-04-01

    Non-linear four-wave interactions are a key physical process in the evolution of wind generated ocean waves. The present generation operational wave models use the Discrete Interaction Approximation (DIA), but it accuracy is poor. It is now generally acknowledged that the DIA should be replaced with a more accurate method to improve predicted spectral shapes and derived parameters. The search for such a method is challenging as one should find a balance between accuracy and computational requirements. Such a method is presented here in the form of a scalable and adaptive method that can mimic both the time consuming exact Snl4 approach and the fast but inaccurate DIA, and everything in between. The method provides an elegant approach to improve the DIA, not by including more arbitrarily shaped wave number configurations, but by a mathematically consistent reduction of an exact method, viz. the WRT method. The adaptiveness is to adapt the abscissa of the locus integrand in relation to the magnitude of the known terms. The adaptiveness is extended to the highest level of the WRT method to select interacting wavenumber configurations in a hierarchical way in relation to their importance. This adaptiveness results in a speed-up of one to three orders of magnitude depending on the measure of accuracy. This definition of accuracy should not be expressed in terms of the quality of the transfer integral for academic spectra but rather in terms of wave model performance in a dynamic run. This has consequences for the balance between the required accuracy and the computational workload for evaluating these interactions. The performance of the scalable method on different scales is illustrated with results from academic spectra, simple growth curves to more complicated field cases using a 3G-wave model.

  5. Interactive and Animated Scalable Vector Graphics and R Data Displays

    Directory of Open Access Journals (Sweden)

    Deborah Nolan

    2012-01-01

    Full Text Available We describe an approach to creating interactive and animated graphical displays using R's graphics engine and Scalable Vector Graphics, an XML vocabulary for describing two-dimensional graphical displays. We use the svg( graphics device in R and then post-process the resulting XML documents. The post-processing identities the elements in the SVG that correspond to the different components of the graphical display, e.g., points, axes, labels, lines. One can then annotate these elements to add interactivity and animation effects. One can also use JavaScript to provide dynamic interactive effects to the plot, enabling rich user interactions and compelling visualizations. The resulting SVG documents can be embedded withinHTML documents and can involve JavaScript code that integrates the SVG and HTML objects. The functionality is provided via the SVGAnnotation package and makes static plots generated via R graphics functions available as stand-alone, interactive and animated plots for the Web and other venues.

  6. Predicting rates of interspecific interaction from phylogenetic trees.

    Science.gov (United States)

    Nuismer, Scott L; Harmon, Luke J

    2015-01-01

    Integrating phylogenetic information can potentially improve our ability to explain species' traits, patterns of community assembly, the network structure of communities, and ecosystem function. In this study, we use mathematical models to explore the ecological and evolutionary factors that modulate the explanatory power of phylogenetic information for communities of species that interact within a single trophic level. We find that phylogenetic relationships among species can influence trait evolution and rates of interaction among species, but only under particular models of species interaction. For example, when interactions within communities are mediated by a mechanism of phenotype matching, phylogenetic trees make specific predictions about trait evolution and rates of interaction. In contrast, if interactions within a community depend on a mechanism of phenotype differences, phylogenetic information has little, if any, predictive power for trait evolution and interaction rate. Together, these results make clear and testable predictions for when and how evolutionary history is expected to influence contemporary rates of species interaction. © 2014 John Wiley & Sons Ltd/CNRS.

  7. jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web.

    Directory of Open Access Journals (Sweden)

    Samuel A Smits

    Full Text Available BACKGROUND: Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. METHODS/PRINCIPAL FINDINGS: We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. CONCLUSIONS/SIGNIFICANCE: jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.

  8. jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web.

    Science.gov (United States)

    Smits, Samuel A; Ouverney, Cleber C

    2010-08-18

    Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.

  9. Dendroscope: An interactive viewer for large phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Franz Markus

    2007-11-01

    Full Text Available Abstract Background Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems. Results We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. Conclusion Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.

  10. Wolfram technologies as an integrated scalable platform for interactive learning

    Science.gov (United States)

    Kaurov, Vitaliy

    2012-02-01

    We rely on technology profoundly with the prospect of even greater integration in the future. Well known challenges in education are a technology-inadequate curriculum and many software platforms that are difficult to scale or interconnect. We'll review an integrated technology, much of it free, that addresses these issues for individuals and small schools as well as for universities. Topics include: Mathematica, a programming environment that offers a diverse range of functionality; natural language programming for getting started quickly and accessing data from Wolfram|Alpha; quick and easy construction of interactive courseware and scientific applications; partnering with publishers to create interactive e-textbooks; course assistant apps for mobile platforms; the computable document format (CDF); teacher-student and student-student collaboration on interactive projects and web publishing at the Wolfram Demonstrations site.

  11. Towards Scalable and Interactive Delivery of Immersive Media.

    NARCIS (Netherlands)

    Niamut, O.A.; Macq, J.F.; Prins, M.J.; Brandenburg, R. van; Verzijp, N.; Alface, P.R.

    2012-01-01

    Within the EU FP7 project FascinatE, a capture, production and delivery system capable of allowing end-users to interactively view and navigate around an ultra-high resolution video panorama showing a live event is being developed. Within this system, network-based processing is used to repurpose

  12. Combining Phylogenetic and Occurrence Information for Risk Assessment of Pest and Pathogen Interactions with Host Plants

    Directory of Open Access Journals (Sweden)

    Ángel L. Robles-Fernández

    2017-08-01

    Full Text Available Phytosanitary agencies conduct plant biosecurity activities, including early detection of potential introduction pathways, to improve control and eradication of pest and pathogen incursions. For such actions, analytical tools based on solid scientific knowledge regarding plant-pest or pathogen relationships for pest risk assessment are needed. Recent evidence indicating that closely related species share a higher chance of becoming infected or attacked by pests has allowed the identification of taxa with different degrees of vulnerability. Here, we use information readily available online about pest-host interactions and their geographic distributions, in combination with host phylogenetic reconstructions, to estimate a pest-host interaction (in some cases infection index in geographic space as a more comprehensive, spatially explicit tool for risk assessment. We demonstrate this protocol using phylogenetic relationships for 20 beetle species and 235 host plant genera: first, we estimate the probability of a host sharing pests, and second, we project the index in geographic space. Overall, the predictions allow identification of the pest-host interaction type (e.g., generalist or specialist, which is largely determined by both host range and phylogenetic constraints. Furthermore, the results can be valuable in terms of identifying hotspots where pests and vulnerable hosts interact. This knowledge is useful for anticipating biological invasions or spreading of disease. We suggest that our understanding of biotic interactions will improve after combining information from multiple dimensions of biodiversity at multiple scales (e.g., phylogenetic signal and host-vector-pathogen geographic distribution.

  13. SciSpark: Highly Interactive and Scalable Model Evaluation and Climate Metrics

    Science.gov (United States)

    Wilson, B. D.; Palamuttam, R. S.; Mogrovejo, R. M.; Whitehall, K. D.; Mattmann, C. A.; Verma, R.; Waliser, D. E.; Lee, H.

    2015-12-01

    Remote sensing data and climate model output are multi-dimensional arrays of massive sizes locked away in heterogeneous file formats (HDF5/4, NetCDF 3/4) and metadata models (HDF-EOS, CF) making it difficult to perform multi-stage, iterative science processing since each stage requires writing and reading data to and from disk. We are developing a lightning fast Big Data technology called SciSpark based on ApacheTM Spark under a NASA AIST grant (PI Mattmann). Spark implements the map-reduce paradigm for parallel computing on a cluster, but emphasizes in-memory computation, "spilling" to disk only as needed, and so outperforms the disk-based ApacheTM Hadoop by 100x in memory and by 10x on disk. SciSpark will enable scalable model evaluation by executing large-scale comparisons of A-Train satellite observations to model grids on a cluster of 10 to 1000 compute nodes. This 2nd generation capability for NASA's Regional Climate Model Evaluation System (RCMES) will compute simple climate metrics at interactive speeds, and extend to quite sophisticated iterative algorithms such as machine-learning based clustering of temperature PDFs, and even graph-based algorithms for searching for Mesocale Convective Complexes. We have implemented a parallel data ingest capability in which the user specifies desired variables (arrays) as several time-sorted lists of URL's (i.e. using OPeNDAP model.nc?varname, or local files). The specified variables are partitioned by time/space and then each Spark node pulls its bundle of arrays into memory to begin a computation pipeline. We also investigated the performance of several N-dim. array libraries (scala breeze, java jblas & netlib-java, and ND4J). We are currently developing science codes using ND4J and studying memory behavior on the JVM. On the pyspark side, many of our science codes already use the numpy and SciPy ecosystems. The talk will cover: the architecture of SciSpark, the design of the scientific RDD (sRDD) data structure, our

  14. Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices

    Directory of Open Access Journals (Sweden)

    Liao Li

    2007-01-01

    Full Text Available Abstract Background Protein-protein interactions are critical for cellular functions. Recently developed computational approaches for predicting protein-protein interactions utilize co-evolutionary information of the interacting partners, e.g., correlations between distance matrices, where each matrix stores the pairwise distances between a protein and its orthologs from a group of reference genomes. Results We proposed a novel, simple method to account for some of the intra-matrix correlations in improving the prediction accuracy. Specifically, the phylogenetic species tree of the reference genomes is used as a guide tree for hierarchical clustering of the orthologous proteins. The distances between these clusters, derived from the original pairwise distance matrix using the Neighbor Joining algorithm, form intermediate distance matrices, which are then transformed and concatenated into a super phylogenetic vector. A support vector machine is trained and tested on pairs of proteins, represented as super phylogenetic vectors, whose interactions are known. The performance, measured as ROC score in cross validation experiments, shows significant improvement of our method (ROC score 0.8446 over that of using Pearson correlations (0.6587. Conclusion We have shown that the phylogenetic tree can be used as a guide to extract intra-matrix correlations in the distance matrices of orthologous proteins, where these correlations are represented as intermediate distance matrices of the ancestral orthologous proteins. Both the unsupervised and supervised learning paradigms benefit from the explicit inclusion of these intermediate distance matrices, and particularly so in the latter case, which offers a better balance between sensitivity and specificity in the prediction of protein-protein interactions.

  15. SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

    Science.gov (United States)

    Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

    2017-09-30

    Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.

  16. SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision.

    Science.gov (United States)

    Wiewiórka, Marek S; Messina, Antonio; Pacholewska, Alicja; Maffioletti, Sergio; Gawrysiak, Piotr; Okoniewski, Michał J

    2014-09-15

    Many time-consuming analyses of next -: generation sequencing data can be addressed with modern cloud computing. The Apache Hadoop-based solutions have become popular in genomics BECAUSE OF: their scalability in a cloud infrastructure. So far, most of these tools have been used for batch data processing rather than interactive data querying. The SparkSeq software has been created to take advantage of a new MapReduce framework, Apache Spark, for next-generation sequencing data. SparkSeq is a general-purpose, flexible and easily extendable library for genomic cloud computing. It can be used to build genomic analysis pipelines in Scala and run them in an interactive way. SparkSeq opens up the possibility of customized ad hoc secondary analyses and iterative machine learning algorithms. This article demonstrates its scalability and overall fast performance by running the analyses of sequencing datasets. Tests of SparkSeq also prove that the use of cache and HDFS block size can be tuned for the optimal performance on multiple worker nodes. Available under open source Apache 2.0 license: https://bitbucket.org/mwiewiorka/sparkseq/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Circuit design for multi-body interactions in superconducting quantum annealing systems with applications to a scalable architecture

    Science.gov (United States)

    Chancellor, N.; Zohren, S.; Warburton, P. A.

    2017-06-01

    Quantum annealing provides a way of solving optimization problems by encoding them as Ising spin models which are implemented using physical qubits. The solution of the optimization problem then corresponds to the ground state of the system. Quantum tunneling is harnessed to enable the system to move to the ground state in a potentially high non-convex energy landscape. A major difficulty in encoding optimization problems in physical quantum annealing devices is the fact that many real world optimization problems require interactions of higher connectivity, as well as multi-body terms beyond the limitations of the physical hardware. In this work we address the question of how to implement multi-body interactions using hardware which natively only provides two-body interactions. The main result is an efficient circuit design of such multi-body terms using superconducting flux qubits in which effective N-body interactions are implemented using N ancilla qubits and only two inductive couplers. It is then shown how this circuit can be used as the unit cell of a scalable architecture by applying it to a recently proposed embedding technique for constructing an architecture of logical qubits with arbitrary connectivity using physical qubits which have nearest-neighbor four-body interactions. It is further shown that this design is robust to non-linear effects in the coupling loops, as well as mismatches in some of the circuit parameters.

  18. MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME

    Science.gov (United States)

    Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

    2017-01-01

    Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments. PMID:28190948

  19. Interface induced spin-orbit interaction in silicon quantum dots and prospects of scalability

    Science.gov (United States)

    Ferdous, Rifat; Wai, Kok; Veldhorst, Menno; Hwang, Jason; Yang, Henry; Klimeck, Gerhard; Dzurak, Andrew; Rahman, Rajib

    A scalable quantum computing architecture requires reproducibility over key qubit properties, like resonance frequency, coherence time etc. Randomness in these properties would necessitate individual knowledge of each qubit in a quantum computer. Spin qubits hosted in Silicon (Si) quantum dots (QD) is promising as a potential building block for a large-scale quantum computer, because of their longer coherence times. The Stark shift of the electron g-factor in these QDs has been used to selectively address multiple qubits. From atomistic tight-binding studies we investigated the effect of interface non-ideality on the Stark shift of the g-factor in a Si QD. We find that based on the location of a monoatomic step at the interface with respect to the dot center both the sign and magnitude of the Stark shift change. Thus the presence of interface steps in these devices will cause variability in electron g-factor and its Stark shift based on the location of the qubit. This behavior will also cause varying sensitivity to charge noise from one qubit to another, which will randomize the dephasing times T2*. This predicted device-to-device variability is experimentally observed recently in three qubits fabricated at a Si/Si02 interface, which validates the issues discussed.

  20. A Scalable and Extensible Interactive Scenario Architecture for Distributed Command and Control Simulations

    Science.gov (United States)

    2004-06-01

    solution. Mateas and Stern proposed a HAP-based architecture for interactive narrative ( Mateas and Stern 2000, 2001). Young proposed a plan-based...interactive scenarios1 is unclear. Mateas and Stern proposed a HAP-based architecture for interactive narratives (2001). Young proposed a plan-based...manager in the Oz Project ( Mateas , 1999). The scenario manager is the essential component of dynamic scenario architecture; it serves as a hidden

  1. Automata-based Optimization of Interaction Protocols for Scalable Multicore Platforms (Technical Report)

    NARCIS (Netherlands)

    S.-S.T.Q. Jongmans (Sung-Shik); S. Halle; F. Arbab (Farhad)

    2014-01-01

    htmlabstractMulticore platforms offer the opportunity for utilizing massively parallel resources. However, programming them is challenging. We need good compilers that optimize commonly occurring synchronization/interaction patterns. To facilitate optimization, a programming language must convey

  2. Functional phylogenetic analysis of LGI proteins identifies an interaction motif crucial for myelination.

    Science.gov (United States)

    Kegel, Linde; Jaegle, Martine; Driegen, Siska; Aunin, Eerik; Leslie, Kris; Fukata, Yuko; Watanabe, Masahiko; Fukata, Masaki; Meijer, Dies

    2014-04-01

    The cellular interactions that drive the formation and maintenance of the insulating myelin sheath around axons are only partially understood. Leucine-rich glioma-inactivated (LGI) proteins play important roles in nervous system development and mutations in their genes have been associated with epilepsy and amyelination. Their function involves interactions with ADAM22 and ADAM23 cell surface receptors, possibly in apposing membranes, thus attenuating cellular interactions. LGI4-ADAM22 interactions are required for axonal sorting and myelination in the developing peripheral nervous system (PNS). Functional analysis revealed that, despite their high homology and affinity for ADAM22, LGI proteins are functionally distinct. To dissect the key residues in LGI proteins required for coordinating axonal sorting and myelination in the developing PNS, we adopted a phylogenetic and computational approach and demonstrate that the mechanism of action of LGI4 depends on a cluster of three amino acids on the outer surface of the LGI4 protein, thus providing a structural basis for the mechanistic differences in LGI protein function in nervous system development and evolution.

  3. On parallel scalability aspects of strongly coupled partitioned fluid-structure-acoustics interaction

    NARCIS (Netherlands)

    Blom, D.S.; Krupp, V.; Van Zuijlen, A.H.; Klimach, H.; Roller, S.; Bijl, H.

    2015-01-01

    Multi-physics simulations, such as fluid-structure-acoustics interaction (FSA), require a high performance computing environment in order to perform the simulation in a reasonable amount of computation time. Currently used coupling methods use a staggered execution of the fluid and solid solver [6],

  4. Observing Graphene Grow: Catalyst–Graphene Interactions during Scalable Graphene Growth on Polycrystalline Copper

    Science.gov (United States)

    2013-01-01

    Complementary in situ X-ray photoelectron spectroscopy (XPS), X-ray diffractometry, and environmental scanning electron microscopy are used to fingerprint the entire graphene chemical vapor deposition process on technologically important polycrystalline Cu catalysts to address the current lack of understanding of the underlying fundamental growth mechanisms and catalyst interactions. Graphene forms directly on metallic Cu during the high-temperature hydrocarbon exposure, whereby an upshift in the binding energies of the corresponding C1s XPS core level signatures is indicative of coupling between the Cu catalyst and the growing graphene. Minor carbon uptake into Cu can under certain conditions manifest itself as carbon precipitation upon cooling. Postgrowth, ambient air exposure even at room temperature decouples the graphene from Cu by (reversible) oxygen intercalation. The importance of these dynamic interactions is discussed for graphene growth, processing, and device integration. PMID:24041311

  5. Observing graphene grow: catalyst-graphene interactions during scalable graphene growth on polycrystalline copper.

    Science.gov (United States)

    Kidambi, Piran R; Bayer, Bernhard C; Blume, Raoul; Wang, Zhu-Jun; Baehtz, Carsten; Weatherup, Robert S; Willinger, Marc-Georg; Schloegl, Robert; Hofmann, Stephan

    2013-10-09

    Complementary in situ X-ray photoelectron spectroscopy (XPS), X-ray diffractometry, and environmental scanning electron microscopy are used to fingerprint the entire graphene chemical vapor deposition process on technologically important polycrystalline Cu catalysts to address the current lack of understanding of the underlying fundamental growth mechanisms and catalyst interactions. Graphene forms directly on metallic Cu during the high-temperature hydrocarbon exposure, whereby an upshift in the binding energies of the corresponding C1s XPS core level signatures is indicative of coupling between the Cu catalyst and the growing graphene. Minor carbon uptake into Cu can under certain conditions manifest itself as carbon precipitation upon cooling. Postgrowth, ambient air exposure even at room temperature decouples the graphene from Cu by (reversible) oxygen intercalation. The importance of these dynamic interactions is discussed for graphene growth, processing, and device integration.

  6. Scalable devices

    KAUST Repository

    Krüger, Jens J.

    2014-01-01

    In computer science in general and in particular the field of high performance computing and supercomputing the term scalable plays an important role. It indicates that a piece of hardware, a concept, an algorithm, or an entire system scales with the size of the problem, i.e., it can not only be used in a very specific setting but it\\'s applicable for a wide range of problems. From small scenarios to possibly very large settings. In this spirit, there exist a number of fixed areas of research on scalability. There are works on scalable algorithms, scalable architectures but what are scalable devices? In the context of this chapter, we are interested in a whole range of display devices, ranging from small scale hardware such as tablet computers, pads, smart-phones etc. up to large tiled display walls. What interests us mostly is not so much the hardware setup but mostly the visualization algorithms behind these display systems that scale from your average smart phone up to the largest gigapixel display walls.

  7. Helicopter model rotor-blade vortex interaction impulsive noise: Scalability and parametric variations

    Science.gov (United States)

    Splettstoesser, W. R.; Schultz, K. J.; Boxwell, D. A.; Schmitz, F. H.

    1984-01-01

    Acoustic data taken in the anechoic Deutsch-Niederlaendischer Windkanal (DNW) have documented the blade vortex interaction (BVI) impulsive noise radiated from a 1/7-scale model main rotor of the AH-1 series helicopter. Averaged model scale data were compared with averaged full scale, inflight acoustic data under similar nondimensional test conditions. At low advance ratios (mu = 0.164 to 0.194), the data scale remarkable well in level and waveform shape, and also duplicate the directivity pattern of BVI impulsive noise. At moderate advance ratios (mu = 0.224 to 0.270), the scaling deteriorates, suggesting that the model scale rotor is not adequately simulating the full scale BVI noise; presently, no proved explanation of this discrepancy exists. Carefully performed parametric variations over a complete matrix of testing conditions have shown that all of the four governing nondimensional parameters - tip Mach number at hover, advance ratio, local inflow ratio, and thrust coefficient - are highly sensitive to BVI noise radiation.

  8. Photon-Mediated Interactions: A Scalable Tool to Create and Sustain Entangled States of N Atoms

    Directory of Open Access Journals (Sweden)

    Camille Aron

    2016-03-01

    Full Text Available We propose and study the use of photon-mediated interactions for the generation of long-range steady-state entanglement between N atoms. Through the judicious use of coherent drives and the placement of the atoms in a network of cavity QED systems, a balance between their unitary and dissipative dynamics can be precisely engineered to stabilize a long-range correlated state of qubits in the steady state. We discuss the general theory behind such a scheme and present an example of how it can be used to drive a register of N atoms to a generalized W state and how the entanglement can be sustained indefinitely. The achievable steady-state fidelities for entanglement and its scaling with the number of qubits are discussed for presently existing superconducting quantum circuits. While the protocol is primarily discussed for a superconducting circuit architecture, it is ideally realized in any cavity QED platform that permits controllable delivery of coherent electromagnetic radiation to specified locations.

  9. Scalable Resolution Display Walls

    KAUST Repository

    Leigh, Jason

    2013-01-01

    This article will describe the progress since 2000 on research and development in 2-D and 3-D scalable resolution display walls that are built from tiling individual lower resolution flat panel displays. The article will describe approaches and trends in display hardware construction, middleware architecture, and user-interaction design. The article will also highlight examples of use cases and the benefits the technology has brought to their respective disciplines. © 1963-2012 IEEE.

  10. A scalable nonlinear fluid-structure interaction solver based on a Schwarz preconditioner with isogeometric unstructured coarse spaces in 3D

    Science.gov (United States)

    Kong, Fande; Cai, Xiao-Chuan

    2017-07-01

    Nonlinear fluid-structure interaction (FSI) problems on unstructured meshes in 3D appear in many applications in science and engineering, such as vibration analysis of aircrafts and patient-specific diagnosis of cardiovascular diseases. In this work, we develop a highly scalable, parallel algorithmic and software framework for FSI problems consisting of a nonlinear fluid system and a nonlinear solid system, that are coupled monolithically. The FSI system is discretized by a stabilized finite element method in space and a fully implicit backward difference scheme in time. To solve the large, sparse system of nonlinear algebraic equations at each time step, we propose an inexact Newton-Krylov method together with a multilevel, smoothed Schwarz preconditioner with isogeometric coarse meshes generated by a geometry preserving coarsening algorithm. Here ;geometry; includes the boundary of the computational domain and the wet interface between the fluid and the solid. We show numerically that the proposed algorithm and implementation are highly scalable in terms of the number of linear and nonlinear iterations and the total compute time on a supercomputer with more than 10,000 processor cores for several problems with hundreds of millions of unknowns.

  11. Automatic selection of reference taxa for protein–protein interaction prediction with phylogenetic profiling

    DEFF Research Database (Denmark)

    Simonsen, Martin; Maetschke, Stefan R.; Ragan, Mark A

    2012-01-01

    : We present three novel methods for automating the selection of RT, using machine learning based on known protein–protein interaction networks. One of these methods in particular, Tree-Based Search, yields greatly improved prediction accuracies. We further show that different methods for constituting...

  12. Functional phylogenetic analysis of LGI proteins identifies an interaction motif crucial for myelination

    NARCIS (Netherlands)

    L. Kegel (Linde); M.M. Jaegle (Martine); M.J.F. Driegen (Siska); E. Aunin (Eerik); K. Leslie (Kris); Y. Fukata (Yuko); M. Watanabe (Masahiko); M. Fukata (Masaki); D.N. Meijer (Dies)

    2014-01-01

    textabstractThe cellular interactions that drive the formation and maintenance of the insulating myelin sheath around axons are only partially understood. Leucine-rich glioma-inactivated (LGI) proteins play important roles in nervous system development and mutations in their genes have been

  13. Visual analytics in scalable visualization environments

    OpenAIRE

    Yamaoka, So

    2011-01-01

    Visual analytics is an interdisciplinary field that facilitates the analysis of the large volume of data through interactive visual interface. This dissertation focuses on the development of visual analytics techniques in scalable visualization environments. These scalable visualization environments offer a high-resolution, integrated virtual space, as well as a wide-open physical space that affords collaborative user interaction. At the same time, the sheer scale of these environments poses ...

  14. Phenotypic Microdiversity and Phylogenetic Signal Analysis of Traits Related to Social Interaction in Bacillus spp. from Sediment Communities.

    Science.gov (United States)

    Rodríguez-Torres, María Dolores; Islas-Robles, África; Gómez-Lunar, Zulema; Delaye, Luis; Hernández-González, Ismael; Souza, Valeria; Travisano, Michael; Olmedo-Álvarez, Gabriela

    2017-01-01

    Understanding the relationship between phylogeny and predicted traits is important to uncover the dimension of the predictive power of a microbial composition approach. Numerous works have addressed the taxonomic composition of bacteria in communities, but little is known about trait heterogeneity in closely related bacteria that co-occur in communities. We evaluated a sample of 467 isolates from the Churince water system of the Cuatro Cienegas Basin (CCB), enriched for Bacillus spp. The 16S rRNA gene revealed a random distribution of taxonomic groups within this genus among 11 sampling sites. A subsample of 141 Bacillus spp. isolates from sediment, with seven well-represented species was chosen to evaluate the heterogeneity and the phylogenetic signal of phenotypic traits that are known to diverge within small clades, such as substrate utilization, and traits that are conserved deep in the lineage, such as prototrophy, swarming and biofilm formation. We were especially interested in evaluating social traits, such as swarming and biofilm formation, for which cooperation is needed to accomplish a multicellular behavior and for which there is little information from natural communities. The phylogenetic distribution of traits, evaluated by the Purvis and Fritz's D statistics approached a Brownian model of evolution. Analysis of the phylogenetic relatedness of the clusters of members sharing the trait using consenTRAIT algorithm, revealed more clustering and deeper phylogenetic signal for prototrophy, biofilm and swimming compared to the data obtained for substrate utilization. The explanation to the observed Brownian evolution of social traits could be either loss due to complete dispensability or to compensated trait loss due to the availability of public goods. Since many of the evaluated traits can be considered to be collective action traits, such as swarming, motility and biofilm formation, the observed microdiversity within taxonomic groups might be explained

  15. Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

    Science.gov (United States)

    Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

    2015-01-01

    The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.

  16. Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa

    Science.gov (United States)

    Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

    2015-01-01

    The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation. PMID:25978319

  17. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms

    OpenAIRE

    Speiser, Daniel I.; Pankey, M. Sabrina; Zaharoff, Alexander K.; Battelle, Barbara A; Heather D. Bracken-Grissom; Breinholt, Jesse W.; Bybee, Seth M.; Cronin, Thomas W.; Garm, Anders Lydik; Lindgren, Annie R; Patel, Nipam H.; Megan L Porter; Protas, Meredith E; Rivera, Ajna S.; Serb, Jeanne M.

    2014-01-01

    Background Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees ...

  18. PKI Scalability Issues

    OpenAIRE

    Slagell, Adam J.; Bonilla, Rafael

    2004-01-01

    This report surveys different PKI technologies such as PKIX and SPKI and the issues of PKI that affect scalability. Much focus is spent on certificate revocation methodologies and status verification systems such as CRLs, Delta-CRLs, CRS, Certificate Revocation Trees, Windowed Certificate Revocation, OCSP, SCVP and DVCS.

  19. Scalable rendering on PC clusters

    Energy Technology Data Exchange (ETDEWEB)

    WYLIE,BRIAN N.; LEWIS,VASILY; SHIRLEY,DAVID NOYES; PAVLAKOS,CONSTANTINE

    2000-04-25

    This case study presents initial results from research targeted at the development of cost-effective scalable visualization and rendering technologies. The implementations of two 3D graphics libraries based on the popular sort-last and sort-middle parallel rendering techniques are discussed. An important goal of these implementations is to provide scalable rendering capability for extremely large datasets (>> 5 million polygons). Applications can use these libraries for either run-time visualization, by linking to an existing parallel simulation, or for traditional post-processing by linking to an interactive display program. The use of parallel, hardware-accelerated rendering on commodity hardware is leveraged to achieve high performance. Current performance results show that, using current hardware (a small 16-node cluster), they can utilize up to 85% of the aggregate graphics performance and achieve rendering rates in excess of 20 million polygons/second using OpenGL{reg_sign} with lighting, Gouraud shading, and individually specified triangles (not t-stripped).

  20. Scalable Reliable SD Erlang Design

    OpenAIRE

    Chechina, Natalia; Trinder, Phil; Ghaffari, Amir; Green, Rickard; Lundin, Kenneth; Virding, Robert

    2014-01-01

    This technical report presents the design of Scalable Distributed (SD) Erlang: a set of language-level changes that aims to enable Distributed Erlang to scale for server applications on commodity hardware with at most 100,000 cores. We cover a number of aspects, specifically anticipated architecture, anticipated failures, scalable data structures, and scalable computation. Other two components that guided us in the design of SD Erlang are design principles and typical Erlang applications. The...

  1. Scalable photoreactor for hydrogen production

    KAUST Repository

    Takanabe, Kazuhiro

    2017-04-06

    Provided herein are scalable photoreactors that can include a membrane-free water- splitting electrolyzer and systems that can include a plurality of membrane-free water- splitting electrolyzers. Also provided herein are methods of using the scalable photoreactors provided herein.

  2. Characterization of the genome of a phylogenetically distinct tospovirus and its interactions with the local lesion-induced host Chenopodium quinoa by whole-transcriptome analyses.

    Directory of Open Access Journals (Sweden)

    Wan-Chen Chou

    Full Text Available Chenopodium quinoa is a natural local lesion host of numerous plant viruses, including tospoviruses (family Bunyaviridae. Groundnut chlorotic fan-spot tospovirus (GCFSV has been shown to consistently induce local lesions on the leaves of C. quinoa 4 days post-inoculation (dpi. To reveal the whole genome of GCFSV and its interactions with C. quinoa, RNA-seq was performed to determine the transcriptome profiles of C. quinoa leaves. The high-throughput reads from infected C. quinoa leaves were used to identify the whole genome sequence of GCFSV and its single nucleotide polymorphisms. Our results indicated that GCFSV is a phylogenetically distinct tospovirus. Moreover, 27,170 coding and 29,563 non-coding sequences of C. quinoa were identified through de novo assembly, mixing reads from mock and infected samples. Several key genes involved in the modulation of hypersensitive response (HR were identified. The expression levels of 4,893 deduced complete genes annotated using the Arabidopsis genome indicated that several HR-related orthologues of pathogenesis-related proteins, transcription factors, mitogen-activated protein kinases, and defense proteins were significantly expressed in leaves that formed local lesions. Here, we also provide new insights into the replication progression of a tospovirus and the molecular regulation of the C. quinoa response to virus infection.

  3. Characterization of the genome of a phylogenetically distinct tospovirus and its interactions with the local lesion-induced host Chenopodium quinoa by whole-transcriptome analyses.

    Science.gov (United States)

    Chou, Wan-Chen; Lin, Shih-Shun; Yeh, Shyi-Dong; Li, Siang-Ling; Peng, Ying-Che; Fan, Ya-Hsu; Chen, Tsung-Chi

    2017-01-01

    Chenopodium quinoa is a natural local lesion host of numerous plant viruses, including tospoviruses (family Bunyaviridae). Groundnut chlorotic fan-spot tospovirus (GCFSV) has been shown to consistently induce local lesions on the leaves of C. quinoa 4 days post-inoculation (dpi). To reveal the whole genome of GCFSV and its interactions with C. quinoa, RNA-seq was performed to determine the transcriptome profiles of C. quinoa leaves. The high-throughput reads from infected C. quinoa leaves were used to identify the whole genome sequence of GCFSV and its single nucleotide polymorphisms. Our results indicated that GCFSV is a phylogenetically distinct tospovirus. Moreover, 27,170 coding and 29,563 non-coding sequences of C. quinoa were identified through de novo assembly, mixing reads from mock and infected samples. Several key genes involved in the modulation of hypersensitive response (HR) were identified. The expression levels of 4,893 deduced complete genes annotated using the Arabidopsis genome indicated that several HR-related orthologues of pathogenesis-related proteins, transcription factors, mitogen-activated protein kinases, and defense proteins were significantly expressed in leaves that formed local lesions. Here, we also provide new insights into the replication progression of a tospovirus and the molecular regulation of the C. quinoa response to virus infection.

  4. Scalable Atomistic Simulation Algorithms for Materials Research

    Directory of Open Access Journals (Sweden)

    Aiichiro Nakano

    2002-01-01

    Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

  5. Scalable Frequent Subgraph Mining

    KAUST Repository

    Abdelhamid, Ehab

    2017-06-19

    A graph is a data structure that contains a set of nodes and a set of edges connecting these nodes. Nodes represent objects while edges model relationships among these objects. Graphs are used in various domains due to their ability to model complex relations among several objects. Given an input graph, the Frequent Subgraph Mining (FSM) task finds all subgraphs with frequencies exceeding a given threshold. FSM is crucial for graph analysis, and it is an essential building block in a variety of applications, such as graph clustering and indexing. FSM is computationally expensive, and its existing solutions are extremely slow. Consequently, these solutions are incapable of mining modern large graphs. This slowness is caused by the underlying approaches of these solutions which require finding and storing an excessive amount of subgraph matches. This dissertation proposes a scalable solution for FSM that avoids the limitations of previous work. This solution is composed of four components. The first component is a single-threaded technique which, for each candidate subgraph, needs to find only a minimal number of matches. The second component is a scalable parallel FSM technique that utilizes a novel two-phase approach. The first phase quickly builds an approximate search space, which is then used by the second phase to optimize and balance the workload of the FSM task. The third component focuses on accelerating frequency evaluation, which is a critical step in FSM. To do so, a machine learning model is employed to predict the type of each graph node, and accordingly, an optimized method is selected to evaluate that node. The fourth component focuses on mining dynamic graphs, such as social networks. To this end, an incremental index is maintained during the dynamic updates. Only this index is processed and updated for the majority of graph updates. Consequently, search space is significantly pruned and efficiency is improved. The empirical evaluation shows that the

  6. Scalable Nanomanufacturing—A Review

    Directory of Open Access Journals (Sweden)

    Khershed Cooper

    2017-01-01

    Full Text Available This article describes the field of scalable nanomanufacturing, its importance and need, its research activities and achievements. The National Science Foundation is taking a leading role in fostering basic research in scalable nanomanufacturing (SNM. From this effort several novel nanomanufacturing approaches have been proposed, studied and demonstrated, including scalable nanopatterning. This paper will discuss SNM research areas in materials, processes and applications, scale-up methods with project examples, and manufacturing challenges that need to be addressed to move nanotechnology discoveries closer to the marketplace.

  7. Scalable Gravity Offload System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — A scalable gravity offload device simulates reduced gravity for the testing of various surface system elements such as mobile robots, excavators, habitats, and...

  8. Open Reading Frame Phylogenetic Analysis on the Cloud

    Science.gov (United States)

    2013-01-01

    Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

  9. Open Reading Frame Phylogenetic Analysis on the Cloud

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

    Full Text Available Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus.

  10. Unrealistic phylogenetic trees may improve phylogenetic footprinting.

    Science.gov (United States)

    Nettling, Martin; Treutler, Hendrik; Cerquides, Jesus; Grosse, Ivo

    2017-06-01

    The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting requires phylogenetic trees with attached substitution probabilities for quantifying the evolution of binding sites, but these trees and substitution probabilities are typically not known and cannot be estimated easily. Here, we investigate the influence of phylogenetic trees with different substitution probabilities on the classification performance of phylogenetic footprinting using synthetic and real data. For synthetic data we find that the classification performance is highest when the substitution probability used for phylogenetic footprinting is similar to that used for data generation. For real data, however, we typically find that the classification performance of phylogenetic footprinting surprisingly increases with increasing substitution probabilities and is often highest for unrealistically high substitution probabilities close to one. This finding suggests that choosing realistic model assumptions might not always yield optimal predictions in general and that choosing unrealistically high substitution probabilities close to one might actually improve the classification performance of phylogenetic footprinting. The proposed PF is implemented in JAVA and can be downloaded from https://github.com/mgledi/PhyFoo. : martin.nettling@informatik.uni-halle.de. Supplementary data are available at Bioinformatics online.

  11. The Evolutionary Ecology of Plant Disease: A Phylogenetic Perspective.

    Science.gov (United States)

    Gilbert, Gregory S; Parker, Ingrid M

    2016-08-04

    An explicit phylogenetic perspective provides useful tools for phytopathology and plant disease ecology because the traits of both plants and microbes are shaped by their evolutionary histories. We present brief primers on phylogenetic signal and the analytical tools of phylogenetic ecology. We review the literature and find abundant evidence of phylogenetic signal in pathogens and plants for most traits involved in disease interactions. Plant nonhost resistance mechanisms and pathogen housekeeping functions are conserved at deeper phylogenetic levels, whereas molecular traits associated with rapid coevolutionary dynamics are more labile at branch tips. Horizontal gene transfer disrupts the phylogenetic signal for some microbial traits. Emergent traits, such as host range and disease severity, show clear phylogenetic signals. Therefore pathogen spread and disease impact are influenced by the phylogenetic structure of host assemblages. Phylogenetically rare species escape disease pressure. Phylogenetic tools could be used to develop predictive tools for phytosanitary risk analysis and reduce disease pressure in multispecies cropping systems.

  12. Scalable algorithms for contact problems

    CERN Document Server

    Dostál, Zdeněk; Sadowská, Marie; Vondrák, Vít

    2016-01-01

    This book presents a comprehensive and self-contained treatment of the authors’ newly developed scalable algorithms for the solutions of multibody contact problems of linear elasticity. The brand new feature of these algorithms is theoretically supported numerical scalability and parallel scalability demonstrated on problems discretized by billions of degrees of freedom. The theory supports solving multibody frictionless contact problems, contact problems with possibly orthotropic Tresca’s friction, and transient contact problems. It covers BEM discretization, jumping coefficients, floating bodies, mortar non-penetration conditions, etc. The exposition is divided into four parts, the first of which reviews appropriate facets of linear algebra, optimization, and analysis. The most important algorithms and optimality results are presented in the third part of the volume. The presentation is complete, including continuous formulation, discretization, decomposition, optimality results, and numerical experimen...

  13. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.

    Science.gov (United States)

    Junier, Thomas; Zdobnov, Evgeny M

    2010-07-01

    We present a suite of Unix shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes. C source code, Python bindings and executables for various platforms are available from http://cegg.unige.ch/newick_utils. The distribution includes a manual and example data. The package is distributed under the BSD License. thomas.junier@unige.ch

  14. Scalable shared-memory multiprocessing

    CERN Document Server

    Lenoski, Daniel E

    1995-01-01

    Dr. Lenoski and Dr. Weber have experience with leading-edge research and practical issues involved in implementing large-scale parallel systems. They were key contributors to the architecture and design of the DASH multiprocessor. Currently, they are involved with commercializing scalable shared-memory technology.

  15. Scalability study of solid xenon

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, J.; Cease, H.; Jaskierny, W. F.; Markley, D.; Pahlka, R. B.; Balakishiyeva, D.; Saab, T.; Filipenko, M.

    2015-04-01

    We report a demonstration of the scalability of optically transparent xenon in the solid phase for use as a particle detector above a kilogram scale. We employed a cryostat cooled by liquid nitrogen combined with a xenon purification and chiller system. A modified {\\it Bridgeman's technique} reproduces a large scale optically transparent solid xenon.

  16. Drawing rooted phylogenetic networks.

    Science.gov (United States)

    Huson, Daniel H

    2009-01-01

    The evolutionary history of a collection of species is usually represented by a phylogenetic tree. Sometimes, phylogenetic networks are used as a means of representing reticulate evolution or of showing uncertainty and incompatibilities in evolutionary datasets. This is often done using unrooted phylogenetic networks such as split networks, due in part, to the availability of software (SplitsTree) for their computation and visualization. In this paper we discuss the problem of drawing rooted phylogenetic networks as cladograms or phylograms in a number of different views that are commonly used for rooted trees. Implementations of the algorithms are available in new releases of the Dendroscope and SplitsTree programs.

  17. Scalable fast multipole accelerated vortex methods

    KAUST Repository

    Hu, Qi

    2014-05-01

    The fast multipole method (FMM) is often used to accelerate the calculation of particle interactions in particle-based methods to simulate incompressible flows. To evaluate the most time-consuming kernels - the Biot-Savart equation and stretching term of the vorticity equation, we mathematically reformulated it so that only two Laplace scalar potentials are used instead of six. This automatically ensuring divergence-free far-field computation. Based on this formulation, we developed a new FMM-based vortex method on heterogeneous architectures, which distributed the work between multicore CPUs and GPUs to best utilize the hardware resources and achieve excellent scalability. The algorithm uses new data structures which can dynamically manage inter-node communication and load balance efficiently, with only a small parallel construction overhead. This algorithm can scale to large-sized clusters showing both strong and weak scalability. Careful error and timing trade-off analysis are also performed for the cutoff functions induced by the vortex particle method. Our implementation can perform one time step of the velocity+stretching calculation for one billion particles on 32 nodes in 55.9 seconds, which yields 49.12 Tflop/s.

  18. Quality scalable video data stream

    OpenAIRE

    Wiegand, T.; Kirchhoffer, H.; Schwarz, H

    2008-01-01

    An apparatus for generating a quality-scalable video data stream (36) is described which comprises means (42) for coding a video signal (18) using block-wise transformation to obtain transform blocks (146, 148) of transformation coefficient values for a picture (140) of the video signal, a predetermined scan order (154, 156, 164, 166) with possible scan positions being defined among the transformation coefficient values within the transform blocks so that in each transform block, for each pos...

  19. Phylogenetic structure in tropical hummingbird communities

    OpenAIRE

    Graham, Catherine H.; Parra, Juan L.; Rahbek, Carsten; McGuire, Jimmy A.

    2009-01-01

    How biotic interactions, current and historical environment, and biogeographic barriers determine community structure is a fundamental question in ecology and evolution, especially in diverse tropical regions. To evaluate patterns of local and regional diversity, we quantified the phylogenetic composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, l...

  20. Scalable Techniques for Formal Verification

    CERN Document Server

    Ray, Sandip

    2010-01-01

    This book presents state-of-the-art approaches to formal verification techniques to seamlessly integrate different formal verification methods within a single logical foundation. It should benefit researchers and practitioners looking to get a broad overview of the spectrum of formal verification techniques, as well as approaches to combining such techniques within a single framework. Coverage includes a range of case studies showing how such combination is fruitful in developing a scalable verification methodology for industrial designs. This book outlines both theoretical and practical issue

  1. Flexible scalable photonic manufacturing method

    Science.gov (United States)

    Skunes, Timothy A.; Case, Steven K.

    2003-06-01

    A process for flexible, scalable photonic manufacturing is described. Optical components are actively pre-aligned and secured to precision mounts. In a subsequent operation, the mounted optical components are passively placed onto a substrate known as an Optical Circuit Board (OCB). The passive placement may be either manual for low volume applications or with a pick-and-place robot for high volume applications. Mating registration features on the component mounts and the OCB facilitate accurate optical alignment. New photonic circuits may be created by changing the layout of the OCB. Predicted yield data from Monte Carlo tolerance simulations for two fiber optic photonic circuits is presented.

  2. Highly Scalable Matching Pursuit Signal Decomposition Algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — In this research, we propose a variant of the classical Matching Pursuit Decomposition (MPD) algorithm with significantly improved scalability and computational...

  3. Perceptual compressive sensing scalability in mobile video

    Science.gov (United States)

    Bivolarski, Lazar

    2011-09-01

    Scalability features embedded within the video sequences allows for streaming over heterogeneous networks to a variety of end devices. Compressive sensing techniques that will allow for lowering the complexity increase the robustness of the video scalability are reviewed. Human visual system models are often used in establishing perceptual metrics that would evaluate quality of video. Combining of perceptual and compressive sensing approach outlined from recent investigations. The performance and the complexity of different scalability techniques are evaluated. Application of perceptual models to evaluation of the quality of compressive sensing scalability is considered in the near perceptually lossless case and to the appropriate coding schemes is reviewed.

  4. Phylogenetic structure in tropical hummingbird communities.

    Science.gov (United States)

    Graham, Catherine H; Parra, Juan L; Rahbek, Carsten; McGuire, Jimmy A

    2009-11-17

    How biotic interactions, current and historical environment, and biogeographic barriers determine community structure is a fundamental question in ecology and evolution, especially in diverse tropical regions. To evaluate patterns of local and regional diversity, we quantified the phylogenetic composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern that is consistent with the idea that competition influences the local composition of hummingbirds. At higher elevations communities are phylogenetically clustered (coexistence of close relatives), consistent with the expectation of environmental filtering, which may result from the challenge of sustaining an expensive means of locomotion at high elevations. We found that communities in the lowlands on opposite sides of the Andes tend to be phylogenetically similar despite their large differences in species composition, a pattern implicating the Andes as an important dispersal barrier. In contrast, along the steep environmental gradient between the lowlands and the Andes we found evidence that species turnover is comprised of relatively distantly related species. The integration of local and regional patterns of diversity across environmental gradients and biogeographic barriers provides insight into the potential underlying mechanisms that have shaped community composition and phylogenetic diversity in one of the most species-rich, complex regions of the world.

  5. Scalable Performance Measurement and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gamblin, Todd [Univ. of North Carolina, Chapel Hill, NC (United States)

    2009-01-01

    Concurrency levels in large-scale, distributed-memory supercomputers are rising exponentially. Modern machines may contain 100,000 or more microprocessor cores, and the largest of these, IBM's Blue Gene/L, contains over 200,000 cores. Future systems are expected to support millions of concurrent tasks. In this dissertation, we focus on efficient techniques for measuring and analyzing the performance of applications running on very large parallel machines. Tuning the performance of large-scale applications can be a subtle and time-consuming task because application developers must measure and interpret data from many independent processes. While the volume of the raw data scales linearly with the number of tasks in the running system, the number of tasks is growing exponentially, and data for even small systems quickly becomes unmanageable. Transporting performance data from so many processes over a network can perturb application performance and make measurements inaccurate, and storing such data would require a prohibitive amount of space. Moreover, even if it were stored, analyzing the data would be extremely time-consuming. In this dissertation, we present novel methods for reducing performance data volume. The first draws on multi-scale wavelet techniques from signal processing to compress systemwide, time-varying load-balance data. The second uses statistical sampling to select a small subset of running processes to generate low-volume traces. A third approach combines sampling and wavelet compression to stratify performance data adaptively at run-time and to reduce further the cost of sampled tracing. We have integrated these approaches into Libra, a toolset for scalable load-balance analysis. We present Libra and show how it can be used to analyze data from large scientific applications scalably.

  6. Genome-wide identification, phylogenetic analysis, expression profiling, and protein–protein interaction properties of TOPLESS gene family members in tomato

    Science.gov (United States)

    Hao, Yanwei; Wang, Xinyu; van der Rest, Benoit; Zouine, Mohamed

    2014-01-01

    Members of the TOPLESS gene family emerged recently as key players in gene repression in several mechanisms, especially in auxin perception. The TOPLESS genes constitute, in ‘higher-plant’ genomes, a small multigenic family comprising four to 11 members. In this study, this family was investigated in tomato, a model plant for Solanaceae species and fleshy fruits. Six open reading frames predicted to encode topless-like proteins (SlTPLs) containing the canonical domains (LisH, CTLH, and two WD40 repeats) were identified in the tomato genome. Nuclear localization was confirmed for all members of the SlTPL family with the exception SlTPL6, which localized at the cytoplasm and was excluded from the nucleus. SlTPL genes displayed distinctive expression patterns in different tomato organs, with SlTPL1 showing the highest levels of transcript accumulation in all tissues tested except in ripening fruit where SlTPL3 and SlTPL4 were the most prominently expressed. To gain insight into the specificity of the different TOPLESS paralogues, a protein–protein interaction map between TOPLESS and auxin/indole-3-acetic acid (Aux/IAA) proteins was built using a yeast two-hybrid approach. The PPI map enabled the distinction of two patterns: TOPLESS isoforms interacting with the majority of Aux/IAA, and isoforms with limited capacity for interaction with these protein partners. Interestingly, evolutionary analyses of the TOPLESS gene family revealed that the highly expressed isoforms (SlTPL1, SlTPL3, and SlTPL4) corresponded to the three TPL-related genes undergoing the strongest purifying selection, while the selection was much weaker for SlTPL6, which was expressed at a low level and encoded a protein lacking the capacity to interact with Aux/IAAs. PMID:24399174

  7. Potential of Scalable Vector Graphics (SVG) for Ocean Science Research

    Science.gov (United States)

    Sears, J. R.

    2002-12-01

    Scalable Vector Graphics (SVG), a graphic format encoded in Extensible Markup Language (XML), is a recent W3C standard. SVG is text-based and platform-neutral, allowing interoperability and a rich array of features that offer significant promise for the presentation and publication of ocean and earth science research. This presentation (a) provides a brief introduction to SVG with real-world examples; (b) reviews browsers, editors, and other SVG tools; and (c) talks about some of the more powerful capabilities of SVG that might be important for ocean and earth science data presentation, such as searchability, animation and scripting, interactivity, accessibility, dynamic SVG, layers, scalability, SVG Text, SVG Audio, server-side SVG, and embedding metadata and data. A list of useful SVG resources is also given.

  8. Quality Scalability Aware Watermarking for Visual Content.

    Science.gov (United States)

    Bhowmik, Deepayan; Abhayaratne, Charith

    2016-11-01

    Scalable coding-based content adaptation poses serious challenges to traditional watermarking algorithms, which do not consider the scalable coding structure and hence cannot guarantee correct watermark extraction in media consumption chain. In this paper, we propose a novel concept of scalable blind watermarking that ensures more robust watermark extraction at various compression ratios while not effecting the visual quality of host media. The proposed algorithm generates scalable and robust watermarked image code-stream that allows the user to constrain embedding distortion for target content adaptations. The watermarked image code-stream consists of hierarchically nested joint distortion-robustness coding atoms. The code-stream is generated by proposing a new wavelet domain blind watermarking algorithm guided by a quantization based binary tree. The code-stream can be truncated at any distortion-robustness atom to generate the watermarked image with the desired distortion-robustness requirements. A blind extractor is capable of extracting watermark data from the watermarked images. The algorithm is further extended to incorporate a bit-plane discarding-based quantization model used in scalable coding-based content adaptation, e.g., JPEG2000. This improves the robustness against quality scalability of JPEG2000 compression. The simulation results verify the feasibility of the proposed concept, its applications, and its improved robustness against quality scalable content adaptation. Our proposed algorithm also outperforms existing methods showing 35% improvement. In terms of robustness to quality scalable video content adaptation using Motion JPEG2000 and wavelet-based scalable video coding, the proposed method shows major improvement for video watermarking.

  9. Microscopic Characterization of Scalable Coherent Rydberg Superatoms

    Directory of Open Access Journals (Sweden)

    Johannes Zeiher

    2015-08-01

    Full Text Available Strong interactions can amplify quantum effects such that they become important on macroscopic scales. Controlling these coherently on a single-particle level is essential for the tailored preparation of strongly correlated quantum systems and opens up new prospects for quantum technologies. Rydberg atoms offer such strong interactions, which lead to extreme nonlinearities in laser-coupled atomic ensembles. As a result, multiple excitation of a micrometer-sized cloud can be blocked while the light-matter coupling becomes collectively enhanced. The resulting two-level system, often called a “superatom,” is a valuable resource for quantum information, providing a collective qubit. Here, we report on the preparation of 2 orders of magnitude scalable superatoms utilizing the large interaction strength provided by Rydberg atoms combined with precise control of an ensemble of ultracold atoms in an optical lattice. The latter is achieved with sub-shot-noise precision by local manipulation of a two-dimensional Mott insulator. We microscopically confirm the superatom picture by in situ detection of the Rydberg excitations and observe the characteristic square-root scaling of the optical coupling with the number of atoms. Enabled by the full control over the atomic sample, including the motional degrees of freedom, we infer the overlap of the produced many-body state with a W state from the observed Rabi oscillations and deduce the presence of entanglement. Finally, we investigate the breakdown of the superatom picture when two Rydberg excitations are present in the system, which leads to dephasing and a loss of coherence.

  10. Microscopic Characterization of Scalable Coherent Rydberg Superatoms

    Science.gov (United States)

    Zeiher, Johannes; Schauß, Peter; Hild, Sebastian; Macrı, Tommaso; Bloch, Immanuel; Gross, Christian

    2015-07-01

    Strong interactions can amplify quantum effects such that they become important on macroscopic scales. Controlling these coherently on a single-particle level is essential for the tailored preparation of strongly correlated quantum systems and opens up new prospects for quantum technologies. Rydberg atoms offer such strong interactions, which lead to extreme nonlinearities in laser-coupled atomic ensembles. As a result, multiple excitation of a micrometer-sized cloud can be blocked while the light-matter coupling becomes collectively enhanced. The resulting two-level system, often called a "superatom," is a valuable resource for quantum information, providing a collective qubit. Here, we report on the preparation of 2 orders of magnitude scalable superatoms utilizing the large interaction strength provided by Rydberg atoms combined with precise control of an ensemble of ultracold atoms in an optical lattice. The latter is achieved with sub-shot-noise precision by local manipulation of a two-dimensional Mott insulator. We microscopically confirm the superatom picture by in situ detection of the Rydberg excitations and observe the characteristic square-root scaling of the optical coupling with the number of atoms. Enabled by the full control over the atomic sample, including the motional degrees of freedom, we infer the overlap of the produced many-body state with a W state from the observed Rabi oscillations and deduce the presence of entanglement. Finally, we investigate the breakdown of the superatom picture when two Rydberg excitations are present in the system, which leads to dephasing and a loss of coherence.

  11. Grassmann Averages for Scalable Robust PCA

    DEFF Research Database (Denmark)

    Hauberg, Søren; Feragen, Aasa; Black, Michael J.

    2014-01-01

    As the collection of large datasets becomes increasingly automated, the occurrence of outliers will increase—“big data” implies “big outliers”. While principal component analysis (PCA) is often used to reduce the size of data, and scalable solutions exist, it is well-known that outliers can arbit......, making it scalable to “big noisy data.” We demonstrate TGA for background modeling, video restoration, and shadow removal. We show scalability by performing robust PCA on the entire Star Wars IV movie....

  12. Scalable, remote administration of Windows NT.

    Energy Technology Data Exchange (ETDEWEB)

    Gomberg, M.; Stacey, C.; Sayre, J.

    1999-06-08

    In the UNIX community there is an overwhelming perception that NT is impossible to manage remotely and that NT administration doesn't scale. This was essentially true with earlier versions of the operating system. Even today, out of the box, NT is difficult to manage remotely. Many tools, however, now make remote management of NT not only possible, but under some circumstances very easy. In this paper we discuss how we at Argonne's Mathematics and Computer Science Division manage all our NT machines remotely from a single console, with minimum locally installed software overhead. We also present NetReg, which is a locally developed tool for scalable registry management. NetReg allows us to apply a registry change to a specified set of machines. It is a command line utility that can be run in either interactive or batch mode and is written in Perl for Win32, taking heavy advantage of the Win32::TieRegistry module.

  13. Scalable Combinatorial Tools for Health Disparities Research

    Directory of Open Access Journals (Sweden)

    Michael A. Langston

    2014-10-01

    Full Text Available Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size and heterogeneity of available data needed to illuminate latent gene x environment interactions. This has prompted the adaptation and application of scalable combinatorial methods, many from genome science research, to the study of population health. Most of these powerful tools are algorithmically sophisticated, highly automated and mathematically abstract. Their utility motivates the main theme of this paper, which is to describe real applications of innovative transdisciplinary models and analyses in an effort to help move the research community closer toward identifying the causal mechanisms and associated environmental contexts underlying health disparities. The public health exposome is used as a contemporary focus for addressing the complex nature of this subject.

  14. Fast and scalable inequality joins

    KAUST Repository

    Khayyat, Zuhair

    2016-09-07

    Inequality joins, which is to join relations with inequality conditions, are used in various applications. Optimizing joins has been the subject of intensive research ranging from efficient join algorithms such as sort-merge join, to the use of efficient indices such as (Formula presented.)-tree, (Formula presented.)-tree and Bitmap. However, inequality joins have received little attention and queries containing such joins are notably very slow. In this paper, we introduce fast inequality join algorithms based on sorted arrays and space-efficient bit-arrays. We further introduce a simple method to estimate the selectivity of inequality joins which is then used to optimize multiple predicate queries and multi-way joins. Moreover, we study an incremental inequality join algorithm to handle scenarios where data keeps changing. We have implemented a centralized version of these algorithms on top of PostgreSQL, a distributed version on top of Spark SQL, and an existing data cleaning system, Nadeef. By comparing our algorithms against well-known optimization techniques for inequality joins, we show our solution is more scalable and several orders of magnitude faster. © 2016 Springer-Verlag Berlin Heidelberg

  15. Scalable encryption using alpha rooting

    Science.gov (United States)

    Wharton, Eric J.; Panetta, Karen A.; Agaian, Sos S.

    2008-04-01

    Full and partial encryption methods are important for subscription based content providers, such as internet and cable TV pay channels. Providers need to be able to protect their products while at the same time being able to provide demonstrations to attract new customers without giving away the full value of the content. If an algorithm were introduced which could provide any level of full or partial encryption in a fast and cost effective manner, the applications to real-time commercial implementation would be numerous. In this paper, we present a novel application of alpha rooting, using it to achieve fast and straightforward scalable encryption with a single algorithm. We further present use of the measure of enhancement, the Logarithmic AME, to select optimal parameters for the partial encryption. When parameters are selected using the measure, the output image achieves a balance between protecting the important data in the image while still containing a good overall representation of the image. We will show results for this encryption method on a number of images, using histograms to evaluate the effectiveness of the encryption.

  16. Finite Element Modeling on Scalable Parallel Computers

    Science.gov (United States)

    Cwik, T.; Zuffada, C.; Jamnejad, V.; Katz, D.

    1995-01-01

    A coupled finite element-integral equation was developed to model fields scattered from inhomogenous, three-dimensional objects of arbitrary shape. This paper outlines how to implement the software on a scalable parallel processor.

  17. Corfu: A Platform for Scalable Consistency

    OpenAIRE

    Wei, Michael

    2017-01-01

    Corfu is a platform for building systems which are extremely scalable, strongly consistent and robust. Unlike other systems which weaken guarantees to provide better performance, we have built Corfu with a resilient fabric tuned and engineered for scalability and strong consistency at its core: the Corfu shared log. On top of the Corfu log, we have built a layer of advanced data services which leverage the properties of the Corfu log. Today, Corfu is already replacing data platforms in commer...

  18. Memory-Scalable GPU Spatial Hierarchy Construction.

    Science.gov (United States)

    Qiming Hou; Xin Sun; Kun Zhou; Lauterbach, C; Manocha, D

    2011-04-01

    Recent GPU algorithms for constructing spatial hierarchies have achieved promising performance for moderately complex models by using the breadth-first search (BFS) construction order. While being able to exploit the massive parallelism on the GPU, the BFS order also consumes excessive GPU memory, which becomes a serious issue for interactive applications involving very complex models with more than a few million triangles. In this paper, we propose to use the partial breadth-first search (PBFS) construction order to control memory consumption while maximizing performance. We apply the PBFS order to two hierarchy construction algorithms. The first algorithm is for kd-trees that automatically balances between the level of parallelism and intermediate memory usage. With PBFS, peak memory consumption during construction can be efficiently controlled without costly CPU-GPU data transfer. We also develop memory allocation strategies to effectively limit memory fragmentation. The resulting algorithm scales well with GPU memory and constructs kd-trees of models with millions of triangles at interactive rates on GPUs with 1 GB memory. Compared with existing algorithms, our algorithm is an order of magnitude more scalable for a given GPU memory bound. The second algorithm is for out-of-core bounding volume hierarchy (BVH) construction for very large scenes based on the PBFS construction order. At each iteration, all constructed nodes are dumped to the CPU memory, and the GPU memory is freed for the next iteration's use. In this way, the algorithm is able to build trees that are too large to be stored in the GPU memory. Experiments show that our algorithm can construct BVHs for scenes with up to 20 M triangles, several times larger than previous GPU algorithms.

  19. Fully scalable video coding in multicast applications

    Science.gov (United States)

    Lerouge, Sam; De Sutter, Robbie; Lambert, Peter; Van de Walle, Rik

    2004-01-01

    The increasing diversity of the characteristics of the terminals and networks that are used to access multimedia content through the internet introduces new challenges for the distribution of multimedia data. Scalable video coding will be one of the elementary solutions in this domain. This type of coding allows to adapt an encoded video sequence to the limitations of the network or the receiving device by means of very basic operations. Algorithms for creating fully scalable video streams, in which multiple types of scalability are offered at the same time, are becoming mature. On the other hand, research on applications that use such bitstreams is only recently emerging. In this paper, we introduce a mathematical model for describing such bitstreams. In addition, we show how we can model applications that use scalable bitstreams by means of definitions that are built on top of this model. In particular, we chose to describe a multicast protocol that is targeted at scalable bitstreams. This way, we will demonstrate that it is possible to define an abstract model for scalable bitstreams, that can be used as a tool for reasoning about such bitstreams and related applications.

  20. Phylogenetic Structure of Foliar Spectral Traits in Tropical Forest Canopies

    Directory of Open Access Journals (Sweden)

    Kelly M. McManus

    2016-02-01

    Full Text Available The Spectranomics approach to tropical forest remote sensing has established a link between foliar reflectance spectra and the phylogenetic composition of tropical canopy tree communities vis-à-vis the taxonomic organization of biochemical trait variation. However, a direct relationship between phylogenetic affiliation and foliar reflectance spectra of species has not been established. We sought to develop this relationship by quantifying the extent to which underlying patterns of phylogenetic structure drive interspecific variation among foliar reflectance spectra within three Neotropical canopy tree communities with varying levels of soil fertility. We interpreted the resulting spectral patterns of phylogenetic signal in the context of foliar biochemical traits that may contribute to the spectral-phylogenetic link. We utilized a multi-model ensemble to elucidate trait-spectral relationships, and quantified phylogenetic signal for spectral wavelengths and traits using Pagel’s lambda statistic. Foliar reflectance spectra showed evidence of phylogenetic influence primarily within the visible and shortwave infrared spectral regions. These regions were also selected by the multi-model ensemble as those most important to the quantitative prediction of several foliar biochemical traits. Patterns of phylogenetic organization of spectra and traits varied across sites and with soil fertility, indicative of the complex interactions between the environmental and phylogenetic controls underlying patterns of biodiversity.

  1. Phylogenetic Comparative Assembly

    Science.gov (United States)

    Husemann, Peter; Stoye, Jens

    Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a contig adjacency graph. From this a layout graph can be computed which indicates putative adjacencies of the contigs in order to aid biologists in finishing the complete genomic sequence.

  2. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  3. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  4. Wanted: Scalable Tracers for Diffusion Measurements

    Science.gov (United States)

    2015-01-01

    Scalable tracers are potentially a useful tool to examine diffusion mechanisms and to predict diffusion coefficients, particularly for hindered diffusion in complex, heterogeneous, or crowded systems. Scalable tracers are defined as a series of tracers varying in size but with the same shape, structure, surface chemistry, deformability, and diffusion mechanism. Both chemical homology and constant dynamics are required. In particular, branching must not vary with size, and there must be no transition between ordinary diffusion and reptation. Measurements using scalable tracers yield the mean diffusion coefficient as a function of size alone; measurements using nonscalable tracers yield the variation due to differences in the other properties. Candidate scalable tracers are discussed for two-dimensional (2D) diffusion in membranes and three-dimensional diffusion in aqueous solutions. Correlations to predict the mean diffusion coefficient of globular biomolecules from molecular mass are reviewed briefly. Specific suggestions for the 3D case include the use of synthetic dendrimers or random hyperbranched polymers instead of dextran and the use of core–shell quantum dots. Another useful tool would be a series of scalable tracers varying in deformability alone, prepared by varying the density of crosslinking in a polymer to make say “reinforced Ficoll” or “reinforced hyperbranched polyglycerol.” PMID:25319586

  5. Scalable L-infinite coding of meshes.

    Science.gov (United States)

    Munteanu, Adrian; Cernea, Dan C; Alecu, Alin; Cornelis, Jan; Schelkens, Peter

    2010-01-01

    The paper investigates the novel concept of local-error control in mesh geometry encoding. In contrast to traditional mesh-coding systems that use the mean-square error as target distortion metric, this paper proposes a new L-infinite mesh-coding approach, for which the target distortion metric is the L-infinite distortion. In this context, a novel wavelet-based L-infinite-constrained coding approach for meshes is proposed, which ensures that the maximum error between the vertex positions in the original and decoded meshes is lower than a given upper bound. Furthermore, the proposed system achieves scalability in L-infinite sense, that is, any decoding of the input stream will correspond to a perfectly predictable L-infinite distortion upper bound. An instantiation of the proposed L-infinite-coding approach is demonstrated for MESHGRID, which is a scalable 3D object encoding system, part of MPEG-4 AFX. In this context, the advantages of scalable L-infinite coding over L-2-oriented coding are experimentally demonstrated. One concludes that the proposed L-infinite mesh-coding approach guarantees an upper bound on the local error in the decoded mesh, it enables a fast real-time implementation of the rate allocation, and it preserves all the scalability features and animation capabilities of the employed scalable mesh codec.

  6. The phylogenetic structure of plant-pollinator networks increases with habitat size and isolation.

    Science.gov (United States)

    Aizen, Marcelo A; Gleiser, Gabriela; Sabatino, Malena; Gilarranz, Luis J; Bascompte, Jordi; Verdú, Miguel

    2016-01-01

    Similarity among species in traits related to ecological interactions is frequently associated with common ancestry. Thus, closely related species usually interact with ecologically similar partners, which can be reinforced by diverse co-evolutionary processes. The effect of habitat fragmentation on the phylogenetic signal in interspecific interactions and correspondence between plant and animal phylogenies is, however, unknown. Here, we address to what extent phylogenetic signal and co-phylogenetic congruence of plant-animal interactions depend on habitat size and isolation by analysing the phylogenetic structure of 12 pollination webs from isolated Pampean hills. Phylogenetic signal in interspecific interactions differed among webs, being stronger for flower-visiting insects than plants. Phylogenetic signal and overall co-phylogenetic congruence increased independently with hill size and isolation. We propose that habitat fragmentation would erode the phylogenetic structure of interaction webs. A decrease in phylogenetic signal and co-phylogenetic correspondence in plant-pollinator interactions could be associated with less reliable mutualism and erratic co-evolutionary change. © 2015 John Wiley & Sons Ltd/CNRS.

  7. Scalable Density-Based Subspace Clustering

    DEFF Research Database (Denmark)

    Müller, Emmanuel; Assent, Ira; Günnemann, Stephan

    2011-01-01

    For knowledge discovery in high dimensional databases, subspace clustering detects clusters in arbitrary subspace projections. Scalability is a crucial issue, as the number of possible projections is exponential in the number of dimensions. We propose a scalable density-based subspace clustering...... method that steers mining to few selected subspace clusters. Our novel steering technique reduces subspace processing by identifying and clustering promising subspaces and their combinations directly. Thereby, it narrows down the search space while maintaining accuracy. Thorough experiments on real...... and synthetic databases show that steering is efficient and scalable, with high quality results. For future work, our steering paradigm for density-based subspace clustering opens research potential for speeding up other subspace clustering approaches as well....

  8. Scalable Open Source Smart Grid Simulator (SGSim)

    DEFF Research Database (Denmark)

    Ebeid, Emad Samuel Malki; Jacobsen, Rune Hylsberg; Quaglia, Davide

    2017-01-01

    The future smart power grid will consist of an unlimited number of smart devices that communicate with control units to maintain the grid’s sustainability, efficiency, and balancing. In order to build and verify such controllers over a large grid, a scalable simulation environment is needed....... This paper presents an open source smart grid simulator (SGSim). The simulator is based on open source SystemC Network Simulation Library (SCNSL) and aims to model scalable smart grid applications. SGSim has been tested under different smart grid scenarios that contain hundreds of thousands of households...... and appliances. By using SGSim, different smart grid control strategies and protocols can be tested, validated and evaluated in a scalable environment....

  9. From Digital Disruption to Business Model Scalability

    DEFF Research Database (Denmark)

    Nielsen, Christian; Lund, Morten; Thomsen, Peter Poulsen

    2017-01-01

    a long time to replicate, business model scalability can be cornered into four dimensions. In many corporate restructuring exercises and Mergers and Acquisitions there is a tendency to look for synergies in the form of cost reductions, lean workflows and market segments. However, this state of mind......This article discusses the terms disruption, digital disruption, business models and business model scalability. It illustrates how managers should be using these terms for the benefit of their business by developing business models capable of achieving exponentially increasing returns to scale...

  10. From Digital Disruption to Business Model Scalability

    DEFF Research Database (Denmark)

    Nielsen, Christian; Lund, Morten; Thomsen, Peter Poulsen

    2017-01-01

    as a response to digital disruption. A series of case studies illustrate that besides frequent existing messages in the business literature relating to the importance of creating agile businesses, both in growing and declining economies, as well as hard to copy value propositions or value propositions that take......This article discusses the terms disruption, digital disruption, business models and business model scalability. It illustrates how managers should be using these terms for the benefit of their business by developing business models capable of achieving exponentially increasing returns to scale...... will seldom lead to business model scalability capable of competing with digital disruption(s)....

  11. Content-Aware Scalability-Type Selection for Rate Adaptation of Scalable Video

    Directory of Open Access Journals (Sweden)

    Tekalp A Murat

    2007-01-01

    Full Text Available Scalable video coders provide different scaling options, such as temporal, spatial, and SNR scalabilities, where rate reduction by discarding enhancement layers of different scalability-type results in different kinds and/or levels of visual distortion depend on the content and bitrate. This dependency between scalability type, video content, and bitrate is not well investigated in the literature. To this effect, we first propose an objective function that quantifies flatness, blockiness, blurriness, and temporal jerkiness artifacts caused by rate reduction by spatial size, frame rate, and quantization parameter scaling. Next, the weights of this objective function are determined for different content (shot types and different bitrates using a training procedure with subjective evaluation. Finally, a method is proposed for choosing the best scaling type for each temporal segment that results in minimum visual distortion according to this objective function given the content type of temporal segments. Two subjective tests have been performed to validate the proposed procedure for content-aware selection of the best scalability type on soccer videos. Soccer videos scaled from 600 kbps to 100 kbps by the proposed content-aware selection of scalability type have been found visually superior to those that are scaled using a single scalability option over the whole sequence.

  12. Scalable Detection and Isolation of Phishing

    NARCIS (Netherlands)

    Moreira Moura, Giovane; Pras, Aiko

    2009-01-01

    This paper presents a proposal for scalable detection and isolation of phishing. The main ideas are to move the protection from end users towards the network provider and to employ the novel bad neighborhood concept, in order to detect and isolate both phishing e-mail senders and phishing web

  13. Scalable Open Source Smart Grid Simulator (SGSim)

    DEFF Research Database (Denmark)

    Ebeid, Emad Samuel Malki; Jacobsen, Rune Hylsberg; Stefanni, Francesco

    2017-01-01

    . This paper presents an open source smart grid simulator (SGSim). The simulator is based on open source SystemC Network Simulation Library (SCNSL) and aims to model scalable smart grid applications. SGSim has been tested under different smart grid scenarios that contain hundreds of thousands of households...

  14. Realization of a scalable airborne radar

    NARCIS (Netherlands)

    Halsema, D. van; Jongh, R.V. de; Es, J. van; Otten, M.P.G.; Vermeulen, B.C.B.; Liempt, L.J. van

    2008-01-01

    Modern airborne ground surveillance radar systems are increasingly based on Active Electronically Scanned Array (AESA) antennas. Efficient use of array technology and the need for radar solutions for various airborne platforms, manned and unmanned, leads to the design of scalable radar systems. The

  15. Scalable Domain Decomposed Monte Carlo Particle Transport

    Energy Technology Data Exchange (ETDEWEB)

    O' Brien, Matthew Joseph [Univ. of California, Davis, CA (United States)

    2013-12-05

    In this dissertation, we present the parallel algorithms necessary to run domain decomposed Monte Carlo particle transport on large numbers of processors (millions of processors). Previous algorithms were not scalable, and the parallel overhead became more computationally costly than the numerical simulation.

  16. Subjective comparison of temporal and quality scalability

    DEFF Research Database (Denmark)

    Korhonen, Jari; Reiter, Ulrich; You, Junyong

    2011-01-01

    and quality scalability. The practical experiments with low resolution video sequences show that in general, distortion is a more crucial factor for the perceived subjective quality than frame rate. However, the results also depend on the content. Moreover,, we discuss the role of other different influence...

  17. Ultrafast Approximation for Phylogenetic Bootstrap

    NARCIS (Netherlands)

    Bui Quang Minh, [No Value; Nguyen, Thi; von Haeseler, Arndt

    Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods such as the RAxML rapid bootstrap (RBS) and

  18. Containment Domains: A Scalable, Efficient and Flexible Resilience Scheme for Exascale Systems

    Directory of Open Access Journals (Sweden)

    Jinsuk Chung

    2013-01-01

    Full Text Available This paper describes and evaluates a scalable and efficient resilience scheme based on the concept of containment domains. Containment domains are a programming construct that enable applications to express resilience needs and to interact with the system to tune and specialize error detection, state preservation and restoration, and recovery schemes. Containment domains have weak transactional semantics and are nested to take advantage of the machine and application hierarchies and to enable hierarchical state preservation, restoration and recovery. We evaluate the scalability and efficiency of containment domains using generalized trace-driven simulation and analytical analysis and show that containment domains are superior to both checkpoint restart and redundant execution approaches.

  19. Ecological and phylogenetic influences on maxillary dentition in snakes

    Directory of Open Access Journals (Sweden)

    Kate Jackson

    2010-12-01

    Full Text Available The maxillary dentition of snakes was used as a system with which to investigate the relative importance of the interacting forces of ecological selective pressures and phylogenetic constraints indetermining morphology. The maxillary morphology of three groups of snakes having different diets, with each group comprising two distinct lineages — boids and colubroids — was examined. Our results suggest that dietary selective pressures may be more significantthan phylogenetic history in shaping maxillary morphology.

  20. Power law tails in phylogenetic systems.

    Science.gov (United States)

    Qin, Chongli; Colwell, Lucy J

    2018-01-23

    Covariance analysis of protein sequence alignments uses coevolving pairs of sequence positions to predict features of protein structure and function. However, current methods ignore the phylogenetic relationships between sequences, potentially corrupting the identification of covarying positions. Here, we use random matrix theory to demonstrate the existence of a power law tail that distinguishes the spectrum of covariance caused by phylogeny from that caused by structural interactions. The power law is essentially independent of the phylogenetic tree topology, depending on just two parameters-the sequence length and the average branch length. We demonstrate that these power law tails are ubiquitous in the large protein sequence alignments used to predict contacts in 3D structure, as predicted by our theory. This suggests that to decouple phylogenetic effects from the interactions between sequence distal sites that control biological function, it is necessary to remove or down-weight the eigenvectors of the covariance matrix with largest eigenvalues. We confirm that truncating these eigenvectors improves contact prediction.

  1. Scalable Quantum Circuit and Control for a Superconducting Surface Code

    Science.gov (United States)

    Versluis, R.; Poletto, S.; Khammassi, N.; Tarasinski, B.; Haider, N.; Michalak, D. J.; Bruno, A.; Bertels, K.; DiCarlo, L.

    2017-09-01

    We present a scalable scheme for executing the error-correction cycle of a monolithic surface-code fabric composed of fast-flux-tunable transmon qubits with nearest-neighbor coupling. An eight-qubit unit cell forms the basis for repeating both the quantum hardware and coherent control, enabling spatial multiplexing. This control uses three fixed frequencies for all single-qubit gates and a unique frequency-detuning pattern for each qubit in the cell. By pipelining the interaction and readout steps of ancilla-based X - and Z -type stabilizer measurements, we can engineer detuning patterns that avoid all second-order transmon-transmon interactions except those exploited in controlled-phase gates, regardless of fabric size. Our scheme is applicable to defect-based and planar logical qubits, including lattice surgery.

  2. Enhanced JPEG2000 Quality Scalability through Block-Wise Layer Truncation

    Directory of Open Access Journals (Sweden)

    Auli-Llinas Francesc

    2010-01-01

    Full Text Available Quality scalability is an important feature of image and video coding systems. In JPEG2000, quality scalability is achieved through the use of quality layers that are formed in the encoder through rate-distortion optimization techniques. Quality layers provide optimal rate-distortion representations of the image when the codestream is transmitted and/or decoded at layer boundaries. Nonetheless, applications such as interactive image transmission, video streaming, or transcoding demand layer fragmentation. The common approach to truncate layers is to keep the initial prefix of the to-be-truncated layer, which may greatly penalize the quality of decoded images, especially when the layer allocation is inadequate. So far, only one method has been proposed in the literature providing enhanced quality scalability for compressed JPEG2000 imagery. However, that method provides quality scalability at the expense of high computational costs, which prevents its application to the aforementioned applications. This paper introduces a Block-Wise Layer Truncation (BWLT that, requiring negligible computational costs, enhances the quality scalability of compressed JPEG2000 images. The main insight behind BWLT is to dismantle and reassemble the to-be-fragmented layer by selecting the most relevant codestream segments of codeblocks within that layer. The selection process is conceived from a rate-distortion model that finely estimates rate-distortion contributions of codeblocks. Experimental results suggest that BWLT achieves near-optimal performance even when the codestream contains a single quality layer.

  3. Trophic phylogenetics: evolutionary influences on body size, feeding, and species associations in grassland arthropods.

    Science.gov (United States)

    Lind, Eric M; Vincent, John B; Weiblen, George D; Cavender-Bares, Jeannine; Borer, Elizabeth T

    2015-04-01

    Contemporary animal-plant interactions such as herbivory are widely understood to be shaped by evolutionary history. Yet questions remain about the role of plant phylogenetic diversity in generating and maintaining herbivore diversity, and whether evolutionary relatedness of producers might predict the composition of consumer communities. We tested for evidence of evolutionary associations among arthropods and the plants on which they were found, using phylogenetic analysis of naturally occurring arthropod assemblages sampled from a plant-diversity manipulation experiment. Considering phylogenetic relationships among more than 900 arthropod consumer taxa and 29 plant species in the experiment, we addressed several interrelated questions. First, our results support the hypothesis that arthropod functional traits such as body size and trophic role are phylogenetically conserved in community ecological samples. Second, herbivores tended to cooccur with closer phylogenetic relatives than would be expected at random, whereas predators and parasitoids did not show phylogenetic association patterns. Consumer specialization, as measured by association through time with monocultures of particular host plant species, showed significant phylogenetic signal, although the. strength of this association varied among plant species. Polycultures of phylogenetically dissimilar plant species supported more phylogenetically dissimilar consumer communities than did phylogenetically similar polycultures. Finally, we separated the effects of plant species richness and relatedness in predicting the phylogenetic distribution of the arthropod assemblages in this experiment. The phylogenetic diversity of plant communities predicted the phylogenetic diversity of herbivore communities even after accounting for plant species richness. The phylogenetic diversity of secondary consumers differed by guild, with predator phylogenetic diversity responding to herbivore relatedness, while parasitoid

  4. Scalable fast multipole methods for vortex element methods

    KAUST Repository

    Hu, Qi

    2012-11-01

    We use a particle-based method to simulate incompressible flows, where the Fast Multipole Method (FMM) is used to accelerate the calculation of particle interactions. The most time-consuming kernelsâ\\'the Biot-Savart equation and stretching term of the vorticity equationâ\\'are mathematically reformulated so that only two Laplace scalar potentials are used instead of six, while automatically ensuring divergence-free far-field computation. Based on this formulation, and on our previous work for a scalar heterogeneous FMM algorithm, we develop a new FMM-based vortex method capable of simulating general flows including turbulence on heterogeneous architectures, which distributes the work between multi-core CPUs and GPUs to best utilize the hardware resources and achieve excellent scalability. The algorithm also uses new data structures which can dynamically manage inter-node communication and load balance efficiently but with only a small parallel construction overhead. This algorithm can scale to large-sized clusters showing both strong and weak scalability. Careful error and timing trade-off analysis are also performed for the cutoff functions induced by the vortex particle method. Our implementation can perform one time step of the velocity+stretching for one billion particles on 32 nodes in 55.9 seconds, which yields 49.12 Tflop/s. © 2012 IEEE.

  5. [Foundations of the new phylogenetics].

    Science.gov (United States)

    Pavlinov, I Ia

    2004-01-01

    Evolutionary idea is the core of the modern biology. Due to this, phylogenetics dealing with historical reconstructions in biology takes a priority position among biological disciplines. The second half of the 20th century witnessed growth of a great interest to phylogenetic reconstructions at macrotaxonomic level which replaced microevolutionary studies dominating during the 30s-60s. This meant shift from population thinking to phylogenetic one but it was not revival of the classical phylogenetics; rather, a new approach emerged that was baptized The New Phylogenetics. It arose as a result of merging of three disciplines which were developing independently during 60s-70s, namely cladistics, numerical phyletics, and molecular phylogenetics (now basically genophyletics). Thus, the new phylogenetics could be defined as a branch of evolutionary biology aimed at elaboration of "parsimonious" cladistic hypotheses by means of numerical methods on the basis of mostly molecular data. Classical phylogenetics, as a historical predecessor of the new one, emerged on the basis of the naturphilosophical worldview which included a superorganismal idea of biota. Accordingly to that view, historical development (the phylogeny) was thought an analogy of individual one (the ontogeny) so its most basical features were progressive parallel developments of "parts" (taxa), supplemented with Darwinian concept of monophyly. Two predominating traditions were diverged within classical phylogenetics according to a particular interpretation of relation between these concepts. One of them (Cope, Severtzow) belittled monophyly and paid most attention to progressive parallel developments of morphological traits. Such an attitude turned this kind of phylogenetics to be rather the semogenetics dealing primarily with evolution of structures and not of taxa. Another tradition (Haeckel) considered both monophyletic and parallel origins of taxa jointly: in the middle of 20th century it was split into

  6. Declarative and Scalable Selection for Map Visualizations

    DEFF Research Database (Denmark)

    Kefaloukos, Pimin Konstantin Balic

    supports the PostgreSQL dialect of SQL. The prototype implementation is a compiler that translates CVL into SQL and stored procedures. (c) TileHeat is a framework and basic algorithm for partial materialization of hot tile sets for scalable map distribution. The framework predicts future map workloads......, there are indications that the method is scalable for databases that contain millions of records, especially if the target language of the compiler is substituted by a cluster-ready variant of SQL. While several realistic use cases for maps have been implemented in CVL, additional non-geographic data visualization uses...... goal. The results for Tileheat show that the prediction method offers a substantial improvement over the current method used by the Danish Geodata Agency. Thus, a large amount of computations can potentially be saved by this public institution, who is responsible for the distribution of government...

  7. A Scalability Model for ECS's Data Server

    Science.gov (United States)

    Menasce, Daniel A.; Singhal, Mukesh

    1998-01-01

    This report presents in four chapters a model for the scalability analysis of the Data Server subsystem of the Earth Observing System Data and Information System (EOSDIS) Core System (ECS). The model analyzes if the planned architecture of the Data Server will support an increase in the workload with the possible upgrade and/or addition of processors, storage subsystems, and networks. The approaches in the report include a summary of the architecture of ECS's Data server as well as a high level description of the Ingest and Retrieval operations as they relate to ECS's Data Server. This description forms the basis for the development of the scalability model of the data server and the methodology used to solve it.

  8. Stencil Lithography for Scalable Micro- and Nanomanufacturing

    Directory of Open Access Journals (Sweden)

    Ke Du

    2017-04-01

    Full Text Available In this paper, we review the current development of stencil lithography for scalable micro- and nanomanufacturing as a resistless and reusable patterning technique. We first introduce the motivation and advantages of stencil lithography for large-area micro- and nanopatterning. Then we review the progress of using rigid membranes such as SiNx and Si as stencil masks as well as stacking layers. We also review the current use of flexible membranes including a compliant SiNx membrane with springs, polyimide film, polydimethylsiloxane (PDMS layer, and photoresist-based membranes as stencil lithography masks to address problems such as blurring and non-planar surface patterning. Moreover, we discuss the dynamic stencil lithography technique, which significantly improves the patterning throughput and speed by moving the stencil over the target substrate during deposition. Lastly, we discuss the future advancement of stencil lithography for a resistless, reusable, scalable, and programmable nanolithography method.

  9. SPRNG Scalable Parallel Random Number Generator LIbrary

    Energy Technology Data Exchange (ETDEWEB)

    2010-03-16

    This revision corrects some errors in SPRNG 1. Users of newer SPRNG versions can obtain the corrected files and build their version with it. This version also improves the scalability of some of the application-based tests in the SPRNG test suite. It also includes an interface to a parallel Mersenne Twister, so that if users install the Mersenne Twister, then they can test this generator with the SPRNG test suite and also use some SPRNG features with that generator.

  10. Bitcoin-NG: A Scalable Blockchain Protocol

    OpenAIRE

    Eyal, Ittay; Gencer, Adem Efe; Sirer, Emin Gun; Renesse, Robbert,

    2015-01-01

    Cryptocurrencies, based on and led by Bitcoin, have shown promise as infrastructure for pseudonymous online payments, cheap remittance, trustless digital asset exchange, and smart contracts. However, Bitcoin-derived blockchain protocols have inherent scalability limits that trade-off between throughput and latency and withhold the realization of this potential. This paper presents Bitcoin-NG, a new blockchain protocol designed to scale. Based on Bitcoin's blockchain protocol, Bitcoin-NG is By...

  11. Stencil Lithography for Scalable Micro- and Nanomanufacturing

    OpenAIRE

    Ke Du; Junjun Ding; Yuyang Liu; Ishan Wathuthanthri; Chang-Hwan Choi

    2017-01-01

    In this paper, we review the current development of stencil lithography for scalable micro- and nanomanufacturing as a resistless and reusable patterning technique. We first introduce the motivation and advantages of stencil lithography for large-area micro- and nanopatterning. Then we review the progress of using rigid membranes such as SiNx and Si as stencil masks as well as stacking layers. We also review the current use of flexible membranes including a compliant SiNx membrane with spring...

  12. Scalable robotic biofabrication of tissue spheroids

    Energy Technology Data Exchange (ETDEWEB)

    Mehesz, A Nagy; Hajdu, Z; Visconti, R P; Markwald, R R; Mironov, V [Advanced Tissue Biofabrication Center, Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC (United States); Brown, J [Department of Mechanical Engineering, Clemson University, Clemson, SC (United States); Beaver, W [York Technical College, Rock Hill, SC (United States); Da Silva, J V L, E-mail: mironovv@musc.edu [Renato Archer Information Technology Center-CTI, Campinas (Brazil)

    2011-06-15

    Development of methods for scalable biofabrication of uniformly sized tissue spheroids is essential for tissue spheroid-based bioprinting of large size tissue and organ constructs. The most recent scalable technique for tissue spheroid fabrication employs a micromolded recessed template prepared in a non-adhesive hydrogel, wherein the cells loaded into the template self-assemble into tissue spheroids due to gravitational force. In this study, we present an improved version of this technique. A new mold was designed to enable generation of 61 microrecessions in each well of a 96-well plate. The microrecessions were seeded with cells using an EpMotion 5070 automated pipetting machine. After 48 h of incubation, tissue spheroids formed at the bottom of each microrecession. To assess the quality of constructs generated using this technology, 600 tissue spheroids made by this method were compared with 600 spheroids generated by the conventional hanging drop method. These analyses showed that tissue spheroids fabricated by the micromolded method are more uniform in diameter. Thus, use of micromolded recessions in a non-adhesive hydrogel, combined with automated cell seeding, is a reliable method for scalable robotic fabrication of uniform-sized tissue spheroids.

  13. DISP: Optimizations towards Scalable MPI Startup

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Huansong [Florida State University, Tallahassee; Pophale, Swaroop S [ORNL; Gorentla Venkata, Manjunath [ORNL; Yu, Weikuan [Florida State University, Tallahassee

    2016-01-01

    Despite the popularity of MPI for high performance computing, the startup of MPI programs faces a scalability challenge as both the execution time and memory consumption increase drastically at scale. We have examined this problem using the collective modules of Cheetah and Tuned in Open MPI as representative implementations. Previous improvements for collectives have focused on algorithmic advances and hardware off-load. In this paper, we examine the startup cost of the collective module within a communicator and explore various techniques to improve its efficiency and scalability. Accordingly, we have developed a new scalable startup scheme with three internal techniques, namely Delayed Initialization, Module Sharing and Prediction-based Topology Setup (DISP). Our DISP scheme greatly benefits the collective initialization of the Cheetah module. At the same time, it helps boost the performance of non-collective initialization in the Tuned module. We evaluate the performance of our implementation on Titan supercomputer at ORNL with up to 4096 processes. The results show that our delayed initialization can speed up the startup of Tuned and Cheetah by an average of 32.0% and 29.2%, respectively, our module sharing can reduce the memory consumption of Tuned and Cheetah by up to 24.1% and 83.5%, respectively, and our prediction-based topology setup can speed up the startup of Cheetah by up to 80%.

  14. A scalable distributed RRT for motion planning

    KAUST Repository

    Jacobs, Sam Ade

    2013-05-01

    Rapidly-exploring Random Tree (RRT), like other sampling-based motion planning methods, has been very successful in solving motion planning problems. Even so, sampling-based planners cannot solve all problems of interest efficiently, so attention is increasingly turning to parallelizing them. However, one challenge in parallelizing RRT is the global computation and communication overhead of nearest neighbor search, a key operation in RRTs. This is a critical issue as it limits the scalability of previous algorithms. We present two parallel algorithms to address this problem. The first algorithm extends existing work by introducing a parameter that adjusts how much local computation is done before a global update. The second algorithm radially subdivides the configuration space into regions, constructs a portion of the tree in each region in parallel, and connects the subtrees,i removing cycles if they exist. By subdividing the space, we increase computation locality enabling a scalable result. We show that our approaches are scalable. We present results demonstrating almost linear scaling to hundreds of processors on a Linux cluster and a Cray XE6 machine. © 2013 IEEE.

  15. Numeric Analysis for Relationship-Aware Scalable Streaming Scheme

    Directory of Open Access Journals (Sweden)

    Heung Ki Lee

    2014-01-01

    Full Text Available Frequent packet loss of media data is a critical problem that degrades the quality of streaming services over mobile networks. Packet loss invalidates frames containing lost packets and other related frames at the same time. Indirect loss caused by losing packets decreases the quality of streaming. A scalable streaming service can decrease the amount of dropped multimedia resulting from a single packet loss. Content providers typically divide one large media stream into several layers through a scalable streaming service and then provide each scalable layer to the user depending on the mobile network. Also, a scalable streaming service makes it possible to decode partial multimedia data depending on the relationship between frames and layers. Therefore, a scalable streaming service provides a way to decrease the wasted multimedia data when one packet is lost. However, the hierarchical structure between frames and layers of scalable streams determines the service quality of the scalable streaming service. Even if whole packets of layers are transmitted successfully, they cannot be decoded as a result of the absence of reference frames and layers. Therefore, the complicated relationship between frames and layers in a scalable stream increases the volume of abandoned layers. For providing a high-quality scalable streaming service, we choose a proper relationship between scalable layers as well as the amount of transmitted multimedia data depending on the network situation. We prove that a simple scalable scheme outperforms a complicated scheme in an error-prone network. We suggest an adaptive set-top box (AdaptiveSTB to lower the dependency between scalable layers in a scalable stream. Also, we provide a numerical model to obtain the indirect loss of multimedia data and apply it to various multimedia streams. Our AdaptiveSTB enhances the quality of a scalable streaming service by removing indirect loss.

  16. Scalable and balanced dynamic hybrid data assimilation

    Science.gov (United States)

    Kauranne, Tuomo; Amour, Idrissa; Gunia, Martin; Kallio, Kari; Lepistö, Ahti; Koponen, Sampsa

    2017-04-01

    Scalability of complex weather forecasting suites is dependent on the technical tools available for implementing highly parallel computational kernels, but to an equally large extent also on the dependence patterns between various components of the suite, such as observation processing, data assimilation and the forecast model. Scalability is a particular challenge for 4D variational assimilation methods that necessarily couple the forecast model into the assimilation process and subject this combination to an inherently serial quasi-Newton minimization process. Ensemble based assimilation methods are naturally more parallel, but large models force ensemble sizes to be small and that results in poor assimilation accuracy, somewhat akin to shooting with a shotgun in a million-dimensional space. The Variational Ensemble Kalman Filter (VEnKF) is an ensemble method that can attain the accuracy of 4D variational data assimilation with a small ensemble size. It achieves this by processing a Gaussian approximation of the current error covariance distribution, instead of a set of ensemble members, analogously to the Extended Kalman Filter EKF. Ensemble members are re-sampled every time a new set of observations is processed from a new approximation of that Gaussian distribution which makes VEnKF a dynamic assimilation method. After this a smoothing step is applied that turns VEnKF into a dynamic Variational Ensemble Kalman Smoother VEnKS. In this smoothing step, the same process is iterated with frequent re-sampling of the ensemble but now using past iterations as surrogate observations until the end result is a smooth and balanced model trajectory. In principle, VEnKF could suffer from similar scalability issues as 4D-Var. However, this can be avoided by isolating the forecast model completely from the minimization process by implementing the latter as a wrapper code whose only link to the model is calling for many parallel and totally independent model runs, all of them

  17. Scalable Creation of Long-Lived Multipartite Entanglement

    Science.gov (United States)

    Kaufmann, H.; Ruster, T.; Schmiegelow, C. T.; Luda, M. A.; Kaushal, V.; Schulz, J.; von Lindenfels, D.; Schmidt-Kaler, F.; Poschinger, U. G.

    2017-10-01

    We demonstrate the deterministic generation of multipartite entanglement based on scalable methods. Four qubits are encoded in 40Ca+, stored in a microstructured segmented Paul trap. These qubits are sequentially entangled by laser-driven pairwise gate operations. Between these, the qubit register is dynamically reconfigured via ion shuttling operations, where ion crystals are separated and merged, and ions are moved in and out of a fixed laser interaction zone. A sequence consisting of three pairwise entangling gates yields a four-ion Greenberger-Horne-Zeilinger state |ψ ⟩=(1 /√{2 })(|0000 ⟩+|1111 ⟩) , and full quantum state tomography reveals a state fidelity of 94.4(3)%. We analyze the decoherence of this state and employ dynamic decoupling on the spatially distributed constituents to maintain 69(5)% coherence at a storage time of 1.1 sec.

  18. Phylogenetic classification of bony fishes.

    Science.gov (United States)

    Betancur-R, Ricardo; Wiley, Edward O; Arratia, Gloria; Acero, Arturo; Bailly, Nicolas; Miya, Masaki; Lecointre, Guillaume; Ortí, Guillermo

    2017-07-06

    Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution

  19. Scalable resource management in high performance computers.

    Energy Technology Data Exchange (ETDEWEB)

    Frachtenberg, E. (Eitan); Petrini, F. (Fabrizio); Fernandez Peinador, J. (Juan); Coll, S. (Salvador)

    2002-01-01

    Clusters of workstations have emerged as an important platform for building cost-effective, scalable and highly-available computers. Although many hardware solutions are available today, the largest challenge in making large-scale clusters usable lies in the system software. In this paper we present STORM, a resource management tool designed to provide scalability, low overhead and the flexibility necessary to efficiently support and analyze a wide range of job scheduling algorithms. STORM achieves these feats by closely integrating the management daemons with the low-level features that are common in state-of-the-art high-performance system area networks. The architecture of STORM is based on three main technical innovations. First, a sizable part of the scheduler runs in the thread processor located on the network interface. Second, we use hardware collectives that are highly scalable both for implementing control heartbeats and to distribute the binary of a parallel job in near-constant time, irrespective of job and machine sizes. Third, we use an I/O bypass protocol that allows fast data movements from the file system to the communication buffers in the network interface and vice versa. The experimental results show that STORM can launch a job with a binary of 12MB on a 64 processor/32 node cluster in less than 0.25 sec on an empty network, in less than 0.45 sec when all the processors are busy computing other jobs, and in less than 0.65 sec when the network is flooded with a background traffic. This paper provides experimental and analytical evidence that these results scale to a much larger number of nodes. To the best of our knowledge, STORM is at least two orders of magnitude faster than existing production schedulers in launching jobs, performing resource management tasks and gang scheduling.

  20. Towards an eco-phylogenetic framework for infectious disease ecology.

    Science.gov (United States)

    Fountain-Jones, Nicholas M; Pearse, William D; Escobar, Luis E; Alba-Casals, Ana; Carver, Scott; Davies, T Jonathan; Kraberger, Simona; Papeş, Monica; Vandegrift, Kurt; Worsley-Tonks, Katherine; Craft, Meggan E

    2017-11-08

    Identifying patterns and drivers of infectious disease dynamics across multiple scales is a fundamental challenge for modern science. There is growing awareness that it is necessary to incorporate multi-host and/or multi-parasite interactions to understand and predict current and future disease threats better, and new tools are needed to help address this task. Eco-phylogenetics (phylogenetic community ecology) provides one avenue for exploring multi-host multi-parasite systems, yet the incorporation of eco-phylogenetic concepts and methods into studies of host pathogen dynamics has lagged behind. Eco-phylogenetics is a transformative approach that uses evolutionary history to infer present-day dynamics. Here, we present an eco-phylogenetic framework to reveal insights into parasite communities and infectious disease dynamics across spatial and temporal scales. We illustrate how eco-phylogenetic methods can help untangle the mechanisms of host-parasite dynamics from individual (e.g. co-infection) to landscape scales (e.g. parasite/host community structure). An improved ecological understanding of multi-host and multi-pathogen dynamics across scales will increase our ability to predict disease threats. © 2017 Cambridge Philosophical Society.

  1. Combined Scalable Video Coding Method for Wireless Transmission

    Directory of Open Access Journals (Sweden)

    Achmad Affandi

    2011-08-01

    Full Text Available Mobile video streaming is one of multimedia services that has developed very rapidly. Recently, bandwidth utilization for wireless transmission is the main problem in the field of multimedia communications. In this research, we offer a combination of scalable methods as the most attractive solution to this problem. Scalable method for wireless communication should adapt to input video sequence. Standard ITU (International Telecommunication Union - Joint Scalable Video Model (JSVM is employed to produce combined scalable video coding (CSVC method that match the required quality of video streaming services for wireless transmission. The investigation in this paper shows that combined scalable technique outperforms the non-scalable one, in using bit rate capacity at certain layer.

  2. Towards a Scalable, Biomimetic, Antibacterial Coating

    Science.gov (United States)

    Dickson, Mary Nora

    Corneal afflictions are the second leading cause of blindness worldwide. When a corneal transplant is unavailable or contraindicated, an artificial cornea device is the only chance to save sight. Bacterial or fungal biofilm build up on artificial cornea devices can lead to serious complications including the need for systemic antibiotic treatment and even explantation. As a result, much emphasis has been placed on anti-adhesion chemical coatings and antibiotic leeching coatings. These methods are not long-lasting, and microorganisms can eventually circumvent these measures. Thus, I have developed a surface topographical antimicrobial coating. Various surface structures including rough surfaces, superhydrophobic surfaces, and the natural surfaces of insects' wings and sharks' skin are promising anti-biofilm candidates, however none meet the criteria necessary for implementation on the surface of an artificial cornea device. In this thesis I: 1) developed scalable fabrication protocols for a library of biomimetic nanostructure polymer surfaces 2) assessed the potential these for poly(methyl methacrylate) nanopillars to kill or prevent formation of biofilm by E. coli bacteria and species of Pseudomonas and Staphylococcus bacteria and improved upon a proposed mechanism for the rupture of Gram-negative bacterial cell walls 3) developed a scalable, commercially viable method for producing antibacterial nanopillars on a curved, PMMA artificial cornea device and 4) developed scalable fabrication protocols for implantation of antibacterial nanopatterned surfaces on the surfaces of thermoplastic polyurethane materials, commonly used in catheter tubings. This project constitutes a first step towards fabrication of the first entirely PMMA artificial cornea device. The major finding of this work is that by precisely controlling the topography of a polymer surface at the nano-scale, we can kill adherent bacteria and prevent biofilm formation of certain pathogenic bacteria

  3. Programming Scala Scalability = Functional Programming + Objects

    CERN Document Server

    Wampler, Dean

    2009-01-01

    Learn how to be more productive with Scala, a new multi-paradigm language for the Java Virtual Machine (JVM) that integrates features of both object-oriented and functional programming. With this book, you'll discover why Scala is ideal for highly scalable, component-based applications that support concurrency and distribution. Programming Scala clearly explains the advantages of Scala as a JVM language. You'll learn how to leverage the wealth of Java class libraries to meet the practical needs of enterprise and Internet projects more easily. Packed with code examples, this book provides us

  4. Scalable and Anonymous Group Communication with MTor

    Directory of Open Access Journals (Sweden)

    Lin Dong

    2016-04-01

    Full Text Available This paper presents MTor, a low-latency anonymous group communication system. We construct MTor as an extension to Tor, allowing the construction of multi-source multicast trees on top of the existing Tor infrastructure. MTor does not depend on an external service to broker the group communication, and avoids central points of failure and trust. MTor’s substantial bandwidth savings and graceful scalability enable new classes of anonymous applications that are currently too bandwidth-intensive to be viable through traditional unicast Tor communication-e.g., group file transfer, collaborative editing, streaming video, and real-time audio conferencing.

  5. Scalable conditional induction variables (CIV) analysis

    DEFF Research Database (Denmark)

    Oancea, Cosmin Eugen; Rauchwerger, Lawrence

    2015-01-01

    representation. Our technique requires no modifications of our dependence tests, which is agnostic to the original shape of the subscripts, and is more powerful than previously reported dependence tests that rely on the pairwise disambiguation of read-write references. We have implemented the CIV analysis in our...... parallelizing compiler and evaluated its impact on five Fortran benchmarks. We have found that that there are many important loops using CIV subscripts and that our analysis can lead to their scalable parallelization. This in turn has led to the parallelization of the benchmark programs they appear in....

  6. Tip-Based Nanofabrication for Scalable Manufacturing

    Directory of Open Access Journals (Sweden)

    Huan Hu

    2017-03-01

    Full Text Available Tip-based nanofabrication (TBN is a family of emerging nanofabrication techniques that use a nanometer scale tip to fabricate nanostructures. In this review, we first introduce the history of the TBN and the technology development. We then briefly review various TBN techniques that use different physical or chemical mechanisms to fabricate features and discuss some of the state-of-the-art techniques. Subsequently, we focus on those TBN methods that have demonstrated potential to scale up the manufacturing throughput. Finally, we discuss several research directions that are essential for making TBN a scalable nano-manufacturing technology.

  7. Scalable Engineering of Quantum Optical Information Processing Architectures (SEQUOIA)

    Science.gov (United States)

    2016-12-13

    scalable architecture for LOQC and cluster state quantum computing (Ballistic or non-ballistic) - With parametric nonlinearities (Kerr, chi-2...Scalable Engineering of Quantum Optical Information-Processing Architectures (SEQUOIA) 5a. CONTRACT NUMBER W31-P4Q-15-C-0045 5b. GRANT NUMBER 5c...Technologies 13 December 2016 “Scalable Engineering of Quantum Optical Information-Processing Architectures (SEQUOIA)” Final R&D Status Report

  8. BLAST-EXPLORER helps you building datasets for phylogenetic analysis

    Directory of Open Access Journals (Sweden)

    Claverie Jean-Michel

    2010-01-01

    Full Text Available Abstract Background The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task. Results To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the Phylogeny.fr platform. Conclusions BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://www.phylogeny.fr

  9. Phylogenetic congruence between subtropical trees and their associated fungi.

    Science.gov (United States)

    Liu, Xubing; Liang, Minxia; Etienne, Rampal S; Gilbert, Gregory S; Yu, Shixiao

    2016-12-01

    Recent studies have detected phylogenetic signals in pathogen-host networks for both soil-borne and leaf-infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next-generation high-throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK, rbcL, atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host-fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant-fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant-fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.

  10. Big data integration: scalability and sustainability

    KAUST Repository

    Zhang, Zhang

    2016-01-26

    Integration of various types of omics data is critically indispensable for addressing most important and complex biological questions. In the era of big data, however, data integration becomes increasingly tedious, time-consuming and expensive, posing a significant obstacle to fully exploit the wealth of big biological data. Here we propose a scalable and sustainable architecture that integrates big omics data through community-contributed modules. Community modules are contributed and maintained by different committed groups and each module corresponds to a specific data type, deals with data collection, processing and visualization, and delivers data on-demand via web services. Based on this community-based architecture, we build Information Commons for Rice (IC4R; http://ic4r.org), a rice knowledgebase that integrates a variety of rice omics data from multiple community modules, including genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequencing data of thousands of rice varieties, plant homologous genes covering multiple diverse plant species, post-translational modifications, rice-related literatures, and community annotations. Taken together, such architecture achieves integration of different types of data from multiple community-contributed modules and accordingly features scalable, sustainable and collaborative integration of big data as well as low costs for database update and maintenance, thus helpful for building IC4R into a comprehensive knowledgebase covering all aspects of rice data and beneficial for both basic and translational researches.

  11. Using MPI to Implement Scalable Libraries

    Science.gov (United States)

    Lusk, Ewing

    MPI is an instantiation of a general-purpose programming model, and high-performance implementations of the MPI standard have provided scalability for a wide range of applications. Ease of use was not an explicit goal of the MPI design process, which emphasized completeness, portability, and performance. Thus it is not surprising that MPI is occasionally criticized for being inconvenient to use and thus a drag on software developer productivity. One approach to the productivity issue is to use MPI to implement simpler programming models. Such models may limit the range of parallel algorithms that can be expressed, yet provide sufficient generality to benefit a significant number of applications, even from different domains.We illustrate this concept with the ADLB (Asynchronous, Dynamic Load-Balancing) library, which can be used to express manager/worker algorithms in such a way that their execution is scalable, even on the largestmachines. ADLB makes sophisticated use ofMPI functionality while providing an extremely simple API for the application programmer.We will describe it in the context of solving Sudoku puzzles and a nuclear physics Monte Carlo application currently running on tens of thousands of processors.

  12. Using the scalable nonlinear equations solvers package

    Energy Technology Data Exchange (ETDEWEB)

    Gropp, W.D.; McInnes, L.C.; Smith, B.F.

    1995-02-01

    SNES (Scalable Nonlinear Equations Solvers) is a software package for the numerical solution of large-scale systems of nonlinear equations on both uniprocessors and parallel architectures. SNES also contains a component for the solution of unconstrained minimization problems, called SUMS (Scalable Unconstrained Minimization Solvers). Newton-like methods, which are known for their efficiency and robustness, constitute the core of the package. As part of the multilevel PETSc library, SNES incorporates many features and options from other parts of PETSc. In keeping with the spirit of the PETSc library, the nonlinear solution routines are data-structure-neutral, making them flexible and easily extensible. This users guide contains a detailed description of uniprocessor usage of SNES, with some added comments regarding multiprocessor usage. At this time the parallel version is undergoing refinement and extension, as we work toward a common interface for the uniprocessor and parallel cases. Thus, forthcoming versions of the software will contain additional features, and changes to parallel interface may result at any time. The new parallel version will employ the MPI (Message Passing Interface) standard for interprocessor communication. Since most of these details will be hidden, users will need to perform only minimal message-passing programming.

  13. Towards Scalable Graph Computation on Mobile Devices

    Science.gov (United States)

    Chen, Yiqi; Lin, Zhiyuan; Pienta, Robert; Kahng, Minsuk; Chau, Duen Horng

    2015-01-01

    Mobile devices have become increasingly central to our everyday activities, due to their portability, multi-touch capabilities, and ever-improving computational power. Such attractive features have spurred research interest in leveraging mobile devices for computation. We explore a novel approach that aims to use a single mobile device to perform scalable graph computation on large graphs that do not fit in the device's limited main memory, opening up the possibility of performing on-device analysis of large datasets, without relying on the cloud. Based on the familiar memory mapping capability provided by today's mobile operating systems, our approach to scale up computation is powerful and intentionally kept simple to maximize its applicability across the iOS and Android platforms. Our experiments demonstrate that an iPad mini can perform fast computation on large real graphs with as many as 272 million edges (Google+ social graph), at a speed that is only a few times slower than a 13″ Macbook Pro. Through creating a real world iOS app with this technique, we demonstrate the strong potential application for scalable graph computation on a single mobile device using our approach. PMID:25859564

  14. Scalability Optimization of Seamless Positioning Service

    Directory of Open Access Journals (Sweden)

    Juraj Machaj

    2016-01-01

    Full Text Available Recently positioning services are getting more attention not only within research community but also from service providers. From the service providers point of view positioning service that will be able to work seamlessly in all environments, for example, indoor, dense urban, and rural, has a huge potential to open new markets. However, such system does not only need to provide accurate position estimates but have to be scalable and resistant to fake positioning requests. In the previous works we have proposed a modular system, which is able to provide seamless positioning in various environments. The system automatically selects optimal positioning module based on available radio signals. The system currently consists of three positioning modules—GPS, GSM based positioning, and Wi-Fi based positioning. In this paper we will propose algorithm which will reduce time needed for position estimation and thus allow higher scalability of the modular system and thus allow providing positioning services to higher amount of users. Such improvement is extremely important, for real world application where large number of users will require position estimates, since positioning error is affected by response time of the positioning server.

  15. An Open Infrastructure for Scalable, Reconfigurable Analysis

    Energy Technology Data Exchange (ETDEWEB)

    de Supinski, B R; Fowler, R; Gamblin, T; Mueller, F; Ratn, P; Schulz, M

    2008-05-15

    Petascale systems will have hundreds of thousands of processor cores so their applications must be massively parallel. Effective use of petascale systems will require efficient interprocess communication through memory hierarchies and complex network topologies. Tools to collect and analyze detailed data about this communication would facilitate its optimization. However, several factors complicate tool design. First, large-scale runs on petascale systems will be a precious commodity, so scalable tools must have almost no overhead. Second, the volume of performance data from petascale runs could easily overwhelm hand analysis and, thus, tools must collect only data that is relevant to diagnosing performance problems. Analysis must be done in-situ, when available processing power is proportional to the data. We describe a tool framework that overcomes these complications. Our approach allows application developers to combine existing techniques for measurement, analysis, and data aggregation to develop application-specific tools quickly. Dynamic configuration enables application developers to select exactly the measurements needed and generic components support scalable aggregation and analysis of this data with little additional effort.

  16. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  17. Network selection, Information filtering and Scalable computation

    Science.gov (United States)

    Ye, Changqing

    -complete factorizations, possibly with a high percentage of missing values. This promotes additional sparsity beyond rank reduction. Computationally, we design methods based on a ``decomposition and combination'' strategy, to break large-scale optimization into many small subproblems to solve in a recursive and parallel manner. On this basis, we implement the proposed methods through multi-platform shared-memory parallel programming, and through Mahout, a library for scalable machine learning and data mining, for mapReduce computation. For example, our methods are scalable to a dataset consisting of three billions of observations on a single machine with sufficient memory, having good timings. Both theoretical and numerical investigations show that the proposed methods exhibit significant improvement in accuracy over state-of-the-art scalable methods.

  18. Scalable Transactions for Web Applications in the Cloud

    NARCIS (Netherlands)

    Zhou, W.; Pierre, G.E.O.; Chi, C.-H.

    2009-01-01

    Cloud Computing platforms provide scalability and high availability properties for web applications but they sacrifice data consistency at the same time. However, many applications cannot afford any data inconsistency. We present a scalable transaction manager for NoSQL cloud database services to

  19. New Complexity Scalable MPEG Encoding Techniques for Mobile Applications

    Directory of Open Access Journals (Sweden)

    Stephan Mietens

    2004-03-01

    Full Text Available Complexity scalability offers the advantage of one-time design of video applications for a large product family, including mobile devices, without the need of redesigning the applications on the algorithmic level to meet the requirements of the different products. In this paper, we present complexity scalable MPEG encoding having core modules with modifications for scalability. The interdependencies of the scalable modules and the system performance are evaluated. Experimental results show scalability giving a smooth change in complexity and corresponding video quality. Scalability is basically achieved by varying the number of computed DCT coefficients and the number of evaluated motion vectors but other modules are designed such they scale with the previous parameters. In the experiments using the “Stefan” sequence, the elapsed execution time of the scalable encoder, reflecting the computational complexity, can be gradually reduced to roughly 50% of its original execution time. The video quality scales between 20 dB and 48 dB PSNR with unity quantizer setting, and between 21.5 dB and 38.5 dB PSNR for different sequences targeting 1500 kbps. The implemented encoder and the scalability techniques can be successfully applied in mobile systems based on MPEG video compression.

  20. Scalable DeNoise-and-Forward in Bidirectional Relay Networks

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Krigslund, Rasmus; Popovski, Petar

    2010-01-01

    In this paper a scalable relaying scheme is proposed based on an existing concept called DeNoise-and-Forward, DNF. We call it Scalable DNF, S-DNF, and it targets the scenario with multiple communication flows through a single common relay. The idea of the scheme is to combine packets at the relay...

  1. Building scalable apps with Redis and Node.js

    CERN Document Server

    Johanan, Joshua

    2014-01-01

    If the phrase scalability sounds alien to you, then this is an ideal book for you. You will not need much Node.js experience as each framework is demonstrated in a way that requires no previous knowledge of the framework. You will be building scalable Node.js applications in no time! Knowledge of JavaScript is required.

  2. A phylogenetic blueprint for a modern whale.

    Science.gov (United States)

    Gatesy, John; Geisler, Jonathan H; Chang, Joseph; Buell, Carl; Berta, Annalisa; Meredith, Robert W; Springer, Mark S; McGowen, Michael R

    2013-02-01

    The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti - toothed whales), and others that batch feed using racks of baleen (Mysticeti - baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological+paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life. Copyright © 2012 Elsevier Inc. All rights reserved.

  3. BASSET: Scalable Gateway Finder in Large Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Tong, H; Papadimitriou, S; Faloutsos, C; Yu, P S; Eliassi-Rad, T

    2010-11-03

    Given a social network, who is the best person to introduce you to, say, Chris Ferguson, the poker champion? Or, given a network of people and skills, who is the best person to help you learn about, say, wavelets? The goal is to find a small group of 'gateways': persons who are close enough to us, as well as close enough to the target (person, or skill) or, in other words, are crucial in connecting us to the target. The main contributions are the following: (a) we show how to formulate this problem precisely; (b) we show that it is sub-modular and thus it can be solved near-optimally; (c) we give fast, scalable algorithms to find such gateways. Experiments on real data sets validate the effectiveness and efficiency of the proposed methods, achieving up to 6,000,000x speedup.

  4. The Concept of Business Model Scalability

    DEFF Research Database (Denmark)

    Nielsen, Christian; Lund, Morten

    2015-01-01

    are leveraged in this value creation, delivery and realization exercise. Central to the mainstream understanding of business models is the value proposition towards the customer and the hypothesis generated is that if the firm delivers to the customer what he/she requires, then there is a good foundation......The power of business models lies in their ability to visualize and clarify how firms’ may configure their value creation processes. Among the key aspects of business model thinking are a focus on what the customer values, how this value is best delivered to the customer and how strategic partners...... for a long-term profitable business. However, the message conveyed in this article is that while providing a good value proposition may help the firm ‘get by’, the really successful businesses of today are those able to reach the sweet-spot of business model scalability. This article introduces and discusses...

  5. Towards scalable Byzantine fault-tolerant replication

    Science.gov (United States)

    Zbierski, Maciej

    2017-08-01

    Byzantine fault-tolerant (BFT) replication is a powerful technique, enabling distributed systems to remain available and correct even in the presence of arbitrary faults. Unfortunately, existing BFT replication protocols are mostly load-unscalable, i.e. they fail to respond with adequate performance increase whenever new computational resources are introduced into the system. This article proposes a universal architecture facilitating the creation of load-scalable distributed services based on BFT replication. The suggested approach exploits parallel request processing to fully utilize the available resources, and uses a load balancer module to dynamically adapt to the properties of the observed client workload. The article additionally provides a discussion on selected deployment scenarios, and explains how the proposed architecture could be used to increase the dependability of contemporary large-scale distributed systems.

  6. A graph algebra for scalable visual analytics.

    Science.gov (United States)

    Shaverdian, Anna A; Zhou, Hao; Michailidis, George; Jagadish, Hosagrahar V

    2012-01-01

    Visual analytics (VA), which combines analytical techniques with advanced visualization features, is fast becoming a standard tool for extracting information from graph data. Researchers have developed many tools for this purpose, suggesting a need for formal methods to guide these tools' creation. Increased data demands on computing requires redesigning VA tools to consider performance and reliability in the context of analysis of exascale datasets. Furthermore, visual analysts need a way to document their analyses for reuse and results justification. A VA graph framework encapsulated in a graph algebra helps address these needs. Its atomic operators include selection and aggregation. The framework employs a visual operator and supports dynamic attributes of data to enable scalable visual exploration of data.

  7. Declarative and Scalable Selection for Map Visualizations

    DEFF Research Database (Denmark)

    Kefaloukos, Pimin Konstantin Balic

    foreground layers is merited. (2) The typical map making professional has changed from a GIS specialist to a busy person with map making as a secondary skill. Today, thematic maps are produced by journalists, aid workers, amateur data enth siasts, and scientists alike. Therefore it is crucial...... that this diverse group of map makers is provided with easy-to-use and expressible thematic map design tools. Such tools should support customized selection of data for maps in scenarios where developer time is a scarce resource. (3) The Web provides access to massive data repositories for thematic maps...... based on an access log of recent requests. The results show that Glossy SQL og CVL can be used to compute cartographic selection by processing one or more complex queries in a relational database. The scalability of the approach has been verified up to half a million objects in the database. Furthermore...

  8. Phylogenetic constrains on mycorrhizal specificity in eight Dendrobium (Orchidaceae) species.

    Science.gov (United States)

    Xing, Xiaoke; Ma, Xueting; Men, Jinxin; Chen, Yanhong; Guo, Shunxing

    2017-05-01

    Plant phylogeny constrains orchid mycorrhizal (OrM) fungal community composition in some orchids. Here, we investigated the structures of the OrM fungal communities of eight Dendrobium species in one niche to determine whether similarities in the OrM fungal communities correlated with the phylogeny of the host plants and whether the Dendrobium-OrM fungal interactions are phylogenetically conserved. A phylogeny based on DNA data was constructed for the eight coexisting Dendrobium species, and the OrM fungal communities were characterized by their roots. There were 31 different fungal lineages associated with the eight Dendrobium species. In total, 82.98% of the identified associations belonging to Tulasnellaceae, and a smaller proportion involved members of the unknown Basidiomycota (9.67%). Community analyses revealed that phylogenetically related Dendrobium tended to interact with a similar set of Tulasnellaceae fungi. The interactions between Dendrobium and Tulasnellaceae fungi were significantly influenced by the phylogenetic relationships among the Dendrobium species. Our results provide evidence that the mycorrhizal specificity in the eight coexisting Dendrobium species was phylogenetically conserved.

  9. Scalable and Media Aware Adaptive Video Streaming over Wireless Networks

    Science.gov (United States)

    Tizon, Nicolas; Pesquet-Popescu, Béatrice

    2008-12-01

    This paper proposes an advanced video streaming system based on scalable video coding in order to optimize resource utilization in wireless networks with retransmission mechanisms at radio protocol level. The key component of this system is a packet scheduling algorithm which operates on the different substreams of a main scalable video stream and which is implemented in a so-called media aware network element. The concerned type of transport channel is a dedicated channel subject to parameters (bitrate, loss rate) variations on the long run. Moreover, we propose a combined scalability approach in which common temporal and SNR scalability features can be used jointly with a partitioning of the image into regions of interest. Simulation results show that our approach provides substantial quality gain compared to classical packet transmission methods and they demonstrate how ROI coding combined with SNR scalability allows to improve again the visual quality.

  10. Phylogenetic Signal in AFLP Data Sets

    NARCIS (Netherlands)

    Koopman, W.J.M.

    2005-01-01

    AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment

  11. Phylogenetic Position of Barbus lacerta Heckel, 1843

    Directory of Open Access Journals (Sweden)

    Mustafa Korkmaz

    2015-11-01

    As a result, five clades come out from phylogenetic reconstruction and in phylogenetic tree Barbus lacerta determined to be sister group of Barbus macedonicus, Barbus oligolepis and Barbus plebejus complex.

  12. Phylogenetics of neotropical Platymiscium (Leguminosae

    DEFF Research Database (Denmark)

    Saslis-Lagoudakis, C. Haris; Chase, Mark W; Robinson, Daniel N

    2008-01-01

    Platymiscium is a neotropical legume genus of forest trees in the Pterocarpus clade of the pantropical "dalbergioid" clade. It comprises 19 species (29 taxa), distributed from Mexico to southern Brazil. This study presents a molecular phylogenetic analysis of Platymiscium and allies inferred from...... twice before the closure of the Isthmus of Panama. Divergence times of the P. pubescens complex, restricted to seasonally dry tropical forests of South America, support pre-Pleistocene divergence in this biome.......Platymiscium is a neotropical legume genus of forest trees in the Pterocarpus clade of the pantropical "dalbergioid" clade. It comprises 19 species (29 taxa), distributed from Mexico to southern Brazil. This study presents a molecular phylogenetic analysis of Platymiscium and allies inferred from...

  13. Phyx: phylogenetic tools for unix.

    Science.gov (United States)

    Brown, Joseph W; Walker, Joseph F; Smith, Stephen A

    2017-06-15

    The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx : a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets. phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx. eebsmith@umich.edu. Supplementary data are available at Bioinformatics online.

  14. Vestige: Maximum likelihood phylogenetic footprinting

    Directory of Open Access Journals (Sweden)

    Maxwell Peter

    2005-05-01

    Full Text Available Abstract Background Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have diverged less than neutral DNA. Vestige is a phylogenetic footprinting package built on the PyEvolve toolkit that uses probabilistic molecular evolutionary modelling to represent aspects of sequence evolution, including the conventional divergence measure employed by other footprinting approaches. In addition to measuring the divergence, Vestige allows the expansion of the definition of a phylogenetic footprint to include variation in the distribution of any molecular evolutionary processes. This is achieved by displaying the distribution of model parameters that represent partitions of molecular evolutionary substitutions. Examination of the spatial incidence of these effects across regions of the genome can identify DNA segments that differ in the nature of the evolutionary process. Results Vestige was applied to a reference dataset of the SCL locus from four species and provided clear identification of the known conserved regions in this dataset. To demonstrate the flexibility to use diverse models of molecular evolution and dissect the nature of the evolutionary process Vestige was used to footprint the Ka/Ks ratio in primate BRCA1 with a codon model of evolution. Two regions of putative adaptive evolution were identified illustrating the ability of Vestige to represent the spatial distribution of distinct molecular evolutionary processes. Conclusion Vestige provides a flexible, open platform for phylogenetic footprinting. Underpinned by the PyEvolve toolkit, Vestige provides a framework for visualising the signatures of evolutionary processes across the genome of numerous organisms simultaneously. By exploiting the maximum-likelihood statistical framework, the complex interplay between mutational

  15. Vestige: maximum likelihood phylogenetic footprinting.

    Science.gov (United States)

    Wakefield, Matthew J; Maxwell, Peter; Huttley, Gavin A

    2005-05-29

    Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have diverged less than neutral DNA. Vestige is a phylogenetic footprinting package built on the PyEvolve toolkit that uses probabilistic molecular evolutionary modelling to represent aspects of sequence evolution, including the conventional divergence measure employed by other footprinting approaches. In addition to measuring the divergence, Vestige allows the expansion of the definition of a phylogenetic footprint to include variation in the distribution of any molecular evolutionary processes. This is achieved by displaying the distribution of model parameters that represent partitions of molecular evolutionary substitutions. Examination of the spatial incidence of these effects across regions of the genome can identify DNA segments that differ in the nature of the evolutionary process. Vestige was applied to a reference dataset of the SCL locus from four species and provided clear identification of the known conserved regions in this dataset. To demonstrate the flexibility to use diverse models of molecular evolution and dissect the nature of the evolutionary process Vestige was used to footprint the Ka/Ks ratio in primate BRCA1 with a codon model of evolution. Two regions of putative adaptive evolution were identified illustrating the ability of Vestige to represent the spatial distribution of distinct molecular evolutionary processes. Vestige provides a flexible, open platform for phylogenetic footprinting. Underpinned by the PyEvolve toolkit, Vestige provides a framework for visualising the signatures of evolutionary processes across the genome of numerous organisms simultaneously. By exploiting the maximum-likelihood statistical framework, the complex interplay between mutational processes, DNA repair and selection can be evaluated both

  16. Phylogenetic analysis of gene expression.

    Science.gov (United States)

    Dunn, Casey W; Luo, Xi; Wu, Zhijin

    2013-11-01

    Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary changes in morphological, physiological, and developmental characters of interest. This will provide entirely new opportunities to identify genes related to particular phenotypes. There are, however, 3 key challenges that must be addressed for such studies to realize their potential. First, data on gene expression must be measured from multiple species, some of which may be field-collected, and parameterized in such a way that they can be compared across species. Second, it will be necessary to develop comparative phylogenetic methods suitable for large multidimensional datasets. In most phylogenetic comparative studies to date, the number n of independent observations (independent contrasts) has been greater than the number p of variables (characters). The behavior of comparative methods for these classic problems is now well understood under a wide variety of conditions. In studies of gene expression, and in studies based on other high-throughput tools, the number n of samples is dwarfed by the number p of variables. The estimated covariance matrices will be singular, complicating their analysis and interpretation, and prone to spurious results. Third, new approaches are needed to investigate the expression of the many genes whose phylogenies are not congruent with species phylogenies due to gene loss, gene duplication, and incomplete lineage sorting. Here we outline general considerations of project design for phylogenetic analyses of gene expression and suggest solutions to these three categories of challenges. These topics are relevant to high-throughput phenotypic data well beyond gene expression.

  17. A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis.

    Science.gov (United States)

    Xiong, Xiong; Zhang, Yanxiao; Yan, Jian; Jain, Surbhi; Chee, Sora; Ren, Bing; Zhao, Huimin

    2017-06-16

    Eukaryotic transcriptional factors (TFs) typically recognize short genomic sequences alone or together with other proteins to modulate gene expression. Mapping of TF-DNA interactions in the genome is crucial for understanding the gene regulatory programs in cells. While chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is commonly used for this purpose, its application is severely limited by the availability of suitable antibodies for TFs. To overcome this limitation, we developed an efficient and scalable strategy named cmChIP-Seq that combines the clustered regularly interspaced short palindromic repeats (CRISPR) technology with microhomology mediated end joining (MMEJ) to genetically engineer a TF with an epitope tag. We demonstrated the utility of this tool by applying it to four TFs in a human colorectal cancer cell line. The highly scalable procedure makes this strategy ideal for ChIP-Seq analysis of TFs in diverse species and cell types.

  18. Comparison of phylogenetic trees through alignment of embedded evolutionary distances

    Directory of Open Access Journals (Sweden)

    Choi Kwangbom

    2009-12-01

    Full Text Available Abstract Background The understanding of evolutionary relationships is a fundamental aspect of modern biology, with the phylogenetic tree being a primary tool for describing these associations. However, comparison of trees for the purpose of assessing similarity and the quantification of various biological processes remains a significant challenge. Results We describe a novel approach for the comparison of phylogenetic distance information based on the alignment of representative high-dimensional embeddings (xCEED: Comparison of Embedded Evolutionary Distances. The xCEED methodology, which utilizes multidimensional scaling and Procrustes-related superimposition approaches, provides the ability to measure the global similarity between trees as well as incongruities between them. We demonstrate the application of this approach to the prediction of coevolving protein interactions and demonstrate its improved performance over the mirrortree, tol-mirrortree, phylogenetic vector projection, and partial correlation approaches. Furthermore, we show its applicability to both the detection of horizontal gene transfer events as well as its potential use in the prediction of interaction specificity between a pair of multigene families. Conclusions These approaches provide additional tools for the study of phylogenetic trees and associated evolutionary processes. Source code is available at http://gomezlab.bme.unc.edu/tools.

  19. Functional and phylogenetic ecology in R

    CERN Document Server

    Swenson, Nathan G

    2014-01-01

    Functional and Phylogenetic Ecology in R is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a uni...

  20. Oracle database performance and scalability a quantitative approach

    CERN Document Server

    Liu, Henry H

    2011-01-01

    A data-driven, fact-based, quantitative text on Oracle performance and scalability With database concepts and theories clearly explained in Oracle's context, readers quickly learn how to fully leverage Oracle's performance and scalability capabilities at every stage of designing and developing an Oracle-based enterprise application. The book is based on the author's more than ten years of experience working with Oracle, and is filled with dependable, tested, and proven performance optimization techniques. Oracle Database Performance and Scalability is divided into four parts that enable reader

  1. A novel 3D scalable video compression algorithm

    Science.gov (United States)

    Somasundaram, Siva; Subbalakshmi, Koduvayur P.

    2003-05-01

    In this paper we propose a scalable video coding scheme that utilizes the embedded block coding with optimal truncation (EBCOT) compression algorithm. Three dimensional spatio-temporal decomposition of the video sequence succeeded by compression using the EBCOT generates a SNR and resolution scalable bit stream. The proposed video coding algorithm not only performs closer to the MPEG-4 video coding standard in compression efficiency but also provides better SNR and resolution scalability. Experimental results show that the performance of the proposed algorithm does better than the 3-D SPIHT (Set Partitioning in Hierarchial Trees) algorithm by 1.5dB.

  2. The Scalable Reasoning System: Lightweight Visualization for Distributed Analytics

    Energy Technology Data Exchange (ETDEWEB)

    Pike, William A.; Bruce, Joseph R.; Baddeley, Robert L.; Best, Daniel M.; Franklin, Lyndsey; May, Richard A.; Rice, Douglas M.; Riensche, Roderick M.; Younkin, Katarina

    2009-03-01

    A central challenge in visual analytics is the creation of accessible, widely distributable analysis applications that bring the benefits of visual discovery to as broad a user base as possible. Moreover, to support the role of visualization in the knowledge creation process, it is advantageous to allow users to describe the reasoning strategies they employ while interacting with analytic environments. We introduce an application suite called the Scalable Reasoning System (SRS), which provides web-based and mobile interfaces for visual analysis. The service-oriented analytic framework that underlies SRS provides a platform for deploying pervasive visual analytic environments across an enterprise. SRS represents a “lightweight” approach to visual analytics whereby thin client analytic applications can be rapidly deployed in a platform-agnostic fashion. Client applications support multiple coordinated views while giving analysts the ability to record evidence, assumptions, hypotheses and other reasoning artifacts. We describe the capabilities of SRS in the context of a real-world deployment at a regional law enforcement organization.

  3. Scalable conditional induction variables (CIV) analysis

    KAUST Repository

    Oancea, Cosmin E.

    2015-02-01

    Subscripts using induction variables that cannot be expressed as a formula in terms of the enclosing-loop indices appear in the low-level implementation of common programming abstractions such as Alter, or stack operations and pose significant challenges to automatic parallelization. Because the complexity of such induction variables is often due to their conditional evaluation across the iteration space of loops we name them Conditional Induction Variables (CIV). This paper presents a flow-sensitive technique that summarizes both such CIV-based and affine subscripts to program level, using the same representation. Our technique requires no modifications of our dependence tests, which is agnostic to the original shape of the subscripts, and is more powerful than previously reported dependence tests that rely on the pairwise disambiguation of read-write references. We have implemented the CIV analysis in our parallelizing compiler and evaluated its impact on five Fortran benchmarks. We have found that that there are many important loops using CIV subscripts and that our analysis can lead to their scalable parallelization. This in turn has led to the parallelization of the benchmark programs they appear in.

  4. Scalable Notch Antenna System for Multiport Applications

    Directory of Open Access Journals (Sweden)

    Abdurrahim Toktas

    2016-01-01

    Full Text Available A novel and compact scalable antenna system is designed for multiport applications. The basic design is built on a square patch with an electrical size of 0.82λ0×0.82λ0 (at 2.4 GHz on a dielectric substrate. The design consists of four symmetrical and orthogonal triangular notches with circular feeding slots at the corners of the common patch. The 4-port antenna can be simply rearranged to 8-port and 12-port systems. The operating band of the system can be tuned by scaling (S the size of the system while fixing the thickness of the substrate. The antenna system with S: 1/1 in size of 103.5×103.5 mm2 operates at the frequency band of 2.3–3.0 GHz. By scaling the antenna with S: 1/2.3, a system of 45×45 mm2 is achieved, and thus the operating band is tuned to 4.7–6.1 GHz with the same scattering characteristic. A parametric study is also conducted to investigate the effects of changing the notch dimensions. The performance of the antenna is verified in terms of the antenna characteristics as well as diversity and multiplexing parameters. The antenna system can be tuned by scaling so that it is applicable to the multiport WLAN, WIMAX, and LTE devices with port upgradability.

  5. Scalable inference for stochastic block models

    KAUST Repository

    Peng, Chengbin

    2017-12-08

    Community detection in graphs is widely used in social and biological networks, and the stochastic block model is a powerful probabilistic tool for describing graphs with community structures. However, in the era of "big data," traditional inference algorithms for such a model are increasingly limited due to their high time complexity and poor scalability. In this paper, we propose a multi-stage maximum likelihood approach to recover the latent parameters of the stochastic block model, in time linear with respect to the number of edges. We also propose a parallel algorithm based on message passing. Our algorithm can overlap communication and computation, providing speedup without compromising accuracy as the number of processors grows. For example, to process a real-world graph with about 1.3 million nodes and 10 million edges, our algorithm requires about 6 seconds on 64 cores of a contemporary commodity Linux cluster. Experiments demonstrate that the algorithm can produce high quality results on both benchmark and real-world graphs. An example of finding more meaningful communities is illustrated consequently in comparison with a popular modularity maximization algorithm.

  6. A Programmable, Scalable-Throughput Interleaver

    Directory of Open Access Journals (Sweden)

    Rijshouwer EJC

    2010-01-01

    Full Text Available The interleaver stages of digital communication standards show a surprisingly large variation in throughput, state sizes, and permutation functions. Furthermore, data rates for 4G standards such as LTE-Advanced will exceed typical baseband clock frequencies of handheld devices. Multistream operation for Software Defined Radio and iterative decoding algorithms will call for ever higher interleave data rates. Our interleave machine is built around 8 single-port SRAM banks and can be programmed to generate up to 8 addresses every clock cycle. The scalable architecture combines SIMD and VLIW concepts with an efficient resolution of bank conflicts. A wide range of cellular, connectivity, and broadcast interleavers have been mapped on this machine, with throughputs up to more than 0.5 Gsymbol/second. Although it was designed for channel interleaving, the application domain of the interleaver extends also to Turbo interleaving. The presented configuration of the architecture is designed as a part of a programmable outer receiver on a prototype board. It offers (near universal programmability to enable the implementation of new interleavers. The interleaver measures 2.09 m in 65 nm CMOS (including memories and proves functional on silicon.

  7. SCTP as scalable video coding transport

    Science.gov (United States)

    Ortiz, Jordi; Graciá, Eduardo Martínez; Skarmeta, Antonio F.

    2013-12-01

    This study presents an evaluation of the Stream Transmission Control Protocol (SCTP) for the transport of the scalable video codec (SVC), proposed by MPEG as an extension to H.264/AVC. Both technologies fit together properly. On the one hand, SVC permits to split easily the bitstream into substreams carrying different video layers, each with different importance for the reconstruction of the complete video sequence at the receiver end. On the other hand, SCTP includes features, such as the multi-streaming and multi-homing capabilities, that permit to transport robustly and efficiently the SVC layers. Several transmission strategies supported on baseline SCTP and its concurrent multipath transfer (CMT) extension are compared with the classical solutions based on the Transmission Control Protocol (TCP) and the Realtime Transmission Protocol (RTP). Using ns-2 simulations, it is shown that CMT-SCTP outperforms TCP and RTP in error-prone networking environments. The comparison is established according to several performance measurements, including delay, throughput, packet loss, and peak signal-to-noise ratio of the received video.

  8. Scalability and interoperability within glideinWMS

    Energy Technology Data Exchange (ETDEWEB)

    Bradley, D.; /Wisconsin U., Madison; Sfiligoi, I.; /Fermilab; Padhi, S.; /UC, San Diego; Frey, J.; /Wisconsin U., Madison; Tannenbaum, T.; /Wisconsin U., Madison

    2010-01-01

    Physicists have access to thousands of CPUs in grid federations such as OSG and EGEE. With the start-up of the LHC, it is essential for individuals or groups of users to wrap together available resources from multiple sites across multiple grids under a higher user-controlled layer in order to provide a homogeneous pool of available resources. One such system is glideinWMS, which is based on the Condor batch system. A general discussion of glideinWMS can be found elsewhere. Here, we focus on recent advances in extending its reach: scalability and integration of heterogeneous compute elements. We demonstrate that the new developments exceed the design goal of over 10,000 simultaneous running jobs under a single Condor schedd, using strong security protocols across global networks, and sustaining a steady-state job completion rate of a few Hz. We also show interoperability across heterogeneous computing elements achieved using client-side methods. We discuss this technique and the challenges in direct access to NorduGrid and CREAM compute elements, in addition to Globus based systems.

  9. Scalable production of biliverdin IXα by Escherichia coli.

    Science.gov (United States)

    Chen, Dong; Brown, Jason D; Kawasaki, Yukie; Bommer, Jerry; Takemoto, Jon Y

    2012-11-23

    Biliverdin IXα is produced when heme undergoes reductive ring cleavage at the α-methene bridge catalyzed by heme oxygenase. It is subsequently reduced by biliverdin reductase to bilirubin IXα which is a potent endogenous antioxidant. Biliverdin IXα, through interaction with biliverdin reductase, also initiates signaling pathways leading to anti-inflammatory responses and suppression of cellular pro-inflammatory events. The use of biliverdin IXα as a cytoprotective therapeutic has been suggested, but its clinical development and use is currently limited by insufficient quantity, uncertain purity, and derivation from mammalian materials. To address these limitations, methods to produce, recover and purify biliverdin IXα from bacterial cultures of Escherichia coli were investigated and developed. Recombinant E. coli strains BL21(HO1) and BL21(mHO1) expressing cyanobacterial heme oxygenase gene ho1 and a sequence modified version (mho1) optimized for E. coli expression, respectively, were constructed and shown to produce biliverdin IXα in batch and fed-batch bioreactor cultures. Strain BL21(mHO1) produced roughly twice the amount of biliverdin IXα than did strain BL21(HO1). Lactose either alone or in combination with glycerol supported consistent biliverdin IXα production by strain BL21(mHO1) (up to an average of 23. 5mg L(-1) culture) in fed-batch mode and production by strain BL21 (HO1) in batch-mode was scalable to 100L bioreactor culture volumes. Synthesis of the modified ho1 gene protein product was determined, and identity of the enzyme reaction product as biliverdin IXα was confirmed by spectroscopic and chromatographic analyses and its ability to serve as a substrate for human biliverdin reductase A. Methods for the scalable production, recovery, and purification of biliverdin IXα by E. coli were developed based on expression of a cyanobacterial ho1 gene. The purity of the produced biliverdin IXα and its ability to serve as substrate for human

  10. Scalable production of biliverdin IXα by Escherichia coli

    Directory of Open Access Journals (Sweden)

    Chen Dong

    2012-11-01

    Full Text Available Abstract Background Biliverdin IXα is produced when heme undergoes reductive ring cleavage at the α-methene bridge catalyzed by heme oxygenase. It is subsequently reduced by biliverdin reductase to bilirubin IXα which is a potent endogenous antioxidant. Biliverdin IXα, through interaction with biliverdin reductase, also initiates signaling pathways leading to anti-inflammatory responses and suppression of cellular pro-inflammatory events. The use of biliverdin IXα as a cytoprotective therapeutic has been suggested, but its clinical development and use is currently limited by insufficient quantity, uncertain purity, and derivation from mammalian materials. To address these limitations, methods to produce, recover and purify biliverdin IXα from bacterial cultures of Escherichia coli were investigated and developed. Results Recombinant E. coli strains BL21(HO1 and BL21(mHO1 expressing cyanobacterial heme oxygenase gene ho1 and a sequence modified version (mho1 optimized for E. coli expression, respectively, were constructed and shown to produce biliverdin IXα in batch and fed-batch bioreactor cultures. Strain BL21(mHO1 produced roughly twice the amount of biliverdin IXα than did strain BL21(HO1. Lactose either alone or in combination with glycerol supported consistent biliverdin IXα production by strain BL21(mHO1 (up to an average of 23. 5mg L-1 culture in fed-batch mode and production by strain BL21 (HO1 in batch-mode was scalable to 100L bioreactor culture volumes. Synthesis of the modified ho1 gene protein product was determined, and identity of the enzyme reaction product as biliverdin IXα was confirmed by spectroscopic and chromatographic analyses and its ability to serve as a substrate for human biliverdin reductase A. Conclusions Methods for the scalable production, recovery, and purification of biliverdin IXα by E. coli were developed based on expression of a cyanobacterial ho1 gene. The purity of the produced biliverdin IXα and

  11. ARC Code TI: Block-GP: Scalable Gaussian Process Regression

    Data.gov (United States)

    National Aeronautics and Space Administration — Block GP is a Gaussian Process regression framework for multimodal data, that can be an order of magnitude more scalable than existing state-of-the-art nonlinear...

  12. Scalable pattern recognition algorithms applications in computational biology and bioinformatics

    CERN Document Server

    Maji, Pradipta

    2014-01-01

    Reviews the development of scalable pattern recognition algorithms for computational biology and bioinformatics Includes numerous examples and experimental results to support the theoretical concepts described Concludes each chapter with directions for future research and a comprehensive bibliography

  13. Scalability of telecom cloud architectures for live-TV distribution

    OpenAIRE

    Asensio Carmona, Adrian; Contreras, Luis Miguel; Ruiz Ramírez, Marc; López Álvarez, Victor; Velasco Esteban, Luis Domingo

    2015-01-01

    A hierarchical distributed telecom cloud architecture for live-TV distribution exploiting flexgrid networking and SBVTs is proposed. Its scalability is compared to that of a centralized architecture. Cost savings as high as 32 % are shown. Peer Reviewed

  14. Evaluating the Scalability of Enterprise JavaBeans Technology

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yan (Jenny); Gorton, Ian; Liu, Anna; Chen, Shiping; Paul A Strooper; Pornsiri Muenchaisri

    2002-12-04

    One of the major problems in building large-scale distributed systems is to anticipate the performance of the eventual solution before it has been built. This problem is especially germane to Internet-based e-business applications, where failure to provide high performance and scalability can lead to application and business failure. The fundamental software engineering problem is compounded by many factors, including individual application diversity, software architecture trade-offs, COTS component integration requirements, and differences in performance of various software and hardware infrastructures. In this paper, we describe the results of an empirical investigation into the scalability of a widely used distributed component technology, Enterprise JavaBeans (EJB). A benchmark application is developed and tested to measure the performance of a system as both the client load and component infrastructure are scaled up. A scalability metric from the literature is then applied to analyze the scalability of the EJB component infrastructure under two different architectural solutions.

  15. Scalable RFCMOS Model for 90 nm Technology

    Directory of Open Access Journals (Sweden)

    Ah Fatt Tong

    2011-01-01

    Full Text Available This paper presents the formation of the parasitic components that exist in the RF MOSFET structure during its high-frequency operation. The parasitic components are extracted from the transistor's S-parameter measurement, and its geometry dependence is studied with respect to its layout structure. Physical geometry equations are proposed to represent these parasitic components, and by implementing them into the RF model, a scalable RFCMOS model, that is, valid up to 49.85 GHz is demonstrated. A new verification technique is proposed to verify the quality of the developed scalable RFCMOS model. The proposed technique can shorten the verification time of the scalable RFCMOS model and ensure that the coded scalable model file is error-free and thus more reliable to use.

  16. Scalable-to-lossless transform domain distributed video coding

    DEFF Research Database (Denmark)

    Huang, Xin; Ukhanova, Ann; Veselov, Anton

    2010-01-01

    Distributed video coding (DVC) is a novel approach providing new features as low complexity encoding by mainly exploiting the source statistics at the decoder based on the availability of decoder side information. In this paper, scalable-tolossless DVC is presented based on extending a lossy...... TransformDomain Wyner-Ziv (TDWZ) distributed video codec with feedback.The lossless coding is obtained by using a reversible integer DCT.Experimental results show that the performance of the proposed scalable-to-lossless TDWZ video codec can outperform alternatives based on the JPEG 2000 standard. The TDWZ...... codec provides frame by frame encoding. Comparing the lossless coding efficiency, the proposed scalable-to-lossless TDWZ video codec can save up to 5%-13% bits compared to JPEG LS and H.264 Intra frame lossless coding and do so as a scalable-to-lossless coding....

  17. Improving the Performance Scalability of the Community Atmosphere Model

    Energy Technology Data Exchange (ETDEWEB)

    Mirin, Arthur [Lawrence Livermore National Laboratory (LLNL); Worley, Patrick H [ORNL

    2012-01-01

    The Community Atmosphere Model (CAM), which serves as the atmosphere component of the Community Climate System Model (CCSM), is the most computationally expensive CCSM component in typical configurations. On current and next-generation leadership class computing systems, the performance of CAM is tied to its parallel scalability. Improving performance scalability in CAM has been a challenge, due largely to algorithmic restrictions necessitated by the polar singularities in its latitude-longitude computational grid. Nevertheless, through a combination of exploiting additional parallelism, implementing improved communication protocols, and eliminating scalability bottlenecks, we have been able to more than double the maximum throughput rate of CAM on production platforms. We describe these improvements and present results on the Cray XT5 and IBM BG/P. The approaches taken are not specific to CAM and may inform similar scalability enhancement activities for other codes.

  18. Parallelism and Scalability in an Image Processing Application

    DEFF Research Database (Denmark)

    Rasmussen, Morten Sleth; Stuart, Matthias Bo; Karlsson, Sven

    2008-01-01

    parallel programs. This paper investigates parallelism and scalability of an embedded image processing application. The major challenges faced when parallelizing the application were to extract enough parallelism from the application and to reduce load imbalance. The application has limited immediately...

  19. Scalable Multiple-Description Image Coding Based on Embedded Quantization

    Directory of Open Access Journals (Sweden)

    Moerman Ingrid

    2007-01-01

    Full Text Available Scalable multiple-description (MD coding allows for fine-grain rate adaptation as well as robust coding of the input source. In this paper, we present a new approach for scalable MD coding of images, which couples the multiresolution nature of the wavelet transform with the robustness and scalability features provided by embedded multiple-description scalar quantization (EMDSQ. Two coding systems are proposed that rely on quadtree coding to compress the side descriptions produced by EMDSQ. The proposed systems are capable of dynamically adapting the bitrate to the available bandwidth while providing robustness to data losses. Experiments performed under different simulated network conditions demonstrate the effectiveness of the proposed scalable MD approach for image streaming over error-prone channels.

  20. Scalable Multiple-Description Image Coding Based on Embedded Quantization

    Directory of Open Access Journals (Sweden)

    Augustin I. Gavrilescu

    2007-02-01

    Full Text Available Scalable multiple-description (MD coding allows for fine-grain rate adaptation as well as robust coding of the input source. In this paper, we present a new approach for scalable MD coding of images, which couples the multiresolution nature of the wavelet transform with the robustness and scalability features provided by embedded multiple-description scalar quantization (EMDSQ. Two coding systems are proposed that rely on quadtree coding to compress the side descriptions produced by EMDSQ. The proposed systems are capable of dynamically adapting the bitrate to the available bandwidth while providing robustness to data losses. Experiments performed under different simulated network conditions demonstrate the effectiveness of the proposed scalable MD approach for image streaming over error-prone channels.

  1. TriG: Next Generation Scalable Spaceborne GNSS Receiver

    Science.gov (United States)

    Tien, Jeffrey Y.; Okihiro, Brian Bachman; Esterhuizen, Stephan X.; Franklin, Garth W.; Meehan, Thomas K.; Munson, Timothy N.; Robison, David E.; Turbiner, Dmitry; Young, Lawrence E.

    2012-01-01

    TriG is the next generation NASA scalable space GNSS Science Receiver. It will track all GNSS and additional signals (i.e. GPS, GLONASS, Galileo, Compass and Doris). Scalable 3U architecture and fully software and firmware recofigurable, enabling optimization to meet specific mission requirements. TriG GNSS EM is currently undergoing testing and is expected to complete full performance testing later this year.

  2. SDC: Scalable description coding for adaptive streaming media

    OpenAIRE

    Quinlan, Jason J.; Zahran, Ahmed H.; Sreenan, Cormac J.

    2012-01-01

    Video compression techniques enable adaptive media streaming over heterogeneous links to end-devices. Scalable Video Coding (SVC) and Multiple Description Coding (MDC) represent well-known techniques for video compression with distinct characteristics in terms of bandwidth efficiency and resiliency to packet loss. In this paper, we present Scalable Description Coding (SDC), a technique to compromise the tradeoff between bandwidth efficiency and error resiliency without sacrificing user-percei...

  3. Analysis of scalability of high-performance 3D image processing platform for virtual colonoscopy

    Science.gov (United States)

    Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

    2014-03-01

    One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. For this purpose, we previously developed a software platform for high-performance 3D medical image processing, called HPC 3D-MIP platform, which employs increasingly available and affordable commodity computing systems such as the multicore, cluster, and cloud computing systems. To achieve scalable high-performance computing, the platform employed size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D-MIP algorithms, supported task scheduling for efficient load distribution and balancing, and consisted of a layered parallel software libraries that allow image processing applications to share the common functionalities. We evaluated the performance of the HPC 3D-MIP platform by applying it to computationally intensive processes in virtual colonoscopy. Experimental results showed a 12-fold performance improvement on a workstation with 12-core CPUs over the original sequential implementation of the processes, indicating the efficiency of the platform. Analysis of performance scalability based on the Amdahl's law for symmetric multicore chips showed the potential of a high performance scalability of the HPC 3DMIP platform when a larger number of cores is available.

  4. Analysis of scalability of high-performance 3D image processing platform for virtual colonoscopy.

    Science.gov (United States)

    Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

    2014-03-19

    One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. For this purpose, we previously developed a software platform for high-performance 3D medical image processing, called HPC 3D-MIP platform, which employs increasingly available and affordable commodity computing systems such as the multicore, cluster, and cloud computing systems. To achieve scalable high-performance computing, the platform employed size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D-MIP algorithms, supported task scheduling for efficient load distribution and balancing, and consisted of a layered parallel software libraries that allow image processing applications to share the common functionalities. We evaluated the performance of the HPC 3D-MIP platform by applying it to computationally intensive processes in virtual colonoscopy. Experimental results showed a 12-fold performance improvement on a workstation with 12-core CPUs over the original sequential implementation of the processes, indicating the efficiency of the platform. Analysis of performance scalability based on the Amdahl's law for symmetric multicore chips showed the potential of a high performance scalability of the HPC 3D-MIP platform when a larger number of cores is available.

  5. Scalable persistent identifier systems for dynamic datasets

    Science.gov (United States)

    Golodoniuc, P.; Cox, S. J. D.; Klump, J. F.

    2016-12-01

    Reliable and persistent identification of objects, whether tangible or not, is essential in information management. Many Internet-based systems have been developed to identify digital data objects, e.g., PURL, LSID, Handle, ARK. These were largely designed for identification of static digital objects. The amount of data made available online has grown exponentially over the last two decades and fine-grained identification of dynamically generated data objects within large datasets using conventional systems (e.g., PURL) has become impractical. We have compared capabilities of various technological solutions to enable resolvability of data objects in dynamic datasets, and developed a dataset-centric approach to resolution of identifiers. This is particularly important in Semantic Linked Data environments where dynamic frequently changing data is delivered live via web services, so registration of individual data objects to obtain identifiers is impractical. We use identifier patterns and pattern hierarchies for identification of data objects, which allows relationships between identifiers to be expressed, and also provides means for resolving a single identifier into multiple forms (i.e. views or representations of an object). The latter can be implemented through (a) HTTP content negotiation, or (b) use of URI querystring parameters. The pattern and hierarchy approach has been implemented in the Linked Data API supporting the United Nations Spatial Data Infrastructure (UNSDI) initiative and later in the implementation of geoscientific data delivery for the Capricorn Distal Footprints project using International Geo Sample Numbers (IGSN). This enables flexible resolution of multi-view persistent identifiers and provides a scalable solution for large heterogeneous datasets.

  6. Myria: Scalable Analytics as a Service

    Science.gov (United States)

    Howe, B.; Halperin, D.; Whitaker, A.

    2014-12-01

    At the UW eScience Institute, we're working to empower non-experts, especially in the sciences, to write and use data-parallel algorithms. To this end, we are building Myria, a web-based platform for scalable analytics and data-parallel programming. Myria's internal model of computation is the relational algebra extended with iteration, such that every program is inherently data-parallel, just as every query in a database is inherently data-parallel. But unlike databases, iteration is a first class concept, allowing us to express machine learning tasks, graph traversal tasks, and more. Programs can be expressed in a number of languages and can be executed on a number of execution environments, but we emphasize a particular language called MyriaL that supports both imperative and declarative styles and a particular execution engine called MyriaX that uses an in-memory column-oriented representation and asynchronous iteration. We deliver Myria over the web as a service, providing an editor, performance analysis tools, and catalog browsing features in a single environment. We find that this web-based "delivery vector" is critical in reaching non-experts: they are insulated from irrelevant effort technical work associated with installation, configuration, and resource management. The MyriaX backend, one of several execution runtimes we support, is a main-memory, column-oriented, RDBMS-on-the-worker system that supports cyclic data flows as a first-class citizen and has been shown to outperform competitive systems on 100-machine cluster sizes. I will describe the Myria system, give a demo, and present some new results in large-scale oceanographic microbiology.

  7. Physical principles for scalable neural recording.

    Science.gov (United States)

    Marblestone, Adam H; Zamft, Bradley M; Maguire, Yael G; Shapiro, Mikhail G; Cybulski, Thaddeus R; Glaser, Joshua I; Amodei, Dario; Stranges, P Benjamin; Kalhor, Reza; Dalrymple, David A; Seo, Dongjin; Alon, Elad; Maharbiz, Michel M; Carmena, Jose M; Rabaey, Jan M; Boyden, Edward S; Church, George M; Kording, Konrad P

    2013-01-01

    Simultaneously measuring the activities of all neurons in a mammalian brain at millisecond resolution is a challenge beyond the limits of existing techniques in neuroscience. Entirely new approaches may be required, motivating an analysis of the fundamental physical constraints on the problem. We outline the physical principles governing brain activity mapping using optical, electrical, magnetic resonance, and molecular modalities of neural recording. Focusing on the mouse brain, we analyze the scalability of each method, concentrating on the limitations imposed by spatiotemporal resolution, energy dissipation, and volume displacement. Based on this analysis, all existing approaches require orders of magnitude improvement in key parameters. Electrical recording is limited by the low multiplexing capacity of electrodes and their lack of intrinsic spatial resolution, optical methods are constrained by the scattering of visible light in brain tissue, magnetic resonance is hindered by the diffusion and relaxation timescales of water protons, and the implementation of molecular recording is complicated by the stochastic kinetics of enzymes. Understanding the physical limits of brain activity mapping may provide insight into opportunities for novel solutions. For example, unconventional methods for delivering electrodes may enable unprecedented numbers of recording sites, embedded optical devices could allow optical detectors to be placed within a few scattering lengths of the measured neurons, and new classes of molecularly engineered sensors might obviate cumbersome hardware architectures. We also study the physics of powering and communicating with microscale devices embedded in brain tissue and find that, while radio-frequency electromagnetic data transmission suffers from a severe power-bandwidth tradeoff, communication via infrared light or ultrasound may allow high data rates due to the possibility of spatial multiplexing. The use of embedded local recording and

  8. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    interaction between a human operator and an artificial actor or agent. We can apply insights from puppetry to develop culturally-aware robots. Here we describe the development of a robotic marionette theatre wherein robotic controllers assume the role of human puppeteers. The system has been built, tested...... including puppetry and dance. However, the aesthetics of these traditions vary across cultures and carry different associative and interpretive meanings. Puppetry offers a useful frame for understanding the relationship between abstract and imitative gestures and behavior, and instantiates the complex...

  9. Global patterns of amphibian phylogenetic diversity

    DEFF Research Database (Denmark)

    Fritz, Susanne; Rahbek, Carsten

    2012-01-01

    phylogeny (2792 species). We combined each tree with global species distributions to map four indices of phylogenetic diversity. To investigate congruence between global spatial patterns of amphibian species richness and phylogenetic diversity, we selected Faith’s phylogenetic diversity (PD) index......Aim  Phylogenetic diversity can provide insight into how evolutionary processes may have shaped contemporary patterns of species richness. Here, we aim to test for the influence of phylogenetic history on global patterns of amphibian species richness, and to identify areas where macroevolutionary...... and the total taxonomic distinctness (TTD) index, because we found that the variance of the other two indices we examined (average taxonomic distinctness and mean root distance) strongly depended on species richness. We then identified regions with unusually high or low phylogenetic diversity given...

  10. Phylogenetic structure in tropical hummingbird communities

    DEFF Research Database (Denmark)

    Graham, Catherine H; Parra, Juan L; Rahbek, Carsten

    2009-01-01

    composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern...... that is consistent with the idea that competition influences the local composition of hummingbirds. At higher elevations communities are phylogenetically clustered (coexistence of close relatives), consistent with the expectation of environmental filtering, which may result from the challenge of sustaining...

  11. Taxonomic colouring of phylogenetic trees of protein sequences

    Directory of Open Access Journals (Sweden)

    Andrade-Navarro Miguel A

    2006-02-01

    Full Text Available Abstract Background Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common. Results We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree. Conclusion PhyloView can be used at http://www.ogic.ca/projects/phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address.

  12. Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks.

    Science.gov (United States)

    Pérez-Valera, Eduardo; Goberna, Marta; Faust, Karoline; Raes, Jeroen; García, Carlos; Verdú, Miguel

    2017-01-01

    Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co-occurrence networks to detect co-presence (bacteria that co-occur) or exclusion (bacteria that do not co-occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co-presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co-presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co-presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  13. Phylogenetic detection of conserved gene clusters in microbial genomes

    Directory of Open Access Journals (Sweden)

    Anton Brian P

    2005-10-01

    Full Text Available Abstract Background Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional selection. Thus, identification of conserved gene clusters that are under functional selection provides an effective channel for gene annotation, microarray screening, and pathway reconstruction. The problem of devising a robust method to identify these conserved gene clusters and to evaluate the significance of the conservation in multiple genomes has a number of implications for comparative, evolutionary and functional genomics as well as synthetic biology. Results In this paper we describe a new method for detecting conserved gene clusters that incorporates the information captured by a genome phylogenetic tree. We show that our method can overcome the common problem of overestimation of significance due to the bias in the genome database and thereby achieve better accuracy when detecting functionally connected gene clusters. Our results can be accessed at database GeneChords http://genomics10.bu.edu/GeneChords. Conclusion The methodology described in this paper gives a scalable framework for discovering conserved gene clusters in microbial genomes. It serves as a platform for many other functional genomic analyses in microorganisms, such as operon prediction, regulatory site prediction, functional annotation of genes, evolutionary origin and development of gene clusters.

  14. Phylogenetic detection of conserved gene clusters in microbial genomes.

    Science.gov (United States)

    Zheng, Yu; Anton, Brian P; Roberts, Richard J; Kasif, Simon

    2005-10-03

    Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional selection. Thus, identification of conserved gene clusters that are under functional selection provides an effective channel for gene annotation, microarray screening, and pathway reconstruction. The problem of devising a robust method to identify these conserved gene clusters and to evaluate the significance of the conservation in multiple genomes has a number of implications for comparative, evolutionary and functional genomics as well as synthetic biology. In this paper we describe a new method for detecting conserved gene clusters that incorporates the information captured by a genome phylogenetic tree. We show that our method can overcome the common problem of overestimation of significance due to the bias in the genome database and thereby achieve better accuracy when detecting functionally connected gene clusters. Our results can be accessed at database GeneChords http://genomics10.bu.edu/GeneChords. The methodology described in this paper gives a scalable framework for discovering conserved gene clusters in microbial genomes. It serves as a platform for many other functional genomic analyses in microorganisms, such as operon prediction, regulatory site prediction, functional annotation of genes, evolutionary origin and development of gene clusters.

  15. Scalable nanohelices for predictive studies and enhanced 3D visualization.

    Science.gov (United States)

    Meagher, Kwyn A; Doblack, Benjamin N; Ramirez, Mercedes; Davila, Lilian P

    2014-11-12

    Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing applications. For predictive simulations, it has become increasingly important to be able to model the structure of nanohelices accurately. To study the effect of local structure on the properties of these complex geometries one must develop realistic models. To date, software packages are rather limited in creating atomistic helical models. This work focuses on producing atomistic models of silica glass (SiO₂) nanoribbons and nanosprings for molecular dynamics (MD) simulations. Using an MD model of "bulk" silica glass, two computational procedures to precisely create the shape of nanoribbons and nanosprings are presented. The first method employs the AWK programming language and open-source software to effectively carve various shapes of silica nanoribbons from the initial bulk model, using desired dimensions and parametric equations to define a helix. With this method, accurate atomistic silica nanoribbons can be generated for a range of pitch values and dimensions. The second method involves a more robust code which allows flexibility in modeling nanohelical structures. This approach utilizes a C++ code particularly written to implement pre-screening methods as well as the mathematical equations for a helix, resulting in greater precision and efficiency when creating nanospring models. Using these codes, well-defined and scalable nanoribbons and nanosprings suited for atomistic simulations can be effectively created. An added value in both open-source codes is that they can be adapted to reproduce different helical structures, independent of material. In addition, a MATLAB graphical user interface (GUI) is used to enhance learning through visualization and interaction for a general user with the atomistic helical structures. One application of these methods is the recent study of nanohelices via MD simulations for

  16. Phylogenetic diversity of cassava green mite, Mononychellus ...

    African Journals Online (AJOL)

    Similarly, the Uganda and Tanzania samples had 99% match to emb/X79902.1 on the 18Sr RNA region. The CGM sequence from coastal Kenya had the highest phylogenetic divergence from the Congo-Benin sequences. A small biogeographic phylogenetic divergence (0-1%) was evident from the analyses among the six ...

  17. Nucleotide diversity and phylogenetic relationships among ...

    Indian Academy of Sciences (India)

    RESEARCH ARTICLE Volume 96 Issue 1 March 2017 pp 135-145 ... Present study revealed that psbA–trnH region are useful in addressing questions of phylogenetic relationships among the Gladiolus cultivars, as these intergenic spacers are more variable and have more phylogenetically informative sites than the ...

  18. Molecular phylogenetics and character evolution of Cannabaceae

    NARCIS (Netherlands)

    Yang, M.Q.; Velzen, van R.; Bakker, F.T.; Sattarian, A.; Li, D.Z.; Yi, T.S.

    2013-01-01

    Cannabaceae includes ten genera that are widely distributed in tropical to temperate regions of the world. Because of limited taxon and character sampling in previous studies, intergeneric phylogenetic relationships within this family have been poorly resolved. We conducted a molecular phylogenetic

  19. Conflicting phylogenetic position of Schizosaccharomyces pombe.

    NARCIS (Netherlands)

    Kuramae, E.E.; Robert, V.; Snel, B.; Boekhout, T.

    2006-01-01

    The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister

  20. Phylogenetic diversity of Amazonian tree communities

    NARCIS (Netherlands)

    Honorio Coronado, E.N.; Dexter, K.G.; Pennington, R.T.; Chave, Jérôme; Lewis, S.L.; Alexiades, M.N.; Alvarez, Esteban; Alves de Oliveira, Atila; Amaral, J.L.; Araujo-Murakami, Alejandro; Arets, E.J.M.M.

    2015-01-01

    Aim: To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location: Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods: We evaluated PD as the total phylogenetic branch

  1. Conflicting phylogenetic position of Schizosaccharomyces pombe

    NARCIS (Netherlands)

    Kuramae, Eiko E.; Robert, Vincent; Snel, Berend; Boekhout, Teun

    2006-01-01

    The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister

  2. Characterization of Escherichia coli Phylogenetic Groups ...

    African Journals Online (AJOL)

    Background: Escherichia coli strains mainly fall into four phylogenetic groups (A, B1, B2, and D) and that virulent extra‑intestinal strains mainly belong to groups B2 and D. Aim: The aim was to determine the association between phylogenetic groups of E. coli causing extraintestinal infections (ExPEC) regarding the site of ...

  3. Global patterns of amphibian phylogenetic diversity

    DEFF Research Database (Denmark)

    Fritz, Susanne; Rahbek, Carsten

    2012-01-01

    Aim  Phylogenetic diversity can provide insight into how evolutionary processes may have shaped contemporary patterns of species richness. Here, we aim to test for the influence of phylogenetic history on global patterns of amphibian species richness, and to identify areas where macroevolutionary...... processes such as diversification and dispersal have left strong signatures on contemporary species richness. Location  Global; equal-area grid cells of approximately 10,000 km2. Methods  We generated an amphibian global supertree (6111 species) and repeated analyses with the largest available molecular...... phylogeny (2792 species). We combined each tree with global species distributions to map four indices of phylogenetic diversity. To investigate congruence between global spatial patterns of amphibian species richness and phylogenetic diversity, we selected Faith’s phylogenetic diversity (PD) index...

  4. The phylogenetics of succession can guide restoration

    DEFF Research Database (Denmark)

    Shooner, Stephanie; Chisholm, Chelsea Lee; Davies, T. Jonathan

    2015-01-01

    on a chronosequence of three abandoned subarctic mine spoil heaps (waste piles) dating from the early 1970s, mid-1970s and early 1980s. The vegetation at each mine site was compared to the surrounding vegetation, and community structure on mines was explored assuming species pools at nested spatial scales. We found...... rehabilitation. However, to date, these two applications have been largely separate. Here, we suggest that information on phylogenetic community structure might help to inform community restoration strategies following major disturbance. Our study examined phylogenetic patterns of succession based...... that the adjacent vegetation was more phylogenetically clustered than the vegetation on the mines, with mines demonstrating weaker phylogenetic community structure. Using simulation models, we showed that phylogenetic dissimilarity between mine sites did not depart from null expectations. However, we found evidence...

  5. Scalability of Knowledge Transfer in Complex Systems of Emergent "living" Communities

    Directory of Open Access Journals (Sweden)

    Susu Nousala

    2013-08-01

    Full Text Available Communities are emergent, holistic living systems. Understanding the impact of social complex systems through spatial interactions via the lens of scalability requires the development of new methodological behavioural approaches. The evolution of social complex systems of cities and their regions can be investigated through the evolution of spatial structures. The clustering of entities within cities, regions and beyond presents behavioural elements for which methodological approaches need to be considered. The emergent aspect of complex entities by their very nature requires an understanding that can embrace unpredictability through emergence. Qualitative methodological approaches can be holistic with the ability to embrace bottom up and top down methods for analysis. Social complex systems develop structures by connecting "like minded" behaviour through scalability. How "mobile" these interactions are, is a concept that can be understood via "inter-organizational" and "interstructural" comparative approaches. How do we indeed convey this adequately or appropriately? Just as a geographical area may contain characteristics that can help to support the formation of an emergent industry cluster, similar behaviours occur through emergent characteristics of complex systems that underpin the sustainability of an organization. The idea that complex systems have tacit structures, capable of displaying emergent behaviour, is not a common concept. These tacit structures can in turn, impact the structural sustainability of physical entities. More often than not, there is a focus on how these concepts of complex systems work, but the "why" questions depends upon scalability. Until recently, social complex adaptive systems were largely over looked due to the tacit nature of these network structures.

  6. Quality Scalability Compression on Single-Loop Solution in HEVC

    Directory of Open Access Journals (Sweden)

    Mengmeng Zhang

    2014-01-01

    Full Text Available This paper proposes a quality scalable extension design for the upcoming high efficiency video coding (HEVC standard. In the proposed design, the single-loop decoder solution is extended into the proposed scalable scenario. A novel interlayer intra/interprediction is added to reduce the amount of bits representation by exploiting the correlation between coding layers. The experimental results indicate that the average Bjøntegaard delta rate decrease of 20.50% can be gained compared with the simulcast encoding. The proposed technique achieved 47.98% Bjøntegaard delta rate reduction compared with the scalable video coding extension of the H.264/AVC. Consequently, significant rate savings confirm that the proposed method achieves better performance.

  7. Technical Report: Scalable Parallel Algorithms for High Dimensional Numerical Integration

    Energy Technology Data Exchange (ETDEWEB)

    Masalma, Yahya [Universidad del Turabo; Jiao, Yu [ORNL

    2010-10-01

    We implemented a scalable parallel quasi-Monte Carlo numerical high-dimensional integration for tera-scale data points. The implemented algorithm uses the Sobol s quasi-sequences to generate random samples. Sobol s sequence was used to avoid clustering effects in the generated random samples and to produce low-discrepancy random samples which cover the entire integration domain. The performance of the algorithm was tested. Obtained results prove the scalability and accuracy of the implemented algorithms. The implemented algorithm could be used in different applications where a huge data volume is generated and numerical integration is required. We suggest using the hyprid MPI and OpenMP programming model to improve the performance of the algorithms. If the mixed model is used, attention should be paid to the scalability and accuracy.

  8. Current parallel I/O limitations to scalable data analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Mascarenhas, Ajith Arthur; Pebay, Philippe Pierre

    2011-07-01

    This report describes the limitations to parallel scalability which we have encountered when applying our otherwise optimally scalable parallel statistical analysis tool kit to large data sets distributed across the parallel file system of the current premier DOE computational facility. This report describes our study to evaluate the effect of parallel I/O on the overall scalability of a parallel data analysis pipeline using our scalable parallel statistics tool kit [PTBM11]. In this goal, we tested it using the Jaguar-pf DOE/ORNL peta-scale platform on a large combustion simulation data under a variety of process counts and domain decompositions scenarios. In this report we have recalled the foundations of the parallel statistical analysis tool kit which we have designed and implemented, with the specific double intent of reproducing typical data analysis workflows, and achieving optimal design for scalable parallel implementations. We have briefly reviewed those earlier results and publications which allow us to conclude that we have achieved both goals. However, in this report we have further established that, when used in conjuction with a state-of-the-art parallel I/O system, as can be found on the premier DOE peta-scale platform, the scaling properties of the overall analysis pipeline comprising parallel data access routines degrade rapidly. This finding is problematic and must be addressed if peta-scale data analysis is to be made scalable, or even possible. In order to attempt to address these parallel I/O limitations, we will investigate the use the Adaptable IO System (ADIOS) [LZL+10] to improve I/O performance, while maintaining flexibility for a variety of IO options, such MPI IO, POSIX IO. This system is developed at ORNL and other collaborating institutions, and is being tested extensively on Jaguar-pf. Simulation code being developed on these systems will also use ADIOS to output the data thereby making it easier for other systems, such as ours, to

  9. Simple, Scalable, Script-Based Science Processor (S4P)

    Science.gov (United States)

    Lynnes, Christopher; Vollmer, Bruce; Berrick, Stephen; Mack, Robert; Pham, Long; Zhou, Bryan; Wharton, Stephen W. (Technical Monitor)

    2001-01-01

    The development and deployment of data processing systems to process Earth Observing System (EOS) data has proven to be costly and prone to technical and schedule risk. Integration of science algorithms into a robust operational system has been difficult. The core processing system, based on commercial tools, has demonstrated limitations at the rates needed to produce the several terabytes per day for EOS, primarily due to job management overhead. This has motivated an evolution in the EOS Data Information System toward a more distributed one incorporating Science Investigator-led Processing Systems (SIPS). As part of this evolution, the Goddard Earth Sciences Distributed Active Archive Center (GES DAAC) has developed a simplified processing system to accommodate the increased load expected with the advent of reprocessing and launch of a second satellite. This system, the Simple, Scalable, Script-based Science Processor (S42) may also serve as a resource for future SIPS. The current EOSDIS Core System was designed to be general, resulting in a large, complex mix of commercial and custom software. In contrast, many simpler systems, such as the EROS Data Center AVHRR IKM system, rely on a simple directory structure to drive processing, with directories representing different stages of production. The system passes input data to a directory, and the output data is placed in a "downstream" directory. The GES DAAC's Simple Scalable Script-based Science Processing System is based on the latter concept, but with modifications to allow varied science algorithms and improve portability. It uses a factory assembly-line paradigm: when work orders arrive at a station, an executable is run, and output work orders are sent to downstream stations. The stations are implemented as UNIX directories, while work orders are simple ASCII files. The core S4P infrastructure consists of a Perl program called stationmaster, which detects newly arrived work orders and forks a job to run the

  10. Natural product synthesis in the age of scalability.

    Science.gov (United States)

    Kuttruff, Christian A; Eastgate, Martin D; Baran, Phil S

    2014-04-01

    The ability to procure useful quantities of a molecule by simple, scalable routes is emerging as an important goal in natural product synthesis. Approaches to molecules that yield substantial material enable collaborative investigations (such as SAR studies or eventual commercial production) and inherently spur innovation in chemistry. As such, when evaluating a natural product synthesis, scalability is becoming an increasingly important factor. In this Highlight, we discuss recent examples of natural product synthesis from our laboratory and others, where the preparation of gram-scale quantities of a target compound or a key intermediate allowed for a deeper understanding of biological activities or enabled further investigational collaborations.

  11. Providing scalable system software for high-end simulations

    Energy Technology Data Exchange (ETDEWEB)

    Greenberg, D. [Sandia National Labs., Albuquerque, NM (United States)

    1997-12-31

    Detailed, full-system, complex physics simulations have been shown to be feasible on systems containing thousands of processors. In order to manage these computer systems it has been necessary to create scalable system services. In this talk Sandia`s research on scalable systems will be described. The key concepts of low overhead data movement through portals and of flexible services through multi-partition architectures will be illustrated in detail. The talk will conclude with a discussion of how these techniques can be applied outside of the standard monolithic MPP system.

  12. Scalable and Hybrid Radio Resource Management for Future Wireless Networks

    DEFF Research Database (Denmark)

    Mino, E.; Luo, Jijun; Tragos, E.

    2007-01-01

    The concept of ubiquitous and scalable system is applied in the IST WINNER II [1] project to deliver optimum performance for different deployment scenarios, from local area to wide area wireless networks. The integration in a unique radio system of a cellular and local area type networks supposes...... describes a proposal for scalable and hybrid radio resource management to efficiently integrate the different WINNER system modes. Index...... a great advantage for the final user and for the operator, compared with the current situation, with disconnected systems, usually with different subscriptions, radio interfaces and terminals. To be a ubiquitous wireless system, the IST project WINNER II has defined three system modes. This contribution...

  13. Scalability limitations of VIA-based technologies in supporting MPI

    Energy Technology Data Exchange (ETDEWEB)

    BRIGHTWELL,RONALD B.; MACCABE,ARTHUR BERNARD

    2000-04-17

    This paper analyzes the scalability limitations of networking technologies based on the Virtual Interface Architecture (VIA) in supporting the runtime environment needed for an implementation of the Message Passing Interface. The authors present an overview of the important characteristics of VIA and an overview of the runtime system being developed as part of the Computational Plant (Cplant) project at Sandia National Laboratories. They discuss the characteristics of VIA that prevent implementations based on this system to meet the scalability and performance requirements of Cplant.

  14. A Scalable Smart Meter Data Generator Using Spark

    DEFF Research Database (Denmark)

    Iftikhar, Nadeem; Liu, Xiufeng; Danalachi, Sergiu

    2017-01-01

    Today, smart meters are being used worldwide. As a matter of fact smart meters produce large volumes of data. Thus, it is important for smart meter data management and analytics systems to process petabytes of data. Benchmarking and testing of these systems require scalable data, however, it can...... be challenging to get large data sets due to privacy and/or data protection regulations. This paper presents a scalable smart meter data generator using Spark that can generate realistic data sets. The proposed data generator is based on a supervised machine learning method that can generate data of any size...

  15. Scalable and portable visualization of large atomistic datasets

    Science.gov (United States)

    Sharma, Ashish; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2004-10-01

    A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms. Program summaryTitle of program: Atomsviewer Catalogue identifier: ADUM Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUM Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics card Operating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5 Programming languages used: C++, C and OpenGL Memory required to execute with typical data: 1 gigabyte of RAM High speed storage required: 60 gigabytes No. of lines in the distributed program including test data, etc.: 550 241 No. of bytes in the distributed program including test data, etc.: 6 258 245 Number of bits in a word: Arbitrary Number of processors used: 1 Has the code been vectorized or parallelized: No Distribution format: tar gzip file Nature of physical problem: Scientific visualization of atomic systems Method of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data

  16. phylo-node: A molecular phylogenetic toolkit using Node.js.

    Directory of Open Access Journals (Sweden)

    Damien M O'Halloran

    Full Text Available Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis.To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines.phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

  17. phylo-node: A molecular phylogenetic toolkit using Node.js.

    Science.gov (United States)

    O'Halloran, Damien M

    2017-01-01

    Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

  18. Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge

    Directory of Open Access Journals (Sweden)

    Mayordomo Elvira

    2011-05-01

    Full Text Available Abstract Background Mitochondrial DNA is an ideal source of information to conduct evolutionary and phylogenetic studies due to its extraordinary properties and abundance. Many insights can be gained from these, including but not limited to screening genetic variation to identify potentially deleterious mutations. However, such advances require efficient solutions to very difficult computational problems, a need that is hampered by the very plenty of data that confers strength to the analysis. Results We develop a systematic, automated methodology to overcome these difficulties, building from readily available, public sequence databases to high-quality alignments and phylogenetic trees. Within each stage in an autonomous workflow, outputs are carefully evaluated and outlier detection rules defined to integrate expert knowledge and automated curation, hence avoiding the manual bottleneck found in past approaches to the problem. Using these techniques, we have performed exhaustive updates to the human mitochondrial phylogeny, illustrating the power and computational scalability of our approach, and we have conducted some initial analyses on the resulting phylogenies. Conclusions The problem at hand demands careful definition of inputs and adequate algorithmic treatment for its solutions to be realistic and useful. It is possible to define formal rules to address the former requirement by refining inputs directly and through their combination as outputs, and the latter are also of help to ascertain the performance of chosen algorithms. Rules can exploit known or inferred properties of datasets to simplify inputs through partitioning, therefore cutting computational costs and affording work on rapidly growing, otherwise intractable datasets. Although expert guidance may be necessary to assist the learning process, low-risk results can be fully automated and have proved themselves convenient and valuable.

  19. Efficient Computation of Popular Phylogenetic Tree Measures

    DEFF Research Database (Denmark)

    Tsirogiannis, Constantinos; Sandel, Brody Steven; Cheliotis, Dimitris

    2012-01-01

    Given a phylogenetic tree $\\mathcal{T}$ of n nodes, and a sample R of its tips (leaf nodes) a very common problem in ecological and evolutionary research is to evaluate a distance measure for the elements in R. Two of the most common measures of this kind are the Mean Pairwise Distance...... software package for processing phylogenetic trees....... ($\\ensuremath{\\mathrm{MPD}} $) and the Phylogenetic Diversity ($\\ensuremath{\\mathrm{PD}} $). In many applications, it is often necessary to compute the expectation and standard deviation of one of these measures over all subsets of tips of $\\mathcal{T}$ that have a certain size. Unfortunately, existing methods...

  20. Scalable Track Initiation for Optical Space Surveillance

    Science.gov (United States)

    Schumacher, P.; Wilkins, M. P.

    2012-09-01

    least cubic and commonly quartic or higher. Therefore, practical implementations require attention to the scalability of the algorithms, when one is dealing with the very large number of observations from large surveillance telescopes. We address two broad categories of algorithms. The first category includes and extends the classical methods of Laplace and Gauss, as well as the more modern method of Gooding, in which one solves explicitly for the apparent range to the target in terms of the given data. In particular, recent ideas offered by Mortari and Karimi allow us to construct a family of range-solution methods that can be scaled to many processors efficiently. We find that the orbit solutions (data association hypotheses) can be ranked by means of a concept we call persistence, in which a simple statistical measure of likelihood is based on the frequency of occurrence of combinations of observations in consistent orbit solutions. Of course, range-solution methods can be expected to perform poorly if the orbit solutions of most interest are not well conditioned. The second category of algorithms addresses this difficulty. Instead of solving for range, these methods attach a set of range hypotheses to each measured line of sight. Then all pair-wise combinations of observations are considered and the family of Lambert problems is solved for each pair. These algorithms also have polynomial complexity, though now the complexity is quadratic in the number of observations and also quadratic in the number of range hypotheses. We offer a novel type of admissible-region analysis, constructing partitions of the orbital element space and deriving rigorous upper and lower bounds on the possible values of the range for each partition. This analysis allows us to parallelize with respect to the element partitions and to reduce the number of range hypotheses that have to be considered in each processor simply by making the partitions smaller. Naturally, there are many ways to

  1. Contrasting biodiversity-ecosystem functioning relationships in phylogenetic and functional diversity.

    Science.gov (United States)

    Steudel, Bastian; Hallmann, Christine; Lorenz, Maike; Abrahamczyk, Stefan; Prinz, Kathleen; Herrfurth, Cornelia; Feussner, Ivo; Martini, Johannes W R; Kessler, Michael

    2016-10-01

    It is well known that ecosystem functioning is positively influenced by biodiversity. Most biodiversity-ecosystem functioning experiments have measured biodiversity based on species richness or phylogenetic relationships. However, theoretical and empirical evidence suggests that ecosystem functioning should be more closely related to functional diversity than to species richness. We applied different metrics of biodiversity in an artificial biodiversity-ecosystem functioning experiment using 64 species of green microalgae in combinations of two to 16 species. We found that phylogenetic and functional diversity were positively correlated with biomass overyield, driven by their strong correlation with species richness. At low species richness, no significant correlation between overyield and functional and phylogenetic diversity was found. However, at high species richness (16 species), we found a positive relationship of overyield with functional diversity and a negative relationship with phylogenetic diversity. We show that negative phylogenetic diversity-ecosystem functioning relationships can result from interspecific growth inhibition. The opposing performances of facilitation (functional diversity) and inhibition (phylogenetic diversity) we observed at the 16 species level suggest that phylogenetic diversity is not always a good proxy for functional diversity and that results from experiments with low species numbers may underestimate negative species interactions. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  2. Quicksilver: Middleware for Scalable Self-Regenerative Systems

    Science.gov (United States)

    2006-04-01

    standard best practice in the area, and hence helped us identify problems that can be justified in terms of real user needs. Our own group may write a...semantics, generally lack efficient, scalable implementations. Systems aproaches usually lack a precise formal specification, limiting the

  3. Scalable learning of probabilistic latent models for collaborative filtering

    DEFF Research Database (Denmark)

    Langseth, Helge; Nielsen, Thomas Dyhre

    2015-01-01

    Collaborative filtering has emerged as a popular way of making user recommendations, but with the increasing sizes of the underlying databases scalability is becoming a crucial issue. In this paper we focus on a recently proposed probabilistic collaborative filtering model that explicitly...

  4. PSOM2—partitioning-based scalable ontology matching using ...

    Indian Academy of Sciences (India)

    B Sathiya

    2017-11-16

    Nov 16, 2017 ... Abstract. The growth and use of semantic web has led to a drastic increase in the size, heterogeneity and number of ontologies that are available on the web. Correspondingly, scalable ontology matching algorithms that will eliminate the heterogeneity among large ontologies have become a necessity.

  5. Cognition-inspired Descriptors for Scalable Cover Song Retrieval

    NARCIS (Netherlands)

    van Balen, J.M.H.; Bountouridis, D.; Wiering, F.; Veltkamp, R.C.

    2014-01-01

    Inspired by representations used in music cognition studies and computational musicology, we propose three simple and interpretable descriptors for use in mid- to high-level computational analysis of musical audio and applications in content-based retrieval. We also argue that the task of scalable

  6. Scalable Directed Self-Assembly Using Ultrasound Waves

    Science.gov (United States)

    2015-09-04

    at Aberdeen Proving Grounds (APG), to discuss a possible collaboration. The idea is to integrate the ultrasound directed self- assembly technique ...difference between the ultrasound technology studied in this project, and other directed self-assembly techniques is its scalability and...deliverable: A scientific tool to predict particle organization, pattern, and orientation, based on the operating and design parameters of the ultrasound

  7. Scalable Robust Principal Component Analysis Using Grassmann Averages.

    Science.gov (United States)

    Hauberg, Sren; Feragen, Aasa; Enficiaud, Raffi; Black, Michael J

    2016-11-01

    In large datasets, manual data verification is impossible, and we must expect the number of outliers to increase with data size. While principal component analysis (PCA) can reduce data size, and scalable solutions exist, it is well-known that outliers can arbitrarily corrupt the results. Unfortunately, state-of-the-art approaches for robust PCA are not scalable. We note that in a zero-mean dataset, each observation spans a one-dimensional subspace, giving a point on the Grassmann manifold. We show that the average subspace corresponds to the leading principal component for Gaussian data. We provide a simple algorithm for computing this Grassmann Average ( GA), and show that the subspace estimate is less sensitive to outliers than PCA for general distributions. Because averages can be efficiently computed, we immediately gain scalability. We exploit robust averaging to formulate the Robust Grassmann Average (RGA) as a form of robust PCA. The resulting Trimmed Grassmann Average ( TGA) is appropriate for computer vision because it is robust to pixel outliers. The algorithm has linear computational complexity and minimal memory requirements. We demonstrate TGA for background modeling, video restoration, and shadow removal. We show scalability by performing robust PCA on the entire Star Wars IV movie; a task beyond any current method. Source code is available online.

  8. Scalable electro-photonic integration concept based on polymer waveguides

    NARCIS (Netherlands)

    Bosman, E.; Steenberge, G. van; Boersma, A.; Wiegersma, S.; Harmsma, P.J.; Karppinen, M.; Korhonen, T.; Offrein, B.J.; Dangel, R.; Daly, A.; Ortsiefer, M.; Justice, J.; Corbett, B.; Dorrestein, S.; Duis, J.

    2016-01-01

    A novel method for fabricating a single mode optical interconnection platform is presented. The method comprises the miniaturized assembly of optoelectronic single dies, the scalable fabrication of polymer single mode waveguides and the coupling to glass fiber arrays providing the I/O's. The low

  9. Coilable Crystalline Fiber (CCF) Lasers and their Scalability

    Science.gov (United States)

    2014-03-01

    highly power scalable, nearly diffraction-limited output laser. 37 References 1. Snitzer, E. Optical Maser Action of Nd 3+ in A Barium Crown Glass ...Electron Devices Directorate Helmuth Meissner Onyx Optics Approved for public release; distribution...lasers, but their composition ( glass ) poses significant disadvantages in pump absorption, gain, and thermal conductivity. All-crystalline fiber lasers

  10. Efficient Enhancement for Spatial Scalable Video Coding Transmission

    Directory of Open Access Journals (Sweden)

    Mayada Khairy

    2017-01-01

    Full Text Available Scalable Video Coding (SVC is an international standard technique for video compression. It is an extension of H.264 Advanced Video Coding (AVC. In the encoding of video streams by SVC, it is suitable to employ the macroblock (MB mode because it affords superior coding efficiency. However, the exhaustive mode decision technique that is usually used for SVC increases the computational complexity, resulting in a longer encoding time (ET. Many other algorithms were proposed to solve this problem with imperfection of increasing transmission time (TT across the network. To minimize the ET and TT, this paper introduces four efficient algorithms based on spatial scalability. The algorithms utilize the mode-distribution correlation between the base layer (BL and enhancement layers (ELs and interpolation between the EL frames. The proposed algorithms are of two categories. Those of the first category are based on interlayer residual SVC spatial scalability. They employ two methods, namely, interlayer interpolation (ILIP and the interlayer base mode (ILBM method, and enable ET and TT savings of up to 69.3% and 83.6%, respectively. The algorithms of the second category are based on full-search SVC spatial scalability. They utilize two methods, namely, full interpolation (FIP and the full-base mode (FBM method, and enable ET and TT savings of up to 55.3% and 76.6%, respectively.

  11. Scalable power selection method for wireless mesh networks

    CSIR Research Space (South Africa)

    Olwal, TO

    2009-01-01

    Full Text Available This paper addresses the problem of a scalable dynamic power control (SDPC) for wireless mesh networks (WMNs) based on IEEE 802.11 standards. An SDPC model that accounts for architectural complexities witnessed in multiple radios and hops...

  12. Estimates of the Sampling Distribution of Scalability Coefficient H

    Science.gov (United States)

    Van Onna, Marieke J. H.

    2004-01-01

    Coefficient "H" is used as an index of scalability in nonparametric item response theory (NIRT). It indicates the degree to which a set of items rank orders examinees. Theoretical sampling distributions, however, have only been derived asymptotically and only under restrictive conditions. Bootstrap methods offer an alternative possibility to…

  13. Phylogenetic relationship among Kenyan sorghum germplasms ...

    African Journals Online (AJOL)

    . The objective of this study was to assess the level of phylogenetic relationships among the Kenyan sorghum germplasms at a known Al tolerance locus. Hierarchical cluster analysis joined at 70% simple matching coefficient using average ...

  14. DySectAPI: Scalable Prescriptive Debugging

    DEFF Research Database (Denmark)

    Jensen, Nicklas Bo; Karlsson, Sven; Quarfot Nielsen, Niklas

    We present the DySectAPI, a tool that allow users to construct probe trees for automatic, event-driven debugging at scale. The traditional, interactive debugging model, whereby users manually step through and inspect their application, does not scale well even for current supercomputers. While...... lightweight debugging models scale well, they can currently only debug a subset of bug classes. DySectAPI fills the gap between these two approaches with a novel user-guided approach. Using both experimental results and analytical modeling we show how DySectAPI scales and can run with a low overhead...

  15. Charles Darwin, beetles and phylogenetics.

    Science.gov (United States)

    Beutel, Rolf G; Friedrich, Frank; Leschen, Richard A B

    2009-11-01

    changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics--yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.

  16. Charles Darwin, beetles and phylogenetics

    Science.gov (United States)

    Beutel, Rolf G.; Friedrich, Frank; Leschen, Richard A. B.

    2009-11-01

    . This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics—yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.

  17. Phylogenetic distribution of fungal sterols.

    Directory of Open Access Journals (Sweden)

    John D Weete

    Full Text Available BACKGROUND: Ergosterol has been considered the "fungal sterol" for almost 125 years; however, additional sterol data superimposed on a recent molecular phylogeny of kingdom Fungi reveals a different and more complex situation. METHODOLOGY/PRINCIPAL FINDINGS: The interpretation of sterol distribution data in a modern phylogenetic context indicates that there is a clear trend from cholesterol and other Delta(5 sterols in the earliest diverging fungal species to ergosterol in later diverging fungi. There are, however, deviations from this pattern in certain clades. Sterols of the diverse zoosporic and zygosporic forms exhibit structural diversity with cholesterol and 24-ethyl -Delta(5 sterols in zoosporic taxa, and 24-methyl sterols in zygosporic fungi. For example, each of the three monophyletic lineages of zygosporic fungi has distinctive major sterols, ergosterol in Mucorales, 22-dihydroergosterol in Dimargaritales, Harpellales, and Kickxellales (DHK clade, and 24-methyl cholesterol in Entomophthorales. Other departures from ergosterol as the dominant sterol include: 24-ethyl cholesterol in Glomeromycota, 24-ethyl cholest-7-enol and 24-ethyl-cholesta-7,24(28-dienol in rust fungi, brassicasterol in Taphrinales and hypogeous pezizalean species, and cholesterol in Pneumocystis. CONCLUSIONS/SIGNIFICANCE: Five dominant end products of sterol biosynthesis (cholesterol, ergosterol, 24-methyl cholesterol, 24-ethyl cholesterol, brassicasterol, and intermediates in the formation of 24-ethyl cholesterol, are major sterols in 175 species of Fungi. Although most fungi in the most speciose clades have ergosterol as a major sterol, sterols are more varied than currently understood, and their distribution supports certain clades of Fungi in current fungal phylogenies. In addition to the intellectual importance of understanding evolution of sterol synthesis in fungi, there is practical importance because certain antifungal drugs (e.g., azoles target reactions in

  18. Fly pollination in Ceropegia (Apocynaceae: Asclepiadoideae): biogeographic and phylogenetic perspectives.

    Science.gov (United States)

    Ollerton, Jeff; Masinde, Siro; Meve, Ulrich; Picker, Mike; Whittington, Andrew

    2009-06-01

    Ceropegia (Apocynaceae subfamily Asclepiadoideae) is a large, Old World genus of >180 species, all of which possess distinctive flask-shaped flowers that temporarily trap pollinators. The taxonomic diversity of pollinators, biogeographic and phylogenetic patterns of pollinator exploitation, and the level of specificity of interactions were assessed in order to begin to understand the role of pollinators in promoting diversification within the genus. Flower visitor and pollinator data for approx. 60 Ceropegia taxa were analysed with reference to the main centres of diversity of the genus and to a cpDNA-nrDNA molecular phylogeny of the genus. Ceropegia spp. interact with flower-visiting Diptera from at least 26 genera in 20 families, of which 11 genera and 11 families are pollinators. Size range of flies was 0.5-4.0 mm and approx. 94 % were females. Ceropegia from particular regions do not use specific fly genera or families, though Arabian Peninsula species are pollinated by a wider range of Diptera families than those in other regions. The basal-most clade interacts with the highest diversity of Diptera families and genera, largely due to one hyper-generalist taxon, C. aristolochioides subsp. deflersiana. Species in the more-derived clades interact with a smaller diversity of Diptera. Approximately 60 % of taxa are so far recorded as interacting with only a single genus of pollinators, the remaining 40 % being less conservative in their interactions. Ceropegia spp. can therefore be ecological specialists or generalists. The genus Ceropegia has largely radiated without evolutionary shifts in pollinator functional specialization, maintaining its interactions with small Diptera. Intriguing biogeographic and phylogenetic patterns may reflect processes of regional dispersal, diversification and subsequent specialization onto a narrower range of pollinators, though some of the findings may be caused by inconsistent sampling. Comparisons are made with other plant genera

  19. Functional & phylogenetic diversity of copepod communities

    Science.gov (United States)

    Benedetti, F.; Ayata, S. D.; Blanco-Bercial, L.; Cornils, A.; Guilhaumon, F.

    2016-02-01

    The diversity of natural communities is classically estimated through species identification (taxonomic diversity) but can also be estimated from the ecological functions performed by the species (functional diversity), or from the phylogenetic relationships among them (phylogenetic diversity). Estimating functional diversity requires the definition of specific functional traits, i.e., phenotypic characteristics that impact fitness and are relevant to ecosystem functioning. Estimating phylogenetic diversity requires the description of phylogenetic relationships, for instance by using molecular tools. In the present study, we focused on the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. First, we implemented a specific trait database for the most commonly-sampled and abundant copepod species of the Mediterranean Sea. Our database includes 191 species, described by seven traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Clustering analysis in the functional trait space revealed that Mediterranean copepods can be gathered into groups that have different ecological roles. Second, we reconstructed a phylogenetic tree using the available sequences of 18S rRNA. Our tree included 154 of the analyzed Mediterranean copepod species. We used these two datasets to describe the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. The replacement component (turn-over) and the species richness difference component (nestedness) of the beta diversity indices were identified. Finally, by comparing various and complementary aspects of plankton diversity (taxonomic, functional, and phylogenetic diversity) we were able to gain a better understanding of the relationships among the zooplankton community, biodiversity, ecosystem function, and environmental forcing.

  20. Reflections on systematics and phylogenetic reconstruction.

    Science.gov (United States)

    Schwartz, Jeffrey H

    2009-06-01

    I attempt to raise questions regarding elements of systematics--primarily in the realm of phylogenetic reconstruction--in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian "phylogenetic systematics", and the schism between (neo)Darwinian descendants of the "modern evolutionary synthesis" and their supposed antagonists, cladists and punctuationalists.

  1. Phylogenetic relationships among megabats, microbats, and primates.

    OpenAIRE

    Mindell, D P; Dick, C. W.; Baker, R. J.

    1991-01-01

    We present 744 nucleotide base positions from the mitochondrial 12S rRNA gene and 236 base positions from the mitochondrial cytochrome oxidase subunit I gene for a microbat, Brachyphylla cavernarum, and a megabat, Pteropus capestratus, in phylogenetic analyses with homologous DNA sequences from Homo sapiens, Mus musculus (house mouse), and Gallus gallus (chicken). We use information on evolutionary rate differences for different types of sequence change to establish phylogenetic character wei...

  2. Fast and scalable inference of multi-sample cancer lineages.

    KAUST Repository

    Popic, Victoria

    2015-05-06

    Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee .

  3. Evaluation of 3D printed anatomically scalable transfemoral prosthetic knee.

    Science.gov (United States)

    Ramakrishnan, Tyagi; Schlafly, Millicent; Reed, Kyle B

    2017-07-01

    This case study compares a transfemoral amputee's gait while using the existing Ossur Total Knee 2000 and our novel 3D printed anatomically scalable transfemoral prosthetic knee. The anatomically scalable transfemoral prosthetic knee is 3D printed out of a carbon-fiber and nylon composite that has a gear-mesh coupling with a hard-stop weight-actuated locking mechanism aided by a cross-linked four-bar spring mechanism. This design can be scaled using anatomical dimensions of a human femur and tibia to have a unique fit for each user. The transfemoral amputee who was tested is high functioning and walked on the Computer Assisted Rehabilitation Environment (CAREN) at a self-selected pace. The motion capture and force data that was collected showed that there were distinct differences in the gait dynamics. The data was used to perform the Combined Gait Asymmetry Metric (CGAM), where the scores revealed that the overall asymmetry of the gait on the Ossur Total Knee was more asymmetric than the anatomically scalable transfemoral prosthetic knee. The anatomically scalable transfemoral prosthetic knee had higher peak knee flexion that caused a large step time asymmetry. This made walking on the anatomically scalable transfemoral prosthetic knee more strenuous due to the compensatory movements in adapting to the different dynamics. This can be overcome by tuning the cross-linked spring mechanism to emulate the dynamics of the subject better. The subject stated that the knee would be good for daily use and has the potential to be adapted as a running knee.

  4. How does cognition evolve? Phylogenetic comparative psychology

    Science.gov (United States)

    Matthews, Luke J.; Hare, Brian A.; Nunn, Charles L.; Anderson, Rindy C.; Aureli, Filippo; Brannon, Elizabeth M.; Call, Josep; Drea, Christine M.; Emery, Nathan J.; Haun, Daniel B. M.; Herrmann, Esther; Jacobs, Lucia F.; Platt, Michael L.; Rosati, Alexandra G.; Sandel, Aaron A.; Schroepfer, Kara K.; Seed, Amanda M.; Tan, Jingzhi; van Schaik, Carel P.; Wobber, Victoria

    2014-01-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

  5. Many-core algorithms for statistical phylogenetics.

    Science.gov (United States)

    Suchard, Marc A; Rambaut, Andrew

    2009-06-01

    Statistical phylogenetics is computationally intensive, resulting in considerable attention meted on techniques for parallelization. Codon-based models allow for independent rates of synonymous and replacement substitutions and have the potential to more adequately model the process of protein-coding sequence evolution with a resulting increase in phylogenetic accuracy. Unfortunately, due to the high number of codon states, computational burden has largely thwarted phylogenetic reconstruction under codon models, particularly at the genomic-scale. Here, we describe novel algorithms and methods for evaluating phylogenies under arbitrary molecular evolutionary models on graphics processing units (GPUs), making use of the large number of processing cores to efficiently parallelize calculations even for large state-size models. We implement the approach in an existing Bayesian framework and apply the algorithms to estimating the phylogeny of 62 complete mitochondrial genomes of carnivores under a 60-state codon model. We see a near 90-fold speed increase over an optimized CPU-based computation and a >140-fold increase over the currently available implementation, making this the first practical use of codon models for phylogenetic inference over whole mitochondrial or microorganism genomes. Source code provided in BEAGLE: Broad-platform Evolutionary Analysis General Likelihood Evaluator, a cross-platform/processor library for phylogenetic likelihood computation (http://beagle-lib.googlecode.com/). We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (http://beast.bio.ed.ac.uk/).

  6. How does cognition evolve? Phylogenetic comparative psychology.

    Science.gov (United States)

    MacLean, Evan L; Matthews, Luke J; Hare, Brian A; Nunn, Charles L; Anderson, Rindy C; Aureli, Filippo; Brannon, Elizabeth M; Call, Josep; Drea, Christine M; Emery, Nathan J; Haun, Daniel B M; Herrmann, Esther; Jacobs, Lucia F; Platt, Michael L; Rosati, Alexandra G; Sandel, Aaron A; Schroepfer, Kara K; Seed, Amanda M; Tan, Jingzhi; van Schaik, Carel P; Wobber, Victoria

    2012-03-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

  7. Maximizing the phylogenetic diversity of seed banks.

    Science.gov (United States)

    Griffiths, Kate E; Balding, Sharon T; Dickie, John B; Lewis, Gwilym P; Pearce, Tim R; Grenyer, Richard

    2015-04-01

    Ex situ conservation efforts such as those of zoos, botanical gardens, and seed banks will form a vital complement to in situ conservation actions over the coming decades. It is therefore necessary to pay the same attention to the biological diversity represented in ex situ conservation facilities as is often paid to protected-area networks. Building the phylogenetic diversity of ex situ collections will strengthen our capacity to respond to biodiversity loss. Since 2000, the Millennium Seed Bank Partnership has banked seed from 14% of the world's plant species. We assessed the taxonomic, geographic, and phylogenetic diversity of the Millennium Seed Bank collection of legumes (Leguminosae). We compared the collection with all known legume genera, their known geographic range (at country and regional levels), and a genus-level phylogeny of the legume family constructed for this study. Over half the phylogenetic diversity of legumes at the genus level was represented in the Millennium Seed Bank. However, pragmatic prioritization of species of economic importance and endangerment has led to the banking of a less-than-optimal phylogenetic diversity and prioritization of range-restricted species risks an underdispersed collection. The current state of the phylogenetic diversity of legumes in the Millennium Seed Bank could be substantially improved through the strategic banking of relatively few additional taxa. Our method draws on tools that are widely applied to in situ conservation planning, and it can be used to evaluate and improve the phylogenetic diversity of ex situ collections. © 2014 Society for Conservation Biology.

  8. Nodal distances for rooted phylogenetic trees.

    Science.gov (United States)

    Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

    2010-08-01

    Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M(n)(R) of real-valued n x n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L(p) metrics on M(n)(R), with p [epsilon] R(>0).

  9. GSKY: A scalable distributed geospatial data server on the cloud

    Science.gov (United States)

    Rozas Larraondo, Pablo; Pringle, Sean; Antony, Joseph; Evans, Ben

    2017-04-01

    Earth systems, environmental and geophysical datasets are an extremely valuable sources of information about the state and evolution of the Earth. Being able to combine information coming from different geospatial collections is in increasing demand by the scientific community, and requires managing and manipulating data with different formats and performing operations such as map reprojections, resampling and other transformations. Due to the large data volume inherent in these collections, storing multiple copies of them is unfeasible and so such data manipulation must be performed on-the-fly using efficient, high performance techniques. Ideally this should be performed using a trusted data service and common system libraries to ensure wide use and reproducibility. Recent developments in distributed computing based on dynamic access to significant cloud infrastructure opens the door for such new ways of processing geospatial data on demand. The National Computational Infrastructure (NCI), hosted at the Australian National University (ANU), has over 10 Petabytes of nationally significant research data collections. Some of these collections, which comprise a variety of observed and modelled geospatial data, are now made available via a highly distributed geospatial data server, called GSKY (pronounced [jee-skee]). GSKY supports on demand processing of large geospatial data products such as satellite earth observation data as well as numerical weather products, allowing interactive exploration and analysis of the data. It dynamically and efficiently distributes the required computations among cloud nodes providing a scalable analysis framework that can adapt to serve large number of concurrent users. Typical geospatial workflows handling different file formats and data types, or blending data in different coordinate projections and spatio-temporal resolutions, is handled transparently by GSKY. This is achieved by decoupling the data ingestion and indexing process as

  10. Decision making uncertainty, imperfection, deliberation and scalability

    CERN Document Server

    Kárný, Miroslav; Wolpert, David

    2015-01-01

    This volume focuses on uncovering the fundamental forces underlying dynamic decision making among multiple interacting, imperfect and selfish decision makers. The chapters are written by leading experts from different disciplines, all considering the many sources of imperfection in decision making, and always with an eye to decreasing the myriad discrepancies between theory and real world human decision making. Topics addressed include uncertainty, deliberation cost and the complexity arising from the inherent large computational scale of decision making in these systems. In particular, analyses and experiments are presented which concern: • task allocation to maximize “the wisdom of the crowd”; • design of a society of “edutainment” robots who account for one anothers’ emotional states; • recognizing and counteracting seemingly non-rational human decision making; • coping with extreme scale when learning causality in networks; • efficiently incorporating expert knowledge in personalized...

  11. Temporal scalability comparison of the H.264/SVC and distributed video codec

    DEFF Research Database (Denmark)

    Huang, Xin; Ukhanova, Ann; Belyaev, Evgeny

    2009-01-01

    The problem of the multimedia scalable video streaming is a current topic of interest. There exist many methods for scalable video coding. This paper is focused on the scalable extension of H.264/AVC (H.264/SVC) and distributed video coding (DVC). The paper presents an efficiency comparison of SVC...

  12. Scalable and Resilient Middleware to Handle Information Exchange during Environment Crisis

    Science.gov (United States)

    Tao, R.; Poslad, S.; Moßgraber, J.; Middleton, S.; Hammitzsch, M.

    2012-04-01

    The EU FP7 TRIDEC project focuses on enabling real-time, intelligent, information management of collaborative, complex, critical decision processes for earth management. A key challenge is to promote a communication infrastructure to facilitate interoperable environment information services during environment events and crises such as tsunamis and drilling, during which increasing volumes and dimensionality of disparate information sources, including sensor-based and human-based ones, can result, and need to be managed. Such a system needs to support: scalable, distributed messaging; asynchronous messaging; open messaging to handling changing clients such as new and retired automated system and human information sources becoming online or offline; flexible data filtering, and heterogeneous access networks (e.g., GSM, WLAN and LAN). In addition, the system needs to be resilient to handle the ICT system failures, e.g. failure, degradation and overloads, during environment events. There are several system middleware choices for TRIDEC based upon a Service-oriented-architecture (SOA), Event-driven-Architecture (EDA), Cloud Computing, and Enterprise Service Bus (ESB). In an SOA, everything is a service (e.g. data access, processing and exchange); clients can request on demand or subscribe to services registered by providers; more often interaction is synchronous. In an EDA system, events that represent significant changes in state can be processed simply, or as streams or more complexly. Cloud computing is a virtualization, interoperable and elastic resource allocation model. An ESB, a fundamental component for enterprise messaging, supports synchronous and asynchronous message exchange models and has inbuilt resilience against ICT failure. Our middleware proposal is an ESB based hybrid architecture model: an SOA extension supports more synchronous workflows; EDA assists the ESB to handle more complex event processing; Cloud computing can be used to increase and

  13. Rearrangement moves on rooted phylogenetic networks.

    Directory of Open Access Journals (Sweden)

    Philippe Gambette

    2017-08-01

    Full Text Available Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide

  14. Rearrangement moves on rooted phylogenetic networks.

    Science.gov (United States)

    Gambette, Philippe; van Iersel, Leo; Jones, Mark; Lafond, Manuel; Pardi, Fabio; Scornavacca, Celine

    2017-08-01

    Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a solid basis for

  15. Scalable active learning for multiclass image classification.

    Science.gov (United States)

    Joshi, Ajay J; Porikli, Fatih; Papanikolopoulos, Nikolaos P

    2012-11-01

    Machine learning techniques for computer vision applications like object recognition, scene classification, etc., require a large number of training samples for satisfactory performance. Especially when classification is to be performed over many categories, providing enough training samples for each category is infeasible. This paper describes new ideas in multiclass active learning to deal with the training bottleneck, making it easier to train large multiclass image classification systems. First, we propose a new interaction modality for training which requires only yes-no type binary feedback instead of a precise category label. The modality is especially powerful in the presence of hundreds of categories. For the proposed modality, we develop a Value-of-Information (VOI) algorithm that chooses informative queries while also considering user annotation cost. Second, we propose an active selection measure that works with many categories and is extremely fast to compute. This measure is employed to perform a fast seed search before computing VOI, resulting in an algorithm that scales linearly with dataset size. Third, we use locality sensitive hashing to provide a very fast approximation to active learning, which gives sublinear time scaling, allowing application to very large datasets. The approximation provides up to two orders of magnitude speedups with little loss in accuracy. Thorough empirical evaluation of classification accuracy, noise sensitivity, imbalanced data, and computational performance on a diverse set of image datasets demonstrates the strengths of the proposed algorithms.

  16. Heterogeneous scalable framework for multiphase flows

    Energy Technology Data Exchange (ETDEWEB)

    Morris, Karla Vanessa [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2013-09-01

    Two categories of challenges confront the developer of computational spray models: those related to the computation and those related to the physics. Regarding the computation, the trend towards heterogeneous, multi- and many-core platforms will require considerable re-engineering of codes written for the current supercomputing platforms. Regarding the physics, accurate methods for transferring mass, momentum and energy from the dispersed phase onto the carrier fluid grid have so far eluded modelers. Significant challenges also lie at the intersection between these two categories. To be competitive, any physics model must be expressible in a parallel algorithm that performs well on evolving computer platforms. This work created an application based on a software architecture where the physics and software concerns are separated in a way that adds flexibility to both. The develop spray-tracking package includes an application programming interface (API) that abstracts away the platform-dependent parallelization concerns, enabling the scientific programmer to write serial code that the API resolves into parallel processes and threads of execution. The project also developed the infrastructure required to provide similar APIs to other application. The API allow object-oriented Fortran applications direct interaction with Trilinos to support memory management of distributed objects in central processing units (CPU) and graphic processing units (GPU) nodes for applications using C++.

  17. Parametric investigation of scalable tactile sensors

    Science.gov (United States)

    Saadatzi, Mohammad Nasser; Yang, Zhong; Baptist, Joshua R.; Sahasrabuddhe, Ritvij R.; Wijayasinghe, Indika B.; Popa, Dan O.

    2017-05-01

    In the near future, robots and humans will share the same environment and perform tasks cooperatively. For intuitive, safe, and reliable physical human-robot interaction (pHRI), sensorized robot skins for tactile measurements of contact are necessary. In a previous study, we presented skins consisting of strain gauge arrays encased in silicone encapsulants. Although these structures could measure normal forces applied directly onto the sensing elements, they also exhibited blind spots and response asymmetry to certain loading patterns. This study presents a parametric investigation of piezoresistive polymeric strain gauge that exhibits a symmetric omniaxial response thanks to its novel star-shaped structure. This strain gauge relies on the use of gold micro-patterned star-shaped structures with a thin layer of PEDOT:PSS which is a flexible polymer with piezoresistive properties. In this paper, the sensor is first modeled and comprehensively analyzed in the finite-element simulation environment COMSOL. Simulations include stress-strain loading for a variety of structure parameters such as gauge lengths, widths, and spacing, as well as multiple load locations relative to the gauge. Subsequently, sensors with optimized configurations obtained through simulations were fabricated using cleanroom photolithographic and spin-coating processes, and then experimentally tested. Results show a trend-wise agreement between experiments and simulations.

  18. Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling.

    Science.gov (United States)

    Sferra, Gabriella; Fratini, Federica; Ponzi, Marta; Pizzi, Elisabetta

    2017-09-05

    Elaboration of powerful methods to predict functional and/or physical protein-protein interactions from genome sequence is one of the main tasks in the post-genomic era. Phylogenetic profiling allows the prediction of protein-protein interactions at a whole genome level in both Prokaryotes and Eukaryotes. For this reason it is considered one of the most promising methods. Here, we propose an improvement of phylogenetic profiling that enables handling of large genomic datasets and infer global protein-protein interactions. This method uses the distance correlation as a new measure of phylogenetic profile similarity. We constructed robust reference sets and developed Phylo-dCor, a parallelized version of the algorithm for calculating the distance correlation that makes it applicable to large genomic data. Using Saccharomyces cerevisiae and Escherichia coli genome datasets, we showed that Phylo-dCor outperforms phylogenetic profiling methods previously described based on the mutual information and Pearson's correlation as measures of profile similarity. In this work, we constructed and assessed robust reference sets and propose the distance correlation as a measure for comparing phylogenetic profiles. To make it applicable to large genomic data, we developed Phylo-dCor, a parallelized version of the algorithm for calculating the distance correlation. Two R scripts that can be run on a wide range of machines are available upon request.

  19. A scalable strategy for high-throughput GFP tagging of endogenous human proteins.

    Science.gov (United States)

    Leonetti, Manuel D; Sekine, Sayaka; Kamiyama, Daichi; Weissman, Jonathan S; Huang, Bo

    2016-06-21

    A central challenge of the postgenomic era is to comprehensively characterize the cellular role of the ∼20,000 proteins encoded in the human genome. To systematically study protein function in a native cellular background, libraries of human cell lines expressing proteins tagged with a functional sequence at their endogenous loci would be very valuable. Here, using electroporation of Cas9 nuclease/single-guide RNA ribonucleoproteins and taking advantage of a split-GFP system, we describe a scalable method for the robust, scarless, and specific tagging of endogenous human genes with GFP. Our approach requires no molecular cloning and allows a large number of cell lines to be processed in parallel. We demonstrate the scalability of our method by targeting 48 human genes and show that the resulting GFP fluorescence correlates with protein expression levels. We next present how our protocols can be easily adapted for the tagging of a given target with GFP repeats, critically enabling the study of low-abundance proteins. Finally, we show that our GFP tagging approach allows the biochemical isolation of native protein complexes for proteomic studies. Taken together, our results pave the way for the large-scale generation of endogenously tagged human cell lines for the proteome-wide analysis of protein localization and interaction networks in a native cellular context.

  20. A scalable multi-DLP pico-projector system for virtual reality

    Science.gov (United States)

    Teubl, F.; Kurashima, C.; Cabral, M.; Fels, S.; Lopes, R.; Zuffo, M.

    2014-03-01

    Virtual Reality (VR) environments can offer immersion, interaction and realistic images to users. A VR system is usually expensive and requires special equipment in a complex setup. One approach is to use Commodity-Off-The-Shelf (COTS) desktop multi-projectors manually or camera based calibrated to reduce the cost of VR systems without significant decrease of the visual experience. Additionally, for non-planar screen shapes, special optics such as lenses and mirrors are required thus increasing costs. We propose a low-cost, scalable, flexible and mobile solution that allows building complex VR systems that projects images onto a variety of arbitrary surfaces such as planar, cylindrical and spherical surfaces. This approach combines three key aspects: 1) clusters of DLP-picoprojectors to provide homogeneous and continuous pixel density upon arbitrary surfaces without additional optics; 2) LED lighting technology for energy efficiency and light control; 3) smaller physical footprint for flexibility purposes. Therefore, the proposed system is scalable in terms of pixel density, energy and physical space. To achieve these goals, we developed a multi-projector software library called FastFusion that calibrates all projectors in a uniform image that is presented to viewers. FastFusion uses a camera to automatically calibrate geometric and photometric correction of projected images from ad-hoc positioned projectors, the only requirement is some few pixels overlapping amongst them. We present results with eight Pico-projectors, with 7 lumens (LED) and DLP 0.17 HVGA Chipset.

  1. Phylogenetic tests of distribution patterns in South Asia: towards an ...

    Indian Academy of Sciences (India)

    The last four decades have seen an increasing integration of phylogenetics and biogeography. However, a dearth of phylogenetic studies has precluded such biogeographic analyses in South Asia until recently. Noting the increase in phylogenetic research and interest in phylogenetic biogeography in the region, we ...

  2. Phylogenetic diversity and relationships among species of genus ...

    African Journals Online (AJOL)

    Fifty six Nicotiana species were used to construct phylogenetic trees and to asses the genetic relationships between them. Genetic distances estimated from RAPD analysis was used to construct phylogenetic trees using Phylogenetic Inference Package (PHYLIP). Since phylogenetic relationships estimated for closely ...

  3. Phylogenetic footprinting to find functional DNA elements.

    Science.gov (United States)

    Ganley, Austen R D; Kobayashi, Takehiko

    2007-01-01

    Phylogenetic footprinting is powerful technique for finding functional elements from sequence data. Functional elements are thought to have greater sequence constraint than nonfunctional elements, and, thus, undergo a slower rate of sequence change through time. Phylogenetic footprinting uses comparisons of homologous sequences from closely related organisms to identify "phylogenetic footprints," regions with slower rates of sequence change than background. This does not require prior characterization of the sequence in question, therefore, it can be used in a wide range of applications. In particular, it is useful for the identification of functional elements in noncoding DNA, which are traditionally difficult to detect. Here, we describe in detail how to perform a simple yet powerful phylogenetic footprinting analysis. As an example, we use ribosomal DNA repeat sequences from various Saccharomyces yeasts to find functional noncoding DNA elements in the intergenic spacer, and explain critical considerations in performing phylogenetic footprinting analyses, including the number of species and species range, and some of the available software. Our methods are broadly applicable and should appeal to molecular biologists with little experience in bioinformatics.

  4. Worldwide phylogenetic relationship of avian poxviruses

    Science.gov (United States)

    Gyuranecz, Miklós; Foster, Jeffrey T.; Dán, Ádám; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly

    2013-01-01

    Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we have expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g. starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

  5. Bounds for phylogenetic network space metrics.

    Science.gov (United States)

    Francis, Andrew; Huber, Katharina T; Moulton, Vincent; Wu, Taoyang

    2018-04-01

    Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which every vertex has degree 1 or 3 and whose leaf-set is a fixed set X of taxa. This space, denoted [Formula: see text], is defined in terms of two operations on networks-the nearest neighbor interchange and triangle operations-which can be used to transform any network with leaf set X into any other network with that leaf set. In particular, it gives rise to a metric d on [Formula: see text] which is given by the smallest number of operations required to transform one network in [Formula: see text] into another in [Formula: see text]. The metric generalizes the well-known NNI-metric on phylogenetic trees which has been intensively studied in the literature. In this paper, we derive a bound for the metric d as well as a related metric [Formula: see text] which arises when restricting d to the subset of [Formula: see text] consisting of all networks with [Formula: see text] vertices, [Formula: see text]. We also introduce two new metrics on networks-the SPR and TBR metrics-which generalize the metrics on phylogenetic trees with the same name and give bounds for these new metrics. We expect our results to eventually have applications to the development and understanding of network search algorithms.

  6. A metric on the space of reduced phylogenetic networks.

    Science.gov (United States)

    Nakhleh, Luay

    2010-01-01

    Phylogenetic networks are leaf-labeled, rooted, acyclic, and directed graphs that are used to model reticulate evolutionary histories. Several measures for quantifying the topological dissimilarity between two phylogenetic networks have been devised, each of which was proven to be a metric on certain restricted classes of phylogenetic networks. A biologically motivated class of phylogenetic networks, namely, reduced phylogenetic networks, was recently introduced. None of the existing measures is a metric on the space of reduced phylogenetic networks. In this paper, we provide a metric on the space of reduced phylogenetic networks that is computable in time polynomial in the size of the networks.

  7. Scalable Computational Chemistry: New Developments and Applications

    Energy Technology Data Exchange (ETDEWEB)

    Alexeev, Yuri [Iowa State Univ., Ames, IA (United States)

    2002-01-01

    The computational part of the thesis is the investigation of titanium chloride (II) as a potential catalyst for the bis-silylation reaction of ethylene with hexaclorodisilane at different levels of theory. Bis-silylation is an important reaction for producing bis(silyl) compounds and new C-Si bonds, which can serve as monomers for silicon containing polymers and silicon carbides. Ab initio calculations on the steps involved in a proposed mechanism are presented. This choice of reactants allows them to study this reaction at reliable levels of theory without compromising accuracy. The calculations indicate that this is a highly exothermic barrierless reaction. The TiCl2 catalyst removes a 50 kcal/mol activation energy barrier required for the reaction without the catalyst. The first step is interaction of TiCl2 with ethylene to form an intermediate that is 60 kcal/mol below the energy of the reactants. This is the driving force for the entire reaction. Dynamic correlation plays a significant role because RHF calculations indicate that the net barrier for the catalyzed reaction is 50 kcal/mol. They conclude that divalent Ti has the potential to become an important industrial catalyst for silylation reactions. In the programming part of the thesis, parallelization of different quantum chemistry methods is presented. The parallelization of code is becoming important aspects of quantum chemistry code development. Two trends contribute to it: the overall desire to study large chemical systems and the desire to employ highly correlated methods which are usually computationally and memory expensive. In the presented distributed data algorithms computation is parallelized and the largest arrays are evenly distributed among CPUs. First, the parallelization of the Hartree-Fock self-consistent field (SCF) method is considered. SCF method is the most common starting point for more accurate calculations. The Fock build (sub step of SCF) from AO integrals is

  8. Scalable graphene coatings for enhanced condensation heat transfer.

    Science.gov (United States)

    Preston, Daniel J; Mafra, Daniela L; Miljkovic, Nenad; Kong, Jing; Wang, Evelyn N

    2015-05-13

    Water vapor condensation is commonly observed in nature and routinely used as an effective means of transferring heat with dropwise condensation on nonwetting surfaces exhibiting heat transfer improvement compared to filmwise condensation on wetting surfaces. However, state-of-the-art techniques to promote dropwise condensation rely on functional hydrophobic coatings that either have challenges with chemical stability or are so thick that any potential heat transfer improvement is negated due to the added thermal resistance of the coating. In this work, we show the effectiveness of ultrathin scalable chemical vapor deposited (CVD) graphene coatings to promote dropwise condensation while offering robust chemical stability and maintaining low thermal resistance. Heat transfer enhancements of 4× were demonstrated compared to filmwise condensation, and the robustness of these CVD coatings was superior to typical hydrophobic monolayer coatings. Our results indicate that graphene is a promising surface coating to promote dropwise condensation of water in industrial conditions with the potential for scalable application via CVD.

  9. On the Scalability of Time-predictable Chip-Multiprocessing

    DEFF Research Database (Denmark)

    Puffitsch, Wolfgang; Schoeberl, Martin

    2012-01-01

    simple processors is not an option for embedded systems with high demands on computing power. In order to provide high performance and predictability we argue to use multiprocessor systems with a time-predictable memory interface. In this paper we present the scalability of a Java chip......Real-time systems need a time-predictable execution platform to be able to determine the worst-case execution time statically. In order to be time-predictable, several advanced processor features, such as out-of-order execution and other forms of speculation, have to be avoided. However, just using......-multiprocessor system that is designed to be time-predictable. Adding time-predictable caches is mandatory to achieve scalability with a shared memory multi-processor system. As Java bytecode retains information about the nature of memory accesses, it is possible to implement a memory hierarchy that takes...

  10. Scientific visualization uncertainty, multifield, biomedical, and scalable visualization

    CERN Document Server

    Chen, Min; Johnson, Christopher; Kaufman, Arie; Hagen, Hans

    2014-01-01

    Based on the seminar that took place in Dagstuhl, Germany in June 2011, this contributed volume studies the four important topics within the scientific visualization field: uncertainty visualization, multifield visualization, biomedical visualization and scalable visualization. • Uncertainty visualization deals with uncertain data from simulations or sampled data, uncertainty due to the mathematical processes operating on the data, and uncertainty in the visual representation, • Multifield visualization addresses the need to depict multiple data at individual locations and the combination of multiple datasets, • Biomedical is a vast field with select subtopics addressed from scanning methodologies to structural applications to biological applications, • Scalability in scientific visualization is critical as data grows and computational devices range from hand-held mobile devices to exascale computational platforms. Scientific Visualization will be useful to practitioners of scientific visualization, ...

  11. Continuity-Aware Scheduling Algorithm for Scalable Video Streaming

    Directory of Open Access Journals (Sweden)

    Atinat Palawan

    2016-05-01

    Full Text Available The consumer demand for retrieving and delivering visual content through consumer electronic devices has increased rapidly in recent years. The quality of video in packet networks is susceptible to certain traffic characteristics: average bandwidth availability, loss, delay and delay variation (jitter. This paper presents a scheduling algorithm that modifies the stream of scalable video to combat jitter. The algorithm provides unequal look-ahead by safeguarding the base layer (without the need for overhead of the scalable video. The results of the experiments show that our scheduling algorithm reduces the number of frames with a violated deadline and significantly improves the continuity of the video stream without compromising the average Y Peek Signal-to-Noise Ratio (PSNR.

  12. Scalable Quantum Photonics with Single Color Centers in Silicon Carbide.

    Science.gov (United States)

    Radulaski, Marina; Widmann, Matthias; Niethammer, Matthias; Zhang, Jingyuan Linda; Lee, Sang-Yun; Rendler, Torsten; Lagoudakis, Konstantinos G; Son, Nguyen Tien; Janzén, Erik; Ohshima, Takeshi; Wrachtrup, Jörg; Vučković, Jelena

    2017-03-08

    Silicon carbide is a promising platform for single photon sources, quantum bits (qubits), and nanoscale sensors based on individual color centers. Toward this goal, we develop a scalable array of nanopillars incorporating single silicon vacancy centers in 4H-SiC, readily available for efficient interfacing with free-space objective and lensed-fibers. A commercially obtained substrate is irradiated with 2 MeV electron beams to create vacancies. Subsequent lithographic process forms 800 nm tall nanopillars with 400-1400 nm diameters. We obtain high collection efficiency of up to 22 kcounts/s optical saturation rates from a single silicon vacancy center while preserving the single photon emission and the optically induced electron-spin polarization properties. Our study demonstrates silicon carbide as a readily available platform for scalable quantum photonics architecture relying on single photon sources and qubits.

  13. Scalable metagenomic taxonomy classification using a reference genome database.

    Science.gov (United States)

    Ames, Sasha K; Hysom, David A; Gardner, Shea N; Lloyd, G Scott; Gokhale, Maya B; Allen, Jonathan E

    2013-09-15

    Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take contents of the sample. Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat allen99@llnl.gov Supplementary data are available at Bioinformatics online.

  14. Semantic Models for Scalable Search in the Internet of Things

    Directory of Open Access Journals (Sweden)

    Dennis Pfisterer

    2013-03-01

    Full Text Available The Internet of Things is anticipated to connect billions of embedded devices equipped with sensors to perceive their surroundings. Thereby, the state of the real world will be available online and in real-time and can be combined with other data and services in the Internet to realize novel applications such as Smart Cities, Smart Grids, or Smart Healthcare. This requires an open representation of sensor data and scalable search over data from diverse sources including sensors. In this paper we show how the Semantic Web technologies RDF (an open semantic data format and SPARQL (a query language for RDF-encoded data can be used to address those challenges. In particular, we describe how prediction models can be employed for scalable sensor search, how these prediction models can be encoded as RDF, and how the models can be queried by means of SPARQL.

  15. Scalable, flexible and high resolution patterning of CVD graphene.

    Science.gov (United States)

    Hofmann, Mario; Hsieh, Ya-Ping; Hsu, Allen L; Kong, Jing

    2014-01-07

    The unique properties of graphene make it a promising material for interconnects in flexible and transparent electronics. To increase the commercial impact of graphene in those applications, a scalable and economical method for producing graphene patterns is required. The direct synthesis of graphene from an area-selectively passivated catalyst substrate can generate patterned graphene of high quality. We here present a solution-based method for producing patterned passivation layers. Various deposition methods such as ink-jet deposition and microcontact printing were explored, that can satisfy application demands for low cost, high resolution and scalable production of patterned graphene. The demonstrated high quality and nanometer precision of grown graphene establishes the potential of this synthesis approach for future commercial applications of graphene. Finally, the ability to transfer high resolution graphene patterns onto complex three-dimensional surfaces affords the vision of graphene-based interconnects in novel electronics.

  16. Scalable Quantum Photonics with Single Color Centers in Silicon Carbide

    Science.gov (United States)

    Radulaski, Marina; Widmann, Matthias; Niethammer, Matthias; Zhang, Jingyuan Linda; Lee, Sang-Yun; Rendler, Torsten; Lagoudakis, Konstantinos G.; Son, Nguyen Tien; Janzén, Erik; Ohshima, Takeshi; Wrachtrup, Jörg; Vučković, Jelena

    2017-03-01

    Silicon carbide is a promising platform for single photon sources, quantum bits (qubits) and nanoscale sensors based on individual color centers. Towards this goal, we develop a scalable array of nanopillars incorporating single silicon vacancy centers in 4H-SiC, readily available for efficient interfacing with free-space objective and lensed-fibers. A commercially obtained substrate is irradiated with 2 MeV electron beams to create vacancies. Subsequent lithographic process forms 800 nm tall nanopillars with 400-1,400 nm diameters. We obtain high collection efficiency, up to 22 kcounts/s optical saturation rates from a single silicon vacancy center, while preserving the single photon emission and the optically induced electron-spin polarization properties. Our study demonstrates silicon carbide as a readily available platform for scalable quantum photonics architecture relying on single photon sources and qubits.

  17. Scalability of DL_POLY on High Performance Computing Platform

    Directory of Open Access Journals (Sweden)

    Mabule Samuel Mabakane

    2017-12-01

    Full Text Available This paper presents a case study on the scalability of several versions of the molecular dynamics code (DL_POLY performed on South Africa‘s Centre for High Performance Computing e1350 IBM Linux cluster, Sun system and Lengau supercomputers. Within this study different problem sizes were designed and the same chosen systems were employed in order to test the performance of DL_POLY using weak and strong scalability. It was found that the speed-up results for the small systems were better than large systems on both Ethernet and Infiniband network. However, simulations of large systems in DL_POLY performed well using Infiniband network on Lengau cluster as compared to e1350 and Sun supercomputer.

  18. Trident: scalable compute archives: workflows, visualization, and analysis

    Science.gov (United States)

    Gopu, Arvind; Hayashi, Soichi; Young, Michael D.; Kotulla, Ralf; Henschel, Robert; Harbeck, Daniel

    2016-08-01

    The Astronomy scientific community has embraced Big Data processing challenges, e.g. associated with time-domain astronomy, and come up with a variety of novel and efficient data processing solutions. However, data processing is only a small part of the Big Data challenge. Efficient knowledge discovery and scientific advancement in the Big Data era requires new and equally efficient tools: modern user interfaces for searching, identifying and viewing data online without direct access to the data; tracking of data provenance; searching, plotting and analyzing metadata; interactive visual analysis, especially of (time-dependent) image data; and the ability to execute pipelines on supercomputing and cloud resources with minimal user overhead or expertise even to novice computing users. The Trident project at Indiana University offers a comprehensive web and cloud-based microservice software suite that enables the straight forward deployment of highly customized Scalable Compute Archive (SCA) systems; including extensive visualization and analysis capabilities, with minimal amount of additional coding. Trident seamlessly scales up or down in terms of data volumes and computational needs, and allows feature sets within a web user interface to be quickly adapted to meet individual project requirements. Domain experts only have to provide code or business logic about handling/visualizing their domain's data products and about executing their pipelines and application work flows. Trident's microservices architecture is made up of light-weight services connected by a REST API and/or a message bus; a web interface elements are built using NodeJS, AngularJS, and HighCharts JavaScript libraries among others while backend services are written in NodeJS, PHP/Zend, and Python. The software suite currently consists of (1) a simple work flow execution framework to integrate, deploy, and execute pipelines and applications (2) a progress service to monitor work flows and sub

  19. Scalable Deployment of Advanced Building Energy Management Systems

    Science.gov (United States)

    2013-06-01

    rooms, classrooms, a quarterdeck with a two-story atrium and office spaces, and a large cafeteria /galley. Buildings 7113 and 7114 are functionally...similar (include barracks, classroom, cafeteria , etc.) and share a common central chilled water plant. 3.1.1 Building 7230 The drill hall (Building...scalability of the proposed approach, and expanded the capabilities developed for a single building to a building campus at Naval Station Great Lakes

  20. Scalable, Self Aligned Printing of Flexible Graphene Micro Supercapacitors (Postprint)

    Science.gov (United States)

    2017-05-11

    reduced graphene oxide: 0.4 mF cm−2)[11,39–41] prepared by conventional micro- fabrication techniques, the printed MSCs offer distinct advan- tages in...AFRL-RX-WP-JA-2017-0318 SCALABLE, SELF-ALIGNED PRINTING OF FLEXIBLE GRAPHENE MICRO-SUPERCAPACITORS (POSTPRINT) Woo Jin Hyun, Chang-Hyun Kim...including suggestions for reducing this burden, to Department of Defense, Washington Headquarters Services, Directorate for Information Operations

  1. Scalable Power-Component Models for Concept Testing

    Science.gov (United States)

    2011-08-16

    Technology: Permanent Magnet Brushless DC machine • Model: Self-generating torque-speed-efficiency map • Future improvements: Induction machine ...system to the standard driveline – Example: BAS System – 3 kW system ISG Block, Rev. 2.0 Revision 2.0 • Four quadrant • PM Brushless Machine • Speed...and systems engineering. • Scope: Scalable, generic MATLAB/Simulink models in three areas: – Electromechanical machines (Integrated Starter

  2. Scalable privacy-preserving big data aggregation mechanism

    OpenAIRE

    Dapeng Wu; Boran Yang; Ruyan Wang

    2016-01-01

    As the massive sensor data generated by large-scale Wireless Sensor Networks (WSNs) recently become an indispensable part of ‘Big Data’, the collection, storage, transmission and analysis of the big sensor data attract considerable attention from researchers. Targeting the privacy requirements of large-scale WSNs and focusing on the energy-efficient collection of big sensor data, a Scalable Privacy-preserving Big Data Aggregation (Sca-PBDA) method is proposed in this paper. Firstly, according...

  3. Fast & scalable pattern transfer via block copolymer nanolithography

    DEFF Research Database (Denmark)

    Li, Tao; Wang, Zhongli; Schulte, Lars

    2015-01-01

    A fully scalable and efficient pattern transfer process based on block copolymer (BCP) self-assembling directly on various substrates is demonstrated. PS-rich and PDMS-rich poly(styrene-b-dimethylsiloxane) (PS-b-PDMS) copolymers are used to give monolayer sphere morphology after spin-casting of s...... on long range lateral order, including fabrication of substrates for catalysis, solar cells, sensors, ultrafiltration membranes and templating of semiconductors or metals....

  4. Economical and scalable synthesis of 6-amino-2-cyanobenzothiazole

    Directory of Open Access Journals (Sweden)

    Jacob R. Hauser

    2016-09-01

    Full Text Available 2-Cyanobenzothiazoles (CBTs are useful building blocks for: 1 luciferin derivatives for bioluminescent imaging; and 2 handles for bioorthogonal ligations. A particularly versatile CBT is 6-amino-2-cyanobenzothiazole (ACBT, which has an amine handle for straight-forward derivatisation. Here we present an economical and scalable synthesis of ACBT based on a cyanation catalysed by 1,4-diazabicyclo[2.2.2]octane (DABCO, and discuss its advantages for scale-up over previously reported routes.

  5. Scalable Cluster-based Routing in Large Wireless Sensor Networks

    OpenAIRE

    Jiandong Li; Xuelian Cai; Jin Yang; Lina Zhu

    2012-01-01

    Large control overhead is the leading factor limiting the scalability of wireless sensor networks (WSNs). Clustering network nodes is an efficient solution, and Passive Clustering (PC) is one of the most efficient clustering methods. In this letter, we propose an improved PC-based route building scheme, named Route Reply (RREP) Broadcast with Passive Clustering (in short RBPC). Through broadcasting RREP packets on an expanding ring to build route, sensor nodes cache their route to the sink no...

  6. Semantic Models for Scalable Search in the Internet of Things

    OpenAIRE

    Dennis Pfisterer; Kay Römer; Richard Mietz; Sven Groppe

    2013-01-01

    The Internet of Things is anticipated to connect billions of embedded devices equipped with sensors to perceive their surroundings. Thereby, the state of the real world will be available online and in real-time and can be combined with other data and services in the Internet to realize novel applications such as Smart Cities, Smart Grids, or Smart Healthcare. This requires an open representation of sensor data and scalable search over data from diverse sources including sensors. In this paper...

  7. Consequences of recombination on traditional phylogenetic analysis

    DEFF Research Database (Denmark)

    Schierup, M H; Hein, J

    2000-01-01

    We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mt......DNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination....... With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may...

  8. Efficient comparative phylogenetics on large trees.

    Science.gov (United States)

    Louca, Stilianos; Doebeli, Michael

    2017-10-30

    Biodiversity databases now comprise hundreds of thousands of sequences and trait records. For example, the Open Tree of Life includes over 1,491,000 metazoan and over 300,000 bacterial taxa. These data provide unique opportunities for analysis of phylogenetic trait distribution and reconstruction of ancestral biodiversity. However, existing tools for comparative phylogenetics scale poorly to such large trees, to the point of being almost unusable. Here we present a new R package, named "castor", for comparative phylogenetics on large trees spanning millions of tips. On large trees castor is often 100-1000 times faster than existing tools. The castor source code, compiled binaries, documentation and usage examples are freely available at the Comprehensive R Archive Network (CRAN). louca.research@gmail.com.

  9. Phylogenetic analysis of the honeybee Sacbrood virus

    Directory of Open Access Journals (Sweden)

    Li You

    2016-06-01

    Full Text Available Sacbrood virus (SBV is one of the most common and harmful viruses to honeybees. It causes failure to pupate and death during larval stage, in adult bees it has an influence on their behavior and even shortens their life-span. In this study, we analyzed the phylogenetic relationships among the SBV isolates from all around the world, with from both Apis cerana and Apis mellifera. Phylogenetic trees were constructed based on three types of nucleotide sequences: complete genome sequence, VP1 gene and SB1-2 fragment of SBV. Moreover, genome recombination analysis was performed to assess the effect of genome recombination on the evolutionary relationship of some SBV isolates. The phylogenetic trees showed that although all the SBV isolates form two major groups, these two groups were not formed strictly according to their host specificity or geographical origin. These results indicate that both host specificity and geographic origin decide the genetic diversity of SBV strains.

  10. Scalable Coverage Maintenance for Dense Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Jun Lu

    2007-06-01

    Full Text Available Owing to numerous potential applications, wireless sensor networks have been attracting significant research effort recently. The critical challenge that wireless sensor networks often face is to sustain long-term operation on limited battery energy. Coverage maintenance schemes can effectively prolong network lifetime by selecting and employing a subset of sensors in the network to provide sufficient sensing coverage over a target region. We envision future wireless sensor networks composed of a vast number of miniaturized sensors in exceedingly high density. Therefore, the key issue of coverage maintenance for future sensor networks is the scalability to sensor deployment density. In this paper, we propose a novel coverage maintenance scheme, scalable coverage maintenance (SCOM, which is scalable to sensor deployment density in terms of communication overhead (i.e., number of transmitted and received beacons and computational complexity (i.e., time and space complexity. In addition, SCOM achieves high energy efficiency and load balancing over different sensors. We have validated our claims through both analysis and simulations.

  11. Design and Implementation of Ceph: A Scalable Distributed File System

    Energy Technology Data Exchange (ETDEWEB)

    Weil, S A; Brandt, S A; Miller, E L; Long, D E; Maltzahn, C

    2006-04-19

    File system designers continue to look to new architectures to improve scalability. Object-based storage diverges from server-based (e.g. NFS) and SAN-based storage systems by coupling processors and memory with disk drives, delegating low-level allocation to object storage devices (OSDs) and decoupling I/O (read/write) from metadata (file open/close) operations. Even recent object-based systems inherit decades-old architectural choices going back to early UNIX file systems, however, limiting their ability to effectively scale to hundreds of petabytes. We present Ceph, a distributed file system that provides excellent performance and reliability with unprecedented scalability. Ceph maximizes the separation between data and metadata management by replacing allocation tables with a pseudo-random data distribution function (CRUSH) designed for heterogeneous and dynamic clusters of unreliable OSDs. We leverage OSD intelligence to distribute data replication, failure detection and recovery with semi-autonomous OSDs running a specialized local object storage file system (EBOFS). Finally, Ceph is built around a dynamic distributed metadata management cluster that provides extremely efficient metadata management that seamlessly adapts to a wide range of general purpose and scientific computing file system workloads. We present performance measurements under a variety of workloads that show superior I/O performance and scalable metadata management (more than a quarter million metadata ops/sec).

  12. Event metadata records as a testbed for scalable data mining

    Science.gov (United States)

    van Gemmeren, P.; Malon, D.

    2010-04-01

    At a data rate of 200 hertz, event metadata records ("TAGs," in ATLAS parlance) provide fertile grounds for development and evaluation of tools for scalable data mining. It is easy, of course, to apply HEP-specific selection or classification rules to event records and to label such an exercise "data mining," but our interest is different. Advanced statistical methods and tools such as classification, association rule mining, and cluster analysis are common outside the high energy physics community. These tools can prove useful, not for discovery physics, but for learning about our data, our detector, and our software. A fixed and relatively simple schema makes TAG export to other storage technologies such as HDF5 straightforward. This simplifies the task of exploiting very-large-scale parallel platforms such as Argonne National Laboratory's BlueGene/P, currently the largest supercomputer in the world for open science, in the development of scalable tools for data mining. Using a domain-neutral scientific data format may also enable us to take advantage of existing data mining components from other communities. There is, further, a substantial literature on the topic of one-pass algorithms and stream mining techniques, and such tools may be inserted naturally at various points in the event data processing and distribution chain. This paper describes early experience with event metadata records from ATLAS simulation and commissioning as a testbed for scalable data mining tool development and evaluation.

  13. Scalable Dynamic Instrumentation for BlueGene/L

    Energy Technology Data Exchange (ETDEWEB)

    Schulz, M; Ahn, D; Bernat, A; de Supinski, B R; Ko, S Y; Lee, G; Rountree, B

    2005-09-08

    Dynamic binary instrumentation for performance analysis on new, large scale architectures such as the IBM Blue Gene/L system (BG/L) poses new challenges. Their scale--with potentially hundreds of thousands of compute nodes--requires new, more scalable mechanisms to deploy and to organize binary instrumentation and to collect the resulting data gathered by the inserted probes. Further, many of these new machines don't support full operating systems on the compute nodes; rather, they rely on light-weight custom compute kernels that do not support daemon-based implementations. We describe the design and current status of a new implementation of the DPCL (Dynamic Probe Class Library) API for BG/L. DPCL provides an easy to use layer for dynamic instrumentation on parallel MPI applications based on the DynInst dynamic instrumentation mechanism for sequential platforms. Our work includes modifying DynInst to control instrumentation from remote I/O nodes and porting DPCL's communication to use MRNet, a scalable data reduction network for collecting performance data. We describe extensions to the DPCL API that support instrumentation of task subsets and aggregation of collected performance data. Overall, our implementation provides a scalable infrastructure that provides efficient binary instrumentation on BG/L.

  14. The intergroup protocols: Scalable group communication for the internet

    Energy Technology Data Exchange (ETDEWEB)

    Berket, Karlo [Univ. of California, Santa Barbara, CA (United States)

    2000-12-04

    Reliable group ordered delivery of multicast messages in a distributed system is a useful service that simplifies the programming of distributed applications. Such a service helps to maintain the consistency of replicated information and to coordinate the activities of the various processes. With the increasing popularity of the Internet, there is an increasing interest in scaling the protocols that provide this service to the environment of the Internet. The InterGroup protocol suite, described in this dissertation, provides such a service, and is intended for the environment of the Internet with scalability to large numbers of nodes and high latency links. The InterGroup protocols approach the scalability problem from various directions. They redefine the meaning of group membership, allow voluntary membership changes, add a receiver-oriented selection of delivery guarantees that permits heterogeneity of the receiver set, and provide a scalable reliability service. The InterGroup system comprises several components, executing at various sites within the system. Each component provides part of the services necessary to implement a group communication system for the wide-area. The components can be categorized as: (1) control hierarchy, (2) reliable multicast, (3) message distribution and delivery, and (4) process group membership. We have implemented a prototype of the InterGroup protocols in Java, and have tested the system performance in both local-area and wide-area networks.

  15. Scalable MPEG-4 Encoder on FPGA Multiprocessor SOC

    Directory of Open Access Journals (Sweden)

    Kulmala Ari

    2006-01-01

    Full Text Available High computational requirements combined with rapidly evolving video coding algorithms and standards are a great challenge for contemporary encoder implementations. Rapid specification changes prefer full programmability and configurability both for software and hardware. This paper presents a novel scalable MPEG-4 video encoder on an FPGA-based multiprocessor system-on-chip (MPSOC. The MPSOC architecture is truly scalable and is based on a vendor-independent intellectual property (IP block interconnection network. The scalability in video encoding is achieved by spatial parallelization where images are divided to horizontal slices. A case design is presented with up to four synthesized processors on an Altera Stratix 1S40 device. A truly portable ANSI-C implementation that supports an arbitrary number of processors gives 11 QCIF frames/s at 50 MHz without processor specific optimizations. The parallelization efficiency is 97% for two processors and 93% with three. The FPGA utilization is 70%, requiring 28 797 logic elements. The implementation effort is significantly lower compared to traditional multiprocessor implementations.

  16. Scalable MPEG-4 Encoder on FPGA Multiprocessor SOC

    Directory of Open Access Journals (Sweden)

    Marko Hännikäinen

    2006-10-01

    Full Text Available High computational requirements combined with rapidly evolving video coding algorithms and standards are a great challenge for contemporary encoder implementations. Rapid specification changes prefer full programmability and configurability both for software and hardware. This paper presents a novel scalable MPEG-4 video encoder on an FPGA-based multiprocessor system-on-chip (MPSOC. The MPSOC architecture is truly scalable and is based on a vendor-independent intellectual property (IP block interconnection network. The scalability in video encoding is achieved by spatial parallelization where images are divided to horizontal slices. A case design is presented with up to four synthesized processors on an Altera Stratix 1S40 device. A truly portable ANSI-C implementation that supports an arbitrary number of processors gives 11 QCIF frames/s at 50 MHz without processor specific optimizations. The parallelization efficiency is 97% for two processors and 93% with three. The FPGA utilization is 70%, requiring 28 797 logic elements. The implementation effort is significantly lower compared to traditional multiprocessor implementations.

  17. Scalability improvements to NRLMOL for DFT calculations of large molecules

    Science.gov (United States)

    Diaz, Carlos Manuel

    Advances in high performance computing (HPC) have provided a way to treat large, computationally demanding tasks using thousands of processors. With the development of more powerful HPC architectures, the need to create efficient and scalable code has grown more important. Electronic structure calculations are valuable in understanding experimental observations and are routinely used for new materials predictions. For the electronic structure calculations, the memory and computation time are proportional to the number of atoms. Memory requirements for these calculations scale as N2, where N is the number of atoms. While the recent advances in HPC offer platforms with large numbers of cores, the limited amount of memory available on a given node and poor scalability of the electronic structure code hinder their efficient usage of these platforms. This thesis will present some developments to overcome these bottlenecks in order to study large systems. These developments, which are implemented in the NRLMOL electronic structure code, involve the use of sparse matrix storage formats and the use of linear algebra using sparse and distributed matrices. These developments along with other related development now allow ground state density functional calculations using up to 25,000 basis functions and the excited state calculations using up to 17,000 basis functions while utilizing all cores on a node. An example on a light-harvesting triad molecule is described. Finally, future plans to further improve the scalability will be presented.

  18. Scalable force directed graph layout algorithms using fast multipole methods

    KAUST Repository

    Yunis, Enas Abdulrahman

    2012-06-01

    We present an extension to ExaFMM, a Fast Multipole Method library, as a generalized approach for fast and scalable execution of the Force-Directed Graph Layout algorithm. The Force-Directed Graph Layout algorithm is a physics-based approach to graph layout that treats the vertices V as repelling charged particles with the edges E connecting them acting as springs. Traditionally, the amount of work required in applying the Force-Directed Graph Layout algorithm is O(|V|2 + |E|) using direct calculations and O(|V| log |V| + |E|) using truncation, filtering, and/or multi-level techniques. Correct application of the Fast Multipole Method allows us to maintain a lower complexity of O(|V| + |E|) while regaining most of the precision lost in other techniques. Solving layout problems for truly large graphs with millions of vertices still requires a scalable algorithm and implementation. We have been able to leverage the scalability and architectural adaptability of the ExaFMM library to create a Force-Directed Graph Layout implementation that runs efficiently on distributed multicore and multi-GPU architectures. © 2012 IEEE.

  19. Scalable Video Coding with Interlayer Signal Decorrelation Techniques

    Directory of Open Access Journals (Sweden)

    Yang Wenxian

    2007-01-01

    Full Text Available Scalability is one of the essential requirements in the compression of visual data for present-day multimedia communications and storage. The basic building block for providing the spatial scalability in the scalable video coding (SVC standard is the well-known Laplacian pyramid (LP. An LP achieves the multiscale representation of the video as a base-layer signal at lower resolution together with several enhancement-layer signals at successive higher resolutions. In this paper, we propose to improve the coding performance of the enhancement layers through efficient interlayer decorrelation techniques. We first show that, with nonbiorthogonal upsampling and downsampling filters, the base layer and the enhancement layers are correlated. We investigate two structures to reduce this correlation. The first structure updates the base-layer signal by subtracting from it the low-frequency component of the enhancement layer signal. The second structure modifies the prediction in order that the low-frequency component in the new enhancement layer is diminished. The second structure is integrated in the JSVM 4.0 codec with suitable modifications in the prediction modes. Experimental results with some standard test sequences demonstrate coding gains up to 1 dB for I pictures and up to 0.7 dB for both I and P pictures.

  20. Event metadata records as a testbed for scalable data mining

    Energy Technology Data Exchange (ETDEWEB)

    Gemmeren, P van; Malon, D, E-mail: gemmeren@anl.go [Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2010-04-01

    At a data rate of 200 hertz, event metadata records ('TAGs,' in ATLAS parlance) provide fertile grounds for development and evaluation of tools for scalable data mining. It is easy, of course, to apply HEP-specific selection or classification rules to event records and to label such an exercise 'data mining,' but our interest is different. Advanced statistical methods and tools such as classification, association rule mining, and cluster analysis are common outside the high energy physics community. These tools can prove useful, not for discovery physics, but for learning about our data, our detector, and our software. A fixed and relatively simple schema makes TAG export to other storage technologies such as HDF5 straightforward. This simplifies the task of exploiting very-large-scale parallel platforms such as Argonne National Laboratory's BlueGene/P, currently the largest supercomputer in the world for open science, in the development of scalable tools for data mining. Using a domain-neutral scientific data format may also enable us to take advantage of existing data mining components from other communities. There is, further, a substantial literature on the topic of one-pass algorithms and stream mining techniques, and such tools may be inserted naturally at various points in the event data processing and distribution chain. This paper describes early experience with event metadata records from ATLAS simulation and commissioning as a testbed for scalable data mining tool development and evaluation.

  1. Probabilistic graphical model representation in phylogenetics.

    Science.gov (United States)

    Höhna, Sebastian; Heath, Tracy A; Boussau, Bastien; Landis, Michael J; Ronquist, Fredrik; Huelsenbeck, John P

    2014-09-01

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  2. The macroecology of phylogenetically structured hummingbird-plant networks

    DEFF Research Database (Denmark)

    González, Ana M. Martín; Dalsgaard, Bo; Nogues, David Bravo

    2015-01-01

    Aim To investigate the association between hummingbird–plant network structure and species richness, phylogenetic signal on species' interaction pattern, insularity and historical and current climate. Location Fifty-four communities along a c. 10,000 km latitudinal gradient across the Americas (39......° N–32° S), ranging from sea level to c. 3700 m a.s.l., located on the mainland and on islands and covering a wide range of climate regimes. Methods We measured the level of specialization and modularity in mutualistic plant–hummingbird interaction networks. Using an ordinary least squares multimodel.......32–0.45, respectively). Specifically, higher levels of specialization and modularity were associated with species-rich communities and communities in which closely related hummingbirds visited distinct sets of flowering species. On the mainland, specialization was also associated with warmer temperatures and greater...

  3. Phylogenetic diversity of plants alters the effect of species richness on invertebrate herbivory.

    Science.gov (United States)

    Dinnage, Russell

    2013-01-01

    Long-standing ecological theory proposes that diverse communities of plants should experience a decrease in herbivory. Yet previous empirical examinations of this hypothesis have revealed that plant species richness increases herbivory in just as many systems as it decreases it. In this study, I ask whether more insight into the role of plant diversity in promoting or suppressing herbivory can be gained by incorporating information about the evolutionary history of species in a community. In an old field system in southern Ontario, I surveyed communities of plants and measured levels of leaf damage on 27 species in 38 plots. I calculated a measure of phylogenetic diversity (PSE) that encapsulates information about the amount of evolutionary history represented in each of the plots and looked for a relationship between levels of herbivory and both species richness and phylogenetic diversity using a generalized linear mixed model (GLMM) that could account for variation in herbivory levels between species. I found that species richness was positively associated with herbivore damage at the plot-level, in keeping with the results from several other recent studies on this question. On the other hand, phylogenetic diversity was associated with decreased herbivory. Importantly, there was also an interaction between species richness and phylogenetic diversity, such that plots with the highest levels of herbivory were plots which had many species but only if those species tended to be closely related to one another. I propose that these results are the consequence of interactions with herbivores whose diets are phylogenetically specialized (for which I introduce the term cladophage), and how phylogenetic diversity may alter their realized host ranges. These results suggest that incorporating a phylogenetic perspective can add valuable additional insight into the role of plant diversity in explaining or predicting levels of herbivory at a whole-community scale.

  4. Scalability of Sustainable Business Models in Hybrid Organizations

    Directory of Open Access Journals (Sweden)

    Adam Jabłoński

    2016-02-01

    Full Text Available The dynamics of change in modern business create new mechanisms for company management to determine their pursuit and the achievement of their high performance. This performance maintained over a long period of time becomes a source of ensuring business continuity by companies. An ontological being enabling the adoption of such assumptions is such a business model that has the ability to generate results in every possible market situation and, moreover, it has the features of permanent adaptability. A feature that describes the adaptability of the business model is its scalability. Being a factor ensuring more work and more efficient work with an increasing number of components, scalability can be applied to the concept of business models as the company’s ability to maintain similar or higher performance through it. Ensuring the company’s performance in the long term helps to build the so-called sustainable business model that often balances the objectives of stakeholders and shareholders, and that is created by the implemented principles of value-based management and corporate social responsibility. This perception of business paves the way for building hybrid organizations that integrate business activities with pro-social ones. The combination of an approach typical of hybrid organizations in designing and implementing sustainable business models pursuant to the scalability criterion seems interesting from the cognitive point of view. Today, hybrid organizations are great spaces for building effective and efficient mechanisms for dialogue between business and society. This requires the appropriate business model. The purpose of the paper is to present the conceptualization and operationalization of scalability of sustainable business models that determine the performance of a hybrid organization in the network environment. The paper presents the original concept of applying scalability in sustainable business models with detailed

  5. Advances in Intelligent Modelling and Simulation Artificial Intelligence-Based Models and Techniques in Scalable Computing

    CERN Document Server

    Khan, Samee; Burczy´nski, Tadeusz

    2012-01-01

    One of the most challenging issues in today’s large-scale computational modeling and design is to effectively manage the complex distributed environments, such as computational clouds, grids, ad hoc, and P2P networks operating under  various  types of users with evolving relationships fraught with  uncertainties. In this context, the IT resources and services usually belong to different owners (institutions, enterprises, or individuals) and are managed by different administrators. Moreover, uncertainties are presented to the system at hand in various forms of information that are incomplete, imprecise, fragmentary, or overloading, which hinders in the full and precise resolve of the evaluation criteria, subsequencing and selection, and the assignment scores. Intelligent scalable systems enable the flexible routing and charging, advanced user interactions and the aggregation and sharing of geographically-distributed resources in modern large-scale systems.   This book presents new ideas, theories, models...

  6. A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data.

    Science.gov (United States)

    Gui, Shupeng; Rice, Andrew P; Chen, Rui; Wu, Liang; Liu, Ji; Miao, Hongyu

    2017-01-31

    Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes from temporal gene expression data, especially for complex eukaryotes like human. Moreover, recent work suggests that these methods still suffer from the curse of dimensionality if a network size increases to 100 or higher. Here we present a novel scalable algorithm for identifying genome-wide gene regulatory network (GRN) structures, and we have verified the algorithm performances by extensive simulation studies based on the DREAM challenge benchmark data. The highlight of our method is that its superior performance does not degenerate even for a network size on the order of 10(4), and is thus readily applicable to large-scale complex networks. Such a breakthrough is achieved by considering both prior biological knowledge and multiple topological properties (i.e., sparsity and hub gene structure) of complex networks in the regularized formulation. We also validate and illustrate the application of our algorithm in practice using the time-course gene expression data from a study on human respiratory epithelial cells in response to influenza A virus (IAV) infection, as well as the CHIP-seq data from ENCODE on transcription factor (TF) and target gene interactions. An interesting finding, owing to the proposed algorithm, is that the biggest hub structures (e.g., top ten) in the GRN all center at some transcription factors in the context of epithelial cell infection by IAV. The proposed algorithm is the first scalable method for large complex network structure identification. The GRN structure identified by our algorithm could reveal possible biological links and help researchers to choose which gene functions to investigate in a biological event. The algorithm described in this article is implemented in MATLAB (Ⓡ) , and the source code is

  7. Undergraduate Students’ Difficulties in Reading and Constructing Phylogenetic Tree

    Science.gov (United States)

    Sa'adah, S.; Tapilouw, F. S.; Hidayat, T.

    2017-02-01

    Representation is a very important communication tool to communicate scientific concepts. Biologists produce phylogenetic representation to express their understanding of evolutionary relationships. The phylogenetic tree is visual representation depict a hypothesis about the evolutionary relationship and widely used in the biological sciences. Phylogenetic tree currently growing for many disciplines in biology. Consequently, learning about phylogenetic tree become an important part of biological education and an interesting area for biology education research. However, research showed many students often struggle with interpreting the information that phylogenetic trees depict. The purpose of this study was to investigate undergraduate students’ difficulties in reading and constructing a phylogenetic tree. The method of this study is a descriptive method. In this study, we used questionnaires, interviews, multiple choice and open-ended questions, reflective journals and observations. The findings showed students experiencing difficulties, especially in constructing a phylogenetic tree. The students’ responds indicated that main reasons for difficulties in constructing a phylogenetic tree are difficult to placing taxa in a phylogenetic tree based on the data provided so that the phylogenetic tree constructed does not describe the actual evolutionary relationship (incorrect relatedness). Students also have difficulties in determining the sister group, character synapomorphy, autapomorphy from data provided (character table) and comparing among phylogenetic tree. According to them building the phylogenetic tree is more difficult than reading the phylogenetic tree. Finding this studies provide information to undergraduate instructor and students to overcome learning difficulties of reading and constructing phylogenetic tree.

  8. Mitochondrial DNA sequence-based phylogenetic relationship ...

    Indian Academy of Sciences (India)

    The phylogenetic relationships among flesh flies of the family Sarcophagidae has been based mainly on the morphology of male genitalia. However, the male genitalic character-based relationships are far from satisfactory. Therefore, in the present study mitochondrial DNA has been used as marker to unravel genetic ...

  9. The Drosophila bipectinata species complex: phylogenetic ...

    Indian Academy of Sciences (India)

    PARUL BANERJEE

    [Banerjee P. and Singh B. N. 2017 The Drosophila bipectinata species complex: phylogenetic relationship among different members based on chromosomal variations. ... understanding the intricacies of speciation (Yang et al. 1972;. Bock 1978 .... tures more number of larvae needs to be checked to confirm homozygosity.

  10. Identification and phylogenetic analysis of filamentous ...

    African Journals Online (AJOL)

    Unique banding patterns were observed from all tested cyanobacterial species and their molecular weights of each band were used to calculate their genetic distance among them. Random amplification of polymorphic DNA (RAPD) was carried out for the phylogenetic characterization of these strains. RAPD fingerprinting ...

  11. DNA barcoding and phylogenetic relationships in Timaliidae.

    Science.gov (United States)

    Huang, Z H; Ke, D H

    2015-06-01

    The Timaliidae, a diverse family of oscine passerine birds, has long been a subject of debate regarding its phylogeny. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used as a powerful marker for identification and phylogenetic studies of animal species. In the present study, we analyzed the COI barcodes of 71 species from 21 genera belonging to the family Timaliidae. Every bird species possessed a barcode distinct from that of other bird species. Kimura two-parameter (K2P) distances were calculated between barcodes. The average genetic distance between species was 18 times higher than the average genetic distance within species. The neighbor-joining method was used to construct a phylogenetic tree and all the species could be discriminated by their distinct clades within the phylogenetic tree. The results indicate that some currently recognized babbler genera might not be monophyletic, with the COI gene data supporting the hypothesis of polyphyly for Garrulax, Alcippe, and Minla. Thus, DNA barcoding is an effective molecular tool for Timaliidae species identification and phylogenetic inference.

  12. Chromosomal evolution and phylogenetic analyses in Tayassu ...

    Indian Academy of Sciences (India)

    The mammalian family Tayassuidae (peccaries) is confined to the New World and comprises three recognized extant species, white-lipped (Tayassu pecari), collared (Pecari tajacu) and chacoan (Catagonus wagneri) peccaries, which exhibit distinct morphological and chromosomal features. The phylogenetic relationships ...

  13. YBYRÁ facilitates comparison of large phylogenetic trees.

    Science.gov (United States)

    Machado, Denis Jacob

    2015-07-01

    The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

  14. Phylogenetic estimation of timescales using ancient DNA

    DEFF Research Database (Denmark)

    Molak, Martyna; Lorenzen, Eline; Shapiro, Beth

    2013-01-01

    analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise...

  15. Coproheme decarboxylases - Phylogenetic prediction versus biochemical experiments.

    Science.gov (United States)

    Pfanzagl, Vera; Holcik, Laurenz; Maresch, Daniel; Gorgone, Giulia; Michlits, Hanna; Furtmüller, Paul G; Hofbauer, Stefan

    2018-02-15

    Coproheme decarboxylases (ChdCs) are enzymes responsible for the catalysis of the terminal step in the coproporphyrin-dependent heme biosynthesis pathway. Phylogenetic analyses confirm that the gene encoding for ChdCs is widespread throughout the bacterial world. It is found in monoderm bacteria (Firmicutes, Actinobacteria), diderm bacteria (e. g. Nitrospirae) and also in Archaea. In order to test phylogenetic prediction ChdC representatives from all clades were expressed and examined for their coproheme decarboxylase activity. Based on available biochemical data and phylogenetic analyses a sequence motif (-Y-P-M/F-X-K/R-) is defined for ChdCs. We show for the first time that in diderm bacteria an active coproheme decarboxylase is present and that the archaeal ChdC homolog from Sulfolobus solfataricus is inactive and its physiological role remains elusive. This shows the limitation of phylogenetic prediction of an enzymatic activity, since the identified sequence motif is equally conserved across all previously defined clades. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Characterization of Escherichia coli Phylogenetic Groups ...

    African Journals Online (AJOL)

    infection, and neonatal meningitis.[1] Phylogenetic analysis has shown that E. coli strains fall into four main groups. (A, B1, B2, and D). It has been found that pathogenic E. coli strains causing extraintestinal infections mainly belong to group B2 and a lesser extent to group D whereas commensal strains belong to group A ...

  17. The First Darwinian Phylogenetic Tree of Plants.

    Science.gov (United States)

    Hoßfeld, Uwe; Watts, Elizabeth; Levit, Georgy S

    2017-02-01

    In 1866, the German zoologist Ernst Haeckel (1834-1919) published the first Darwinian trees of life in the history of biology in his book General Morphology of Organisms. We take a specific look at the first phylogenetic trees for the plant kingdom that Haeckel created as part of this two-volume work. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Tree models for macroevolution and phylogenetic analysis.

    Science.gov (United States)

    Jones, Graham R

    2011-12-01

    It has long been recognized that phylogenetic trees are more unbalanced than those generated by a Yule process. Recently, the degree of this imbalance has been quantified using the large set of phylogenetic trees available in the TreeBASE data set. In this article, a more precise analysis of imbalance is undertaken. Trees simulated under a range of models are compared with trees from TreeBASE and two smaller data sets. Several simple models can match the amount of imbalance measured in real data. Most of them also match the variance of imbalance among empirical trees to a remarkable degree. Statistics are developed to measure balance and to distinguish between trees with the same overall imbalance. The match between models and data for these statistics is investigated. In particular, age-dependent (Bellman-Harris) branching process are studied in detail. It remains difficult to separate the process of macroevolution from biases introduced by sampling. The lessons for phylogenetic analysis are clearer. In particular, the use of the usual proportional to distinguishable arrangements (uniform) prior on tree topologies in Bayesian phylogenetic analysis is not recommended.

  19. Transcript variations, phylogenetic tree and chromosomal ...

    Indian Academy of Sciences (India)

    Transcript variations, phylogenetic tree and chromosomal localization of porcine aryl hydrocarbon receptor (AhR) and AhR nuclear translocator (ARNT) genes ... Prawochenskiego 5, 10-720 Olsztyn, Poland; Department of Genetics and Animal Breeding, Poznan University of Life Science, Wolynska 33, 60-637 Poznan, ...

  20. Mitochondrial DNA sequence-based phylogenetic relationship ...

    Indian Academy of Sciences (India)

    Introduction. Mitochondrial DNA (mtDNA) has been one of the most widely used molecular markers for phylogenetic studies in animals, because of its simple genomic structure (Avise. 2004). Among insects, the maximum .... 2007 Population structure of the malaria vector Anopheles dar- lingi in Rondonia, Brazilian Amazon, ...

  1. Scalable fabrication of nanomaterials based piezoresistivity sensors with enhanced performance

    Science.gov (United States)

    Hoang, Phong Tran

    Nanomaterials are small structures that have at least one dimension less than 100 nanometers. Depending on the number of dimensions that are not confined to the nanoscale range, nanomaterials can be classified into 0D, 1D and 2D types. Due to their small sizes, nanoparticles possess exceptional physical and chemical properties which opens a unique possibility for the next generation of strain sensors that are cheap, multifunctional, high sensitivity and reliability. Over the years, thanks to the development of new nanomaterials and the printing technologies, a number of printing techniques have been developed to fabricate a wide range of electronic devices on diverse substrates. Nanomaterials based thin film devices can be readily patterned and fabricated in a variety of ways, including printing, spraying and laser direct writing. In this work, we review the piezoresistivity of nanomaterials of different categories and study various printing approaches to utilize their excellent properties in the fabrication of scalable and printable thin film strain gauges. CNT-AgNP composite thin films were fabricated using a solution based screen printing process. By controlling the concentration ratio of CNTs to AgNPs in the nanocomposites and the supporting substrates, we were able to engineer the crack formation to achieve stable and high sensitivity sensors. The crack formation in the composite films lead to piezoresistive sensors with high GFs up to 221.2. Also, with a simple, low cost, and easy to scale up fabrication process they may find use as an alternative to traditional strain sensors. By using computer controlled spray coating system, we can achieve uniform and high quality CNTs thin films for the fabrication of strain sensors and transparent / flexible electrodes. A simple diazonium salt treatment of the pristine SWCNT thin film has been identified to be efficient in greatly enhancing the piezoresistive sensitivity of SWCNT thin film based piezoresistive sensors

  2. Cnidarian phylogenetic relationships as revealed by mitogenomics.

    Science.gov (United States)

    Kayal, Ehsan; Roure, Béatrice; Philippe, Hervé; Collins, Allen G; Lavrov, Dennis V

    2013-01-09

    Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) - cnidarians with a reproductive polyp and the absence of a medusa stage - and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) - cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in

  3. Cnidarian phylogenetic relationships as revealed by mitogenomics

    Science.gov (United States)

    2013-01-01

    Background Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) – cnidarians with a reproductive polyp and the absence of a medusa stage – and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) – cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. Results We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Conclusions Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that

  4. Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

    Science.gov (United States)

    Roswitha Schmickl; Aaron Liston; Vojtěch Zeisek; Kenneth Oberlander; Kevin Weitemier; Shannon C. K. Straub; Richard C. Cronn; Léanne L. Dreyer; Jan. Suda

    2016-01-01

    Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds...

  5. A Metric on the Space of Partly Reduced Phylogenetic Networks

    Directory of Open Access Journals (Sweden)

    Juan Wang

    2016-01-01

    Full Text Available Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, such as recombination between genes, hybridization between lineages, and horizontal gene transfer. The researchers have designed several measures for computing the dissimilarity between two phylogenetic networks, and each measure has been proven to be a metric on a special kind of phylogenetic networks. However, none of the existing measures is a metric on the space of partly reduced phylogenetic networks. In this paper, we provide a metric, de-distance, on the space of partly reduced phylogenetic networks, which is polynomial-time computable.

  6. A Metric on the Space of Partly Reduced Phylogenetic Networks.

    Science.gov (United States)

    Wang, Juan

    2016-01-01

    Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, such as recombination between genes, hybridization between lineages, and horizontal gene transfer. The researchers have designed several measures for computing the dissimilarity between two phylogenetic networks, and each measure has been proven to be a metric on a special kind of phylogenetic networks. However, none of the existing measures is a metric on the space of partly reduced phylogenetic networks. In this paper, we provide a metric, d e -distance, on the space of partly reduced phylogenetic networks, which is polynomial-time computable.

  7. Highly scalable multichannel mesh electronics for stable chronic brain electrophysiology

    Science.gov (United States)

    Fu, Tian-Ming; Hong, Guosong; Viveros, Robert D.; Zhou, Tao

    2017-01-01

    Implantable electrical probes have led to advances in neuroscience, brain−machine interfaces, and treatment of neurological diseases, yet they remain limited in several key aspects. Ideally, an electrical probe should be capable of recording from large numbers of neurons across multiple local circuits and, importantly, allow stable tracking of the evolution of these neurons over the entire course of study. Silicon probes based on microfabrication can yield large-scale, high-density recording but face challenges of chronic gliosis and instability due to mechanical and structural mismatch with the brain. Ultraflexible mesh electronics, on the other hand, have demonstrated negligible chronic immune response and stable long-term brain monitoring at single-neuron level, although, to date, it has been limited to 16 channels. Here, we present a scalable scheme for highly multiplexed mesh electronics probes to bridge the gap between scalability and flexibility, where 32 to 128 channels per probe were implemented while the crucial brain-like structure and mechanics were maintained. Combining this mesh design with multisite injection, we demonstrate stable 128-channel local field potential and single-unit recordings from multiple brain regions in awake restrained mice over 4 mo. In addition, the newly integrated mesh is used to validate stable chronic recordings in freely behaving mice. This scalable scheme for mesh electronics together with demonstrated long-term stability represent important progress toward the realization of ideal implantable electrical probes allowing for mapping and tracking single-neuron level circuit changes associated with learning, aging, and neurodegenerative diseases. PMID:29109247

  8. AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa

    Directory of Open Access Journals (Sweden)

    Meier-Kolthoff Jan

    2007-10-01

    Full Text Available Abstract Background Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. The sophisticated statistical test for host-parasite co-phylogenetic analyses implemented in Parafit does not allow it to handle large datasets in reasonable times. The Parafit and DistPCoA programs are the by far most compute-intensive components of the Parafit analysis pipeline. We present AxParafit and AxPcoords (Ax stands for Accelerated which are highly optimized versions of Parafit and DistPCoA respectively. Results Both programs have been entirely re-written in C. Via optimization of the algorithm and the C code as well as integration of highly tuned BLAS and LAPACK methods AxParafit runs 5–61 times faster than Parafit with a lower memory footprint (up to 35% reduction while the performance benefit increases with growing dataset size. The MPI-based parallel implementation of AxParafit shows good scalability on up to 128 processors, even on medium-sized datasets. The parallel analysis with AxParafit on 128 CPUs for a medium-sized dataset with an 512 by 512 association matrix is more than 1,200/128 times faster per processor than the sequential Parafit run. AxPcoords is 8–26 times faster than DistPCoA and numerically stable on large datasets. We outline the substantial benefits of using parallel AxParafit by example of a large-scale empirical study on smut fungi and their host plants. To the best of our knowledge, this study represents the largest co-phylogenetic analysis to date. Conclusion The highly efficient AxPcoords and AxParafit programs allow for large-scale co-phylogenetic analyses on several thousands of taxa for the first time. In addition, AxParafit and AxPcoords have been integrated into the easy-to-use CopyCat tool.

  9. Highly Scalable Trip Grouping for Large Scale Collective Transportation Systems

    DEFF Research Database (Denmark)

    Gidofalvi, Gyozo; Pedersen, Torben Bach; Risch, Tore

    2008-01-01

    Transportation-related problems, like road congestion, parking, and pollution, are increasing in most cities. In order to reduce traffic, recent work has proposed methods for vehicle sharing, for example for sharing cabs by grouping "closeby" cab requests and thus minimizing transportation cost...... and utilizing cab space. However, the methods published so far do not scale to large data volumes, which is necessary to facilitate large-scale collective transportation systems, e.g., ride-sharing systems for large cities. This paper presents highly scalable trip grouping algorithms, which generalize previous...

  10. SAR++: A Multi-Channel Scalable and Reconfigurable SAR System

    DEFF Research Database (Denmark)

    Høeg, Flemming; Christensen, Erik Lintz

    2002-01-01

    SAR++ is a technology program aiming at developing know-how and technology needed to design the next generation civilian SAR systems. Technology has reached a state, which allows major parts of the digital subsystem to be built using custom-off-the-shelf (COTS) components. A design goal...... is to design a modular, scalable and reconfigurable SAR system using such components, in order to ensure maximum flexibility for the users of the actual system and for future system updates. Having these aspects in mind the SAR++ system is presented with focus on the digital subsystem architecture...

  11. Scalable brain network construction on white matter fibers

    Science.gov (United States)

    Chung, Moo K.; Adluru, Nagesh; Dalton, Kim M.; Alexander, Andrew L.; Davidson, Richard J.

    2011-03-01

    DTI offers a unique opportunity to characterize the structural connectivity of the human brain non-invasively by tracing white matter fiber tracts. Whole brain tractography studies routinely generate up to half million tracts per brain, which serves as edges in an extremely large 3D graph with up to half million edges. Currently there is no agreed-upon method for constructing the brain structural network graphs out of large number of white matter tracts. In this paper, we present a scalable iterative framework called the ɛ-neighbor method for building a network graph and apply it to testing abnormal connectivity in autism.

  12. Using overlay network architectures for scalable video distribution

    Science.gov (United States)

    Patrikakis, Charalampos Z.; Despotopoulos, Yannis; Fafali, Paraskevi; Cha, Jihun; Kim, Kyuheon

    2004-11-01

    Within the last years, the enormous growth of Internet based communication as well as the rapid increase of available processing power has lead to the widespread use of multimedia streaming as a means to convey information. This work aims at providing an open architecture designed to support scalable streaming to a large number of clients using application layer multicast. The architecture is based on media relay nodes that can be deployed transparently to any existing media distribution scheme, which can support media streamed using the RTP and RTSP protocols. The architecture is based on overlay networks at application level, featuring rate adaptation mechanisms for responding to network congestion.

  13. Design for scalability in 3D computer graphics architectures

    DEFF Research Database (Denmark)

    Holten-Lund, Hans Erik

    2002-01-01

    This thesis describes useful methods and techniques for designing scalable hybrid parallel rendering architectures for 3D computer graphics. Various techniques for utilizing parallelism in a pipelines system are analyzed. During the Ph.D study a prototype 3D graphics architecture named Hybris has...... been developed. Hybris is a prototype rendering architeture which can be tailored to many specific 3D graphics applications and implemented in various ways. Parallel software implementations for both single and multi-processor Windows 2000 system have been demonstrated. Working hardware...... as a case study and an application of the Hybris graphics architecture....

  14. Scalable web services for the PSIPRED Protein Analysis Workbench.

    Science.gov (United States)

    Buchan, Daniel W A; Minneci, Federico; Nugent, Tim C O; Bryson, Kevin; Jones, David T

    2013-07-01

    Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.

  15. A Scalable Framework to Detect Personal Health Mentions on Twitter.

    Science.gov (United States)

    Yin, Zhijun; Fabbri, Daniel; Rosenbloom, S Trent; Malin, Bradley

    2015-06-05

    Biomedical research has traditionally been conducted via surveys and the analysis of medical records. However, these resources are limited in their content, such that non-traditional domains (eg, online forums and social media) have an opportunity to supplement the view of an individual's health. The objective of this study was to develop a scalable framework to detect personal health status mentions on Twitter and assess the extent to which such information is disclosed. We collected more than 250 million tweets via the Twitter streaming API over a 2-month period in 2014. The corpus was filtered down to approximately 250,000 tweets, stratified across 34 high-impact health issues, based on guidance from the Medical Expenditure Panel Survey. We created a labeled corpus of several thousand tweets via a survey, administered over Amazon Mechanical Turk, that documents when terms correspond to mentions of personal health issues or an alternative (eg, a metaphor). We engineered a scalable classifier for personal health mentions via feature selection and assessed its potential over the health issues. We further investigated the utility of the tweets by determining the extent to which Twitter users disclose personal health status. Our investigation yielded several notable findings. First, we find that tweets from a small subset of the health issues can train a scalable classifier to detect health mentions. Specifically, training on 2000 tweets from four health issues (cancer, depression, hypertension, and leukemia) yielded a classifier with precision of 0.77 on all 34 health issues. Second, Twitter users disclosed personal health status for all health issues. Notably, personal health status was disclosed over 50% of the time for 11 out of 34 (33%) investigated health issues. Third, the disclosure rate was dependent on the health issue in a statistically significant manner (PTwitter in a scalable manner. These mentions correspond to the health issues of the Twitter users

  16. A Scalable Architecture of a Structured LDPC Decoder

    Science.gov (United States)

    Lee, Jason Kwok-San; Lee, Benjamin; Thorpe, Jeremy; Andrews, Kenneth; Dolinar, Sam; Hamkins, Jon

    2004-01-01

    We present a scalable decoding architecture for a certain class of structured LDPC codes. The codes are designed using a small (n,r) protograph that is replicated Z times to produce a decoding graph for a (Z x n, Z x r) code. Using this architecture, we have implemented a decoder for a (4096,2048) LDPC code on a Xilinx Virtex-II 2000 FPGA, and achieved decoding speeds of 31 Mbps with 10 fixed iterations. The implemented message-passing algorithm uses an optimized 3-bit non-uniform quantizer that operates with 0.2dB implementation loss relative to a floating point decoder.

  17. Scalable implementation of boson sampling with trapped ions.

    Science.gov (United States)

    Shen, C; Zhang, Z; Duan, L-M

    2014-02-07

    Boson sampling solves a classically intractable problem by sampling from a probability distribution given by matrix permanents. We propose a scalable implementation of boson sampling using local transverse phonon modes of trapped ions to encode the bosons. The proposed scheme allows deterministic preparation and high-efficiency readout of the bosons in the Fock states and universal mode mixing. With the state-of-the-art trapped ion technology, it is feasible to realize boson sampling with tens of bosons by this scheme, which would outperform the most powerful classical computers and constitute an effective disproof of the famous extended Church-Turing thesis.

  18. Scalable video on demand adaptive Internet-based distribution

    CERN Document Server

    Zink, Michael

    2013-01-01

    In recent years, the proliferation of available video content and the popularity of the Internet have encouraged service providers to develop new ways of distributing content to clients. Increasing video scaling ratios and advanced digital signal processing techniques have led to Internet Video-on-Demand applications, but these currently lack efficiency and quality. Scalable Video on Demand: Adaptive Internet-based Distribution examines how current video compression and streaming can be used to deliver high-quality applications over the Internet. In addition to analysing the problems

  19. Empirical Evaluation of Superposition Coded Multicasting for Scalable Video

    KAUST Repository

    Chun Pong Lau

    2013-03-01

    In this paper we investigate cross-layer superposition coded multicast (SCM). Previous studies have proven its effectiveness in exploiting better channel capacity and service granularities via both analytical and simulation approaches. However, it has never been practically implemented using a commercial 4G system. This paper demonstrates our prototype in achieving the SCM using a standard 802.16 based testbed for scalable video transmissions. In particular, to implement the superposition coded (SPC) modulation, we take advantage a novel software approach, namely logical SPC (L-SPC), which aims to mimic the physical layer superposition coded modulation. The emulation results show improved throughput comparing with generic multicast method.

  20. Phylogenetic relatedness predicts priority effects in nectar yeast communities.

    Science.gov (United States)

    Peay, Kabir G; Belisle, Melinda; Fukami, Tadashi

    2012-02-22

    Priority effects, in which the outcome of species interactions depends on the order of their arrival, are a key component of many models of community assembly. Yet, much remains unknown about how priority effects vary in strength among species in a community and what factors explain this variation. We experimented with a model natural community in laboratory microcosms that allowed us to quantify the strength of priority effects for most of the yeast species found in the floral nectar of a hummingbird-pollinated shrub at a biological preserve in northern California. We found that priority effects were widespread, with late-arriving species experiencing strong negative effects from early-arriving species. However, the magnitude of priority effects varied across species pairs. This variation was phylogenetically non-random, with priority effects stronger between closer relatives. Analysis of carbon and amino acid consumption profiles indicated that competition between closer relatives was more intense owing to higher ecological similarity, consistent with Darwin's naturalization hypothesis. These results suggest that phylogenetic relatedness between potential colonists may explain the strength of priority effects and, as a consequence, the degree to which community assembly is historically contingent.

  1. Towards an integrated phylogenetic classification of the Tremellomycetes

    NARCIS (Netherlands)

    Liu, X. -Z.; Wang, Q. -M.; Goeker, M.; Groenewald, M.; Kachalkin, A. V.; Lumbsch, H. T.; Millanes, A. M.; Wedin, M.; Yurkov, A. M.; Boekhout, T.; Bai, F. -Y.

    Abstract Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic

  2. ANALYZING AVIATION SAFETY REPORTS: FROM TOPIC MODELING TO SCALABLE MULTI-LABEL CLASSIFICATION

    Data.gov (United States)

    National Aeronautics and Space Administration — ANALYZING AVIATION SAFETY REPORTS: FROM TOPIC MODELING TO SCALABLE MULTI-LABEL CLASSIFICATION AMRUDIN AGOVIC*, HANHUAI SHAN, AND ARINDAM BANERJEE Abstract. The...

  3. Implementing a hardware-friendly wavelet entropy codec for scalable video

    Science.gov (United States)

    Eeckhaut, Hendrik; Christiaens, Mark; Devos, Harald; Stroobandt, Dirk

    2005-11-01

    In the RESUME project (Reconfigurable Embedded Systems for Use in Multimedia Environments) we explore the benefits of an implementation of scalable multimedia applications using reconfigurable hardware by building an FPGA implementation of a scalable wavelet-based video decoder. The term "scalable" refers to a design that can easily accommodate changes in quality of service with minimal computational overhead. This is important for portable devices that have different Quality of Service (QoS) requirements and have varying power restrictions. The scalable video decoder consists of three major blocks: a Wavelet Entropy Decoder (WED), an Inverse Discrete Wavelet Transformer (IDWT) and a Motion Compensator (MC). The WED decodes entropy encoded parts of the video stream into wavelet transformed frames. These frames are decoded bitlayer per bitlayer. The more bitlayers are decoded the higher the image quality (scalability in image quality). Resolution scalability is obtained as an inherent property of the IDWT. Finally framerate scalability is achieved through hierarchical motion compensation. In this article we present the results of our investigation into the hardware implementation of such a scalable video codec. In particular we found that the implementation of the entropy codec is a significant bottleneck. We present an alternative, hardware-friendly algorithm for entropy coding with excellent data locality (both temporal and spatial), streaming capabilities, a high degree of parallelism, a smaller memory footprint and state-of-the-art compression while maintaining all required scalability properties. These claims are supported by an effective hardware implementation on an FPGA.

  4. SCALABLE TIME SERIES CHANGE DETECTION FOR BIOMASS MONITORING USING GAUSSIAN PROCESS

    Data.gov (United States)

    National Aeronautics and Space Administration — SCALABLE TIME SERIES CHANGE DETECTION FOR BIOMASS MONITORING USING GAUSSIAN PROCESS VARUN CHANDOLA AND RANGA RAJU VATSAVAI Abstract. Biomass monitoring,...

  5. Traffic and Quality Characterization of the H.264/AVC Scalable Video Coding Extension

    Directory of Open Access Journals (Sweden)

    Geert Van der Auwera

    2008-01-01

    Full Text Available The recent scalable video coding (SVC extension to the H.264/AVC video coding standard has unprecedented compression efficiency while supporting a wide range of scalability modes, including temporal, spatial, and quality (SNR scalability, as well as combined spatiotemporal SNR scalability. The traffic characteristics, especially the bit rate variabilities, of the individual layer streams critically affect their network transport. We study the SVC traffic statistics, including the bit rate distortion and bit rate variability distortion, with long CIF resolution video sequences and compare them with the corresponding MPEG-4 Part 2 traffic statistics. We consider (i temporal scalability with three temporal layers, (ii spatial scalability with a QCIF base layer and a CIF enhancement layer, as well as (iii quality scalability modes FGS and MGS. We find that the significant improvement in RD efficiency of SVC is accompanied by substantially higher traffic variabilities as compared to the equivalent MPEG-4 Part 2 streams. We find that separately analyzing the traffic of temporal-scalability only encodings gives reasonable estimates of the traffic statistics of the temporal layers embedded in combined spatiotemporal encodings and in the base layer of combined FGS-temporal encodings. Overall, we find that SVC achieves significantly higher compression ratios than MPEG-4 Part 2, but produces unprecedented levels of traffic variability, thus presenting new challenges for the network transport of scalable video.

  6. Phylogenetic Analysis of PRRSV from Danish Pigs

    DEFF Research Database (Denmark)

    Hjulsager, Charlotte Kristiane; Breum, Solvej Østergaard; Larsen, Lars Erik

    by phylogenetic analysis, in order to asses the applicability of vaccines currently used to control PRRSV infection in Danish pig herds. Materials and methods Lung tissue from samples submitted to the National Veterinary Institute during 2003-2008 for PRRSV diagnosis were screened for PRRSV by real-time RT......-PCR, essentially as described by Egli et al. 2001, on RNA extracted with RNeasy Mini Kit (QIAGEN). Complete open reading frames (ORF) ORF5 and ORF7 were PCR amplified as described (Oleksiewicz et al. 1998) and sequenced. Sequences were aligned and Neighbour-Joining trees were constructed with ClustalX. Trees were...... visualized with NJ-plot software. Genbank entries of Danish PRRSV sequences from the 1990’ties were included in the phylogenetic analysis. Translated sequences were aligned with current vaccine isolates. Results Both PRRSV EU and US type viruses were isolated from material submitted from Danish pigs...

  7. Molecular phylogenetics of mastodon and Tyrannosaurus rex.

    Science.gov (United States)

    Organ, Chris L; Schweitzer, Mary H; Zheng, Wenxia; Freimark, Lisa M; Cantley, Lewis C; Asara, John M

    2008-04-25

    We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.

  8. Phylogenetic paleobiogeography of Late Ordovician Laurentian brachiopods

    Directory of Open Access Journals (Sweden)

    Jennifer E. Bauer

    2014-12-01

    Full Text Available Phylogenetic biogeographic analysis of four brachiopod genera was used to uncover large-scale geologic drivers of Late Ordovician biogeographic differentiation in Laurentia. Previously generated phylogenetic hypotheses were converted into area cladograms, ancestral geographic ranges were optimized and speciation events characterized as via dispersal or vicariance, when possible. Area relationships were reconstructed using Lieberman-modified Brooks Parsimony Analysis. The resulting area cladograms indicate tectonic and oceanographic changes were the primary geologic drivers of biogeographic patterns within the focal taxa. The Taconic tectophase contributed to the separation of the Appalachian and Central basins as well as the two midcontinent basins, whereas sea level rise following the Boda Event promoted interbasinal dispersal. Three migration pathways into the Cincinnati Basin were recognized, which supports the multiple pathway hypothesis for the Richmondian Invasion.

  9. Using Pot-Magnets to Enable Stable and Scalable Electromagnetic Tactile Displays.

    Science.gov (United States)

    Zarate, Juan Jose; Shea, Herbert

    2017-01-01

    We present the design, fabrication, characterization, and psychophysical testing of a scalable haptic display based on electromagnetic (EM) actuators. The display consists of a 4 × 4 array of taxels, each of which can be in a raised or a lowered position, thus generating different static configurations. One of the most challenging aspects when designing densely-packed arrays of EM actuators is obtaining large actuation forces while simultaneously generating only weak interactions between neighboring taxels. In this work, we introduce a lightweight and effective magnetic shielding architecture. The moving part of each taxel is a cylindrical permanent magnet embedded in a ferromagnetic pot, forming a pot-magnet. An array of planar microcoils attracts or repels each pot-magnet. This configuration reduces the interaction between neighboring magnets by more than one order of magnitude, while the coil/magnet interaction is only reduced by 10 percent. For 4 mm diameter pins on an 8 mm pitch, we obtained displacements of 0.55 mm and forces of 40 mN using 1.7 W. We measured the accuracy of human perception under two actuation configurations which differed in the force versus displacement curve. We obtained 91 percent of correct answers in pulling configuration and 100 percent in pushing configuration.

  10. Bayesian phylogenetic estimation of fossil ages

    Science.gov (United States)

    Drummond, Alexei J.; Stadler, Tanja

    2016-01-01

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. This article is part of the themed issue ‘Dating species divergences

  11. Bayesian phylogenetic estimation of fossil ages.

    Science.gov (United States)

    Drummond, Alexei J; Stadler, Tanja

    2016-07-19

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using

  12. NAPP: the Nucleic Acid Phylogenetic Profile Database

    OpenAIRE

    Ott, Alban; Idali, Anouar; Marchais, Antonin; Gautheret, Daniel

    2017-01-01

    Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to ...

  13. Scalable and Fault Tolerant Failure Detection and Consensus

    Energy Technology Data Exchange (ETDEWEB)

    Katti, Amogh [University of Reading, UK; Di Fatta, Giuseppe [University of Reading, UK; Naughton III, Thomas J [ORNL; Engelmann, Christian [ORNL

    2015-01-01

    Future extreme-scale high-performance computing systems will be required to work under frequent component failures. The MPI Forum's User Level Failure Mitigation proposal has introduced an operation, MPI_Comm_shrink, to synchronize the alive processes on the list of failed processes, so that applications can continue to execute even in the presence of failures by adopting algorithm-based fault tolerance techniques. This MPI_Comm_shrink operation requires a fault tolerant failure detection and consensus algorithm. This paper presents and compares two novel failure detection and consensus algorithms. The proposed algorithms are based on Gossip protocols and are inherently fault-tolerant and scalable. The proposed algorithms were implemented and tested using the Extreme-scale Simulator. The results show that in both algorithms the number of Gossip cycles to achieve global consensus scales logarithmically with system size. The second algorithm also shows better scalability in terms of memory and network bandwidth usage and a perfect synchronization in achieving global consensus.

  14. ENDEAVOUR: A Scalable SDN Architecture for Real-World IXPs

    KAUST Repository

    Antichi, Gianni

    2017-10-25

    Innovation in interdomain routing has remained stagnant for over a decade. Recently, IXPs have emerged as economically-advantageous interconnection points for reducing path latencies and exchanging ever increasing traffic volumes among, possibly, hundreds of networks. Given their far-reaching implications on interdomain routing, IXPs are the ideal place to foster network innovation and extend the benefits of SDN to the interdomain level. In this paper, we present, evaluate, and demonstrate ENDEAVOUR, an SDN platform for IXPs. ENDEAVOUR can be deployed on a multi-hop IXP fabric, supports a large number of use cases, and is highly-scalable while avoiding broadcast storms. Our evaluation with real data from one of the largest IXPs, demonstrates the benefits and scalability of our solution: ENDEAVOUR requires around 70% fewer rules than alternative SDN solutions thanks to our rule partitioning mechanism. In addition, by providing an open source solution, we invite everyone from the community to experiment (and improve) our implementation as well as adapt it to new use cases.

  15. Performance and Scalability Evaluation of the Ceph Parallel File System

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Feiyi [ORNL; Nelson, Mark [Inktank Storage, Inc.; Oral, H Sarp [ORNL; Settlemyer, Bradley W [ORNL; Atchley, Scott [ORNL; Caldwell, Blake A [ORNL; Hill, Jason J [ORNL

    2013-01-01

    Ceph is an open-source and emerging parallel distributed file and storage system technology. By design, Ceph assumes running on unreliable and commodity storage and network hardware and provides reliability and fault-tolerance through controlled object placement and data replication. We evaluated the Ceph technology for scientific high-performance computing (HPC) environments. This paper presents our evaluation methodology, experiments, results and observations from mostly parallel I/O performance and scalability perspectives. Our work made two unique contributions. First, our evaluation is performed under a realistic setup for a large-scale capability HPC environment using a commercial high-end storage system. Second, our path of investigation, tuning efforts, and findings made direct contributions to Ceph's development and improved code quality, scalability, and performance. These changes should also benefit both Ceph and HPC communities at large. Throughout the evaluation, we observed that Ceph still is an evolving technology under fast-paced development and showing great promises.

  16. The Node Monitoring Component of a Scalable Systems Software Environment

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Samuel James [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    This research describes Fountain, a suite of programs used to monitor the resources of a cluster. A cluster is a collection of individual computers that are connected via a high speed communication network. They are traditionally used by users who desire more resources, such as processing power and memory, than any single computer can provide. A common drawback to effectively utilizing such a large-scale system is the management infrastructure, which often does not often scale well as the system grows. Large-scale parallel systems provide new research challenges in the area of systems software, the programs or tools that manage the system from boot-up to running a parallel job. The approach presented in this thesis utilizes a collection of separate components that communicate with each other to achieve a common goal. While systems software comprises a broad array of components, this thesis focuses on the design choices for a node monitoring component. We will describe Fountain, an implementation of the Scalable Systems Software (SSS) node monitor specification. It is targeted at aggregate node monitoring for clusters, focusing on both scalability and fault tolerance as its design goals. It leverages widely used technologies such as XML and HTTP to present an interface to other components in the SSS environment.

  17. Towards Scalable Strain Gauge-Based Joint Torque Sensors.

    Science.gov (United States)

    Khan, Hamza; D'Imperio, Mariapaola; Cannella, Ferdinando; Caldwell, Darwin G; Cuschieri, Alfred; Semini, Claudio

    2017-08-18

    During recent decades, strain gauge-based joint torque sensors have been commonly used to provide high-fidelity torque measurements in robotics. Although measurement of joint torque/force is often required in engineering research and development, the gluing and wiring of strain gauges used as torque sensors pose difficulties during integration within the restricted space available in small joints. The problem is compounded by the need for a scalable geometric design to measure joint torque. In this communication, we describe a novel design of a strain gauge-based mono-axial torque sensor referred to as square-cut torque sensor (SCTS), the significant features of which are high degree of linearity, symmetry, and high scalability in terms of both size and measuring range. Most importantly, SCTS provides easy access for gluing and wiring of the strain gauges on sensor surface despite the limited available space. We demonstrated that the SCTS was better in terms of symmetry (clockwise and counterclockwise rotation) and more linear. These capabilities have been shown through finite element modeling (ANSYS) confirmed by observed data obtained by load testing experiments. The high performance of SCTS was confirmed by studies involving changes in size, material and/or wings width and thickness. Finally, we demonstrated that the SCTS can be successfully implementation inside the hip joints of miniaturized hydraulically actuated quadruped robot-MiniHyQ. This communication is based on work presented at the 18th International Conference on Climbing and Walking Robots (CLAWAR).

  18. Developing a scalable artificial photosynthesis technology through nanomaterials by design.

    Science.gov (United States)

    Lewis, Nathan S

    2016-12-06

    An artificial photosynthetic system that directly produces fuels from sunlight could provide an approach to scalable energy storage and a technology for the carbon-neutral production of high-energy-density transportation fuels. A variety of designs are currently being explored to create a viable artificial photosynthetic system, and the most technologically advanced systems are based on semiconducting photoelectrodes. Here, I discuss the development of an approach that is based on an architecture, first conceived around a decade ago, that combines arrays of semiconducting microwires with flexible polymeric membranes. I highlight the key steps that have been taken towards delivering a fully functional solar fuels generator, which have exploited advances in nanotechnology at all hierarchical levels of device construction, and include the discovery of earth-abundant electrocatalysts for fuel formation and materials for the stabilization of light absorbers. Finally, I consider the remaining scientific and engineering challenges facing the fulfilment of an artificial photosynthetic system that is simultaneously safe, robust, efficient and scalable.

  19. A highly scalable peptide-based assay system for proteomics.

    Directory of Open Access Journals (Sweden)

    Igor A Kozlov

    Full Text Available We report a scalable and cost-effective technology for generating and screening high-complexity customizable peptide sets. The peptides are made as peptide-cDNA fusions by in vitro transcription/translation from pools of DNA templates generated by microarray-based synthesis. This approach enables large custom sets of peptides to be designed in silico, manufactured cost-effectively in parallel, and assayed efficiently in a multiplexed fashion. The utility of our peptide-cDNA fusion pools was demonstrated in two activity-based assays designed to discover protease and kinase substrates. In the protease assay, cleaved peptide substrates were separated from uncleaved and identified by digital sequencing of their cognate cDNAs. We screened the 3,011 amino acid HCV proteome for susceptibility to cleavage by the HCV NS3/4A protease and identified all 3 known trans cleavage sites with high specificity. In the kinase assay, peptide substrates phosphorylated by tyrosine kinases were captured and identified by sequencing of their cDNAs. We screened a pool of 3,243 peptides against Abl kinase and showed that phosphorylation events detected were specific and consistent with the known substrate preferences of Abl kinase. Our approach is scalable and adaptable to other protein-based assays.

  20. Scalable privacy-preserving big data aggregation mechanism

    Directory of Open Access Journals (Sweden)

    Dapeng Wu

    2016-08-01

    Full Text Available As the massive sensor data generated by large-scale Wireless Sensor Networks (WSNs recently become an indispensable part of ‘Big Data’, the collection, storage, transmission and analysis of the big sensor data attract considerable attention from researchers. Targeting the privacy requirements of large-scale WSNs and focusing on the energy-efficient collection of big sensor data, a Scalable Privacy-preserving Big Data Aggregation (Sca-PBDA method is proposed in this paper. Firstly, according to the pre-established gradient topology structure, sensor nodes in the network are divided into clusters. Secondly, sensor data is modified by each node according to the privacy-preserving configuration message received from the sink. Subsequently, intra- and inter-cluster data aggregation is employed during the big sensor data reporting phase to reduce energy consumption. Lastly, aggregated results are recovered by the sink to complete the privacy-preserving big data aggregation. Simulation results validate the efficacy and scalability of Sca-PBDA and show that the big sensor data generated by large-scale WSNs is efficiently aggregated to reduce network resource consumption and the sensor data privacy is effectively protected to meet the ever-growing application requirements.

  1. The dust acoustic waves in three dimensional scalable complex plasma

    CERN Document Server

    Zhukhovitskii, D I

    2015-01-01

    Dust acoustic waves in the bulk of a dust cloud in complex plasma of low pressure gas discharge under microgravity conditions are considered. The dust component of complex plasma is assumed a scalable system that conforms to the ionization equation of state (IEOS) developed in our previous study. We find singular points of this IEOS that determine the behavior of the sound velocity in different regions of the cloud. The fluid approach is utilized to deduce the wave equation that includes the neutral drag term. It is shown that the sound velocity is fully defined by the particle compressibility, which is calculated on the basis of the scalable IEOS. The sound velocities and damping rates calculated for different 3D complex plasmas both in ac and dc discharges demonstrate a good correlation with experimental data that are within the limits of validity of the theory. The theory provides interpretation for the observed independence of the sound velocity on the coordinate and for a weak dependence on the particle ...

  2. Developing a scalable artificial photosynthesis technology through nanomaterials by design

    Science.gov (United States)

    Lewis, Nathan S.

    2016-12-01

    An artificial photosynthetic system that directly produces fuels from sunlight could provide an approach to scalable energy storage and a technology for the carbon-neutral production of high-energy-density transportation fuels. A variety of designs are currently being explored to create a viable artificial photosynthetic system, and the most technologically advanced systems are based on semiconducting photoelectrodes. Here, I discuss the development of an approach that is based on an architecture, first conceived around a decade ago, that combines arrays of semiconducting microwires with flexible polymeric membranes. I highlight the key steps that have been taken towards delivering a fully functional solar fuels generator, which have exploited advances in nanotechnology at all hierarchical levels of device construction, and include the discovery of earth-abundant electrocatalysts for fuel formation and materials for the stabilization of light absorbers. Finally, I consider the remaining scientific and engineering challenges facing the fulfilment of an artificial photosynthetic system that is simultaneously safe, robust, efficient and scalable.

  3. Scalable Nernst thermoelectric power using a coiled galfenol wire

    Directory of Open Access Journals (Sweden)

    Zihao Yang

    2017-09-01

    Full Text Available The Nernst thermopower usually is considered far too weak in most metals for waste heat recovery. However, its transverse orientation gives it an advantage over the Seebeck effect on non-flat surfaces. Here, we experimentally demonstrate the scalable generation of a Nernst voltage in an air-cooled metal wire coiled around a hot cylinder. In this geometry, a radial temperature gradient generates an azimuthal electric field in the coil. A Galfenol (Fe0.85Ga0.15 wire is wrapped around a cartridge heater, and the voltage drop across the wire is measured as a function of axial magnetic field. As expected, the Nernst voltage scales linearly with the length of the wire. Based on heat conduction and fluid dynamic equations, finite-element method is used to calculate the temperature gradient across the Galfenol wire and determine the Nernst coefficient. A giant Nernst coefficient of -2.6 μV/KT at room temperature is estimated, in agreement with measurements on bulk Galfenol. We expect that the giant Nernst effect in Galfenol arises from its magnetostriction, presumably through enhanced magnon-phonon coupling. Our results demonstrate the feasibility of a transverse thermoelectric generator capable of scalable output power from non-flat heat sources.

  4. Scalable Nernst thermoelectric power using a coiled galfenol wire

    Science.gov (United States)

    Yang, Zihao; Codecido, Emilio A.; Marquez, Jason; Zheng, Yuanhua; Heremans, Joseph P.; Myers, Roberto C.

    2017-09-01

    The Nernst thermopower usually is considered far too weak in most metals for waste heat recovery. However, its transverse orientation gives it an advantage over the Seebeck effect on non-flat surfaces. Here, we experimentally demonstrate the scalable generation of a Nernst voltage in an air-cooled metal wire coiled around a hot cylinder. In this geometry, a radial temperature gradient generates an azimuthal electric field in the coil. A Galfenol (Fe0.85Ga0.15) wire is wrapped around a cartridge heater, and the voltage drop across the wire is measured as a function of axial magnetic field. As expected, the Nernst voltage scales linearly with the length of the wire. Based on heat conduction and fluid dynamic equations, finite-element method is used to calculate the temperature gradient across the Galfenol wire and determine the Nernst coefficient. A giant Nernst coefficient of -2.6 μV/KT at room temperature is estimated, in agreement with measurements on bulk Galfenol. We expect that the giant Nernst effect in Galfenol arises from its magnetostriction, presumably through enhanced magnon-phonon coupling. Our results demonstrate the feasibility of a transverse thermoelectric generator capable of scalable output power from non-flat heat sources.

  5. Silicon nanophotonics for scalable quantum coherent feedback networks

    Energy Technology Data Exchange (ETDEWEB)

    Sarovar, Mohan; Brif, Constantin [Sandia National Laboratories, Livermore, CA (United States); Soh, Daniel B.S. [Sandia National Laboratories, Livermore, CA (United States); Stanford University, Edward L. Ginzton Laboratory, Stanford, CA (United States); Cox, Jonathan; DeRose, Christopher T.; Camacho, Ryan; Davids, Paul [Sandia National Laboratories, Albuquerque, NM (United States)

    2016-12-15

    The emergence of coherent quantum feedback control (CQFC) as a new paradigm for precise manipulation of dynamics of complex quantum systems has led to the development of efficient theoretical modeling and simulation tools and opened avenues for new practical implementations. This work explores the applicability of the integrated silicon photonics platform for implementing scalable CQFC networks. If proven successful, on-chip implementations of these networks would provide scalable and efficient nanophotonic components for autonomous quantum information processing devices and ultra-low-power optical processing systems at telecommunications wavelengths. We analyze the strengths of the silicon photonics platform for CQFC applications and identify the key challenges to both the theoretical formalism and experimental implementations. In particular, we determine specific extensions to the theoretical CQFC framework (which was originally developed with bulk-optics implementations in mind), required to make it fully applicable to modeling of linear and nonlinear integrated optics networks. We also report the results of a preliminary experiment that studied the performance of an in situ controllable silicon nanophotonic network of two coupled cavities and analyze the properties of this device using the CQFC formalism. (orig.)

  6. Towards Scalable Strain Gauge-Based Joint Torque Sensors

    Science.gov (United States)

    D’Imperio, Mariapaola; Cannella, Ferdinando; Caldwell, Darwin G.; Cuschieri, Alfred

    2017-01-01

    During recent decades, strain gauge-based joint torque sensors have been commonly used to provide high-fidelity torque measurements in robotics. Although measurement of joint torque/force is often required in engineering research and development, the gluing and wiring of strain gauges used as torque sensors pose difficulties during integration within the restricted space available in small joints. The problem is compounded by the need for a scalable geometric design to measure joint torque. In this communication, we describe a novel design of a strain gauge-based mono-axial torque sensor referred to as square-cut torque sensor (SCTS), the significant features of which are high degree of linearity, symmetry, and high scalability in terms of both size and measuring range. Most importantly, SCTS provides easy access for gluing and wiring of the strain gauges on sensor surface despite the limited available space. We demonstrated that the SCTS was better in terms of symmetry (clockwise and counterclockwise rotation) and more linear. These capabilities have been shown through finite element modeling (ANSYS) confirmed by observed data obtained by load testing experiments. The high performance of SCTS was confirmed by studies involving changes in size, material and/or wings width and thickness. Finally, we demonstrated that the SCTS can be successfully implementation inside the hip joints of miniaturized hydraulically actuated quadruped robot-MiniHyQ. This communication is based on work presented at the 18th International Conference on Climbing and Walking Robots (CLAWAR). PMID:28820446

  7. Posterior Predictive Bayesian Phylogenetic Model Selection

    Science.gov (United States)

    Lewis, Paul O.; Xie, Wangang; Chen, Ming-Hui; Fan, Yu; Kuo, Lynn

    2014-01-01

    We present two distinctly different posterior predictive approaches to Bayesian phylogenetic model selection and illustrate these methods using examples from green algal protein-coding cpDNA sequences and flowering plant rDNA sequences. The Gelfand–Ghosh (GG) approach allows dissection of an overall measure of model fit into components due to posterior predictive variance (GGp) and goodness-of-fit (GGg), which distinguishes this method from the posterior predictive P-value approach. The conditional predictive ordinate (CPO) method provides a site-specific measure of model fit useful for exploratory analyses and can be combined over sites yielding the log pseudomarginal likelihood (LPML) which is useful as an overall measure of model fit. CPO provides a useful cross-validation approach that is computationally efficient, requiring only a sample from the posterior distribution (no additional simulation is required). Both GG and CPO add new perspectives to Bayesian phylogenetic model selection based on the predictive abilities of models and complement the perspective provided by the marginal likelihood (including Bayes Factor comparisons) based solely on the fit of competing models to observed data. [Bayesian; conditional predictive ordinate; CPO; L-measure; LPML; model selection; phylogenetics; posterior predictive.] PMID:24193892

  8. Phylogenetic Classification of Seed Plants of Taiwan.

    Science.gov (United States)

    Lin, Cheng-Tao; Chung, Kuo-Fang

    2017-11-21

    Biological classification, the hierarchical arrangement of scientific names of organisms, constitutes the core infrastructure of biological databases. For an efficient management of biological databases, adopting a stable and universal biological classification system is crucial. Currently in Taiwan Biodiversity Information Facility (TaiBIF; http://taibif.tw/ ), the national portal website that integrates Taiwan's biodiversity information databases, angiosperms are arranged according to Cronquist's System of Classification, which is not compatible with current trend of the Angiosperm Phylogeny Group (APG) classification. To consolidate the function and management of the database, TaiBIF is moving to adopt the APG IV classification and Christenhusz et al. (Phytotaxa 19:55-70, 2011)'s classification of gymnosperms, which we summarize as the Phylogenetic Classification of Seed Plants of Taiwan. The Phylogenetic Classification of Seed Plants of Taiwan places gymnosperms in five families [vs. eight families in the Flora of Taiwan (FOT)] and angiosperms in 210 families (vs. 193 families in FOT). Three FOT gymnosperm families are synonymized in current treatment. Of the 210 APG IV families, familial circumscriptions of 114 families are identical with FOT and 50 families are recircumscription of FOT, with 46 families newly added. Of the 29 FOT families not included in current classification, two families are excluded and 27 families are synonymized. The adoption of the Phylogenetic Classification of Seed Plants of Taiwan in TaiBIF will provide better service and efficient management of the nation's biodiversity information databases.

  9. A Consistent Phylogenetic Backbone for the Fungi

    Science.gov (United States)

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-01-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

  10. Incongruencies in Vaccinia Virus Phylogenetic Trees

    Directory of Open Access Journals (Sweden)

    Chad Smithson

    2014-10-01

    Full Text Available Over the years, as more complete poxvirus genomes have been sequenced, phylogenetic studies of these viruses have become more prevalent. In general, the results show similar relationships between the poxvirus species; however, some inconsistencies are notable. Previous analyses of the viral genomes contained within the vaccinia virus (VACV-Dryvax vaccine revealed that their phylogenetic relationships were sometimes clouded by low bootstrapping confidence. To analyze the VACV-Dryvax genomes in detail, a new tool-set was developed and integrated into the Base-By-Base bioinformatics software package. Analyses showed that fewer unique positions were present in each VACV-Dryvax genome than expected. A series of patterns, each containing several single nucleotide polymorphisms (SNPs were identified that were counter to the results of the phylogenetic analysis. The VACV genomes were found to contain short DNA sequence blocks that matched more distantly related clades. Additionally, similar non-conforming SNP patterns were observed in (1 the variola virus clade; (2 some cowpox clades; and (3 VACV-CVA, the direct ancestor of VACV-MVA. Thus, traces of past recombination events are common in the various orthopoxvirus clades, including those associated with smallpox and cowpox viruses.

  11. Phylogenetic analysis of Artemisia L. (Asteraceae) based on ...

    African Journals Online (AJOL)

    A phylogenetic analysis of Artemisia based on 9 micromorphological characters of pollens was conducted using Wagner parsimony method. In the resulting phylogenetic tree, relationships among different Artemisia species are shown. This study also presents the phylogenetic associations among 4 sections within the ...

  12. A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks

    NARCIS (Netherlands)

    K.T. Huber; L.J.J. van Iersel (Leo); S.M. Kelk (Steven); R. Suchecki

    2010-01-01

    htmlabstractRecently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for reconstructing level-1 phylogenetic networks - a type of

  13. Experimental plant communities develop phylogenetically overdispersed abundance distributions during assembly

    OpenAIRE

    Allan, Eric; Jenkins, Tania; Alexander J. F. Fergus; Roscher, Christiane; Fischer, Markus; Petermann, Jana; Wolfgang W Weisser; Schmid, Bernhard

    2013-01-01

    The importance of competition between similar species in driving community assembly is much debated. Recently, phylogenetic patterns in species composition have been investigated to help resolve this question: phylogenetic clustering is taken to imply environmental filtering, and phylogenetic overdispersion to indicate limiting similarity between species. We used experimental plant communities with random species compositions and initially even abundance distributions to examine the developme...

  14. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and phylogenetic analysis showed that our isolates have high homology with Japanese isolates. Key words: Hepatitis C virus, core, phylogenetic analysis, Pakistan. INTRODUCTION.

  15. Metagenomic approaches to understanding phylogenetic diversity in quorum sensing

    Science.gov (United States)

    Kimura, Nobutada

    2014-01-01

    Quorum sensing, a form of cell–cell communication among bacteria, allows bacteria to synchronize their behaviors at the population level in order to control behaviors such as luminescence, biofilm formation, signal turnover, pigment production, antibiotics production, swarming, and virulence. A better understanding of quorum-sensing systems will provide us with greater insight into the complex interaction mechanisms used widely in the Bacteria and even the Archaea domain in the environment. Metagenomics, the use of culture-independent sequencing to study the genomic material of microorganisms, has the potential to provide direct information about the quorum-sensing systems in uncultured bacteria. This article provides an overview of the current knowledge of quorum sensing focused on phylogenetic diversity, and presents examples of studies that have used metagenomic techniques. Future technologies potentially related to quorum-sensing systems are also discussed. PMID:24429899

  16. Investigating the Role of Biogeochemical Processes in the Northern High Latitudes on Global Climate Feedbacks Using an Efficient Scalable Earth System Model

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Atul K. [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2016-09-14

    The overall objectives of this DOE funded project is to combine scientific and computational challenges in climate modeling by expanding our understanding of the biogeophysical-biogeochemical processes and their interactions in the northern high latitudes (NHLs) using an earth system modeling (ESM) approach, and by adopting an adaptive parallel runtime system in an ESM to achieve efficient and scalable climate simulations through improved load balancing algorithms.

  17. CloudTPS: Scalable Transactions for Web Applications in the Cloud

    NARCIS (Netherlands)

    Zhou, W.; Pierre, G.E.O.; Chi, C.-H.

    2010-01-01

    NoSQL Cloud data services provide scalability and high availability properties for web applications but at the same time they sacrifice data consistency. However, many applications cannot afford any data inconsistency. CloudTPS is a scalable transaction manager to allow cloud database services to

  18. Scalable nanostructuring on polymer by a SiC stamp: optical and wetting effects

    DEFF Research Database (Denmark)

    Argyraki, Aikaterini; Lu, Weifang; Petersen, Paul Michael

    2015-01-01

    A method for fabricating scalable antireflective nanostructures on polymer surfaces (polycarbonate) is demonstrated. The transition from small scale fabrication of nanostructures to a scalable replication technique can be quite challenging. In this work, an area per print corresponding to a 2-inch...

  19. Extending JPEG-LS for low-complexity scalable video coding

    DEFF Research Database (Denmark)

    Ukhanova, Anna; Sergeev, Anton; Forchhammer, Søren

    2011-01-01

    JPEG-LS, the well-known international standard for lossless and near-lossless image compression, was originally designed for non-scalable applications. In this paper we propose a scalable modification of JPEG-LS and compare it with the leading image and video coding standards JPEG2000 and H.264/SVC...

  20. Scalable Multifunction Active Phased Array Systems: from concept to implementation; 2006BU1-IS

    NARCIS (Netherlands)

    LaMana, M.; Huizing, A.

    2006-01-01

    The SMRF (Scalable Multifunction Radio Frequency Systems) concept has been launched in the WEAG (Western European Armament Group) context, recently restructured into the EDA (European Defence Agency). A derived concept is introduced here, namely the SMRF-APAS (Scalable Multifunction Radio

  1. A NEaT Design for reliable and scalable network stacks

    NARCIS (Netherlands)

    Hruby, Tomas; Giuffrida, Cristiano; Sambuc, Lionel; Bos, Herbert; Tanenbaum, Andrew S.

    2016-01-01

    Operating systems provide a wide range of services, which are crucial for the increasingly high reliability and scalability demands of modern applications. Providing both reliability and scalability at the same time is hard. Commodity OS architectures simply lack the design abstractions to do so for

  2. Final Report: Center for Programming Models for Scalable Parallel Computing

    Energy Technology Data Exchange (ETDEWEB)

    Mellor-Crummey, John [William Marsh Rice University

    2011-09-13

    As part of the Center for Programming Models for Scalable Parallel Computing, Rice University collaborated with project partners in the design, development and deployment of language, compiler, and runtime support for parallel programming models to support application development for the “leadership-class” computer systems at DOE national laboratories. Work over the course of this project has focused on the design, implementation, and evaluation of a second-generation version of Coarray Fortran. Research and development efforts of the project have focused on the CAF 2.0 language, compiler, runtime system, and supporting infrastructure. This has involved working with the teams that provide infrastructure for CAF that we rely on, implementing new language and runtime features, producing an open source compiler that enabled us to evaluate our ideas, and evaluating our design and implementation through the use of benchmarks. The report details the research, development, findings, and conclusions from this work.

  3. Optimization of Hierarchical Modulation for Use of Scalable Media

    Directory of Open Access Journals (Sweden)

    Heneghan Conor

    2010-01-01

    Full Text Available This paper studies the Hierarchical Modulation, a transmission strategy of the approaching scalable multimedia over frequency-selective fading channel for improving the perceptible quality. An optimization strategy for Hierarchical Modulation and convolutional encoding, which can achieve the target bit error rates with minimum global signal-to-noise ratio in a single-user scenario, is suggested. This strategy allows applications to make a free choice of relationship between Higher Priority (HP and Lower Priority (LP stream delivery. The similar optimization can be used in multiuser scenario. An image transport task and a transport task of an H.264/MPEG4 AVC video embedding both QVGA and VGA resolutions are simulated as the implementation example of this optimization strategy, and demonstrate savings in SNR and improvement in Peak Signal-to-Noise Ratio (PSNR for the particular examples shown.

  4. Hierarchical Sets: Analyzing Pangenome Structure through Scalable Set Visualizations

    DEFF Research Database (Denmark)

    Pedersen, Thomas Lin

    2017-01-01

    information to increase in knowledge. As the pangenome data structure is essentially a collection of sets we explore the potential for scalable set visualization as a tool for pangenome analysis. We present a new hierarchical clustering algorithm based on set arithmetics that optimizes the intersection sizes...... along the branches. The intersection and union sizes along the hierarchy are visualized using a composite dendrogram and icicle plot, which, in pangenome context, shows the evolution of pangenome and core size along the evolutionary hierarchy. Outlying elements, i.e. elements whose presence pattern do...... of hierarchical sets by applying it to a pangenome based on 113 Escherichia and Shigella genomes and find it provides a powerful addition to pangenome analysis. The described clustering algorithm and visualizations are implemented in the hierarchicalSets R package available from CRAN (https...

  5. Scalable Spectrum Sharing Mechanism for Local Area Networks Deployment

    DEFF Research Database (Denmark)

    Da Costa, Gustavo Wagner Oliveira; Cattoni, Andrea Fabio; Kovacs, Istvan Zsolt

    2010-01-01

    The availability on the market of powerful and lightweight mobile devices has led to a fast diffusion of mobile services for end users and the trend is shifting from voice based services to multimedia contents distribution. The current access networks are, however, able to support relatively low...... data rates and with limited Quality of Service (QoS). In order to extend the access to high data rate services to wireless users, the International Telecommunication Union (ITU) established new requirements for future wireless communication technologies of up to 1Gbps in low mobility and up to 100Mbps...... management (RRM) functionalities in a CR framework, able to minimize the inter-OLA interferences. A Game Theory-inspired scalable algorithm is introduced to enable a distributed resource allocation in competitive radio environments. The proof-ofconcept simulation results demonstrate the effectiveness...

  6. Center for Programming Models for Scalable Parallel Computing

    Energy Technology Data Exchange (ETDEWEB)

    John Mellor-Crummey

    2008-02-29

    Rice University's achievements as part of the Center for Programming Models for Scalable Parallel Computing include: (1) design and implemention of cafc, the first multi-platform CAF compiler for distributed and shared-memory machines, (2) performance studies of the efficiency of programs written using the CAF and UPC programming models, (3) a novel technique to analyze explicitly-parallel SPMD programs that facilitates optimization, (4) design, implementation, and evaluation of new language features for CAF, including communication topologies, multi-version variables, and distributed multithreading to simplify development of high-performance codes in CAF, and (5) a synchronization strength reduction transformation for automatically replacing barrier-based synchronization with more efficient point-to-point synchronization. The prototype Co-array Fortran compiler cafc developed in this project is available as open source software from http://www.hipersoft.rice.edu/caf.

  7. Scalable Domain Decomposition Preconditioners for Heterogeneous Elliptic Problems

    Directory of Open Access Journals (Sweden)

    Pierre Jolivet

    2014-01-01

    Full Text Available Domain decomposition methods are, alongside multigrid methods, one of the dominant paradigms in contemporary large-scale partial differential equation simulation. In this paper, a lightweight implementation of a theoretically and numerically scalable preconditioner is presented in the context of overlapping methods. The performance of this work is assessed by numerical simulations executed on thousands of cores, for solving various highly heterogeneous elliptic problems in both 2D and 3D with billions of degrees of freedom. Such problems arise in computational science and engineering, in solid and fluid mechanics. While focusing on overlapping domain decomposition methods might seem too restrictive, it will be shown how this work can be applied to a variety of other methods, such as non-overlapping methods and abstract deflation based preconditioners. It is also presented how multilevel preconditioners can be used to avoid communication during an iterative process such as a Krylov method.

  8. Scalable Fabrication of 2D Semiconducting Crystals for Future Electronics

    Directory of Open Access Journals (Sweden)

    Jiantong Li

    2015-12-01

    Full Text Available Two-dimensional (2D layered materials are anticipated to be promising for future electronics. However, their electronic applications are severely restricted by the availability of such materials with high quality and at a large scale. In this review, we introduce systematically versatile scalable synthesis techniques in the literature for high-crystallinity large-area 2D semiconducting materials, especially transition metal dichalcogenides, and 2D material-based advanced structures, such as 2D alloys, 2D heterostructures and 2D material devices engineered at the wafer scale. Systematic comparison among different techniques is conducted with respect to device performance. The present status and the perspective for future electronics are discussed.

  9. MOSDEN: A Scalable Mobile Collaborative Platform for Opportunistic Sensing Applications

    Directory of Open Access Journals (Sweden)

    Prem Prakash Jayaraman

    2014-05-01

    Full Text Available Mobile smartphones along with embedded sensors have become an efficient enabler for various mobile applications including opportunistic sensing. The hi-tech advances in smartphones are opening up a world of possibilities. This paper proposes a mobile collaborative platform called MOSDEN that enables and supports opportunistic sensing at run time. MOSDEN captures and shares sensor data acrossmultiple apps, smartphones and users. MOSDEN supports the emerging trend of separating sensors from application-specific processing, storing and sharing. MOSDEN promotes reuse and re-purposing of sensor data hence reducing the efforts in developing novel opportunistic sensing applications. MOSDEN has been implemented on Android-based smartphones and tablets. Experimental evaluations validate the scalability and energy efficiency of MOSDEN and its suitability towards real world applications. The results of evaluation and lessons learned are presented and discussed in this paper.

  10. A Modular, Scalable, Extensible, and Transparent Optical Packet Buffer

    Science.gov (United States)

    Small, Benjamin A.; Shacham, Assaf; Bergman, Keren

    2007-04-01

    We introduce a novel optical packet switching buffer architecture that is composed of multiple building-block modules, allowing for a large degree of scalability. The buffer supports independent and simultaneous read and write processes without packet rejection or misordering and can be considered a fully functional packet buffer. It can easily be programmed to support two prioritization schemes: first-in first-out (FIFO) and last-in first-out (LIFO). Because the system leverages semiconductor optical amplifiers as switching elements, wideband packets can be routed transparently. The operation of the system is discussed with illustrative packet sequences, which are then verified on an actual implementation composed of conventional fiber-optic componentry.

  11. Vortex Filaments in Grids for Scalable, Fine Smoke Simulation.

    Science.gov (United States)

    Meng, Zhang; Weixin, Si; Yinling, Qian; Hanqiu, Sun; Jing, Qin; Heng, Pheng-Ann

    2015-01-01

    Vortex modeling can produce attractive visual effects of dynamic fluids, which are widely applicable for dynamic media, computer games, special effects, and virtual reality systems. However, it is challenging to effectively simulate intensive and fine detailed fluids such as smoke with fast increasing vortex filaments and smoke particles. The authors propose a novel vortex filaments in grids scheme in which the uniform grids dynamically bridge the vortex filaments and smoke particles for scalable, fine smoke simulation with macroscopic vortex structures. Using the vortex model, their approach supports the trade-off between simulation speed and scale of details. After computing the whole velocity, external control can be easily exerted on the embedded grid to guide the vortex-based smoke motion. The experimental results demonstrate the efficiency of using the proposed scheme for a visually plausible smoke simulation with macroscopic vortex structures.

  12. Scalable, ultra-resistant structural colors based on network metamaterials

    CERN Document Server

    Galinski, Henning; Dong, Hao; Gongora, Juan S Totero; Favaro, Grégory; Döbeli, Max; Spolenak, Ralph; Fratalocchi, Andrea; Capasso, Federico

    2016-01-01

    Structural colours have drawn wide attention for their potential as a future printing technology for various applications, ranging from biomimetic tissues to adaptive camouflage materials. However, an efficient approach to realise robust colours with a scalable fabrication technique is still lacking, hampering the realisation of practical applications with this platform. Here we develop a new approach based on large scale network metamaterials, which combine dealloyed subwavelength structures at the nanoscale with loss-less, ultra-thin dielectrics coatings. By using theory and experiments, we show how sub-wavelength dielectric coatings control a mechanism of resonant light coupling with epsilon-near-zero (ENZ) regions generated in the metallic network, manifesting the formation of highly saturated structural colours that cover a wide portion of the spectrum. Ellipsometry measurements report the efficient observation of these colours even at angles of $70$ degrees. The network-like architecture of these nanoma...

  13. Photonic Architecture for Scalable Quantum Information Processing in Diamond

    Directory of Open Access Journals (Sweden)

    Kae Nemoto

    2014-08-01

    Full Text Available Physics and information are intimately connected, and the ultimate information processing devices will be those that harness the principles of quantum mechanics. Many physical systems have been identified as candidates for quantum information processing, but none of them are immune from errors. The challenge remains to find a path from the experiments of today to a reliable and scalable quantum computer. Here, we develop an architecture based on a simple module comprising an optical cavity containing a single negatively charged nitrogen vacancy center in diamond. Modules are connected by photons propagating in a fiber-optical network and collectively used to generate a topological cluster state, a robust substrate for quantum information processing. In principle, all processes in the architecture can be deterministic, but current limitations lead to processes that are probabilistic but heralded. We find that the architecture enables large-scale quantum information processing with existing technology.

  14. A Practical and Scalable Tool to Find Overlaps between Sequences

    Science.gov (United States)

    Haj Rachid, Maan

    2015-01-01

    The evolution of the next generation sequencing technology increases the demand for efficient solutions, in terms of space and time, for several bioinformatics problems. This paper presents a practical and easy-to-implement solution for one of these problems, namely, the all-pairs suffix-prefix problem, using a compact prefix tree. The paper demonstrates an efficient construction of this time-efficient and space-economical tree data structure. The paper presents techniques for parallel implementations of the proposed solution. Experimental evaluation indicates superior results in terms of space and time over existing solutions. Results also show that the proposed technique is highly scalable in a parallel execution environment. PMID:25961045

  15. A Practical and Scalable Tool to Find Overlaps between Sequences

    Directory of Open Access Journals (Sweden)

    Maan Haj Rachid

    2015-01-01

    Full Text Available The evolution of the next generation sequencing technology increases the demand for efficient solutions, in terms of space and time, for several bioinformatics problems. This paper presents a practical and easy-to-implement solution for one of these problems, namely, the all-pairs suffix-prefix problem, using a compact prefix tree. The paper demonstrates an efficient construction of this time-efficient and space-economical tree data structure. The paper presents techniques for parallel implementations of the proposed solution. Experimental evaluation indicates superior results in terms of space and time over existing solutions. Results also show that the proposed technique is highly scalable in a parallel execution environment.

  16. CloudETL: Scalable Dimensional ETL for Hadoop and Hive

    DEFF Research Database (Denmark)

    Xiufeng, Liu; Thomsen, Christian; Pedersen, Torben Bach

    Extract-Transform-Load (ETL) programs process data from sources into data warehouses (DWs). Due to the rapid growth of data volumes, there is an increasing demand for systems that can scale on demand. Recently, much attention has been given to MapReduce which is a framework for highly parallel...... handling of massive data sets in cloud environments. The MapReduce-based Hive has been proposed as a DBMS-like system for DWs and provides good and scalable analytical features. It is,however, still challenging to do proper dimensional ETL processing with Hive; for example, UPDATEs are not supported which...... makes handling of slowly changing dimensions (SCDs) very difficult. To remedy this, we here present the cloud-enabled ETL framework CloudETL. CloudETL uses the open source MapReduce implementation Hadoop to parallelize the ETL execution and to process data into Hive. The user defines the ETL process...

  17. A Software and Hardware IPTV Architecture for Scalable DVB Distribution

    Directory of Open Access Journals (Sweden)

    Georg Acher

    2009-01-01

    Full Text Available Many standards and even more proprietary technologies deal with IP-based television (IPTV. But none of them can transparently map popular public broadcast services such as DVB or ATSC to IPTV with acceptable effort. In this paper we explain why we believe that such a mapping using a light weight framework is an important step towards all-IP multimedia. We then present the NetCeiver architecture: it is based on well-known standards such as IPv6, and it allows zero configuration. The use of multicast streaming makes NetCeiver highly scalable. We also describe a low cost FPGA implementation of the proposed NetCeiver architecture, which can concurrently stream services from up to six full transponders.

  18. Adaptive Streaming of Scalable Videos over P2PTV

    Directory of Open Access Journals (Sweden)

    Youssef Lahbabi

    2015-01-01

    Full Text Available In this paper, we propose a new Scalable Video Coding (SVC quality-adaptive peer-to-peer television (P2PTV system executed at the peers and at the network. The quality adaptation mechanisms are developed as follows: on one hand, the Layer Level Initialization (LLI is used for adapting the video quality with the static resources at the peers in order to avoid long startup times. On the other hand, the Layer Level Adjustment (LLA is invoked periodically to adjust the SVC layer to the fluctuation of the network conditions with the aim of predicting the possible stalls before their occurrence. Our results demonstrate that our mechanisms allow quickly adapting the video quality to various system changes while providing best Quality of Experience (QoE that matches current resources of the peer devices and instantaneous throughput available at the network state.

  19. Final Report. Center for Scalable Application Development Software

    Energy Technology Data Exchange (ETDEWEB)

    Mellor-Crummey, John [Rice Univ., Houston, TX (United States)

    2014-10-26

    The Center for Scalable Application Development Software (CScADS) was established as a part- nership between Rice University, Argonne National Laboratory, University of California Berkeley, University of Tennessee – Knoxville, and University of Wisconsin – Madison. CScADS pursued an integrated set of activities with the aim of increasing the productivity of DOE computational scientists by catalyzing the development of systems software, libraries, compilers, and tools for leadership computing platforms. Principal Center activities were workshops to engage the research community in the challenges of leadership computing, research and development of open-source software, and work with computational scientists to help them develop codes for leadership computing platforms. This final report summarizes CScADS activities at Rice University in these areas.

  20. Scalable and Flexible SLA Management Approach for Cloud

    Directory of Open Access Journals (Sweden)

    SHAUKAT MEHMOOD

    2017-01-01

    Full Text Available Cloud Computing is a cutting edge technology in market now a days. In Cloud Computing environment the customer should pay bills to use computing resources. Resource allocation is a primary task in a cloud environment. Significance of resources allocation and availability increase many fold because income of the cloud depends on how efficiently it provides the rented services to the clients. SLA (Service Level Agreement is signed between the cloud Services Provider and the Cloud Services Consumer to maintain stipulated QoS (Quality of Service. It is noted that SLAs are violated due to several reasons. These may include system malfunctions and change in workload conditions. Elastic and adaptive approaches are required to prevent SLA violations. We propose an application level monitoring novel scheme to prevent SLA violations. It is based on elastic and scalable characteristics. It is easy to deploy and use. It focuses on application level monitoring.

  1. A Scalable Framework and Prototype for CAS e-Science

    Directory of Open Access Journals (Sweden)

    Yuanchun Zhou

    2007-07-01

    Full Text Available Based on the Small-World model of CAS e-Science and the power low of Internet, this paper presents a scalable CAS e-Science Grid framework based on virtual region called Virtual Region Grid Framework (VRGF. VRGF takes virtual region and layer as logic manage-unit. In VRGF, the mode of intra-virtual region is pure P2P, and the model of inter-virtual region is centralized. Therefore, VRGF is decentralized framework with some P2P properties. Further more, VRGF is able to achieve satisfactory performance on resource organizing and locating at a small cost, and is well adapted to the complicated and dynamic features of scientific collaborations. We have implemented a demonstration VRGF based Grid prototype—SDG.

  2. MSDLSR: Margin Scalable Discriminative Least Squares Regression for Multicategory Classification.

    Science.gov (United States)

    Wang, Lingfeng; Zhang, Xu-Yao; Pan, Chunhong

    2016-12-01

    In this brief, we propose a new margin scalable discriminative least squares regression (MSDLSR) model for multicategory classification. The main motivation behind the MSDLSR is to explicitly control the margin of DLSR model. We first prove that the DLSR is a relaxation of the traditional L2 -support vector machine. Based on this fact, we further provide a theorem on the margin of DLSR. With this theorem, we add an explicit constraint on DLSR to restrict the number of zeros of dragging values, so as to control the margin of DLSR. The new model is called MSDLSR. Theoretically, we analyze the determination of the margin and support vectors of MSDLSR. Extensive experiments illustrate that our method outperforms the current state-of-the-art approaches on various machine leaning and real-world data sets.

  3. Optimization of Hierarchical Modulation for Use of Scalable Media

    Science.gov (United States)

    Liu, Yongheng; Heneghan, Conor

    2010-12-01

    This paper studies the Hierarchical Modulation, a transmission strategy of the approaching scalable multimedia over frequency-selective fading channel for improving the perceptible quality. An optimization strategy for Hierarchical Modulation and convolutional encoding, which can achieve the target bit error rates with minimum global signal-to-noise ratio in a single-user scenario, is suggested. This strategy allows applications to make a free choice of relationship between Higher Priority (HP) and Lower Priority (LP) stream delivery. The similar optimization can be used in multiuser scenario. An image transport task and a transport task of an H.264/MPEG4 AVC video embedding both QVGA and VGA resolutions are simulated as the implementation example of this optimization strategy, and demonstrate savings in SNR and improvement in Peak Signal-to-Noise Ratio (PSNR) for the particular examples shown.

  4. Simplifying Scalable Graph Processing with a Domain-Specific Language

    KAUST Repository

    Hong, Sungpack

    2014-01-01

    Large-scale graph processing, with its massive data sets, requires distributed processing. However, conventional frameworks for distributed graph processing, such as Pregel, use non-traditional programming models that are well-suited for parallelism and scalability but inconvenient for implementing non-trivial graph algorithms. In this paper, we use Green-Marl, a Domain-Specific Language for graph analysis, to intuitively describe graph algorithms and extend its compiler to generate equivalent Pregel implementations. Using the semantic information captured by Green-Marl, the compiler applies a set of transformation rules that convert imperative graph algorithms into Pregel\\'s programming model. Our experiments show that the Pregel programs generated by the Green-Marl compiler perform similarly to manually coded Pregel implementations of the same algorithms. The compiler is even able to generate a Pregel implementation of a complicated graph algorithm for which a manual Pregel implementation is very challenging.

  5. Scalable load-balance measurement for SPMD codes

    Energy Technology Data Exchange (ETDEWEB)

    Gamblin, T; de Supinski, B R; Schulz, M; Fowler, R; Reed, D

    2008-08-05

    Good load balance is crucial on very large parallel systems, but the most sophisticated algorithms introduce dynamic imbalances through adaptation in domain decomposition or use of adaptive solvers. To observe and diagnose imbalance, developers need system-wide, temporally-ordered measurements from full-scale runs. This potentially requires data collection from multiple code regions on all processors over the entire execution. Doing this instrumentation naively can, in combination with the application itself, exceed available I/O bandwidth and storage capacity, and can induce severe behavioral perturbations. We present and evaluate a novel technique for scalable, low-error load balance measurement. This uses a parallel wavelet transform and other parallel encoding methods. We show that our technique collects and reconstructs system-wide measurements with low error. Compression time scales sublinearly with system size and data volume is several orders of magnitude smaller than the raw data. The overhead is low enough for online use in a production environment.

  6. Polytomy identification in microbial phylogenetic reconstruction

    Directory of Open Access Journals (Sweden)

    Lin Guan

    2011-12-01

    Full Text Available Abstract Background A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies for simplicity, although polytomies (multifurcating branches may reflect more accurate evolutionary relationships. To represent the true evolutionary relationships, it is important to systematically identify the polytomies from a bifurcating tree and generate a taxonomy-compatible multifurcating tree. For this purpose we propose a novel approach, "PolyPhy", which would classify a set of bifurcating branches of a phylogenetic tree into a set of branches with dichotomies and polytomies by considering genome distances among genomes and tree topological properties. Results PolyPhy employs a machine learning technique, BLR (Bayesian logistic regression classifier, to identify possible bifurcating subtrees as polytomies from the trees resulted from ComPhy. Other than considering genome-scale distances between all pairs of species, PolyPhy also takes into account different properties of tree topology between dichotomy and polytomy, such as long-branch retraction and short-branch contraction, and quantifies these properties into comparable rates among different sub-branches. We extract three tree topological features, 'LR' (Leaf rate, 'IntraR' (Intra-subset branch rate and 'InterR' (Inter-subset branch rate, all of which are calculated from bifurcating tree branch sets for classification. We have achieved F-measure (balanced measure between precision and recall of 81% with about 0.9 area under the curve (AUC of ROC. Conclusions PolyPhy is a fast and robust method to identify polytomies from phylogenetic trees based on genome-wide inference of evolutionary relationships among genomes. The software package and test data can be downloaded from http://digbio.missouri.edu/ComPhy/phyloTreeBiNonBi-1.0.zip.

  7. High-resolution phylogenetic microbial community profiling

    Energy Technology Data Exchange (ETDEWEB)

    Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

    2014-03-17

    The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

  8. Molecular phylogenetic study in genus Hydra.

    Science.gov (United States)

    Kawaida, Hitomi; Shimizu, Hiroshi; Fujisawa, Toshitaka; Tachida, Hidenori; Kobayakawa, Yoshitaka

    2010-11-15

    Among 8000-9000 species of Cnidaria, only several dozens of species of Hydrozoa have been found in the fresh water. Hydra is such a fresh water polyp and has been used as a good material for research in developmental biology, regeneration and pattern formation. Although the genus Hydra has only a few ten species, its distribution is cosmopolitan. The phylogenetic relationship between hydra species is fascinating from the aspect of evolutionary biology and biogeography. However, only a few molecular phylogenetic studies have been reported on hydra. Therefore, we conducted a molecular phylogenetic study of the genus Hydra based on mitochondrial and nuclear nucleotide sequences using a hydra collection that has been kept in the National Institute of Genetics (NIG) of Japan. The results support the idea that four species groups comprise the genus Hydra. Within the viridissima group (green hydra) and braueri group, genetic distances between strains were relatively large. In contrast, genetic distances between strains among the vulgaris and oligactis groups were small irrespective of their geographic distribution. The vulgaris group strains were classified at least (as far as our investigated samples) into three sub-groups, vulgaris sub-group, carnea sub-group, and H. sp. (K5 and K6) sub-group. All of the vulgaris sub-group and H. sp. (K5 and K6) sub-group strains were collected in Eurasia. The carnea sub-group strains in NIG collection were all collected in North America. A few newly collected samples in Japan, however, suggested belonging to the carnea sub-group according to the molecular phylogenic analysis. This suggests a trans-Pacific distribution of the carnea sub-group hydra. Copyright © 2010 Elsevier B.V. All rights reserved.

  9. Using tree diversity to compare phylogenetic heuristics.

    Science.gov (United States)

    Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

    2009-04-29

    Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees-especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest.

  10. Polytomy identification in microbial phylogenetic reconstruction.

    Science.gov (United States)

    Lin, Guan Ning; Zhang, Chao; Xu, Dong

    2011-01-01

    A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies) for simplicity, although polytomies (multifurcating branches) may reflect more accurate evolutionary relationships. To represent the true evolutionary relationships, it is important to systematically identify the polytomies from a bifurcating tree and generate a taxonomy-compatible multifurcating tree. For this purpose we propose a novel approach, "PolyPhy", which would classify a set of bifurcating branches of a phylogenetic tree into a set of branches with dichotomies and polytomies by considering genome distances among genomes and tree topological properties. PolyPhy employs a machine learning technique, BLR (Bayesian logistic regression) classifier, to identify possible bifurcating subtrees as polytomies from the trees resulted from ComPhy. Other than considering genome-scale distances between all pairs of species, PolyPhy also takes into account different properties of tree topology between dichotomy and polytomy, such as long-branch retraction and short-branch contraction, and quantifies these properties into comparable rates among different sub-branches. We extract three tree topological features, 'LR' (Leaf rate), 'IntraR' (Intra-subset branch rate) and 'InterR' (Inter-subset branch rate), all of which are calculated from bifurcating tree branch sets for classification. We have achieved F-measure (balanced measure between precision and recall) of 81% with about 0.9 area under the curve (AUC) of ROC. PolyPhy is a fast and robust method to identify polytomies from phylogenetic trees based on genome-wide inference of evolutionary relationships among genomes. The software package and test data can be downloaded from http://digbio.missouri.edu/ComPhy/phyloTreeBiNonBi-1.0.zip.

  11. Phylogenetic and biogeographic analysis of sphaerexochine trilobites.

    Directory of Open Access Journals (Sweden)

    Curtis R Congreve

    Full Text Available BACKGROUND: Sphaerexochinae is a speciose and widely distributed group of cheirurid trilobites. Their temporal range extends from the earliest Ordovician through the Silurian, and they survived the end Ordovician mass extinction event (the second largest mass extinction in Earth history. Prior to this study, the individual evolutionary relationships within the group had yet to be determined utilizing rigorous phylogenetic methods. Understanding these evolutionary relationships is important for producing a stable classification of the group, and will be useful in elucidating the effects the end Ordovician mass extinction had on the evolutionary and biogeographic history of the group. METHODOLOGY/PRINCIPAL FINDINGS: Cladistic parsimony analysis of cheirurid trilobites assigned to the subfamily Sphaerexochinae was conducted to evaluate phylogenetic patterns and produce a hypothesis of relationship for the group. This study utilized the program TNT, and the analysis included thirty-one taxa and thirty-nine characters. The results of this analysis were then used in a Lieberman-modified Brooks Parsimony Analysis to analyze biogeographic patterns during the Ordovician-Silurian. CONCLUSIONS/SIGNIFICANCE: The genus Sphaerexochus was found to be monophyletic, consisting of two smaller clades (one composed entirely of Ordovician species and another composed of Silurian and Ordovician species. By contrast, the genus Kawina was found to be paraphyletic. It is a basal grade that also contains taxa formerly assigned to Cydonocephalus. Phylogenetic patterns suggest Sphaerexochinae is a relatively distinctive trilobite clade because it appears to have been largely unaffected by the end Ordovician mass extinction. Finally, the biogeographic analysis yields two major conclusions about Sphaerexochus biogeography: Bohemia and Avalonia were close enough during the Silurian to exchange taxa; and during the Ordovician there was dispersal between Eastern Laurentia and

  12. fastBMA: scalable network inference and transitive reduction.

    Science.gov (United States)

    Hung, Ling-Hong; Shi, Kaiyuan; Wu, Migao; Young, William Chad; Raftery, Adrian E; Yeung, Ka Yee

    2017-10-01

    Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel, and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminating redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem. We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time series yeast and human datasets. When using a single CPU core, fastBMA is up to 100 times faster than the next fastest method, LASSO, with increased accuracy. It is a memory-efficient, parallel, and distributed application that scales to human genome-wide expression data. A 10 000-gene regulation network can be obtained in a matter of hours using a 32-core cloud cluster (2 nodes of 16 cores). fastBMA is a significant improvement over its predecessor ScanBMA. It is more accurate and orders of magnitude faster than other fast network inference methods such as the 1 based on LASSO. The improved scalability allows it to calculate networks from genome scale data in a reasonable time frame. The transitive reduction method can improve accuracy in denser networks. fastBMA is available as code (M.I.T. license) from GitHub (https://github.com/lhhunghimself/fastBMA), as part of the updated networkBMA Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/networkBMA.html) and as ready-to-deploy Docker images (https://hub.docker.com/r/biodepot/fastbma/). © The Authors 2017. Published by Oxford University Press.

  13. Bubble pump: scalable strategy for in-plane liquid routing.

    Science.gov (United States)

    Oskooei, Ali; Günther, Axel

    2015-07-07

    We present an on-chip liquid routing technique intended for application in well-based microfluidic systems that require long-term active pumping at low to medium flowrates. Our technique requires only one fluidic feature layer, one pneumatic control line and does not rely on flexible membranes and mechanical or moving parts. The presented bubble pump is therefore compatible with both elastomeric and rigid substrate materials and the associated scalable manufacturing processes. Directed liquid flow was achieved in a microchannel by an in-series configuration of two previously described "bubble gates", i.e., by gas-bubble enabled miniature gate valves. Only one time-dependent pressure signal is required and initiates at the upstream (active) bubble gate a reciprocating bubble motion. Applied at the downstream (passive) gate a time-constant gas pressure level is applied. In its rest state, the passive gate remains closed and only temporarily opens while the liquid pressure rises due to the active gate's reciprocating bubble motion. We have designed, fabricated and consistently operated our bubble pump with a variety of working liquids for >72 hours. Flow rates of 0-5.5 μl min(-1), were obtained and depended on the selected geometric dimensions, working fluids and actuation frequencies. The maximum operational pressure was 2.9 kPa-9.1 kPa and depended on the interfacial tension of the working fluids. Attainable flow rates compared favorably with those of available micropumps. We achieved flow rate enhancements of 30-100% by operating two bubble pumps in tandem and demonstrated scalability of the concept in a multi-well format with 12 individually and uniformly perfused microchannels (variation in flow rate bubble pump may provide active flow control for analytical and point-of-care diagnostic devices, as well as for microfluidic cells culture and organ-on-chip platforms.

  14. ParaText : scalable text modeling and analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Dunlavy, Daniel M.; Stanton, Eric T.; Shead, Timothy M.

    2010-06-01

    Automated processing, modeling, and analysis of unstructured text (news documents, web content, journal articles, etc.) is a key task in many data analysis and decision making applications. As data sizes grow, scalability is essential for deep analysis. In many cases, documents are modeled as term or feature vectors and latent semantic analysis (LSA) is used to model latent, or hidden, relationships between documents and terms appearing in those documents. LSA supplies conceptual organization and analysis of document collections by modeling high-dimension feature vectors in many fewer dimensions. While past work on the scalability of LSA modeling has focused on the SVD, the goal of our work is to investigate the use of distributed memory architectures for the entire text analysis process, from data ingestion to semantic modeling and analysis. ParaText is a set of software components for distributed processing, modeling, and analysis of unstructured text. The ParaText source code is available under a BSD license, as an integral part of the Titan toolkit. ParaText components are chained-together into data-parallel pipelines that are replicated across processes on distributed-memory architectures. Individual components can be replaced or rewired to explore different computational strategies and implement new functionality. ParaText functionality can be embedded in applications on any platform using the native C++ API, Python, or Java. The ParaText MPI Process provides a 'generic' text analysis pipeline in a command-line executable that can be used for many serial and parallel analysis tasks. ParaText can also be deployed as a web service accessible via a RESTful (HTTP) API. In the web service configuration, any client can access the functionality provided by ParaText using commodity protocols ... from standard web browsers to custom clients written in any language.

  15. Performance and complexity of color gamut scalable coding

    Science.gov (United States)

    He, Yuwen; Ye, Yan; Xiu, Xiaoyu

    2015-09-01

    Wide color gamut such as BT.2020 allows pictures to be rendered with sharper details and more vivid colors. It is considered an essential video parameter for next generation content generation, and has recently drawn significant commercial interest. As the upgrade cycle of content production work flow and consumer displays take place, current generation and next generation video content are expected to co-exist. Thus, maintaining backward compatibility becomes an important consideration for efficient content delivery systems. The scalable extension of HEVC (SHVC) was recently finalized in the second version of the HEVC specifications. SHVC provides a color mapping tool to improve scalable coding efficiency when the base layer and the enhancement layer video signals are in a different color gamut. The SHVC color mapping tool uses a 3D Look-Up Table (3D LUT) based cross-color linear model to efficiently convert the video in the base layer color gamut into the enhancement layer color gamut. Due to complexity concerns, certain limitations, including limiting the maximum 3D LUT size to 8x2x2, were applied to the color mapping process in SHVC. In this paper, we investigate the complexity and performance trade-off of the 3D LUT based color mapping process. Specifically, we explore the performance benefits of enlarging the size of the 3D LUT with various linear models. In order to reduce computational complexity, a simplified linear model is used within each 3D LUT partition. Simulation results are provided to detail the various performance vs. complexity trade-offs achievable in the proposed design.

  16. BBCA: Improving the scalability of *BEAST using random binning.

    Science.gov (United States)

    Zimmermann, Théo; Mirarab, Siavash; Warnow, Tandy

    2014-01-01

    Species tree estimation can be challenging in the presence of gene tree conflict due to incomplete lineage sorting (ILS), which can occur when the time between speciation events is short relative to the population size. Of the many methods that have been developed to estimate species trees in the presence of ILS, *BEAST, a Bayesian method that co-estimates the species tree and gene trees given sequence alignments on multiple loci, has generally been shown to have the best accuracy. However, *BEAST is extremely computationally intensive so that it cannot be used with large numbers of loci; hence, *BEAST is not suitable for genome-scale analyses. We present BBCA (boosted binned coalescent-based analysis), a method that can be used with *BEAST (and other such co-estimation methods) to improve scalability. BBCA partitions the loci randomly into subsets, uses *BEAST on each subset to co-estimate the gene trees and species tree for the subset, and then combines the newly estimated gene trees together using MP-EST, a popular coalescent-based summary method. We compare time-restricted versions of BBCA and *BEAST on simulated datasets, and show that BBCA is at least as accurate as *BEAST, and achieves better convergence rates for large numbers of loci. Phylogenomic analysis using *BEAST is currently limited to datasets with a small number of loci, and analyses with even just 100 loci can be computationally challenging. BBCA uses a very simple divide-and-conquer approach that makes it possible to use *BEAST on datasets containing hundreds of loci. This study shows that BBCA provides excellent accuracy and is highly scalable.

  17. The phylogenetic problem of Huia (Amphibia: Ranidae).

    Science.gov (United States)

    Stuart, Bryan L

    2008-01-01

    A taxonomic consensus for the diverse and pan-global frog family Ranidae is lacking. A recently proposed classification of living amphibians [Frost, D.R., Grant, T., Faivovich, J., Bain, R. H., Haas, A., Haddad, C.F.B., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M., Wheeler, W.C., 2006. The amphibian tree of life. B. Am. Mus. Nat. Hist. 297, 1-370] included expansion of the Southeast Asian ranid frog genus Huia from seven to 47 species, but without having studied the type species of Huia. This study tested the monophyly of this concept of Huia by sampling the type species and putative members of Huia. Molecular phylogenetic analyses consistently recovered the type species H. cavitympanum as the sister taxon to other Bornean-endemic species in the genus Meristogenys, rendering all previously published concepts of Huia as polyphyletic. Members of Huia sensu [Frost, D.R., Grant, T., Faivovich, J., Bain, R. H., Haas, A., Haddad, C.F.B., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M., Wheeler, W.C., 2006. The amphibian tree of life. B. Am. Mus. Nat. Hist. 297, 1-370.] appear in four places within the family Ranidae. A clade containing the type species of Odorrana is phylogenetically unrelated to the type species of Huia, and Odorrana is removed from synonymy with Huia. These findings underscore the need to include relevant type species in phylogenetic studies before proposing sweeping taxonomic changes. The molecular phylogenetic analyses revealed a high degree of homoplasy in larval and adult morphology of Asian ranid frogs. Detailed studies are needed to identify morphological synapomorphies that unite members in these major clades of ranid frogs.

  18. Phylogenetic analysis of ancient DNA using BEAST.

    Science.gov (United States)

    Ho, Simon Y W

    2012-01-01

    Under exceptional circumstances, it is possible to obtain DNA sequences from samples that are up to hundreds of thousands of years old. These data provide an opportunity to look directly at past genetic diversity, to trace the evolutionary process through time, and to infer demographic and phylogeographic trends. Ancient DNA (aDNA) data sets have some degree of intrinsic temporal structure because the sequences have been obtained from samples of different ages. When analyzing these data sets, it is usually necessary to take the sampling times into account. A number of phylogenetic methods have been designed with this purpose in mind. Here I describe the steps involved in Bayesian phylogenetic analysis of aDNA data. I outline a procedure that can be used to co-estimate the genealogical relationships, mutation rate, evolutionary timescale, and demographic history of the study species in a single analytical framework. A number of modifications to the methodology can be made in order to deal with complicating factors such as postmortem damage, sequences from undated samples, and data sets with low information content.

  19. Epitope discovery with phylogenetic hidden Markov models.

    LENUS (Irish Health Repository)

    Lacerda, Miguel

    2010-05-01

    Existing methods for the prediction of immunologically active T-cell epitopes are based on the amino acid sequence or structure of pathogen proteins. Additional information regarding the locations of epitopes may be acquired by considering the evolution of viruses in hosts with different immune backgrounds. In particular, immune-dependent evolutionary patterns at sites within or near T-cell epitopes can be used to enhance epitope identification. We have developed a mutation-selection model of T-cell epitope evolution that allows the human leukocyte antigen (HLA) genotype of the host to influence the evolutionary process. This is one of the first examples of the incorporation of environmental parameters into a phylogenetic model and has many other potential applications where the selection pressures exerted on an organism can be related directly to environmental factors. We combine this novel evolutionary model with a hidden Markov model to identify contiguous amino acid positions that appear to evolve under immune pressure in the presence of specific host immune alleles and that therefore represent potential epitopes. This phylogenetic hidden Markov model provides a rigorous probabilistic framework that can be combined with sequence or structural information to improve epitope prediction. As a demonstration, we apply the model to a data set of HIV-1 protein-coding sequences and host HLA genotypes.

  20. NAPP: the Nucleic Acid Phylogenetic Profile Database.

    Science.gov (United States)

    Ott, Alban; Idali, Anouar; Marchais, Antonin; Gautheret, Daniel

    2012-01-01

    Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to identify previously undetected RNA genes or elements. Furthermore, as NAPP clusters contain both coding and non-coding sequences with similar occurrence profiles, they can be analyzed under a functional perspective. We recently improved the NAPP pipeline and applied it to a collection of 949 bacterial and 68 archaeal species. The database and web interface available at http://napp.u-psud.fr/ enable detailed analysis of NAPP clusters enriched in non-coding RNAs, graphical display of phylogenetic profiles, visualization of predicted RNAs in their genome context and extraction of predicted RNAs for use with genome browsers or other software.

  1. Phylogenetically-Informed Priorities for Amphibian Conservation

    Science.gov (United States)

    Isaac, Nick J. B.; Redding, David W.; Meredith, Helen M.; Safi, Kamran

    2012-01-01

    The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species’ threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list) for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species’ phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our ‘top 100‘ list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history. PMID:22952807

  2. Phylogenetic relationships among megabats, microbats, and primates.

    Science.gov (United States)

    Mindell, D P; Dick, C W; Baker, R J

    1991-11-15

    We present 744 nucleotide base positions from the mitochondrial 12S rRNA gene and 236 base positions from the mitochondrial cytochrome oxidase subunit I gene for a microbat, Brachyphylla cavernarum, and a megabat, Pteropus capestratus, in phylogenetic analyses with homologous DNA sequences from Homo sapiens, Mus musculus (house mouse), and Gallus gallus (chicken). We use information on evolutionary rate differences for different types of sequence change to establish phylogenetic character weights, and we consider alternative rRNA alignment strategies in finding that this mtDNA data set clearly supports bat monophyly. This result is found despite variations in outgroup used, gap coding scheme, and order of input for DNA sequences in multiple alignment bouts. These findings are congruent with morphological characters including details of wing structure as well as cladistic analyses of amino acid sequences for three globin genes and indicate that neurological similarities between megabats and primates are due to either retention of primitive characters or to convergent evolution rather than to inheritance from a common ancestor. This finding also indicates a single origin for flight among mammals.

  3. Phylogenetics of Theileria species in small ruminants.

    Science.gov (United States)

    Sparagano, Olivier A E; Spitalska, Eva; Namavari, Mehdi; Torina, Alessandra; Cannella, Vincenza; Caracappa, Santo

    2006-10-01

    Our study is based on the collection of blood and ticks from sheep in Iran and Italy. Polymerase chain reaction (PCR) testing was performed to target the 18S rRNA gene and RLB was performed using previously published probes. In Italy and Iran 78.7% and 76.0% of the sheep were PCR positive, which after sequencing and RLB showed that they were Theileria ovis and Theileria lestoquardi, respectively. Phylogenetic analysis was performed using the Clustal W multiple sequence alignment program and our sequences were compared with more than 50 others already published in the EMBL database. Our T. lestoquardi sequences linked with other T. lestoquardi sequences from Iran, Tanzania, and Sudan and Theileria annulata showed the importance of having species-specific probes between these two species. However, distinctive clades were found between T. lestoquardi ticks and those found in sheep blood. Italian T. ovis seemed to be closer to Theileria spp. from Namibia and Iran than with other T. ovis from Spain, Turkey, Tanzania, and Sudan adding some information to the controversy about this species. However, some confusion was found on the existing database where the location of pathogens, years, and species names was inaccurate and when available sequences were not always appropriately used. This article will discuss our results and some comparisons with other phylogenetic approaches.

  4. Triboelectric Charging at the Nanostructured Solid/Liquid Interface for Area-Scalable Wave Energy Conversion and Its Use in Corrosion Protection.

    Science.gov (United States)

    Zhao, Xue Jiao; Zhu, Guang; Fan, You Jun; Li, Hua Yang; Wang, Zhong Lin

    2015-07-28

    We report a flexible and area-scalable energy-harvesting technique for converting kinetic wave energy. Triboelectrification as a result of direct interaction between a dynamic wave and a large-area nanostructured solid surface produces an induced current among an array of electrodes. An integration method ensures that the induced current between any pair of electrodes can be constructively added up, which enables significant enhancement in output power and realizes area-scalable integration of electrode arrays. Internal and external factors that affect the electric output are comprehensively discussed. The produced electricity not only drives small electronics but also achieves effective impressed current cathodic protection. This type of thin-film-based device is a potentially practical solution of on-site sustained power supply at either coastal or off-shore sites wherever a dynamic wave is available. Potential applications include corrosion protection, pollution degradation, water desalination, and wireless sensing for marine surveillance.

  5. GASPRNG: GPU accelerated scalable parallel random number generator library

    Science.gov (United States)

    Gao, Shuang; Peterson, Gregory D.

    2013-04-01

    Graphics processors represent a promising technology for accelerating computational science applications. Many computational science applications require fast and scalable random number generation with good statistical properties, so they use the Scalable Parallel Random Number Generators library (SPRNG). We present the GPU Accelerated SPRNG library (GASPRNG) to accelerate SPRNG in GPU-based high performance computing systems. GASPRNG includes code for a host CPU and CUDA code for execution on NVIDIA graphics processing units (GPUs) along with a programming interface to support various usage models for pseudorandom numbers and computational science applications executing on the CPU, GPU, or both. This paper describes the implementation approach used to produce high performance and also describes how to use the programming interface. The programming interface allows a user to be able to use GASPRNG the same way as SPRNG on traditional serial or parallel computers as well as to develop tightly coupled programs executing primarily on the GPU. We also describe how to install GASPRNG and use it. To help illustrate linking with GASPRNG, various demonstration codes are included for the different usage models. GASPRNG on a single GPU shows up to 280x speedup over SPRNG on a single CPU core and is able to scale for larger systems in the same manner as SPRNG. Because GASPRNG generates identical streams of pseudorandom numbers as SPRNG, users can be confident about the quality of GASPRNG for scalable computational science applications. Catalogue identifier: AEOI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOI_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: UTK license. No. of lines in distributed program, including test data, etc.: 167900 No. of bytes in distributed program, including test data, etc.: 1422058 Distribution format: tar.gz Programming language: C and CUDA. Computer: Any PC or

  6. Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM

    Science.gov (United States)

    Quax, Rick; van de Vijver, David A. M. C.; Frentz, Dineke; Sloot, Peter M. A.

    2013-09-01

    The HIV-1 epidemic in Europe is primarily sustained by a dynamic topology of sexual interactions among MSM who have individual immune systems and behavior. This epidemiological process shapes the phylogeny of the virus population. Both fields of epidemic modeling and phylogenetics have a long history, however it remains difficult to use phylogenetic data to infer epidemiological parameters such as the structure of the sexual network and the per-act infectiousness. This is because phylogenetic data is necessarily incomplete and ambiguous. Here we show that the cluster-size distribution indeed contains information about epidemiological parameters using detailed numberical experiments. We simulate the HIV epidemic among MSM many times using the Monte Carlo method with all parameter values and their ranges taken from literature. For each simulation and the corresponding set of parameter values we calculate the likelihood of reproducing an observed cluster-size distribution. The result is an estimated likelihood distribution of all parameters from the phylogenetic data, in particular the structure of the sexual network, the per-act infectiousness, and the risk behavior reduction upon diagnosis. These likelihood distributions encode the knowledge provided by the observed cluster-size distrbution, which we quantify using information theory. Our work suggests that the growing body of genetic data of patients can be exploited to understand the underlying epidemiological process.

  7. A Scalable Gaussian Process Analysis Algorithm for Biomass Monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Chandola, Varun [ORNL; Vatsavai, Raju [ORNL

    2011-01-01

    Biomass monitoring is vital for studying the carbon cycle of earth's ecosystem and has several significant implications, especially in the context of understanding climate change and its impacts. Recently, several change detection methods have been proposed to identify land cover changes in temporal profiles (time series) of vegetation collected using remote sensing instruments, but do not satisfy one or both of the two requirements of the biomass monitoring problem, i.e., {\\em operating in online mode} and {\\em handling periodic time series}. In this paper, we adapt Gaussian process regression to detect changes in such time series in an online fashion. While Gaussian process (GP) have been widely used as a kernel based learning method for regression and classification, their applicability to massive spatio-temporal data sets, such as remote sensing data, has been limited owing to the high computational costs involved. We focus on addressing the scalability issues associated with the proposed GP based change detection algorithm. This paper makes several significant contributions. First, we propose a GP based online time series change detection algorithm and demonstrate its effectiveness in detecting different types of changes in {\\em Normalized Difference Vegetation Index} (NDVI) data obtained from a study area in Iowa, USA. Second, we propose an efficient Toeplitz matrix based solution which significantly improves the computational complexity and memory requirements of the proposed GP based method. Specifically, the proposed solution can analyze a time series of length $t$ in $O(t^2)$ time while maintaining a $O(t)$ memory footprint, compared to the $O(t^3)$ time and $O(t^2)$ memory requirement of standard matrix manipulation based methods. Third, we describe a parallel version of the proposed solution which can be used to simultaneously analyze a large number of time series. We study three different parallel implementations: using threads, MPI, and a

  8. Towards Reliable, Scalable, and Energy Efficient Cognitive Radio Systems

    KAUST Repository

    Sboui, Lokman

    2017-11-01

    The cognitive radio (CR) concept is expected to be adopted along with many technologies to meet the requirements of the next generation of wireless and mobile systems, the 5G. Consequently, it is important to determine the performance of the CR systems with respect to these requirements. In this thesis, after briefly describing the 5G requirements, we present three main directions in which we aim to enhance the CR performance. The first direction is the reliability. We study the achievable rate of a multiple-input multiple-output (MIMO) relay-assisted CR under two scenarios; an unmanned aerial vehicle (UAV) one-way relaying (OWR) and a fixed two-way relaying (TWR). We propose special linear precoding schemes that enable the secondary user (SU) to take advantage of the primary-free channel eigenmodes. We study the SU rate sensitivity to the relay power, the relay gain, the UAV altitude, the number of antennas and the line of sight availability. The second direction is the scalability. We first study a multiple access channel (MAC) with multiple SUs scenario. We propose a particular linear precoding and SUs selection scheme maximizing their sum-rate. We show that the proposed scheme provides a significant sum-rate improvement as the number of SUs increases. Secondly, we expand our scalability study to cognitive cellular networks. We propose a low-complexity algorithm for base station activation/deactivation and dynamic spectrum management maximizing the profits of primary and secondary networks subject to green constraints. We show that our proposed algorithms achieve performance close to those obtained with the exhaustive search method. The third direction is the energy efficiency (EE). We present a novel power allocation scheme based on maximizing the EE of both single-input and single-output (SISO) and MIMO systems. We solve a non-convex problem and derive explicit expressions of the corresponding optimal power. When the instantaneous channel is not available, we

  9. Spatial predictions of phylogenetic diversity in conservation decision making.

    Science.gov (United States)

    Pio, Dorothea V; Broennimann, Olivier; Barraclough, Timothy G; Reeves, Gail; Rebelo, Anthony G; Thuiller, Wilfried; Guisan, Antoine; Salamin, Nicolas

    2011-12-01

    Considering genetic relatedness among species has long been argued as an important step toward measuring biological diversity more accurately, rather than relying solely on species richness. Some researchers have correlated measures of phylogenetic diversity and species richness across a series of sites and suggest that values of phylogenetic diversity do not differ enough from those of species richness to justify their inclusion in conservation planning. We compared predictions of species richness and 10 measures of phylogenetic diversity by creating distribution models for 168 individual species of a species-rich plant family, the Cape Proteaceae. When we used average amounts of land set aside for conservation to compare areas selected on the basis of species richness with areas selected on the basis of phylogenetic diversity, correlations between species richness and different measures of phylogenetic diversity varied considerably. Correlations between species richness and measures that were based on the length of phylogenetic tree branches and tree shape were weaker than those that were based on tree shape alone. Elevation explained up to 31% of the segregation of species rich versus phylogenetically rich areas. Given these results, the increased availability of molecular data, and the known ecological effect of phylogenetically rich communities, consideration of phylogenetic diversity in conservation decision making may be feasible and informative. ©2011 Society for Conservation Biology.

  10. Improvement of phylogenetic method to analyze compositional heterogeneity.

    Science.gov (United States)

    Zhang, Zehua; Guo, Kecheng; Pan, Gaofeng; Tang, Jijun; Guo, Fei

    2017-09-21

    Phylogenetic analysis is a key way to understand current research in the biological processes and detect theory in evolution of natural selection. The evolutionary relationship between species is generally reflected in the form of phylogenetic trees. Many methods for constructing phylogenetic trees, are based on the optimization criteria. We extract the biological data via modeling features, and then compare these characteristics to study the biological evolution between species. Here, we use maximum likelihood and Bayesian inference method to establish phylogenetic trees; multi-chain Markov chain Monte Carlo sampling method can be used to select optimal phylogenetic tree, resolving local optimum problem. The correlation model of phylogenetic analysis assumes that phylogenetic trees are built on homogeneous data, however there exists a large deviation in the presence of heterogeneous data. We use conscious detection to solve compositional heterogeneity. Our method is evaluated on two sets of experimental data, a group of bacterial 16S ribosomal RNA gene data, and a group of genetic data with five homologous species. Our method can obtain accurate phylogenetic trees on the homologous data, and also detect the compositional heterogeneity of experimental data. We provide an efficient method to enhance the accuracy of generated phylogenetic tree.

  11. Isolation and phylogenetic analysis of zinc resistant Acinetobacter ...

    African Journals Online (AJOL)

    Isolation and phylogenetic analysis of zinc resistant Acinetobacter sp. and its potential for bioremediation. Fatemeh Bagheri Bejestani, Maryam Ghane, Marjan Mirhosseininia, Ozra Bagheri Bejestani ...

  12. Molecular phylogenetic analysis of Nitrobacter spp.

    Science.gov (United States)

    Orso, S; Gouy, M; Navarro, E; Normand, P

    1994-01-01

    The phylogeny of bacteria belonging to the genus Nitrobacter was investigated by sequencing the whole 16S rRNA gene. The average level of similarity for the three Nitrobacter strains examined was high (99.2%), and the similarity level between Nitrobacter winogradskyi and Nitrobacter sp. strain LL, which represent two different genomic species, was even higher (99.6%). When all of the Nitrobacter strains and their phylogenetic neighbors Bradyrhizobium and Rhodopseudomonas species were considered, the average similarity level was 98.1%. When complete sequences were used, Nitrobacter hamburgensis clustered with the two other Nitrobacter strains, while this was not the case when partial sequences were used. The two Rhodopseudomonas palustris strains examined exhibited a low similarity level (97.6%) and were not clustered.

  13. Inferring Phylogenetic Networks from Gene Order Data

    Directory of Open Access Journals (Sweden)

    Alexey Anatolievich Morozov

    2013-01-01

    Full Text Available Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary, sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm. Binary encoding can also be useful, but only when the methods mentioned above cannot be used.

  14. Mitochondrial genome organization and vertebrate phylogenetics

    Directory of Open Access Journals (Sweden)

    Pereira Sérgio Luiz

    2000-01-01

    Full Text Available With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some new rearrangements seem to be typical of monophyletic groups and the use of data from these groups may be useful for answering phylogenetic questions involving vertebrate higher taxonomic levels. Other features such as the secondary structure of tRNA, and the start and stop codons of protein-coding genes may also be useful in comparisons of vertebrate mitochondrial genomes.

  15. The Shapley Value of Phylogenetic Trees

    CERN Document Server

    Haake, Claus-Jochen; Su, Francis Edward

    2007-01-01

    Every weighted tree corresponds naturally to a cooperative game that we call a "tree game"; it assigns to each subset of leaves the sum of the weights of the minimal subtree spanned by those leaves. In the context of phylogenetic trees, the leaves are species and this assignment captures the diversity present in the coalition of species considered. We consider the Shapley value of tree games and suggest a biological interpretation. We determine the linear transformation M that shows the dependence of the Shapley value on the edge weights of the tree, and we also compute a null space basis of M. Both depend on the "split counts" of the tree. Finally, we characterize the Shapley value on tree games by four axioms, a counterpart to Shapley's original theorem on the larger class of cooperative games.

  16. Phylogenetic approaches to microbial community classification.

    Science.gov (United States)

    Ning, Jie; Beiko, Robert G

    2015-10-05

    The microbiota from different body sites are dominated by different major groups of microbes, but the variations within a body site such as the mouth can be more subtle. Accurate predictive models can serve as useful tools for distinguishing sub-sites and understanding key organisms and their roles and can highlight deviations from expected distributions of microbes. Good classification depends on choosing the right combination of classifier, feature representation, and learning model. Machine-learning procedures have been used in the past for supervised classification, but increased attention to feature representation and selection may produce better models and predictions. We focused our attention on the classification of nine oral sites and dental plaque in particular, using data collected from the Human Microbiome Project. A key focus of our representations was the use of phylogenetic information, both as the basis for custom kernels and as a way to represent sets of microbes to the classifier. We also used the PICRUSt software, which draws on phylogenetic relationships to predict molecular functions and to generate additional features for the classifier. Custom kernels based on the UniFrac measure of community dissimilarity did not improve performance. However, feature representation was vital to classification accuracy, with microbial clade and function representations providing useful information to the classifier; combining the two types of features did not yield increased prediction accuracy. Many of the best-performing clades and functions had clear associations with oral microflora. The classification of oral microbiota remains a challenging problem; our best accuracy on the plaque dataset was approximately 81 %. Perfect accuracy may be unattainable due to the close proximity of the sites and intra-individual variation. However, further exploration of the space of both classifiers and feature representations is likely to increase the accuracy of

  17. A nonlinear scalable model for designing ionic polymer-metal composite actuator systems

    Science.gov (United States)

    McDaid, A. J.; Aw, K. C.; Hämmerle, E.; Xie, S. Q.

    2009-07-01

    This paper proposes a conclusive scalable model for Ionic Polymer Metal Composites (IPMC) actuators and their interactions with mechanical systems and external loads. This dynamic, nonlinear model accurately predicts the displacement and force actuation in air for a large range of input voltages. The model addresses all the requirements of a useful design tool for IPMC actuators and is intended for robotic and bio-mimetic (artificial muscle) applications which operate at low frequencies. The response of the IPMC is modeled in three stages, (i) a nonlinear equivalent electrical circuit to predict the current drawn, (ii) an electro-mechanical coupling term, representing the conversion of ion flux to a stress generated in the polymer membrane and (iii) a mechanical beam model which includes an electrically induced torque for the polymer. Mechanical outputs are in the rotational coordinate system, 'tip angle' and 'torque output', to give more practical results for the design and simulation of mechanisms. Model parameters are obtained using the dynamic time response and results are presented demonstrating excellent correspondence between the model and experimental results. This newly developed model is a large step forward, aiding in the progression of IPMCs towards wide acceptance as replacements to traditional actuators.

  18. Scalable, high-performance 3D imaging software platform: system architecture and application to virtual colonoscopy.

    Science.gov (United States)

    Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli; Brett, Bevin

    2012-01-01

    One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. In this work, we have developed a software platform that is designed to support high-performance 3D medical image processing for a wide range of applications using increasingly available and affordable commodity computing systems: multi-core, clusters, and cloud computing systems. To achieve scalable, high-performance computing, our platform (1) employs size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D image processing algorithms; (2) supports task scheduling for efficient load distribution and balancing; and (3) consists of a layered parallel software libraries that allow a wide range of medical applications to share the same functionalities. We evaluated the performance of our platform by applying it to an electronic cleansing system in virtual colonoscopy, with initial experimental results showing a 10 times performance improvement on an 8-core workstation over the original sequential implementation of the system.

  19. Trial prospector: matching patients with cancer research studies using an automated and scalable approach.

    Science.gov (United States)

    Sahoo, Satya S; Tao, Shiqiang; Parchman, Andrew; Luo, Zhihui; Cui, Licong; Mergler, Patrick; Lanese, Robert; Barnholtz-Sloan, Jill S; Meropol, Neal J; Zhang, Guo-Qiang

    2014-01-01

    Cancer is responsible for approximately 7.6 million deaths per year worldwide. A 2012 survey in the United Kingdom found dramatic improvement in survival rates for childhood cancer because of increased participation in clinical trials. Unfortunately, overall patient participation in cancer clinical studies is low. A key logistical barrier to patient and physician participation is the time required for identification of appropriate clinical trials for individual patients. We introduce the Trial Prospector tool that supports end-to-end management of cancer clinical trial recruitment workflow with (a) structured entry of trial eligibility criteria, (b) automated extraction of patient data from multiple sources, (c) a scalable matching algorithm, and (d) interactive user interface (UI) for physicians with both matching results and a detailed explanation of causes for ineligibility of available trials. We report the results from deployment of Trial Prospector at the National Cancer Institute (NCI)-designated Case Comprehensive Cancer Center (Case CCC) with 1,367 clinical trial eligibility evaluations performed with 100% accuracy.

  20. Flash NanoPrecipitation as a scalable platform for the production of structured and hybrid nanocolloids

    Science.gov (United States)

    Lee, Victoria; Sosa, Chris; Liu, Rui; Prud'Homme, Robert; Priestley, Rodney

    Geometrically-structured polymer nanocolloids have been widely investigated for their unique properties, which are derived from their anisotropy. Decoration with inorganic nanoparticles in a controlled manner could induce another level of functionality into structured nanocolloids that could enable applications in fields such as re-writeable electronics and biphasic catalysis. Here, Flash NanoPrecipitation (FNP) is demonstrated as a one-step and scalable process platform to manufacture hybrid polymer-inorganic nanocolloids in which one phase is selectively decorated with a metal nanocatalyst by tuning the interactions between the feed ingredients. For instance, by modifying polymer end-group functionality, we are able to tune the location of the metal nanocatalyst, including placement at the Janus nanocolloid circumference. Moreover, the addition of surfactant to the system is shown to transform the Janus nanocolloid structure from spherical to dumbbell or snowman while still maintaining control over nanocatalyst location. Considering the flexibility and continuous nature of the FNP process, it offers an industrial-scale platform for manufacturing of nanomaterials that are anticipated to impact many technologies.

  1. Highly Efficient and Scalable Separation of Semiconducting Carbon Nanotubes via Weak Field Centrifugation

    Science.gov (United States)

    Reis, Wieland G.; Weitz, R. Thomas; Kettner, Michel; Kraus, Alexander; Schwab, Matthias Georg; Tomović, Željko; Krupke, Ralph; Mikhael, Jules

    2016-05-01

    The identification of scalable processes that transfer random mixtures of single-walled carbon nanotubes (SWCNTs) into fractions featuring a high content of semiconducting species is crucial for future application of SWCNTs in high-performance electronics. Herein we demonstrate a highly efficient and simple separation method that relies on selective interactions between tailor-made amphiphilic polymers and semiconducting SWCNTs in the presence of low viscosity separation media. High purity individualized semiconducting SWCNTs or even self-organized semiconducting sheets are separated from an as-produced SWCNT dispersion via a single weak field centrifugation run. Absorption and Raman spectroscopy are applied to verify the high purity of the obtained SWCNTs. Furthermore SWCNT - network field-effect transistors were fabricated, which exhibit high ON/OFF ratios (105) and field-effect mobilities (17 cm2/Vs). In addition to demonstrating the feasibility of high purity separation by a novel low complexity process, our method can be readily transferred to large scale production.

  2. Towards Scalable Deep Learning via I/O Analysis and Optimization

    Energy Technology Data Exchange (ETDEWEB)

    Pumma, Sarunya; Si, Min; Feng, Wu-Chun; Balaji, Pavan

    2017-01-01

    Deep learning systems have been growing in prominence as a way to automatically characterize objects, trends, and anomalies. Given the importance of deep learning systems, researchers have been investigating techniques to optimize such systems. An area of particular interest has been using large supercomputing systems to quickly generate effective deep learning networks: a phase often referred to as “training” of the deep learning neural network. As we scale existing deep learning frameworks—such as Caffe—on these large supercomputing systems, we notice that the parallelism can help improve the computation tremendously, leaving data I/O as the major bottleneck limiting the overall system scalability. In this paper, we first present a detailed analysis of the performance bottlenecks of Caffe on large supercomputing systems. Our analysis shows that the I/O subsystem of Caffe—LMDB—relies on memory-mapped I/O to access its database, which can be highly inefficient on large-scale systems because of its interaction with the process scheduling system and the network-based parallel filesystem. Based on this analysis, we then present LMDBIO, our optimized I/O plugin for Caffe that takes into account the data access pattern of Caffe in order to vastly improve I/O performance. Our experimental results show that LMDBIO can improve the overall execution time of Caffe by nearly 20-fold in some cases.

  3. Using common table expressions to build a scalable Boolean query generator for clinical data warehouses.

    Science.gov (United States)

    Harris, Daniel R; Henderson, Darren W; Kavuluru, Ramakanth; Stromberg, Arnold J; Johnson, Todd R

    2014-09-01

    We present a custom, Boolean query generator utilizing common-table expressions (CTEs) that is capable of scaling with big datasets. The generator maps user-defined Boolean queries, such as those interactively created in clinical-research and general-purpose healthcare tools, into SQL. We demonstrate the effectiveness of this generator by integrating our study into the Informatics for Integrating Biology and the Bedside (i2b2) query tool and show that it is capable of scaling. Our custom generator replaces and outperforms the default query generator found within the Clinical Research Chart cell of i2b2. In our experiments, 16 different types of i2b2 queries were identified by varying four constraints: date, frequency, exclusion criteria, and whether selected concepts occurred in the same encounter. We generated nontrivial, random Boolean queries based on these 16 types; the corresponding SQL queries produced by both generators were compared by execution times. The CTE-based solution significantly outperformed the default query generator and provided a much more consistent response time across all query types (M = 2.03, SD = 6.64 versus M = 75.82, SD = 238.88 s). Without costly hardware upgrades, we provide a scalable solution based on CTEs with very promising empirical results centered on performance gains. The evaluation methodology used for this provides a means of profiling clinical data warehouse performance.

  4. Continuous and scalable polymer capsule processing for inertial fusion energy target shell fabrication using droplet microfluidics.

    Science.gov (United States)

    Li, Jin; Lindley-Start, Jack; Porch, Adrian; Barrow, David

    2017-07-24

    High specification, polymer capsules, to produce inertial fusion energy targets, were continuously fabricated using surfactant-free, inertial centralisation, and ultrafast polymerisation, in a scalable flow reactor. Laser-driven, inertial confinement fusion depends upon the interaction of high-energy lasers and hydrogen isotopes, contained within small, spherical and concentric target shells, causing a nuclear fusion reaction at ~150 M°C. Potentially, targets will be consumed at ~1 M per day per reactor, demanding a 5000x unit cost reduction to ~$0.20, and is a critical, key challenge. Experimentally, double emulsions were used as templates for capsule-shells, and were formed at 20 Hz, on a fluidic chip. Droplets were centralised in a dynamic flow, and their shapes both evaluated, and mathematically modeled, before subsequent shell solidification. The shells were photo-cured individually, on-the-fly, with precisely-actuated, millisecond-length (70 ms), uniform-intensity UV pulses, delivered through eight, radially orchestrated light-pipes. The near 100% yield rate of uniform shells had a minimum 99.0% concentricity and sphericity, and the solidification processing period was significantly reduced, over conventional batch methods. The data suggest the new possibility of a continuous, on-the-fly, IFE target fabrication process, employing sequential processing operations within a continuous enclosed duct system, which may include cryogenic fuel-filling, and shell curing, to produce ready-to-use IFE targets.

  5. Shifts in the phylogenetic structure of arbuscular mycorrhizal fungi in response to experimental nitrogen and carbon dioxide additions.

    Science.gov (United States)

    Mueller, Rebecca C; Bohannan, Brendan J M

    2015-09-01

    Global N inputs and atmospheric CO2 concentrations have increased as a result of human activities, and are predicted to increase along with population growth, with potentially negative effects on biodiversity. Using taxonomic and phylogenetic measures, we examined the response of arbuscular mycorrhizal fungi (AMF) to experimental manipulations of N and CO2 at the Jasper Ridge Global Change Experiment. No significant interactions between N and CO2 were observed, but individual effects of N and CO2 were found. Elevated CO2 resulted in changes in phylogenetic similarity, and a shift to phylogenetic clustering of AMF communities. N addition resulted in higher phylogenetic diversity and evenness, with no shifts in community composition and no significant signal for phylogenetic clustering. N addition resulted in an increase in both available N and the N:P ratio in N-amended plots, which suggests that changing patterns of nutrient limitation could have lead to altered species interactions. These findings suggest that elevated levels of N and CO2 altered patterns of AMF community assembly, with potential effects on ecosystem function.

  6. High-performance scalable Information Service for the ATLAS experiment

    CERN Document Server

    Kolos, S; The ATLAS collaboration; Hauser, R

    2012-01-01

    The ATLAS experiment is being operated by highly distributed computing system which is constantly producing a lot of status information which is used to monitor the experiment operational conditions as well as to access the quality of the physics data being taken. For example the ATLAS High Level Trigger(HLT) algorithms are executed on the online computing farm consisting from about 1500 nodes. Each HLT algorithm is producing few thousands histograms, which have to be integrated over the whole farm and carefully analyzed in order to properly tune the event rejection. In order to handle such non-physics data the Information Service (IS) facility has been developed in the scope of the ATLAS TDAQ project. The IS provides high-performance scalable solution for information exchange in distributed environment. In the course of an ATLAS data taking session the IS handles about hundred gigabytes of information which is being constantly updated with the update interval varying from a second to few tens of seconds. IS ...

  7. Scalable service architecture for providing strong service guarantees

    Science.gov (United States)

    Christin, Nicolas; Liebeherr, Joerg

    2002-07-01

    For the past decade, a lot of Internet research has been devoted to providing different levels of service to applications. Initial proposals for service differentiation provided strong service guarantees, with strict bounds on delays, loss rates, and throughput, but required high overhead in terms of computational complexity and memory, both of which raise scalability concerns. Recently, the interest has shifted to service architectures with low overhead. However, these newer service architectures only provide weak service guarantees, which do not always address the needs of applications. In this paper, we describe a service architecture that supports strong service guarantees, can be implemented with low computational complexity, and only requires to maintain little state information. A key mechanism of the proposed service architecture is that it addresses scheduling and buffer management in a single algorithm. The presented architecture offers no solution for controlling the amount of traffic that enters the network. Instead, we plan on exploiting feedback mechanisms of TCP congestion control algorithms for the purpose of regulating the traffic entering the network.

  8. Scalable TCP-friendly Video Distribution for Heterogeneous Clients

    Science.gov (United States)

    Zink, Michael; Griwodz, Carsten; Schmitt, Jens; Steinmetz, Ralf

    2003-01-01

    This paper investigates an architecture and implementation for the use of a TCP-friendly protocol in a scalable video distribution system for hierarchically encoded layered video. The design supports a variety of heterogeneous clients, because recent developments have shown that access network and client capabilities differ widely in today's Internet. The distribution system presented here consists of videos servers, proxy caches and clients that make use of a TCP-friendly rate control (TFRC) to perform congestion controlled streaming of layer encoded video. The data transfer protocol of the system is RTP compliant, yet it integrates protocol elements for congestion control with protocols elements for retransmission that is necessary for lossless transfer of contents into proxy caches. The control protocol RTSP is used to negotiate capabilities, such as support for congestion control or retransmission. By tests performed with our experimental platform in a lab test and over the Internet, we show that congestion controlled streaming of layer encoded video through proxy caches is a valid means of supporting heterogeneous clients. We show that filtering of layers depending on a TFRC-controlled permissible bandwidth allows the preferred delivery of the most relevant layers to end-systems while additional layers can be delivered to the cache server. We experiment with uncontrolled delivery from the proxy cache to the client as well, which may result in random loss and bandwidth waste but also a higher goodput, and compare these two approaches.

  9. Quality Guidelines for Scalable Eco Skills in Vet Delivery

    Directory of Open Access Journals (Sweden)

    Liviu MOLDOVAN

    2016-06-01

    Full Text Available In a sustainable economy the assessment of Eco skills provided in a Vocational Education and Training (VET course is performed by the amount of knowledge applied on the job a period after the course ends. To this end VET providers have a current need of quality guidelines for scalable Eco skills and sustainable training evaluation. The purpose of the paper is to present some results of the project entitled “European Quality Assurance in VET towards new Eco Skills and Environmentally Sustainable Economy”, as regards Eco skills categorisation and elaboration of a scale to be used in the green methodology for learning assessment. In the research methodology, the Eco skills are categorised and exemplified for jobs at different levels into generic skills and specific skills evidenced from relevant publications in the field. Than the new Eco skills scale is developed which is organized into six steps: from “Level 1 - Introductory” up to “Level 6 - Expert”. The Eco skills scale is a useful input in the learning assessment process.

  10. GenePING: secure, scalable management of personal genomic data

    Directory of Open Access Journals (Sweden)

    Kohane Isaac S

    2006-04-01

    Full Text Available Abstract Background Patient genomic data are rapidly becoming part of clinical decision making. Within a few years, full genome expression profiling and genotyping will be affordable enough to perform on every individual. The management of such sizeable, yet fine-grained, data in compliance with privacy laws and best practices presents significant security and scalability challenges. Results We present the design and implementation of GenePING, an extension to the PING personal health record system that supports secure storage of large, genome-sized datasets, as well as efficient sharing and retrieval of individual datapoints (e.g. SNPs, rare mutations, gene expression levels. Even with full access to the raw GenePING storage, an attacker cannot discover any stored genomic datapoint on any single patient. Given a large-enough number of patient records, an attacker cannot discover which data corresponds to which patient, or even the size of a given patient's record. The computational overhead of GenePING's security features is a small constant, making the system usable, even in emergency care, on today's hardware. Conclusion GenePING is the first personal health record management system to support the efficient and secure storage and sharing of large genomic datasets. GenePING is available online at http://ping.chip.org/genepinghtml, licensed under the LGPL.

  11. The design of a scalable, fixed-time computer benchmark

    Energy Technology Data Exchange (ETDEWEB)

    Gustafson, J.; Rover, D.; Elbert, S.; Carter, M.

    1990-10-01

    By using the principle of fixed time benchmarking, it is possible to compare a very wide range of computers, from a small personal computer to the most powerful parallel supercomputer, an a single scale. Fixed-time benchmarks promise far greater longevity than those based on a particular problem size, and are more appropriate for grand challenge'' capability comparison. We present the design of a benchmark, SLALOM{trademark}, that scales automatically to the computing power available, and corrects several deficiencies in various existing benchmarks: it is highly scalable, it solves a real problem, it includes input and output times, and it can be run on parallel machines of all kinds, using any convenient language. The benchmark provides a reasonable estimate of the size of problem solvable on scientific computers. Results are presented that span six orders of magnitude for contemporary computers of various architectures. The benchmarks also can be used to demonstrate a new source of superlinear speedup in parallel computers. 15 refs., 14 figs., 3 tabs.

  12. A Scalable Distributed Approach to Mobile Robot Vision

    Science.gov (United States)

    Kuipers, Benjamin; Browning, Robert L.; Gribble, William S.

    1997-01-01

    This paper documents our progress during the first year of work on our original proposal entitled 'A Scalable Distributed Approach to Mobile Robot Vision'. We are pursuing a strategy for real-time visual identification and tracking of complex objects which does not rely on specialized image-processing hardware. In this system perceptual schemas represent objects as a graph of primitive features. Distributed software agents identify and track these features, using variable-geometry image subwindows of limited size. Active control of imaging parameters and selective processing makes simultaneous real-time tracking of many primitive features tractable. Perceptual schemas operate independently from the tracking of primitive features, so that real-time tracking of a set of image features is not hurt by latency in recognition of the object that those features make up. The architecture allows semantically significant features to be tracked with limited expenditure of computational resources, and allows the visual computation to be distributed across a network of processors. Early experiments are described which demonstrate the usefulness of this formulation, followed by a brief overview of our more recent progress (after the first year).

  13. A highly scalable, interoperable clinical decision support service.

    Science.gov (United States)

    Goldberg, Howard S; Paterno, Marilyn D; Rocha, Beatriz H; Schaeffer, Molly; Wright, Adam; Erickson, Jessica L; Middleton, Blackford

    2014-02-01

    To create a clinical decision support (CDS) system that is shareable across healthcare delivery systems and settings over large geographic regions. The enterprise clinical rules service (ECRS) realizes nine design principles through a series of enterprise java beans and leverages off-the-shelf rules management systems in order to provide consistent, maintainable, and scalable decision support in a variety of settings. The ECRS is deployed at Partners HealthCare System (PHS) and is in use for a series of trials by members of the CDS consortium, including internally developed systems at PHS, the Regenstrief Institute, and vendor-based systems deployed at locations in Oregon and New Jersey. Performance measures indicate that the ECRS provides sub-second response time when measured apart from services required to retrieve data and assemble the continuity of care document used as input. We consider related work, design decisions, comparisons with emerging national standards, and discuss uses and limitations of the ECRS. ECRS design, implementation, and use in CDS consortium trials indicate that it provides the flexibility and modularity needed for broad use and performs adequately. Future work will investigate additional CDS patterns, alternative methods of data passing, and further optimizations in ECRS performance.

  14. Scalable and versatile graphene functionalized with the Mannich condensate.

    Science.gov (United States)

    Liao, Ruijuan; Tang, Zhenghai; Lin, Tengfei; Guo, Baochun

    2013-03-01

    The functionalized graphene (JTPG) is fabricated by chemical conversion of graphene oxide (GO), using tea polyphenols (TP) as the reducer and stabilizer, followed by further derivatization through the Mannich reaction between the pyrogallol groups on TP and Jeffamine M-2070. JTPG exhibits solubility in a broad spectrum of solvents, long-term stability and single-layered dispersion in water and organic solvents, which are substantiated by AFM, TEM, and XRD. The paper-like JTPG hybrids prepared by vacuum-assisted filtration exhibits an unusual combination of high toughness (tensile strength of ~275 MPa and break strain of ~8%) and high electrical conductivity (~700 S/m). Still, JTPG is revealed to be very promising in the fabrication of polymer/graphene composites due to the excellent solubility in the solvent with low boiling point and low toxicity. Accordingly, as an example, nitrile rubber/JTPG composites are fabricated by the solution compounding in acetone. The resulted composite shows low threshold percolation at 0.23 vol.% of graphene. The versatilities both in dispersibility and performance, together with the scalable process of JTPG, enable a new way to scale up the fabrication of the graphene-based polymer composites or hybrids with high performance.

  15. Scalable and responsive event processing in the cloud

    Science.gov (United States)

    Suresh, Visalakshmi; Ezhilchelvan, Paul; Watson, Paul

    2013-01-01

    Event processing involves continuous evaluation of queries over streams of events. Response-time optimization is traditionally done over a fixed set of nodes and/or by using metrics measured at query-operator levels. Cloud computing makes it easy to acquire and release computing nodes as required. Leveraging this flexibility, we propose a novel, queueing-theory-based approach for meeting specified response-time targets against fluctuating event arrival rates by drawing only the necessary amount of computing resources from a cloud platform. In the proposed approach, the entire processing engine of a distinct query is modelled as an atomic unit for predicting response times. Several such units hosted on a single node are modelled as a multiple class M/G/1 system. These aspects eliminate intrusive, low-level performance measurements at run-time, and also offer portability and scalability. Using model-based predictions, cloud resources are efficiently used to meet response-time targets. The efficacy of the approach is demonstrated through cloud-based experiments. PMID:23230164

  16. Scalable bonding of nanofibrous polytetrafluoroethylene (PTFE) membranes on microstructures

    Science.gov (United States)

    Mortazavi, Mehdi; Fazeli, Abdolreza; Moghaddam, Saeed

    2018-01-01

    Expanded polytetrafluoroethylene (ePTFE) nanofibrous membranes exhibit high porosity (80%–90%), high gas permeability, chemical inertness, and superhydrophobicity, which makes them a suitable choice in many demanding fields including industrial filtration, medical implants, bio-/nano- sensors/actuators and microanalysis (i.e. lab-on-a-chip). However, one of the major challenges that inhibit implementation of such membranes is their inability to bond to other materials due to their intrinsic low surface energy and chemical inertness. Prior attempts to improve adhesion of ePTFE membranes to other surfaces involved surface chemical treatments which have not been successful due to degradation of the mechanical integrity and the breakthrough pressure of the membrane. Here, we report a simple and scalable method of bonding ePTFE membranes to different surfaces via the introduction of an intermediate adhesive layer. While a variety of adhesives can be used with this technique, the highest bonding performance is obtained for adhesives that have moderate contact angles with the substrate and low contact angles with the membrane. A thin layer of an adhesive can be uniformly applied onto micro-patterned substrates with feature sizes down to 5 µm using a roll-coating process. Membrane-based microchannel and micropillar devices with burst pressures of up to 200 kPa have been successfully fabricated and tested. A thin layer of the membrane remains attached to the substrate after debonding, suggesting that mechanical interlocking through nanofiber engagement is the main mechanism of adhesion.

  17. An open, interoperable, and scalable prehospital information technology network architecture.

    Science.gov (United States)

    Landman, Adam B; Rokos, Ivan C; Burns, Kevin; Van Gelder, Carin M; Fisher, Roger M; Dunford, James V; Cone, David C; Bogucki, Sandy

    2011-01-01

    Some of the most intractable challenges in prehospital medicine include response time optimization, inefficiencies at the emergency medical services (EMS)-emergency department (ED) interface, and the ability to correlate field interventions with patient outcomes. Information technology (IT) can address these and other concerns by ensuring that system and patient information is received when and where it is needed, is fully integrated with prior and subsequent patient information, and is securely archived. Some EMS agencies have begun adopting information technologies, such as wireless transmission of 12-lead electrocardiograms, but few agencies have developed a comprehensive plan for management of their prehospital information and integration with other electronic medical records. This perspective article highlights the challenges and limitations of integrating IT elements without a strategic plan, and proposes an open, interoperable, and scalable prehospital information technology (PHIT) architecture. The two core components of this PHIT architecture are 1) routers with broadband network connectivity to share data between ambulance devices and EMS system information services and 2) an electronic patient care report to organize and archive all electronic prehospital data. To successfully implement this comprehensive PHIT architecture, data and technology requirements must be based on best available evidence, and the system must adhere to health data standards as well as privacy and security regulations. Recent federal legislation prioritizing health information technology may position federal agencies to help design and fund PHIT architectures.

  18. PET protection optimization for streaming scalable videos with multiple transmissions.

    Science.gov (United States)

    Xiong, Ruiqin; Taubman, David S; Sivaraman, Vijay

    2013-11-01

    This paper investigates priority encoding transmission (PET) protection for streaming scalably compressed video streams over erasure channels, for the scenarios where a small number of retransmissions are allowed. In principle, the optimal protection depends not only on the importance of each stream element, but also on the expected channel behavior. By formulating a collection of hypotheses concerning its own behavior in future transmissions, limited-retransmission PET (LR-PET) effectively constructs channel codes spanning multiple transmission slots and thus offers better protection efficiency than the original PET. As the number of transmission opportunities increases, the optimization for LR-PET becomes very challenging because the number of hypothetical retransmission paths increases exponentially. As a key contribution, this paper develops a method to derive the effective recovery-probability versus redundancy-rate characteristic for the LR-PET procedure with any number of transmission opportunities. This significantly accelerates the protection assignment procedure in the original LR-PET with only two transmissions, and also makes a quick and optimal protection assignment feasible for scenarios where more transmissions are possible. This paper also gives a concrete proof to the redundancy embedding property of the channel codes formed by LR-PET, which allows for a decoupled optimization for sequentially dependent source elements with convex utility-length characteristic. This essentially justifies the source-independent construction of the protection convex hull for LR-PET.

  19. Scalability Issues for Remote Sensing Infrastructure: A Case Study.

    Science.gov (United States)

    Liu, Yang; Picard, Sean; Williamson, Carey

    2017-04-29

    For the past decade, a team of University of Calgary researchers has operated a large "sensor Web" to collect, analyze, and share scientific data from remote measurement instruments across northern Canada. This sensor Web receives real-time data streams from over a thousand Internet-connected sensors, with a particular emphasis on environmental data (e.g., space weather, auroral phenomena, atmospheric imaging). Through research collaborations, we had the opportunity to evaluate the performance and scalability of their remote sensing infrastructure. This article reports the lessons learned from our study, which considered both data collection and data dissemination aspects of their system. On the data collection front, we used benchmarking techniques to identify and fix a performance bottleneck in the system's memory management for TCP data streams, while also improving system efficiency on multi-core architectures. On the data dissemination front, we used passive and active network traffic measurements to identify and reduce excessive network traffic from the Web robots and JavaScript techniques used for data sharing. While our results are from one specific sensor Web system, the lessons learned may apply to other scientific Web sites with remote sensing infrastructure.

  20. Hierarchical sets: analyzing pangenome structure through scalable set visualizations.

    Science.gov (United States)

    Pedersen, Thomas Lin

    2017-06-01

    The increase in available microbial genome sequences has resulted in an increase in the size of the pangenomes being analyzed. Current pangenome visualizations are not intended for the pangenome sizes possible today and new approaches are necessary in order to convert the increase in available information to increase in knowledge. As the pangenome data structure is essentially a collection of sets we explore the potential for scalable set visualization as a tool for pangenome analysis. We present a new hierarchical clustering algorithm based on set arithmetics that optimizes the intersection sizes along the branches. The intersection and union sizes along the hierarchy are visualized using a composite dendrogram and icicle plot, which, in pangenome context, shows the evolution of pangenome and core size along the evolutionary hierarchy. Outlying elements, i.e. elements whose presence pattern do not correspond with the hierarchy, can be visualized using hierarchical edge bundles. When applied to pangenome data this plot shows putative horizontal gene transfers between the genomes and can highlight relationships between genomes that is not represented by the hierarchy. We illustrate the utility of hierarchical sets by applying it to a pangenome based on 113 Escherichia and Shigella genomes and find it provides a powerful addition to pangenome analysis. The described clustering algorithm and visualizations are implemented in the hierarchicalSets R package available from CRAN ( https://cran.r-project.org/web/packages/hierarchicalSets ). thomasp85@gmail.com. Supplementary data are available at Bioinformatics online.

  1. Scalable Pressure Sensor Based on Electrothermally Operated Resonator

    KAUST Repository

    Hajjaj, Amal Z.

    2017-11-03

    We experimentally demonstrate a new pressure sensor that offers the flexibility of being scalable to small sizes up to the nano regime. Unlike conventional pressure sensors that rely on large diaphragms and big-surface structures, the principle of operation here relies on convective cooling of the air surrounding an electrothermally heated resonant structure, which can be a beam or a bridge. This concept is demonstrated using an electrothermally tuned and electrostatically driven MEMS resonator, which is designed to be deliberately curved. We show that the variation of pressure can be tracked accurately by monitoring the change in the resonance frequency of the resonator at a constant electrothermal voltage. We show that the range of the sensed pressure and the sensitivity of detection are controllable by the amount of the applied electrothermal voltage. Theoretically, we verify the device concept using a multi-physics nonlinear finite element model. The proposed pressure sensor is simple in principle and design and offers the possibility of further miniaturization to the nanoscale.

  2. A Scalable Architecture for VoIP Conferencing

    Directory of Open Access Journals (Sweden)

    R Venkatesha Prasad

    2003-10-01

    Full Text Available Real-Time services are traditionally supported on circuit switched network. However, there is a need to port these services on packet switched network. Architecture for audio conferencing application over the Internet in the light of ITU-T H.323 recommendations is considered. In a conference, considering packets only from a set of selected clients can reduce speech quality degradation because mixing packets from all clients can lead to lack of speech clarity. A distributed algorithm and architecture for selecting clients for mixing is suggested here based on a new quantifier of the voice activity called "Loudness Number" (LN. The proposed system distributes the computation load and reduces the load on client terminals. The highlights of this architecture are scalability, bandwidth saving and speech quality enhancement. Client selection for playing out tries to mimic a physical conference where the most vocal participants attract more attention. The contributions of the paper are expected to aid H.323 recommendations implementations for Multipoint Processors (MP. A working prototype based on the proposed architecture is already functional.

  3. Scalable Metropolis Monte Carlo for simulation of hard shapes

    Science.gov (United States)

    Anderson, Joshua A.; Eric Irrgang, M.; Glotzer, Sharon C.

    2016-07-01

    We design and implement a scalable hard particle Monte Carlo simulation toolkit (HPMC), and release it open source as part of HOOMD-blue. HPMC runs in parallel on many CPUs and many GPUs using domain decomposition. We employ BVH trees instead of cell lists on the CPU for fast performance, especially with large particle size disparity, and optimize inner loops with SIMD vector intrinsics on the CPU. Our GPU kernel proposes many trial moves in parallel on a checkerboard and uses a block-level queue to redistribute work among threads and avoid divergence. HPMC supports a wide variety of shape classes, including spheres/disks, unions of spheres, convex polygons, convex spheropolygons, concave polygons, ellipsoids/ellipses, convex polyhedra, convex spheropolyhedra, spheres cut by planes, and concave polyhedra. NVT and NPT ensembles can be run in 2D or 3D triclinic boxes. Additional integration schemes permit Frenkel-Ladd free energy computations and implicit depletant simulations. In a benchmark system of a fluid of 4096 pentagons, HPMC performs 10 million sweeps in 10 min on 96 CPU cores on XSEDE Comet. The same simulation would take 7.6 h in serial. HPMC also scales to large system sizes, and the same benchmark with 16.8 million particles runs in 1.4 h on 2048 GPUs on OLCF Titan.

  4. Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

    Directory of Open Access Journals (Sweden)

    Carlos Pulido-Quetglas

    2017-03-01

    Full Text Available CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs. This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. We here present CRISPETa, a pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. Multiple sgRNA pairs are returned for each target, and any number of targets can be analyzed in parallel, making CRISPETa equally useful for focussed or high-throughput studies. Fast run-times are achieved using a pre-computed off-target database. sgRNA pair designs are output in a convenient format for visualisation and oligonucleotide ordering. We present pre-designed, high-coverage library designs for entire classes of protein-coding and non-coding elements in human, mouse, zebrafish, Drosophila melanogaster and Caenorhabditis elegans. In human cells, we reproducibly observe deletion efficiencies of ≥50% for CRISPETa designs targeting an enhancer and exonic fragment of the MALAT1 oncogene. In the latter case, deletion results in production of desired, truncated RNA. CRISPETa will be useful for researchers seeking to harness CRISPR for targeted genomic deletion, in a variety of model organisms, from single-target to high-throughput scales.

  5. Scalability of Phase Change Materials in Nanostructure Template

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2015-01-01

    Full Text Available The scalability of In2Se3, one of the phase change materials, is investigated. By depositing the material onto a nanopatterned substrate, individual In2Se3 nanoclusters are confined in the nanosize pits with well-defined shape and dimension permitting the systematic study of the ultimate scaling limit of its use as a phase change memory element. In2Se3 of progressively smaller volume is heated inside a transmission electron microscope operating in diffraction mode. The volume at which the amorphous-crystalline transition can no longer be observed is taken as the ultimate scaling limit, which is approximately 5 nm3 for In2Se3. The physics for the existence of scaling limit is discussed. Using phase change memory elements in memory hierarchy is believed to reduce its energy consumption because they consume zero leakage power in memory cells. Therefore, the phase change memory applications are of great importance in terms of energy saving.

  6. Scalable Virtual Network Mapping Algorithm for Internet-Scale Networks

    Science.gov (United States)

    Yang, Qiang; Wu, Chunming; Zhang, Min

    The proper allocation of network resources from a common physical substrate to a set of virtual networks (VNs) is one of the key technical challenges of network virtualization. While a variety of state-of-the-art algorithms have been proposed in an attempt to address this issue from different facets, the challenge still remains in the context of large-scale networks as the existing solutions mainly perform in a centralized manner which requires maintaining the overall and up-to-date information of the underlying substrate network. This implies the restricted scalability and computational efficiency when the network scale becomes large. This paper tackles the virtual network mapping problem and proposes a novel hierarchical algorithm in conjunction with a substrate network decomposition approach. By appropriately transforming the underlying substrate network into a collection of sub-networks, the hierarchical virtual network mapping algorithm can be carried out through a global virtual network mapping algorithm (GVNMA) and a local virtual network mapping algorithm (LVNMA) operated in the network central server and within individual sub-networks respectively with their cooperation and coordination as necessary. The proposed algorithm is assessed against the centralized approaches through a set of numerical simulation experiments for a range of network scenarios. The results show that the proposed hierarchical approach can be about 5-20 times faster for VN mapping tasks than conventional centralized approaches with acceptable communication overhead between GVNCA and LVNCA for all examined networks, whilst performs almost as well as the centralized solutions.

  7. Scalable multi-GPU implementation of the MAGFLOW simulator

    Directory of Open Access Journals (Sweden)

    Giovanni Gallo

    2011-12-01

    Full Text Available We have developed a robust and scalable multi-GPU (Graphics Processing Unit version of the cellular-automaton-based MAGFLOW lava simulator. The cellular automaton is partitioned into strips that are assigned to different GPUs, with minimal overlapping. For each GPU, a host thread is launched to manage allocation, deallocation, data transfer and kernel launches; the main host thread coordinates all of the GPUs, to ensure temporal coherence and data integrity. The overlapping borders and maximum temporal step need to be exchanged among the GPUs at the beginning of every evolution of the cellular automaton; data transfers are asynchronous with respect to the computations, to cover the introduced overhead. It is not required to have GPUs of the same speed or capacity; the system runs flawlessly on homogeneous and heterogeneous hardware. The speed-up factor differs from that which is ideal (#GPUs× only for a constant overhead loss of about 4E−2 · T · #GPUs, with T as the total simulation time.

  8. Parallel peak pruning for scalable SMP contour tree computation

    Energy Technology Data Exchange (ETDEWEB)

    Carr, Hamish A. [Univ. of Leeds (United Kingdom); Weber, Gunther H. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Davis, CA (United States); Sewell, Christopher M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ahrens, James P. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-03-09

    As data sets grow to exascale, automated data analysis and visualisation are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance. Unfortunately, the predominant algorithms for computing the contour tree are explicitly serial, and founded on serial metaphors, which has limited the scalability of this form of analysis. While there is some work on distributed contour tree computation, and separately on hybrid GPU-CPU computation, there is no efficient algorithm with strong formal guarantees on performance allied with fast practical performance. Here in this paper, we report the first shared SMP algorithm for fully parallel contour tree computation, withfor-mal guarantees of O(lgnlgt) parallel steps and O(n lgn) work, and implementations with up to 10x parallel speed up in OpenMP and up to 50x speed up in NVIDIA Thrust.

  9. Scalable, ultra-resistant structural colors based on network metamaterials

    KAUST Repository

    Galinski, Henning

    2017-05-05

    Structural colors have drawn wide attention for their potential as a future printing technology for various applications, ranging from biomimetic tissues to adaptive camouflage materials. However, an efficient approach to realize robust colors with a scalable fabrication technique is still lacking, hampering the realization of practical applications with this platform. Here, we develop a new approach based on large-scale network metamaterials that combine dealloyed subwavelength structures at the nanoscale with lossless, ultra-thin dielectric coatings. By using theory and experiments, we show how subwavelength dielectric coatings control a mechanism of resonant light coupling with epsilon-near-zero regions generated in the metallic network, generating the formation of saturated structural colors that cover a wide portion of the spectrum. Ellipsometry measurements support the efficient observation of these colors, even at angles of 70°. The network-like architecture of these nanomaterials allows for high mechanical resistance, which is quantified in a series of nano-scratch tests. With such remarkable properties, these metastructures represent a robust design technology for real-world, large-scale commercial applications.

  10. Nano-islands Based Charge Trapping Memory: A Scalability Study

    KAUST Repository

    Elatab, Nazek

    2017-10-19

    Zinc-oxide (ZnO) and zirconia (ZrO2) metal oxides have been studied extensively in the past few decades with several potential applications including memory devices. In this work, a scalability study, based on the ITRS roadmap, is conducted on memory devices with ZnO and ZrO2 nano-islands charge trapping layer. Both nano-islands are deposited using atomic layer deposition (ALD), however, the different sizes, distribution and properties of the materials result in different memory performance. The results show that at the 32-nm node charge trapping memory with 127 ZrO2 nano-islands can provide a 9.4 V memory window. However, with ZnO only 31 nano-islands can provide a window of 2.5 V. The results indicate that ZrO2 nano-islands are more promising than ZnO in scaled down devices due to their higher density, higher-k, and absence of quantum confinement effects.

  11. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.

    Science.gov (United States)

    Fröhlich, Fabian; Kaltenbacher, Barbara; Theis, Fabian J; Hasenauer, Jan

    2017-01-01

    Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large- and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics.

  12. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.

    Directory of Open Access Journals (Sweden)

    Fabian Fröhlich

    2017-01-01

    Full Text Available Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large- and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics.

  13. Mindfulness and Compassion: An Examination of Mechanism and Scalability

    Science.gov (United States)

    Lim, Daniel; Condon, Paul; DeSteno, David

    2015-01-01

    Emerging evidence suggests that meditation engenders prosocial behaviors meant to benefit others. However, the robustness, underlying mechanisms, and potential scalability of such effects remain open to question. The current experiment employed an ecologically valid situation that exposed participants to a person in visible pain. Following three-week, mobile-app based training courses in mindfulness meditation or cognitive skills (i.e., an active control condition), participants arrived at a lab individually to complete purported measures of cognitive ability. Upon entering a public waiting area outside the lab that contained three chairs, participants seated themselves in the last remaining unoccupied chair; confederates occupied the other two. As the participant sat and waited, a third confederate using crutches and a large walking boot entered the waiting area while displaying discomfort. Compassionate responding was assessed by whether participants gave up their seat to allow the uncomfortable confederate to sit, thereby relieving her pain. Participants’ levels of empathic accuracy was also assessed. As predicted, participants assigned to the mindfulness meditation condition gave up their seats more frequently than did those assigned to the active control group. In addition, empathic accuracy was not increased by mindfulness practice, suggesting that mindfulness-enhanced compassionate behavior does not stem from associated increases in the ability to decode the emotional experiences of others. PMID:25689827

  14. Scalable and cost-effective NGS genotyping in the cloud.

    Science.gov (United States)

    Souilmi, Yassine; Lancaster, Alex K; Jung, Jae-Yoon; Rizzo, Ettore; Hawkins, Jared B; Powles, Ryan; Amzazi, Saaïd; Ghazal, Hassan; Tonellato, Peter J; Wall, Dennis P

    2015-10-15

    While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of NGS will not be realized until robust and routine whole genome sequencing data can be accurately rendered to medically actionable reports within a time window of hours and at scales of economy in the 10's of dollars. We take a step towards addressing this challenge, by using COSMOS, a cloud-enabled workflow management system, to develop GenomeKey, an NGS whole genome analysis workflow. COSMOS implements complex workflows making optimal use of high-performance compute clusters. Here we show that the Amazon Web Service (AWS) implementation of GenomeKey via COSMOS provides a fast, scalable, and cost-effective analysis of both public benchmarking and large-scale heterogeneous clinical NGS datasets. Our systematic benchmarking reveals important new insights and considerations to produce clinical turn-around of whole genome analysis optimization and workflow management including strategic batching of individual genomes and efficient cluster resource configuration.

  15. Scalable transfer of vertical graphene nanosheets for flexible supercapacitor applications

    Science.gov (United States)

    Sahoo, Gopinath; Ghosh, Subrata; Polaki, S. R.; Mathews, Tom; Kamruddin, M.

    2017-10-01

    Vertical graphene nanosheets (VGN) are the material of choice for application in next-generation electronic devices. The growing demand for VGN-based flexible devices for the electronics industry brings in restriction on VGN growth temperature. The difficulty associated with the direct growth of VGN on flexible substrates can be overcome by adopting an effective strategy of transferring the well-grown VGN onto arbitrary flexible substrates through a soft chemistry route. In the present study, we report an inexpensive and scalable technique for the polymer-free transfer of VGN onto arbitrary substrates without disrupting its morphology, structure, and properties. After transfer, the morphology, chemical structure, and electrical properties are analyzed by scanning electron microscopy, Raman spectroscopy, x-ray photoelectron spectroscopy, and four-probe resistive methods, respectively. The wetting properties are studied from the water contact angle measurements. The observed results indicate the retention of morphology, surface chemistry, structure, and electronic properties. Furthermore, the storage capacity of the transferred VGN-based binder-free and current collector-free flexible symmetric supercapacitor device is studied. A very low sheet resistance of 670 Ω/□ and excellent supercapacitance of 158 μF cm-2 with 86% retention after 10 000 cycles show the prospect of the damage-free VGN transfer approach for the fabrication of flexible nanoelectronic devices.

  16. Toward a Scalable and Sustainable Intervention for Complementary Food Safety.

    Science.gov (United States)

    Rahman, Musarrat J; Nizame, Fosiul A; Nuruzzaman, Mohammad; Akand, Farhana; Islam, Mohammad Aminul; Parvez, Sarker Masud; Stewart, Christine P; Unicomb, Leanne; Luby, Stephen P; Winch, Peter J

    2016-06-01

    Contaminated complementary foods are associated with diarrhea and malnutrition among children aged 6 to 24 months. However, existing complementary food safety intervention models are likely not scalable and sustainable. To understand current behaviors, motivations for these behaviors, and the potential barriers to behavior change and to identify one or two simple actions that can address one or few food contamination pathways and have potential to be sustainably delivered to a larger population. Data were collected from 2 rural sites in Bangladesh through semistructured observations (12), video observations (12), in-depth interviews (18), and focus group discussions (3). Although mothers report preparing dedicated foods for children, observations show that these are not separate from family foods. Children are regularly fed store-bought foods that are perceived to be bad for children. Mothers explained that long storage durations, summer temperatures, flies, animals, uncovered food, and unclean utensils are threats to food safety. Covering foods, storing foods on elevated surfaces, and reheating foods before consumption are methods believed to keep food safe. Locally made cabinet-like hardware is perceived to be acceptable solution to address reported food safety threats. Conventional approaches that include teaching food safety and highlighting benefits such as reduced contamination may be a disincentive for rural mothers who need solutions for their physical environment. We propose extending existing beneficial behaviors by addressing local preferences of taste and convenience. © The Author(s) 2016.

  17. Detailed Modeling and Evaluation of a Scalable Multilevel Checkpointing System

    Energy Technology Data Exchange (ETDEWEB)

    Mohror, Kathryn [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Moody, Adam [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bronevetsky, Greg [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); de Supinski, Bronis R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2014-09-01

    High-performance computing (HPC) systems are growing more powerful by utilizing more components. As the system mean time before failure correspondingly drops, applications must checkpoint frequently to make progress. But, at scale, the cost of checkpointing becomes prohibitive. A solution to this problem is multilevel checkpointing, which employs multiple types of checkpoints in a single run. Moreover, lightweight checkpoints can handle the most common failure modes, while more expensive checkpoints can handle severe failures. We designed a multilevel checkpointing library, the Scalable Checkpoint/Restart (SCR) library, that writes lightweight checkpoints to node-local storage in addition to the parallel file system. We present probabilistic Markov models of SCR's performance. We show that on future large-scale systems, SCR can lead to a gain in machine efficiency of up to 35 percent, and reduce the load on the parallel file system by a factor of two. In addition, we predict that checkpoint scavenging, or only writing checkpoints to the parallel file system on application termination, can reduce the load on the parallel file system by 20 × on today's systems and still maintain high application efficiency.

  18. Scalable Photogrammetric Motion Capture System "mosca": Development and Application

    Science.gov (United States)

    Knyaz, V. A.

    2015-05-01

    Wide variety of applications (from industrial to entertainment) has a need for reliable and accurate 3D information about motion of an object and its parts. Very often the process of movement is rather fast as in cases of vehicle movement, sport biomechanics, animation of cartoon characters. Motion capture systems based on different physical principles are used for these purposes. The great potential for obtaining high accuracy and high degree of automation has vision-based system due to progress in image processing and analysis. Scalable inexpensive motion capture system is developed as a convenient and flexible tool for solving various tasks requiring 3D motion analysis. It is based on photogrammetric techniques of 3D measurements and provides high speed image acquisition, high accuracy of 3D measurements and highly automated processing of captured data. Depending on the application the system can be easily modified for different working areas from 100 mm to 10 m. The developed motion capture system uses from 2 to 4 technical vision cameras for video sequences of object motion acquisition. All cameras work in synchronization mode at frame rate up to 100 frames per second under the control of personal computer providing the possibility for accurate calculation of 3D coordinates of interest points. The system was used for a set of different applications fields and demonstrated high accuracy and high level of automation.

  19. TDCCREC: AN EFFICIENT AND SCALABLE WEB-BASED RECOMMENDATION SYSTEM

    Directory of Open Access Journals (Sweden)

    K.Latha

    2010-10-01

    Full Text Available Web browsers are provided with complex information space where the volume of information available to them is huge. There comes the Recommender system which effectively recommends web pages that are related to the current webpage, to provide the user with further customized reading material. To enhance the performance of the recommender systems, we include an elegant proposed web based recommendation system; Truth Discovery based Content and Collaborative RECommender (TDCCREC which is capable of addressing scalability. Existing approaches such as Learning automata deals with usage and navigational patterns of users. On the other hand, Weighted Association Rule is applied for recommending web pages by assigning weights to each page in all the transactions. Both of them have their own disadvantages. The websites recommended by the search engines have no guarantee for information correctness and often delivers conflicting information. To solve them, content based filtering and collaborative filtering techniques are introduced for recommending web pages to the active user along with the trustworthiness of the website and confidence of facts which outperforms the existing methods. Our results show how the proposed recommender system performs better in predicting the next request of web users.

  20. Scalable Multicore Motion Planning Using Lock-Free Concurrency.

    Science.gov (United States)

    Ichnowski, Jeffrey; Alterovitz, Ron

    2014-10-01

    We present PRRT (Parallel RRT) and PRRT* (Parallel RRT*), sampling-based methods for feasible and optimal motion planning designed for modern multicore CPUs. We parallelize RRT and RRT* such that all threads concurrently build a single motion planning tree. Parallelization in this manner requires that data structures, such as the nearest neighbor search tree and the motion planning tree, are safely shared across multiple threads. Rather than rely on traditional locks which can result in slowdowns due to lock contention, we introduce algorithms based on lock-free concurrency using atomic operations. We further improve scalability by using partition-based sampling (which shrinks each core's working data set to improve cache efficiency) and parallel work-saving (in reducing the number of rewiring steps performed in PRRT*). Because PRRT and PRRT* are CPU-based, they can be directly integrated with existing libraries. We demonstrate that PRRT and PRRT* scale well as core counts increase, in some cases exhibiting superlinear speedup, for scenarios such as the Alpha Puzzle and Cubicles scenarios and the Aldebaran Nao robot performing a 2-handed task.

  1. Scalable Fast Rate-Distortion Optimization for H.264/AVC

    Directory of Open Access Journals (Sweden)

    Yu Hongtao

    2006-01-01

    Full Text Available The latest H.264/AVC video coding standard aims at significantly improving compression performance compared to all existing video coding standards. In order to achieve this, variable block-size inter- and intra-coding, with block sizes as large as and as small as , is used to enable very precise depiction of motion and texture details. The Lagrangian rate-distortion optimization (RDO can be employed to select the best coding mode. However, exhaustively searching through all coding modes is computationally expensive. This paper proposes a scalable fast RDO algorithm to effectively choose the best coding mode without exhaustively searching through all the coding modes. The statistical properties of MBs are analyzed to determine the order of coding modes in the mode decision priority queue such that the most probable mode will be checked first, followed by the second most probable mode, and so forth. The process will be terminated as soon as the computed rate-distortion (RD cost is below a threshold which is content adaptive and is also dependent on the RD cost of the previous MBs. By adjusting the threshold we can choose a good tradeoff between timesaving and peak signal-to-noise (PSNR ratio. Experimental results show that the proposed fast RDO algorithm can drastically reduce the encoding time up to 50% with negligible loss of coding efficiency.

  2. Scalable Parallel Density-based Clustering and Applications

    Science.gov (United States)

    Patwary, Mostofa Ali

    2014-04-01

    Recently, density-based clustering algorithms (DBSCAN and OPTICS) have gotten significant attention of the scientific community due to their unique capability of discovering arbitrary shaped clusters and eliminating noise data. These algorithms have several applications, which require high performance computing, including finding halos and subhalos (clusters) from massive cosmology data in astrophysics, analyzing satellite images, X-ray crystallography, and anomaly detection. However, parallelization of these algorithms are extremely challenging as they exhibit inherent sequential data access order, unbalanced workload resulting in low parallel efficiency. To break the data access sequentiality and to achieve high parallelism, we develop new parallel algorithms, both for DBSCAN and OPTICS, designed using graph algorithmic techniques. For example, our parallel DBSCAN algorithm exploits the similarities between DBSCAN and computing connected components. Using datasets containing up to a billion floating point numbers, we show that our parallel density-based clustering algorithms significantly outperform the existing algorithms, achieving speedups up to 27.5 on 40 cores on shared memory architecture and speedups up to 5,765 using 8,192 cores on distributed memory architecture. In our experiments, we found that while achieving the scalability, our algorithms produce clustering results with comparable quality to the classical algorithms.

  3. Mindfulness and compassion: an examination of mechanism and scalability.

    Science.gov (United States)

    Lim, Daniel; Condon, Paul; DeSteno, David

    2015-01-01

    Emerging evidence suggests that meditation engenders prosocial behaviors meant to benefit others. However, the robustness, underlying mechanisms, and potential scalability of such effects remain open to question. The current experiment employed an ecologically valid situation that exposed participants to a person in visible pain. Following three-week, mobile-app based training courses in mindfulness meditation or cognitive skills (i.e., an active control condition), participants arrived at a lab individually to complete purported measures of cognitive ability. Upon entering a public waiting area outside the lab that contained three chairs, participants seated themselves in the last remaining unoccupied chair; confederates occupied the other two. As the participant sat and waited, a third confederate using crutches and a large walking boot entered the waiting area while displaying discomfort. Compassionate responding was assessed by whether participants gave up their seat to allow the uncomfortable confederate to sit, thereby relieving her pain. Participants' levels of empathic accuracy was also assessed. As predicted, participants assigned to the mindfulness meditation condition gave up their seats more frequently than did those assigned to the active control group. In addition, empathic accuracy was not increased by mindfulness practice, suggesting that mindfulness-enhanced compassionate behavior does not stem from associated increases in the ability to decode the emotional experiences of others.

  4. Mindfulness and compassion: an examination of mechanism and scalability.

    Directory of Open Access Journals (Sweden)

    Daniel Lim

    Full Text Available Emerging evidence suggests that meditation engenders prosocial behaviors meant to benefit others. However, the robustness, underlying mechanisms, and potential scalability of such effects remain open to question. The current experiment employed an ecologically valid situation that exposed participants to a person in visible pain. Following three-week, mobile-app based training courses in mindfulness meditation or cognitive skills (i.e., an active control condition, participants arrived at a lab individually to complete purported measures of cognitive ability. Upon entering a public waiting area outside the lab that contained three chairs, participants seated themselves in the last remaining unoccupied chair; confederates occupied the other two. As the participant sat and waited, a third confederate using crutches and a large walking boot entered the waiting area while displaying discomfort. Compassionate responding was assessed by whether participants gave up their seat to allow the uncomfortable confederate to sit, thereby relieving her pain. Participants' levels of empathic accuracy was also assessed. As predicted, participants assigned to the mindfulness meditation condition gave up their seats more frequently than did those assigned to the active control group. In addition, empathic accuracy was not increased by mindfulness practice, suggesting that mindfulness-enhanced compassionate behavior does not stem from associated increases in the ability to decode the emotional experiences of others.

  5. High Performance Storage System Scalability: Architecture, Implementation, and Experience

    Energy Technology Data Exchange (ETDEWEB)

    Watson, R W

    2005-01-05

    The High Performance Storage System (HPSS) provides scalable hierarchical storage management (HSM), archive, and file system services. Its design, implementation and current dominant use are focused on HSM and archive services. It is also a general-purpose, global, shared, parallel file system, potentially useful in other application domains. When HPSS design and implementation began over a decade ago, scientific computing power and storage capabilities at a site, such as a DOE national laboratory, was measured in a few 10s of gigaops, data archived in HSMs in a few 10s of terabytes at most, data throughput rates to an HSM in a few megabytes/s, and daily throughput with the HSM in a few gigabytes/day. At that time, the DOE national laboratories and IBM HPSS design team recognized that we were headed for a data storage explosion driven by computing power rising to teraops/petaops requiring data stored in HSMs to rise to petabytes and beyond, data transfer rates with the HSM to rise to gigabytes/s and higher, and daily throughput with a HSM in 10s of terabytes/day. This paper discusses HPSS architectural, implementation and deployment experiences that contributed to its success in meeting the above orders of magnitude scaling targets. We also discuss areas that need additional attention as we continue significant scaling into the future.

  6. CX: A Scalable, Robust Network for Parallel Computing

    Directory of Open Access Journals (Sweden)

    Peter Cappello

    2002-01-01

    Full Text Available CX, a network-based computational exchange, is presented. The system's design integrates variations of ideas from other researchers, such as work stealing, non-blocking tasks, eager scheduling, and space-based coordination. The object-oriented API is simple, compact, and cleanly separates application logic from the logic that supports interprocess communication and fault tolerance. Computations, of course, run to completion in the presence of computational hosts that join and leave the ongoing computation. Such hosts, or producers, use task caching and prefetching to overlap computation with interprocessor communication. To break a potential task server bottleneck, a network of task servers is presented. Even though task servers are envisioned as reliable, the self-organizing, scalable network of n- servers, described as a sibling-connected height-balanced fat tree, tolerates a sequence of n-1 server failures. Tasks are distributed throughout the server network via a simple "diffusion" process. CX is intended as a test bed for research on automated silent auctions, reputation services, authentication services, and bonding services. CX also provides a test bed for algorithm research into network-based parallel computation.

  7. SAChES: Scalable Adaptive Chain-Ensemble Sampling.

    Energy Technology Data Exchange (ETDEWEB)

    Swiler, Laura Painton [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ray, Jaideep [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Ebeida, Mohamed Salah [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Huang, Maoyi [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hou, Zhangshuan [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bao, Jie [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Ren, Huiying [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2017-08-01

    We present the development of a parallel Markov Chain Monte Carlo (MCMC) method called SAChES, Scalable Adaptive Chain-Ensemble Sampling. This capability is targed to Bayesian calibration of com- putationally expensive simulation models. SAChES involves a hybrid of two methods: Differential Evo- lution Monte Carlo followed by Adaptive Metropolis. Both methods involve parallel chains. Differential evolution allows one to explore high-dimensional parameter spaces using loosely coupled (i.e., largely asynchronous) chains. Loose coupling allows the use of large chain ensembles, with far more chains than the number of parameters to explore. This reduces per-chain sampling burden, enables high-dimensional inversions and the use of computationally expensive forward models. The large number of chains can also ameliorate the impact of silent-errors, which may affect only a few chains. The chain ensemble can also be sampled to provide an initial condition when an aberrant chain is re-spawned. Adaptive Metropolis takes the best points from the differential evolution and efficiently hones in on the poste- rior density. The multitude of chains in SAChES is leveraged to (1) enable efficient exploration of the parameter space; and (2) ensure robustness to silent errors which may be unavoidable in extreme-scale computational platforms of the future. This report outlines SAChES, describes four papers that are the result of the project, and discusses some additional results.

  8. Scalability Issues for Remote Sensing Infrastructure: A Case Study

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2017-04-01

    Full Text Available For the past decade, a team of University of Calgary researchers has operated a large “sensor Web” to collect, analyze, and share scientific data from remote measurement instruments across northern Canada. This sensor Web receives real-time data streams from over a thousand Internet-connected sensors, with a particular emphasis on environmental data (e.g., space weather, auroral phenomena, atmospheric imaging. Through research collaborations, we had the opportunity to evaluate the performance and scalability of their remote sensing infrastructure. This article reports the lessons learned from our study, which considered both data collection and data dissemination aspects of their system. On the data collection front, we used benchmarking techniques to identify and fix a performance bottleneck in the system’s memory management for TCP data streams, while also improving system efficiency on multi-core architectures. On the data dissemination front, we used passive and active network traffic measurements to identify and reduce excessive network traffic from the Web robots and JavaScript techniques used for data sharing. While our results are from one specific sensor Web system, the lessons learned may apply to other scientific Web sites with remote sensing infrastructure.

  9. Techno-Economic Analysis of Scalable Coal-Based Fuel Cells

    Energy Technology Data Exchange (ETDEWEB)

    Chuang, Steven S. C. [Univ. of Akron, OH (United States)

    2014-08-31

    Researchers at The University of Akron (UA) have demonstrated the technical feasibility of a laboratory coal fuel cell that can economically convert high sulfur coal into electricity with near zero negative environmental impact. Scaling up this coal fuel cell technology to the megawatt scale for the nation’s electric power supply requires two key elements: (i) developing the manufacturing technology for the components of the coal-based fuel cell, and (ii) long term testing of a kW scale fuel cell pilot plant. This project was expected to develop a scalable coal fuel cell manufacturing process through testing, demonstrating the feasibility of building a large-scale coal fuel cell power plant. We have developed a reproducible tape casting technique for the mass production of the planner fuel cells. Low cost interconnect and cathode current collector material was identified and current collection was improved. In addition, this study has demonstrated that electrochemical oxidation of carbon can take place on the Ni anode surface and the CO and CO2 product produced can further react with carbon to initiate the secondary reactions. One important secondary reaction is the reaction of carbon with CO2 to produce CO. We found CO and carbon can be electrochemically oxidized simultaneously inside of the anode porous structure and on the surface of anode for producing electricity. Since CH4 produced from coal during high temperature injection of coal into the anode chamber can cause severe deactivation of Ni-anode, we have studied how CH4 can interact with CO2 to produce in the anode chamber. CO produced was found able to inhibit coking and allow the rate of anode deactivation to be decreased. An injection system was developed to inject the solid carbon and coal fuels without bringing air into the anode chamber. Five planner fuel cells connected in a series configuration and tested. Extensive studies on the planner fuels

  10. Conservation biology of Malagasy strepsirhines: a phylogenetic approach.

    Science.gov (United States)

    Lehman, Shawn M

    2006-06-01

    The phylogenetic diversity of extant lemurs represents one of the most important but least studied aspects of the conservation biology of primates. The phylogenetic diversity of a species is inversely proportional to the relative number and closeness of its phylogenetic relatives. Phylogenetic diversity can then be used to determine conservation priorities for specific biogeographic regions. Although Malagasy strepsirhines represent the highest phylogenetic diversity among primates at the global level, there are few phylogenetic data on species-specific and regional conservation plans for lemurs in Madagascar. Therefore, in this paper the following questions are addressed for extant lemurs: 1) how does the measure of taxonomic uniqueness used by Mittermeier et al. (1992 Lemurs of Madagascar; Gland, Switzerland: IUCN) equate with an index of phylogenetic diversity, 2) what are the regional conservation priorities based on analyses of phylogenetic diversity in extant lemurs, and 3) what conservation recommendations can be made based on analyses of phylogenetic diversity in lemurs? Taxonomic endemicity standardized weight (TESW) indices of phylogenetic diversity were used to determine the evolutionary component of biodiversity and to prioritize regions for conserving lemur taxa. TESW refers to the standardization of phylogenetic diversity indices for widespread taxa and endemicity of species. The phylogenetic data came from recent genetic studies of Malagasy strepsirhines at the species level. Lemur species were assigned as being either present or absent in six biogeographic regions. TESW indices were combined with data on lemur complementarity and protected areas to assign conservation priorities at the regional level. Although there were no overall differences between taxonomic ranks and phylogenetic rankings, there were significant differences for the top-ranked taxa. The phylogenetic component of lemur diversity is greatest for Daubentonia madagascariensis

  11. Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

    Science.gov (United States)

    Sa'adah, S.; Hidayat, T.; Sudargo, Fransisca

    2017-04-01

    The Phylogenetic tree is a visual representation depicts a hypothesis about the evolutionary relationship among taxa. Evolutionary experts use this representation to evaluate the evidence for evolution. The phylogenetic tree is currently growing for many disciplines in biology. Consequently, learning about the phylogenetic tree has become an important part of biological education and an interesting area of biology education research. Skill to understanding and reasoning of the phylogenetic tree, (called tree thinking) is an important skill for biology students. However, research showed many students have difficulty in interpreting, constructing, and comparing among the phylogenetic tree, as well as experiencing a misconception in the understanding of the phylogenetic tree. Students are often not taught how to reason about evolutionary relationship depicted in the diagram. Students are also not provided with information about the underlying theory and process of phylogenetic. This study aims to investigate the initial ability of undergraduate students in understanding and reasoning of the phylogenetic tree. The research method is the descriptive method. Students are given multiple choice questions and an essay that representative by tree thinking elements. Each correct answer made percentages. Each student is also given questionnaires. The results showed that the undergraduate students’ initial ability in understanding and reasoning phylogenetic tree is low. Many students are not able to answer questions about the phylogenetic tree. Only 19 % undergraduate student who answered correctly on indicator evaluate the evolutionary relationship among taxa, 25% undergraduate student who answered correctly on indicator applying concepts of the clade, 17% undergraduate student who answered correctly on indicator determines the character evolution, and only a few undergraduate student who can construct the phylogenetic tree.

  12. Tropical Refuges with Exceptionally High Phylogenetic Diversity Reveal Contrasting Phylogenetic Structures

    Directory of Open Access Journals (Sweden)

    Lara Pugliesi

    2015-01-01

    Full Text Available Loss of phylogenetic diversity (PD has gained increasing attention in conservation biology. However, PD is not equally distributed in a phylogeny and can be better assessed when species relatedness (phylogenetic structure: PS is also considered. Here, we investigate PD and PS in two refuges of biodiversity in northeastern Brazil: the Bahia Costal Forest (BCF in the Atlantic Forest domain and Chapada Diamantina (CD in the Caatinga domain. We used geographic data of 205 species at two spatial scales and a chronogram of Apocynaceae based on matK sequences to estimate PD and PS. Our results show an exceptionally high PD in both refuges, overdispersed in BCF and clustered in CD, although this difference is less evident or absent for recent relationships, especially at a smaller spatial scale. Overall, PS suggests long-term competitive exclusion under climatic stability, currently balanced by habitat filtering, in BCF, and biome conservatism and limited dispersal leading to in situ diversification and high density of microendemics in CD. The phylogenetically clustered flora in CD, also threatened by climate changes, are naturally more vulnerable than BCF. Therefore, while in situ conservation may ensure protection of biodiversity in BCF, emergency ex situ conservation is strongly recommended in CD.

  13. Performances of the PIPER scalable child human body model in accident reconstruction.

    Science.gov (United States)

    Giordano, Chiara; Li, Xiaogai; Kleiven, Svein

    2017-01-01

    Human body models (HBMs) have the potential to provide significant insights into the pediatric response to impact. This study describes a scalable/posable approach to perform child accident reconstructions using the Position and Personalize Advanced Human Body Models for Injury Prediction (PIPER) scalable child HBM of different ages and in different positions obtained by the PIPER tool. Overall, the PIPER scalable child HBM managed reasonably well to predict the injury severity and location of the children involved in real-life crash scenarios documented in the medical records. The developed methodology and workflow is essential for future work to determine child injury tolerances based on the full Child Advanced Safety Project for European Roads (CASPER) accident reconstruction database. With the workflow presented in this study, the open-source PIPER scalable HBM combined with the PIPER tool is also foreseen to have implications for improved safety designs for a better protection of children in traffic accidents.

  14. On the scalability of uncoordinated multiple access for the Internet of Things

    KAUST Repository

    Chisci, Giovanni

    2017-11-16

    The Internet of things (IoT) will entail massive number of wireless connections with sporadic traffic patterns. To support the IoT traffic, several technologies are evolving to support low power wide area (LPWA) wireless communications. However, LPWA networks rely on variations of uncoordinated spectrum access, either for data transmissions or scheduling requests, thus imposing a scalability problem to the IoT. This paper presents a novel spatiotemporal model to study the scalability of the ALOHA medium access. In particular, the developed mathematical model relies on stochastic geometry and queueing theory to account for spatial and temporal attributes of the IoT. To this end, the scalability of the ALOHA is characterized by the percentile of IoT devices that can be served while keeping their queues stable. The results highlight the scalability problem of ALOHA and quantify the extend to which ALOHA can support in terms of number of devices, traffic requirement, and transmission rate.

  15. Scalable software-defined optical networking with high-performance routing and wavelength assignment algorithms.

    Science.gov (United States)

    Lee, Chankyun; Cao, Xiaoyuan; Yoshikane, Noboru; Tsuritani, Takehiro; Rhee, June-Koo Kevin

    2015-10-19

    The feasibility of software-defined optical networking (SDON) for a practical application critically depends on scalability of centralized control performance. The paper, highly scalable routing and wavelength assignment (RWA) algorithms are investigated on an OpenFlow-based SDON testbed for proof-of-concept demonstration. Efficient RWA algorithms are proposed to achieve high performance in achieving network capacity with reduced computation cost, which is a significant attribute in a scalable centralized-control SDON. The proposed heuristic RWA algorithms differ in the orders of request processes and in the procedures of routing table updates. Combined in a shortest-path-based routing algorithm, a hottest-request-first processing policy that considers demand intensity and end-to-end distance information offers both the highest throughput of networks and acceptable computation scalability. We further investigate trade-off relationship between network throughput and computation complexity in routing table update procedure by a simulation study.

  16. Design of a Scalable Modular Production System for a Two-Stage Food Service Franchise System

    National Research Council Canada - National Science Library

    Matt, D. T; Rauch, E

    2012-01-01

    .... The purpose of this research is to examine the case of a European fresh food manufacturer's approach to introduce a scalable modular production concept for an international two-stage gastronomy...

  17. Quantum Computing and Control by Optical Manipulation of Molecular Coherences: Towards Scalability

    Science.gov (United States)

    2007-09-14

    coherence. Also, significant progress has been made in approaching the single molecule limit in TFRCARS implementations - a crucial step in considering scalable quantum computing using the molecular Hilbert space and nonlinear optics.

  18. Scalable Metadata Management for a Large Multi-Source Seismic Data Repository

    Energy Technology Data Exchange (ETDEWEB)

    Gaylord, J. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Dodge, D. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Magana-Zook, S. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Barno, J. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Knapp, D. R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Thomas, J. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sullivan, D. S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ruppert, S. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Mellors, R. J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-05-26

    In this work, we implemented the key metadata management components of a scalable seismic data ingestion framework to address limitations in our existing system, and to position it for anticipated growth in volume and complexity.

  19. JPEG2000-Compatible Scalable Scheme for Wavelet-Based Video Coding

    Directory of Open Access Journals (Sweden)

    Thomas André

    2007-03-01

    Full Text Available We present a simple yet efficient scalable scheme for wavelet-based video coders, able to provide on-demand spatial, temporal, and SNR scalability, and fully compatible with the still-image coding standard JPEG2000. Whereas hybrid video coders must undergo significant changes in order to support scalability, our coder only requires a specific wavelet filter for temporal analysis, as well as an adapted bit allocation procedure based on models of rate-distortion curves. Our study shows that scalably encoded sequences have the same or almost the same quality than nonscalably encoded ones, without a significant increase in complexity. A full compatibility with Motion JPEG2000, which tends to be a serious candidate for the compression of high-definition video sequences, is ensured.

  20. JPEG2000-Compatible Scalable Scheme for Wavelet-Based Video Coding

    Directory of Open Access Journals (Sweden)

    André Thomas

    2007-01-01

    Full Text Available We present a simple yet efficient scalable scheme for wavelet-based video coders, able to provide on-demand spatial, temporal, and SNR scalability, and fully compatible with the still-image coding standard JPEG2000. Whereas hybrid video coders must undergo significant changes in order to support scalability, our coder only requires a specific wavelet filter for temporal analysis, as well as an adapted bit allocation procedure based on models of rate-distortion curves. Our study shows that scalably encoded sequences have the same or almost the same quality than nonscalably encoded ones, without a significant increase in complexity. A full compatibility with Motion JPEG2000, which tends to be a serious candidate for the compression of high-definition video sequences, is ensured.