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Sample records for improved large-scale proteomics

  1. Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification.

    PubMed

    McAlister, Graeme C; Phanstiel, Doug; Wenger, Craig D; Lee, M Violet; Coon, Joshua J

    2010-01-01

    Using a newly developed dual-cell quadrupole linear ion trap-orbitrap hybrid mass spectrometer (dcQLT-orbitrap), we demonstrate the utility of collecting high-resolution tandem mass spectral data for large-scale shotgun proteomics. Multiple nanoLC-MS/MS experiments on both an older generation quadrupole linear ion trap-orbitrap hybrid (QLT-orbitrap) and the dcQLT-orbitrap, using both resonant-excitation CAD and beam-type CAD (HCD), were performed. Resulting from various technological advances (e.g., a stacked ring ion guide AP inlet, a dual cell QLT), the dcQLT-orbitrap exhibited increased duty cycle (approximately 1.5-2 times) and sensitivity for both CAD (ion trap detection) and HCD (orbitrap detection) methods. As compared to the older system, the dcQLT-orbitrap produced significantly more unique peptide identifications for both methods (approximately 30% improvement for CAD and approximately 115% improvement for HCD). The sizable improvement of the HCD method on the dcQLT-orbitrap system outperforms the current standard method of CAD with ion trap detection for large-scale analysis. Finally, we demonstrate that the increased HCD performance translates to a direct and substantial improvement in protein quantitation precision using isobaric tags. PMID:19938823

  2. Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification

    PubMed Central

    McAlister, Graeme C.; Phanstiel, Doug; Wenger, Craig D.; Lee, M. Violet; Coon, Joshua J.

    2009-01-01

    Using a newly developed dual-cell quadrupole linear ion trap-orbitrap hybrid mass spectrometer (dcQLT-orbitrap), we demonstrate the utility of collecting high-resolution tandem mass spectral data for large-scale shotgun proteomics. Multiple nanoLC-MS/MS experiments on both an older generation quadrupole linear ion trap-orbitrap hybrid (QLT-orbitrap) and the dcQLT-orbitrap, using both resonant-excitation CAD and beam-type CAD (HCD) were performed. Resulting from various technological advances (e.g., a stacked ring ion guide AP inlet, a dual cell QLT, etc.), the dcQLT-orbitrap exhibited increased duty cycle (~1.5–2×) and sensitivity for both CAD (ion trap detection) and HCD (orbitrap detection) methods. As compared to the older system, the dcQLT-orbitrap produced significantly more unique peptide identification for both methods (~30% improvement for CAD and ~115% improvement for HCD). The sizeable improvement of the HCD method on the dcQLT-orbitrap system, outperforms the current standard method of CAD with ion trap detection for large-scale analysis. Finally, we demonstrate that the increased HCD performance translates to a direct and substantial improvement in protein quantitation precision using isobaric tags. PMID:19938823

  3. Large-scale characterization of the murine cardiac proteome.

    PubMed

    Cosme, Jake; Emili, Andrew; Gramolini, Anthony O

    2013-01-01

    Cardiomyopathies are diseases of the heart that result in impaired cardiac muscle function. This dysfunction can progress to an inability to supply blood to the body. Cardiovascular diseases play a large role in overall global morbidity. Investigating the protein changes in the heart during disease can uncover pathophysiological mechanisms and potential therapeutic targets. Establishing a global protein expression "footprint" can facilitate more targeted studies of diseases of the heart.In the technical review presented here, we present methods to elucidate the heart's proteome through subfractionation of the cellular compartments to reduce sample complexity and improve detection of lower abundant proteins during multidimensional protein identification technology analysis. Analysis of the cytosolic, microsomal, and mitochondrial subproteomes separately in order to characterize the murine cardiac proteome is advantageous by simplifying complex cardiac protein mixtures. In combination with bioinformatic analysis and genome correlation, large-scale protein changes can be identified at the cellular compartment level in this animal model. PMID:23606244

  4. Proteomics beyond large-scale protein expression analysis.

    PubMed

    Boersema, Paul J; Kahraman, Abdullah; Picotti, Paola

    2015-08-01

    Proteomics is commonly referred to as the application of high-throughput approaches to protein expression analysis. Typical results of proteomics studies are inventories of the protein content of a sample or lists of differentially expressed proteins across multiple conditions. Recently, however, an explosion of novel proteomics workflows has significantly expanded proteomics beyond the analysis of protein expression. Targeted proteomics methods, for example, enable the analysis of the fine dynamics of protein systems, such as a specific pathway or a network of interacting proteins, and the determination of protein complex stoichiometries. Structural proteomics tools allow extraction of restraints for structural modeling and identification of structurally altered proteins on a proteome-wide scale. Other variations of the proteomic workflow can be applied to the large-scale analysis of protein activity, location, degradation and turnover. These exciting developments provide new tools for multi-level 'omics' analysis and for the modeling of biological networks in the context of systems biology studies. PMID:25636126

  5. Detecting differential protein expression in large-scale population proteomics

    SciTech Connect

    Ryu, Soyoung; Qian, Weijun; Camp, David G.; Smith, Richard D.; Tompkins, Ronald G.; Davis, Ronald W.; Xiao, Wenzhong

    2014-06-17

    Mass spectrometry-based high-throughput quantitative proteomics shows great potential in clinical biomarker studies, identifying and quantifying thousands of proteins in biological samples. However, methods are needed to appropriately handle issues/challenges unique to mass spectrometry data in order to detect as many biomarker proteins as possible. One issue is that different mass spectrometry experiments generate quite different total numbers of quantified peptides, which can result in more missing peptide abundances in an experiment with a smaller total number of quantified peptides. Another issue is that the quantification of peptides is sometimes absent, especially for less abundant peptides and such missing values contain the information about the peptide abundance. Here, we propose a Significance Analysis for Large-scale Proteomics Studies (SALPS) that handles missing peptide intensity values caused by the two mechanisms mentioned above. Our model has a robust performance in both simulated data and proteomics data from a large clinical study. Because varying patients’ sample qualities and deviating instrument performances are not avoidable for clinical studies performed over the course of several years, we believe that our approach will be useful to analyze large-scale clinical proteomics data.

  6. HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.

    PubMed

    Bryan, Kenneth; Jarboui, Mohamed-Ali; Raso, Cinzia; Bernal-Llinares, Manuel; McCann, Brendan; Rauch, Jens; Boldt, Karsten; Lynn, David J

    2016-06-01

    Recent advances in mass-spectrometry-based proteomics are now facilitating ambitious large-scale investigations of the spatial and temporal dynamics of the proteome; however, the increasing size and complexity of these data sets is overwhelming current downstream computational methods, specifically those that support the postquantification analysis pipeline. Here we present HiQuant, a novel application that enables the design and execution of a postquantification workflow, including common data-processing steps, such as assay normalization and grouping, and experimental replicate quality control and statistical analysis. HiQuant also enables the interpretation of results generated from large-scale data sets by supporting interactive heatmap analysis and also the direct export to Cytoscape and Gephi, two leading network analysis platforms. HiQuant may be run via a user-friendly graphical interface and also supports complete one-touch automation via a command-line mode. We evaluate HiQuant's performance by analyzing a large-scale, complex interactome mapping data set and demonstrate a 200-fold improvement in the execution time over current methods. We also demonstrate HiQuant's general utility by analyzing proteome-wide quantification data generated from both a large-scale public tyrosine kinase siRNA knock-down study and an in-house investigation into the temporal dynamics of the KSR1 and KSR2 interactomes. Download HiQuant, sample data sets, and supporting documentation at http://hiquant.primesdb.eu . PMID:27086506

  7. Large-Scale Proteomic Analysis of the Human Spliceosome

    PubMed Central

    Rappsilber, Juri; Ryder, Ursula; Lamond, Angus I.; Mann, Matthias

    2002-01-01

    In a previous proteomic study of the human spliceosome, we identified 42 spliceosome-associated factors, including 19 novel ones. Using enhanced mass spectrometric tools and improved databases, we now report identification of 311 proteins that copurify with splicing complexes assembled on two separate pre-mRNAs. All known essential human splicing factors were found, and 96 novel proteins were identified, of which 55 contain domains directly linking them to functions in splicing/RNA processing. We also detected 20 proteins related to transcription, which indicates a direct connection between this process and splicing. This investigation provides the most detailed inventory of human spliceosome-associated factors to date, and the data indicate a number of interesting links coordinating splicing with other steps in the gene expression pathway. PMID:12176931

  8. Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

    PubMed Central

    Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L.

    2015-01-01

    Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include mass spectrometry to define protein sequence, protein:protein interactions, and protein post-translational modifications. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative mass spectrometry proteomics. It supports all major operating systems and instrument vendors via open data formats. Here we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of tandem mass spectrometry datasets, as well as some major upcoming features. PMID:25631240

  9. Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.

    PubMed

    Deutsch, Eric W; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L

    2015-08-01

    Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include MS to define protein sequence, protein:protein interactions, and protein PTMs. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative MS proteomics. It supports all major operating systems and instrument vendors via open data formats. Here, we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of MS/MS datasets, as well as some major upcoming features. PMID:25631240

  10. The Revolution and Evolution of Shotgun Proteomics for Large-Scale Proteome Analysis

    PubMed Central

    Yates, John R.

    2013-01-01

    Mass spectrometry has evolved at an exponential rate over the last 100 years. Innovations in the development of mass spectrometers have created powerful instruments capable of analyzing a wide range of targets, from rare atoms and molecules to very large molecules such as a proteins, protein complexes and DNA. These performance gains have been driven by sustaining innovations, punctuated by the occasional disruptive innovation. The use of mass spectrometry for proteome analysis was driven by disruptive innovations that created a capability for large-scale analysis of proteins and modifications. PMID:23294060

  11. Large-scale proteomic analysis of membrane proteins

    SciTech Connect

    Ahram, Mamoun; Springer, David L.

    2004-10-01

    Proteomic analysis of membrane proteins is promising in identification of novel candidates as drug targets and/or disease biomarkers. Despite notable technological developments, obstacles related to extraction and solubilization of membrane proteins are frequently encountered. A critical discussion of the different preparative methods of membrane proteins is offered in relation to downstream proteomic applications, mainly gel-based analyses and mass spectrometry. Unknown proteins are often identified by high-throughput profiling of membrane proteins. In search for novel membrane proteins, analysis of protein sequences using computational tools is performed to predict for the presence of transmembrane domains. Here, we also present these bioinformatic tools with the human proteome as a case study. Along with technological innovations, advancements in the areas of sample preparation and computational prediction of membrane proteins will lead to exciting discoveries.

  12. Large-Scale Organizational Performance Improvement.

    ERIC Educational Resources Information Center

    Pilotto, Rudy; Young, Jonathan O'Donnell

    1999-01-01

    Describes the steps involved in a performance improvement program in the context of a large multinational corporation. Highlights include a training program for managers that explained performance improvement; performance matrices; divisionwide implementation, including strategic planning; organizationwide training of all personnel; and the…

  13. The Challenge of Large-Scale Literacy Improvement

    ERIC Educational Resources Information Center

    Levin, Ben

    2010-01-01

    This paper discusses the challenge of making large-scale improvements in literacy in schools across an entire education system. Despite growing interest and rhetoric, there are very few examples of sustained, large-scale change efforts around school-age literacy. The paper reviews 2 instances of such efforts, in England and Ontario. After…

  14. The value of using multiple proteases for large-scale mass spectrometry-based proteomics

    PubMed Central

    Swaney, Danielle L.; Wenger, Craig D.; Coon, Joshua J.

    2009-01-01

    Large-scale protein sequencing methods rely on enzymatic digestion of complex protein mixtures to generate a collection of peptides for mass spectrometric analysis. Here we examine the use of multiple proteases (trypsin, LysC, ArgC, AspN, and GluC) to improve both protein identification and characterization in the model organism Saccharomyces cerevisiae. Using a data-dependent, decision tree-based algorithm to tailor MS2 fragmentation method to peptide precursor, we identified 92,095 unique peptides (609,665 total) mapping to 3,908 proteins at a 1% false discovery rate (FDR). These results were a significant improvement upon data from a single protease digest (trypsin) – 27,822 unique peptides corresponding to 3,313 proteins. The additional 595 protein identifications were mainly from those at low abundances (i.e., < 1,000 copies/cell); sequence coverage for these proteins was likewise improved nearly 3-fold. We demonstrate that large portions of the proteome are simply inaccessible following digestion with a single protease and that multiple proteases, rather than technical replicates, provide a direct route to increase both protein identifications and proteome sequence coverage. PMID:20113005

  15. Value of using multiple proteases for large-scale mass spectrometry-based proteomics.

    PubMed

    Swaney, Danielle L; Wenger, Craig D; Coon, Joshua J

    2010-03-01

    Large-scale protein sequencing methods rely on enzymatic digestion of complex protein mixtures to generate a collection of peptides for mass spectrometric analysis. Here we examine the use of multiple proteases (trypsin, LysC, ArgC, AspN, and GluC) to improve both protein identification and characterization in the model organism Saccharomyces cerevisiae. Using a data-dependent, decision tree-based algorithm to tailor MS(2) fragmentation method to peptide precursor, we identified 92 095 unique peptides (609 665 total) mapping to 3908 proteins at a 1% false discovery rate (FDR). These results were a significant improvement upon data from a single protease digest (trypsin) - 27 822 unique peptides corresponding to 3313 proteins. The additional 595 protein identifications were mainly from those at low abundances (i.e., < 1000 copies/cell); sequence coverage for these proteins was likewise improved nearly 3-fold. We demonstrate that large portions of the proteome are simply inaccessible following digestion with a single protease and that multiple proteases, rather than technical replicates, provide a direct route to increase both protein identifications and proteome sequence coverage. PMID:20113005

  16. Evaluating the use of HILIC in large-scale, multi dimensional proteomics: Horses for courses?

    PubMed Central

    Bensaddek, Dalila; Nicolas, Armel; Lamond, Angus I.

    2015-01-01

    Despite many recent advances in instrumentation, the sheer complexity of biological samples remains a major challenge in large-scale proteomics experiments, reflecting both the large number of protein isoforms and the wide dynamic range of their expression levels. However, while the dynamic range of expression levels for different components of the proteome is estimated to be ∼107–8, the equivalent dynamic range of LC–MS is currently limited to ∼106. Sample pre-fractionation has therefore become routinely used in large-scale proteomics to reduce sample complexity during MS analysis and thus alleviate the problem of ion suppression and undersampling. There is currently a wide range of chromatographic techniques that can be applied as a first dimension separation. Here, we systematically evaluated the use of hydrophilic interaction liquid chromatography (HILIC), in comparison with hSAX, as a first dimension for peptide fractionation in a bottom-up proteomics workflow. The data indicate that in addition to its role as a useful pre-enrichment method for PTM analysis, HILIC can provide a robust, orthogonal and high-resolution method for increasing the depth of proteome coverage in large-scale proteomics experiments. The data also indicate that the choice of using either HILIC, hSAX, or other methods, is best made taking into account the specific types of biological analyses being performed. PMID:26869852

  17. PROTEOME-3D: An Interactive Bioinformatics Tool for Large-Scale Data Exploration and Knowledge Discovery*

    PubMed Central

    Lundgren, Deborah H.; Eng, Jimmy; Wright, Michael E.; Han, David K.

    2006-01-01

    Comprehensive understanding of biological systems requires efficient and systematic assimilation of high-throughput datasets in the context of the existing knowledge base. A major limitation in the field of proteomics is the lack of an appropriate software platform that can synthesize a large number of experimental datasets in the context of the existing knowledge base. Here, we describe a software platform, termed PROTEOME-3D, that utilizes three essential features for systematic analysis of proteomics data: creation of a scalable, queryable, customized database for identified proteins from published literature; graphical tools for displaying proteome landscapes and trends from multiple large-scale experiments; and interactive data analysis that facilitates identification of crucial networks and pathways. Thus, PROTEOME-3D offers a standardized platform to analyze high-throughput experimental datasets for the identification of crucial players in co-regulated pathways and cellular processes. PMID:12960178

  18. PROTEOME-3D: an interactive bioinformatics tool for large-scale data exploration and knowledge discovery.

    PubMed

    Lundgren, Deborah H; Eng, Jimmy; Wright, Michael E; Han, David K

    2003-11-01

    Comprehensive understanding of biological systems requires efficient and systematic assimilation of high-throughput datasets in the context of the existing knowledge base. A major limitation in the field of proteomics is the lack of an appropriate software platform that can synthesize a large number of experimental datasets in the context of the existing knowledge base. Here, we describe a software platform, termed PROTEOME-3D, that utilizes three essential features for systematic analysis of proteomics data: creation of a scalable, queryable, customized database for identified proteins from published literature; graphical tools for displaying proteome landscapes and trends from multiple large-scale experiments; and interactive data analysis that facilitates identification of crucial networks and pathways. Thus, PROTEOME-3D offers a standardized platform to analyze high-throughput experimental datasets for the identification of crucial players in co-regulated pathways and cellular processes. PMID:12960178

  19. Expediting SRM assay development for large-scale targeted proteomics experiments

    SciTech Connect

    Wu, Chaochao; Shi, Tujin; Brown, Joseph N.; He, Jintang; Gao, Yuqian; Fillmore, Thomas L.; Shukla, Anil K.; Moore, Ronald J.; Camp, David G.; Rodland, Karin D.; Qian, Weijun; Liu, Tao; Smith, Richard D.

    2014-10-03

    Due to their high sensitivity and specificity, targeted proteomics measurements, e.g. selected reaction monitoring (SRM), are becoming increasingly popular for biological and translational applications. Selection of optimal transitions and optimization of collision energy (CE) are important assay development steps for achieving sensitive detection and accurate quantification; however, these steps can be labor-intensive, especially for large-scale applications. Herein, we explored several options for accelerating SRM assay development evaluated in the context of a relatively large set of 215 synthetic peptide targets. We first showed that HCD fragmentation is very similar to CID in triple quadrupole (QQQ) instrumentation, and by selection of top six y fragment ions from HCD spectra, >86% of top transitions optimized from direct infusion on QQQ instrument are covered. We also demonstrated that the CE calculated by existing prediction tools was less accurate for +3 precursors, and a significant increase in intensity for transitions could be obtained using a new CE prediction equation constructed from the present experimental data. Overall, our study illustrates the feasibility of expediting the development of larger numbers of high-sensitivity SRM assays through automation of transitions selection and accurate prediction of optimal CE to improve both SRM throughput and measurement quality.

  20. Expediting SRM Assay Development for Large-Scale Targeted Proteomics Experiments

    PubMed Central

    2015-01-01

    Because of its high sensitivity and specificity, selected reaction monitoring (SRM)-based targeted proteomics has become increasingly popular for biological and translational applications. Selection of optimal transitions and optimization of collision energy (CE) are important assay development steps for achieving sensitive detection and accurate quantification; however, these steps can be labor-intensive, especially for large-scale applications. Herein, we explored several options for accelerating SRM assay development evaluated in the context of a relatively large set of 215 synthetic peptide targets. We first showed that HCD fragmentation is very similar to that of CID in triple quadrupole (QQQ) instrumentation and that by selection of the top 6 y fragment ions from HCD spectra, >86% of the top transitions optimized from direct infusion with QQQ instrumentation are covered. We also demonstrated that the CE calculated by existing prediction tools was less accurate for 3+ precursors and that a significant increase in intensity for transitions could be obtained using a new CE prediction equation constructed from the present experimental data. Overall, our study illustrated the feasibility of expediting the development of larger numbers of high-sensitivity SRM assays through automation of transition selection and accurate prediction of optimal CE to improve both SRM throughput and measurement quality. PMID:25145539

  1. Expediting SRM assay development for large-scale targeted proteomics experiments

    SciTech Connect

    Wu, Chaochao; Shi, Tujin; Brown, Joseph N.; He, Jintang; Gao, Yuqian; Fillmore, Thomas L.; Shukla, Anil K.; Moore, Ronald J.; Camp, David G.; Rodland, Karin D.; Qian, Weijun; Liu, Tao; Smith, Richard D.

    2014-08-22

    Due to their high sensitivity and specificity, targeted proteomics measurements, e.g. selected reaction monitoring (SRM), are becoming increasingly popular for biological and translational applications. Selection of optimal transitions and optimization of collision energy (CE) are important assay development steps for achieving sensitive detection and accurate quantification; however, these steps can be labor-intensive, especially for large-scale applications. Herein, we explored several options for accelerating SRM assay development evaluated in the context of a relatively large set of 215 synthetic peptide targets. We first showed that HCD fragmentation is very similar to CID in triple quadrupole (QQQ) instrumentation, and by selection of top six y fragment ions from HCD spectra, >86% of top transitions optimized from direct infusion on QQQ instrument are covered. We also demonstrated that the CE calculated by existing prediction tools was less accurate for +3 precursors, and a significant increase in intensity for transitions could be obtained using a new CE prediction equation constructed from the present experimental data. Overall, our study illustrates the feasibility of expediting the development of larger numbers of high-sensitivity SRM assays through automation of transitions selection and accurate prediction of optimal CE to improve both SRM throughput and measurement quality.

  2. Expediting SRM assay development for large-scale targeted proteomics experiments

    DOE PAGESBeta

    Wu, Chaochao; Shi, Tujin; Brown, Joseph N.; He, Jintang; Gao, Yuqian; Fillmore, Thomas L.; Shukla, Anil K.; Moore, Ronald J.; Camp, David G.; Rodland, Karin D.; et al

    2014-08-22

    Due to their high sensitivity and specificity, targeted proteomics measurements, e.g. selected reaction monitoring (SRM), are becoming increasingly popular for biological and translational applications. Selection of optimal transitions and optimization of collision energy (CE) are important assay development steps for achieving sensitive detection and accurate quantification; however, these steps can be labor-intensive, especially for large-scale applications. Herein, we explored several options for accelerating SRM assay development evaluated in the context of a relatively large set of 215 synthetic peptide targets. We first showed that HCD fragmentation is very similar to CID in triple quadrupole (QQQ) instrumentation, and by selection ofmore » top six y fragment ions from HCD spectra, >86% of top transitions optimized from direct infusion on QQQ instrument are covered. We also demonstrated that the CE calculated by existing prediction tools was less accurate for +3 precursors, and a significant increase in intensity for transitions could be obtained using a new CE prediction equation constructed from the present experimental data. Overall, our study illustrates the feasibility of expediting the development of larger numbers of high-sensitivity SRM assays through automation of transitions selection and accurate prediction of optimal CE to improve both SRM throughput and measurement quality.« less

  3. Determination of burn patient outcome by large-scale quantitative discovery proteomics

    PubMed Central

    Finnerty, Celeste C.; Jeschke, Marc G.; Qian, Wei-Jun; Kaushal, Amit; Xiao, Wenzhong; Liu, Tao; Gritsenko, Marina A.; Moore, Ronald J.; Camp, David G.; Moldawer, Lyle L.; Elson, Constance; Schoenfeld, David; Gamelli, Richard; Gibran, Nicole; Klein, Matthew; Arnoldo, Brett; Remick, Daniel; Smith, Richard D.; Davis, Ronald; Tompkins, Ronald G.; Herndon, David N.

    2013-01-01

    Objective Emerging proteomics techniques can be used to establish proteomic outcome signatures and to identify candidate biomarkers for survival following traumatic injury. We applied high-resolution liquid chromatography-mass spectrometry (LC-MS) and multiplex cytokine analysis to profile the plasma proteome of survivors and non-survivors of massive burn injury to determine the proteomic survival signature following a major burn injury. Design Proteomic discovery study. Setting Five burn hospitals across the U.S. Patients Thirty-two burn patients (16 non-survivors and 16 survivors), 19–89 years of age, were admitted within 96 h of injury to the participating hospitals with burns covering >20% of the total body surface area and required at least one surgical intervention. Interventions None. Measurements and Main Results We found differences in circulating levels of 43 proteins involved in the acute phase response, hepatic signaling, the complement cascade, inflammation, and insulin resistance. Thirty-two of the proteins identified were not previously known to play a role in the response to burn. IL-4, IL-8, GM-CSF, MCP-1, and β2-microglobulin correlated well with survival and may serve as clinical biomarkers. Conclusions These results demonstrate the utility of these techniques for establishing proteomic survival signatures and for use as a discovery tool to identify candidate biomarkers for survival. This is the first clinical application of a high-throughput, large-scale LC-MS-based quantitative plasma proteomic approach for biomarker discovery for the prediction of patient outcome following burn, trauma or critical illness. PMID:23507713

  4. Large-scale differential proteome analysis in Plasmodium falciparum under drug treatment.

    PubMed

    Prieto, Judith Helena; Fischer, Elisabeth; Koncarevic, Sasa; Yates, John; Becker, Katja

    2015-01-01

    Here, we establish a methodology for large-scale quantitative proteomics using SIL (stable isotope labeling) to examine protein expression changes in trophozoite stages of the malaria parasite Plasmodium falciparum following drug treatment. For this purpose, exposure to (13)C6 (15)N1-isoleucine was optimized in order to obtain 99% atomic enrichment. Proteome fractionation with anion exchange chromatography was used to reduce sample complexity and increase quantitative coverage of protein expression. Tryptic peptides of subfractions were subjected to SCX/RP separation, measured by LC-MS/MS, and quantified using the software tool Census. In drug-treated parasites, we identified a total number of 1,253 proteins, thus increasing the overall number of proteins so far identified in the trophozoite stage by 30% in the previous literature. A relative quantification was obtained for more than 800 proteins. About 5% of proteins showed a clear up- or downregulation upon drug treatment. PMID:25388121

  5. Improving Design Efficiency for Large-Scale Heterogeneous Circuits

    NASA Astrophysics Data System (ADS)

    Gregerson, Anthony

    Despite increases in logic density, many Big Data applications must still be partitioned across multiple computing devices in order to meet their strict performance requirements. Among the most demanding of these applications is high-energy physics (HEP), which uses complex computing systems consisting of thousands of FPGAs and ASICs to process the sensor data created by experiments at particles accelerators such as the Large Hadron Collider (LHC). Designing such computing systems is challenging due to the scale of the systems, the exceptionally high-throughput and low-latency performance constraints that necessitate application-specific hardware implementations, the requirement that algorithms are efficiently partitioned across many devices, and the possible need to update the implemented algorithms during the lifetime of the system. In this work, we describe our research to develop flexible architectures for implementing such large-scale circuits on FPGAs. In particular, this work is motivated by (but not limited in scope to) high-energy physics algorithms for the Compact Muon Solenoid (CMS) experiment at the LHC. To make efficient use of logic resources in multi-FPGA systems, we introduce Multi-Personality Partitioning, a novel form of the graph partitioning problem, and present partitioning algorithms that can significantly improve resource utilization on heterogeneous devices while also reducing inter-chip connections. To reduce the high communication costs of Big Data applications, we also introduce Information-Aware Partitioning, a partitioning method that analyzes the data content of application-specific circuits, characterizes their entropy, and selects circuit partitions that enable efficient compression of data between chips. We employ our information-aware partitioning method to improve the performance of the hardware validation platform for evaluating new algorithms for the CMS experiment. Together, these research efforts help to improve the efficiency

  6. Intact mass detection, interpretation, and visualization to automate Top-Down proteomics on a large scale

    PubMed Central

    Durbin, Kenneth R.; Tran, John C.; Zamdborg, Leonid; Sweet, Steve M. M.; Catherman, Adam D.; Lee, Ji Eun; Li, Mingxi; Kellie, John F.; Kelleher, Neil L.

    2011-01-01

    Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms for processing MS1 data from both isotopically resolved (FT) and charge-state resolved (ion trap) LC-MS data, which are then linked to their fragment ions for database searching using ProSight. Automated determination of human keratin and tubulin isoforms is one result. Optimized for the intricacies of whole proteins, new software modules visualize proteome-scale data based on the LC retention time and intensity of intact masses and enable selective detection of PTMs to automatically screen for acetylation, phosphorylation, and methylation. Software functionality was demonstrated using comparative LC-MS data from yeast strains in addition to human cells undergoing chemical stress. We further these advances as a key aspect of realizing Top-Down MS on a proteomic scale. PMID:20848673

  7. Large scale systematic proteomic quantification from non-metastatic to metastatic colorectal cancer

    NASA Astrophysics Data System (ADS)

    Yin, Xuefei; Zhang, Yang; Guo, Shaowen; Jin, Hong; Wang, Wenhai; Yang, Pengyuan

    2015-07-01

    A systematic proteomic quantification of formalin-fixed, paraffin-embedded (FFPE) colorectal cancer tissues from stage I to stage IIIC was performed in large scale. 1017 proteins were identified with 338 proteins in quantitative changes by label free method, while 341 proteins were quantified with significant expression changes among 6294 proteins by iTRAQ method. We found that proteins related to migration expression increased and those for binding and adherent decreased during the colorectal cancer development according to the gene ontology (GO) annotation and ingenuity pathway analysis (IPA). The integrin alpha 5 (ITA5) in integrin family was focused, which was consistent with the metastasis related pathway. The expression level of ITA5 decreased in metastasis tissues and the result has been further verified by Western blotting. Another two cell migration related proteins vitronectin (VTN) and actin-related protein (ARP3) were also proved to be up-regulated by both mass spectrometry (MS) based quantification results and Western blotting. Up to now, our result shows one of the largest dataset in colorectal cancer proteomics research. Our strategy reveals a disease driven omics-pattern for the metastasis colorectal cancer.

  8. Large-scale label-free quantitative proteomics of the pea aphid-Buchnera symbiosis.

    PubMed

    Poliakov, Anton; Russell, Calum W; Ponnala, Lalit; Hoops, Harold J; Sun, Qi; Douglas, Angela E; van Wijk, Klaas J

    2011-06-01

    Many insects are nutritionally dependent on symbiotic microorganisms that have tiny genomes and are housed in specialized host cells called bacteriocytes. The obligate symbiosis between the pea aphid Acyrthosiphon pisum and the γ-proteobacterium Buchnera aphidicola (only 584 predicted proteins) is particularly amenable for molecular analysis because the genomes of both partners have been sequenced. To better define the symbiotic relationship between this aphid and Buchnera, we used large-scale, high accuracy tandem mass spectrometry (nanoLC-LTQ-Orbtrap) to identify aphid and Buchnera proteins in the whole aphid body, purified bacteriocytes, isolated Buchnera cells and the residual bacteriocyte fraction. More than 1900 aphid and 400 Buchnera proteins were identified. All enzymes in amino acid metabolism annotated in the Buchnera genome were detected, reflecting the high (68%) coverage of the proteome and supporting the core function of Buchnera in the aphid symbiosis. Transporters mediating the transport of predicted metabolites were present in the bacteriocyte. Label-free spectral counting combined with hierarchical clustering, allowed to define the quantitative distribution of a subset of these proteins across both symbiotic partners, yielding no evidence for the selective transfer of protein among the partners in either direction. This is the first quantitative proteome analysis of bacteriocyte symbiosis, providing a wealth of information about molecular function of both the host cell and bacterial symbiont. PMID:21421797

  9. Large-scale proteome comparative analysis of developing rhizomes of the ancient vascular plant equisetum hyemale.

    PubMed

    Balbuena, Tiago Santana; He, Ruifeng; Salvato, Fernanda; Gang, David R; Thelen, Jay J

    2012-01-01

    Horsetail (Equisetum hyemale) is a widespread vascular plant species, whose reproduction is mainly dependent on the growth and development of the rhizomes. Due to its key evolutionary position, the identification of factors that could be involved in the existence of the rhizomatous trait may contribute to a better understanding of the role of this underground organ for the successful propagation of this and other plant species. In the present work, we characterized the proteome of E. hyemale rhizomes using a GeLC-MS spectral-counting proteomics strategy. A total of 1,911 and 1,860 non-redundant proteins were identified in the rhizomes apical tip and elongation zone, respectively. Rhizome-characteristic proteins were determined by comparisons of the developing rhizome tissues to developing roots. A total of 87 proteins were found to be up-regulated in both horsetail rhizome tissues in relation to developing roots. Hierarchical clustering indicated a vast dynamic range in the regulation of the 87 characteristic proteins and revealed, based on the regulation profile, the existence of nine major protein groups. Gene ontology analyses suggested an over-representation of the terms involved in macromolecular and protein biosynthetic processes, gene expression, and nucleotide and protein binding functions. Spatial difference analysis between the rhizome apical tip and the elongation zone revealed that only eight proteins were up-regulated in the apical tip including RNA-binding proteins and an acyl carrier protein, as well as a KH domain protein and a T-complex subunit; while only seven proteins were up-regulated in the elongation zone including phosphomannomutase, galactomannan galactosyltransferase, endoglucanase 10 and 25, and mannose-1-phosphate guanyltransferase subunits alpha and beta. This is the first large-scale characterization of the proteome of a plant rhizome. Implications of the findings were discussed in relation to other underground organs and related

  10. Large-Scale Proteome Comparative Analysis of Developing Rhizomes of the Ancient Vascular Plant Equisetum Hyemale

    PubMed Central

    Balbuena, Tiago Santana; He, Ruifeng; Salvato, Fernanda; Gang, David R.; Thelen, Jay J.

    2012-01-01

    Horsetail (Equisetum hyemale) is a widespread vascular plant species, whose reproduction is mainly dependent on the growth and development of the rhizomes. Due to its key evolutionary position, the identification of factors that could be involved in the existence of the rhizomatous trait may contribute to a better understanding of the role of this underground organ for the successful propagation of this and other plant species. In the present work, we characterized the proteome of E. hyemale rhizomes using a GeLC-MS spectral-counting proteomics strategy. A total of 1,911 and 1,860 non-redundant proteins were identified in the rhizomes apical tip and elongation zone, respectively. Rhizome-characteristic proteins were determined by comparisons of the developing rhizome tissues to developing roots. A total of 87 proteins were found to be up-regulated in both horsetail rhizome tissues in relation to developing roots. Hierarchical clustering indicated a vast dynamic range in the regulation of the 87 characteristic proteins and revealed, based on the regulation profile, the existence of nine major protein groups. Gene ontology analyses suggested an over-representation of the terms involved in macromolecular and protein biosynthetic processes, gene expression, and nucleotide and protein binding functions. Spatial difference analysis between the rhizome apical tip and the elongation zone revealed that only eight proteins were up-regulated in the apical tip including RNA-binding proteins and an acyl carrier protein, as well as a KH domain protein and a T-complex subunit; while only seven proteins were up-regulated in the elongation zone including phosphomannomutase, galactomannan galactosyltransferase, endoglucanase 10 and 25, and mannose-1-phosphate guanyltransferase subunits alpha and beta. This is the first large-scale characterization of the proteome of a plant rhizome. Implications of the findings were discussed in relation to other underground organs and related

  11. Toward Improved Support for Loosely Coupled Large Scale Simulation Workflows

    SciTech Connect

    Boehm, Swen; Elwasif, Wael R; Naughton, III, Thomas J; Vallee, Geoffroy R

    2014-01-01

    High-performance computing (HPC) workloads are increasingly leveraging loosely coupled large scale simula- tions. Unfortunately, most large-scale HPC platforms, including Cray/ALPS environments, are designed for the execution of long-running jobs based on coarse-grained launch capabilities (e.g., one MPI rank per core on all allocated compute nodes). This assumption limits capability-class workload campaigns that require large numbers of discrete or loosely coupled simulations, and where time-to-solution is an untenable pacing issue. This paper describes the challenges related to the support of fine-grained launch capabilities that are necessary for the execution of loosely coupled large scale simulations on Cray/ALPS platforms. More precisely, we present the details of an enhanced runtime system to support this use case, and report on initial results from early testing on systems at Oak Ridge National Laboratory.

  12. Simulating subsurface heterogeneity improves large-scale water resources predictions

    NASA Astrophysics Data System (ADS)

    Hartmann, A. J.; Gleeson, T.; Wagener, T.; Wada, Y.

    2014-12-01

    Heterogeneity is abundant everywhere across the hydrosphere. It exists in the soil, the vadose zone and the groundwater. In large-scale hydrological models, subsurface heterogeneity is usually not considered. Instead average or representative values are chosen for each of the simulated grid cells, not incorporating any sub-grid variability. This may lead to unreliable predictions when the models are used for assessing future water resources availability, floods or droughts, or when they are used for recommendations for more sustainable water management. In this study we use a novel, large-scale model that takes into account sub-grid heterogeneity for the simulation of groundwater recharge by using statistical distribution functions. We choose all regions over Europe that are comprised by carbonate rock (~35% of the total area) because the well understood dissolvability of carbonate rocks (karstification) allows for assessing the strength of subsurface heterogeneity. Applying the model with historic data and future climate projections we show that subsurface heterogeneity lowers the vulnerability of groundwater recharge on hydro-climatic extremes and future changes of climate. Comparing our simulations with the PCR-GLOBWB model we can quantify the deviations of simulations for different sub-regions in Europe.

  13. Discovery of O-GlcNAc-modified Proteins in Published Large-scale Proteome Data*

    PubMed Central

    Hahne, Hannes; Gholami, Amin Moghaddas; Kuster, Bernhard

    2012-01-01

    The attachment of N-acetylglucosamine to serine or threonine residues (O-GlcNAc) is a post-translational modification on nuclear and cytoplasmic proteins with emerging roles in numerous cellular processes, such as signal transduction, transcription, and translation. It is further presumed that O-GlcNAc can exhibit a site-specific, dynamic and possibly functional interplay with phosphorylation. O-GlcNAc proteins are commonly identified by tandem mass spectrometry following some form of biochemical enrichment. In the present study, we assessed if, and to which extent, O-GlcNAc-modified proteins can be discovered from existing large-scale proteome data sets. To this end, we conceived a straightforward O-GlcNAc identification strategy based on our recently developed Oscore software that automatically analyzes tandem mass spectra for the presence and intensity of O-GlcNAc diagnostic fragment ions. Using the Oscore, we discovered hundreds of O-GlcNAc peptides not initially identified in these studies, and most of which have not been described before. Merely re-searching this data extended the number of known O-GlcNAc proteins by almost 100 suggesting that this modification exists even more widely than previously anticipated and the modification is often sufficiently abundant to be detected without enrichment. However, a comparison of O-GlcNAc and phospho-identifications from the very same data indicates that the O-GlcNAc modification is considerably less abundant than phosphorylation. The discovery of numerous doubly modified peptides (i.e. peptides with one or multiple O-GlcNAc or phosphate moieties), suggests that O-GlcNAc and phosphorylation are not necessarily mutually exclusive, but can occur simultaneously at adjacent sites. PMID:22661428

  14. Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM)*

    PubMed Central

    Gallien, Sebastien; Kim, Sang Yoon; Domon, Bruno

    2015-01-01

    Targeted high-resolution and accurate mass analyses performed on fast sequencing mass spectrometers have opened new avenues for quantitative proteomics. More specifically, parallel reaction monitoring (PRM) implemented on quadrupole-orbitrap instruments exhibits exquisite selectivity to discriminate interferences from analytes. Furthermore, the instrument trapping capability enhances the sensitivity of the measurements. The PRM technique, applied to the analysis of limited peptide sets (typically 50 peptides or less) in a complex matrix, resulted in an improved detection and quantification performance as compared with the reference method of selected reaction monitoring performed on triple quadrupole instruments. However, the implementation of PRM for the analysis of large peptide numbers requires the adjustment of mass spectrometry acquisition parameters, which affects dramatically the quality of the generated data, and thus the overall output of an experiment. A newly designed data acquisition scheme enabled the analysis of moderate-to-large peptide numbers while retaining a high performance level. This new method, called internal standard triggered-parallel reaction monitoring (IS-PRM), relies on added internal standards and the on-the-fly adjustment of acquisition parameters to drive in real-time measurement of endogenous peptides. The acquisition time management was designed to maximize the effective time devoted to measure the analytes in a time-scheduled targeted experiment. The data acquisition scheme alternates between two PRM modes: a fast low-resolution “watch mode” and a “quantitative mode” using optimized parameters ensuring data quality. The IS-PRM method exhibited a highly effective use of the instrument time. Applied to the analysis of large peptide sets (up to 600) in complex samples, the method showed an unprecedented combination of scale and analytical performance, with limits of quantification in the low amol range. The successful

  15. Colloquium on Large Scale Improvement: Implications for AISI

    ERIC Educational Resources Information Center

    McEwen, Nelly, Ed.

    2008-01-01

    The Alberta Initiative for School Improvement (AISI) is a province-wide partnership program whose goal is to improve student learning and performance by fostering initiatives that reflect the unique needs and circumstances of each school authority. It is currently ending its third cycle and ninth year of implementation. "The Colloquium on Large…

  16. Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis.

    PubMed

    Kremer, Lukas P M; Leufken, Johannes; Oyunchimeg, Purevdulam; Schulze, Stefan; Fufezan, Christian

    2016-03-01

    Proteomics data integration has become a broad field with a variety of programs offering innovative algorithms to analyze increasing amounts of data. Unfortunately, this software diversity leads to many problems as soon as the data is analyzed using more than one algorithm for the same task. Although it was shown that the combination of multiple peptide identification algorithms yields more robust results, it is only recently that unified approaches are emerging; however, workflows that, for example, aim to optimize search parameters or that employ cascaded style searches can only be made accessible if data analysis becomes not only unified but also and most importantly scriptable. Here we introduce Ursgal, a Python interface to many commonly used bottom-up proteomics tools and to additional auxiliary programs. Complex workflows can thus be composed using the Python scripting language using a few lines of code. Ursgal is easily extensible, and we have made several database search engines (X!Tandem, OMSSA, MS-GF+, Myrimatch, MS Amanda), statistical postprocessing algorithms (qvality, Percolator), and one algorithm that combines statistically postprocessed outputs from multiple search engines ("combined FDR") accessible as an interface in Python. Furthermore, we have implemented a new algorithm ("combined PEP") that combines multiple search engines employing elements of "combined FDR", PeptideShaker, and Bayes' theorem. PMID:26709623

  17. Efficient Processing of Models for Large-scale Shotgun Proteomics Data.

    PubMed

    Grover, Himanshu; Gopalakrishnan, Vanathi

    2012-01-01

    Mass-spectrometry (MS) based proteomics has become a key enabling technology for the systems approach to biology, providing insights into the protein complement of an organism. Bioinformatics analyses play a critical role in interpretation of large, and often replicated, MS datasets generated across laboratories and institutions. A significant amount of computational effort in the workflow is spent on the identification of protein and peptide components of complex biological samples, and consists of a series of steps relying on large database searches and intricate scoring algorithms. In this work, we share our efforts and experience in efficient handling of these large MS datasets through database indexing and parallelization based on multiprocessor architectures. We also identify important challenges and opportunities that are relevant specifically to the task of peptide and protein identification, and more generally to similar multi-step problems that are inherently parallelizable. PMID:25309967

  18. Efficient Processing of Models for Large-scale Shotgun Proteomics Data

    PubMed Central

    Grover, Himanshu

    2013-01-01

    Mass-spectrometry (MS) based proteomics has become a key enabling technology for the systems approach to biology, providing insights into the protein complement of an organism. Bioinformatics analyses play a critical role in interpretation of large, and often replicated, MS datasets generated across laboratories and institutions. A significant amount of computational effort in the workflow is spent on the identification of protein and peptide components of complex biological samples, and consists of a series of steps relying on large database searches and intricate scoring algorithms. In this work, we share our efforts and experience in efficient handling of these large MS datasets through database indexing and parallelization based on multiprocessor architectures. We also identify important challenges and opportunities that are relevant specifically to the task of peptide and protein identification, and more generally to similar multi-step problems that are inherently parallelizable. PMID:25309967

  19. DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics

    PubMed Central

    Wright, James C; Choudhary, Jyoti S

    2016-01-01

    Accurate statistical evaluation of sequence database peptide identifications from tandem mass spectra is essential in mass spectrometry based proteomics experiments. These statistics are dependent on accurately modelling random identifications. The target-decoy approach has risen to become the de facto approach to calculating FDR in proteomic datasets. The main principle of this approach is to search a set of decoy protein sequences that emulate the size and composition of the target protein sequences searched whilst not matching real proteins in the sample. To do this, it is commonplace to reverse or shuffle the proteins and peptides in the target database. However, these approaches have their drawbacks and limitations. A key confounding issue is the peptide redundancy between target and decoy databases leading to inaccurate FDR estimation. This inaccuracy is further amplified at the protein level and when searching large sequence databases such as those used for proteogenomics. Here, we present a unifying hybrid method to quickly and efficiently generate decoy sequences with minimal overlap between target and decoy peptides. We show that applying a reversed decoy approach can produce up to 5% peptide redundancy and many more additional peptides will have the exact same precursor mass as a target peptide. Our hybrid method addresses both these issues by first switching proteolytic cleavage sites with preceding amino acid, reversing the database and then shuffling any redundant sequences. This flexible hybrid method reduces the peptide overlap between target and decoy peptides to about 1% of peptides, making a more robust decoy model suitable for large search spaces. We also demonstrate the anti-conservative effect of redundant peptides on the calculation of q-values in mouse brain tissue data. PMID:27418748

  20. Review of Software Tools for Design and Analysis of Large scale MRM Proteomic Datasets

    PubMed Central

    Colangelo, Christopher M.; Chung, Lisa; Bruce, Can; Cheung, Kei-Hoi

    2013-01-01

    Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow. PMID:23702368

  1. Review of software tools for design and analysis of large scale MRM proteomic datasets.

    PubMed

    Colangelo, Christopher M; Chung, Lisa; Bruce, Can; Cheung, Kei-Hoi

    2013-06-15

    Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow. PMID:23702368

  2. Large-Scale High School Reform through School Improvement Networks: Exploring Possibilities for "Developmental Evaluation"

    ERIC Educational Resources Information Center

    Peurach, Donald J.; Lenhoff, Sarah Winchell; Glazer, Joshua L.

    2016-01-01

    Recognizing school improvement networks as a leading strategy for large-scale high school reform, this analysis examines developmental evaluation as an approach to examining school improvement networks as "learning systems" able to produce, use, and refine practical knowledge in large numbers of schools. Through a case study of one…

  3. Accuracy improvement in laser stripe extraction for large-scale triangulation scanning measurement system

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Liu, Wei; Li, Xiaodong; Yang, Fan; Gao, Peng; Jia, Zhenyuan

    2015-10-01

    Large-scale triangulation scanning measurement systems are widely used to measure the three-dimensional profile of large-scale components and parts. The accuracy and speed of the laser stripe center extraction are essential for guaranteeing the accuracy and efficiency of the measuring system. However, in the process of large-scale measurement, multiple factors can cause deviation of the laser stripe center, including the spatial light intensity distribution, material reflectivity characteristics, and spatial transmission characteristics. A center extraction method is proposed for improving the accuracy of the laser stripe center extraction based on image evaluation of Gaussian fitting structural similarity and analysis of the multiple source factors. First, according to the features of the gray distribution of the laser stripe, evaluation of the Gaussian fitting structural similarity is estimated to provide a threshold value for center compensation. Then using the relationships between the gray distribution of the laser stripe and the multiple source factors, a compensation method of center extraction is presented. Finally, measurement experiments for a large-scale aviation composite component are carried out. The experimental results for this specific implementation verify the feasibility of the proposed center extraction method and the improved accuracy for large-scale triangulation scanning measurements.

  4. Psychology in an Interdisciplinary Setting: A Large-Scale Project to Improve University Teaching

    ERIC Educational Resources Information Center

    Koch, Franziska D.; Vogt, Joachim

    2015-01-01

    At a German university of technology, a large-scale project was funded as a part of the "Quality Pact for Teaching", a programme launched by the German Federal Ministry of Education and Research to improve the quality of university teaching and study conditions. The project aims at intensifying interdisciplinary networking in teaching,…

  5. Large-scale Analysis of Thermo-stable, Mammalian Proteins Provides Insights into the Intrinsically Disordered Proteome

    PubMed Central

    Galea, Charles A.; High, Anthony; Obenauer, John C.; Mishra, Ashutosh; Park, Cheon-Gil; Punta, Marco; Schlessinger, Avner; Ma, Jing; Rost, Burkhard; Slaughter, Clive A.; Kriwacki, Richard W.

    2009-01-01

    Intrinsically disordered proteins are predicted to be highly abundant and play broad biological roles in eukaryotic cells. In particular, by virtue of their structural malleability and propensity to interact with multiple binding partners, disordered proteins are thought to be specialized for roles in signaling and regulation. However, these concepts are based on in silico analyses of translated whole genome sequences, not on large-scale analyses of proteins expressed in living cells. Therefore, whether these concepts broadly apply to expressed proteins is currently unknown. Previous studies have shown that heat-treatment of cell extracts lead to partial enrichment of soluble, disordered proteins. Based on this observation, we sought to address the current dearth of knowledge about expressed, disordered proteins by performing a large-scale proteomics study of thermo-stable proteins isolated from mouse fibroblast cells. Using novel multidimensional chromatography methods and mass spectrometry, we identified a total of 1,320 thermo-stable proteins from these cells. Further, we used a variety of bioinformatics methods to analyze the structural and biological properties of these proteins. Interestingly, more than 900 of these expressed proteins were predicted to be substantially disordered. These were divided into two categories, with 514 predicted to be predominantly disordered and 395 predicted to exhibit both disordered and ordered/folded features. In addition, 411 of the thermo-stable proteins were predicted to be folded. Despite the use of heat treatment (60 min. at 98 °C) to partially enrich for disordered proteins, which might have been expected to select for small proteins, the sequences of these proteins exhibited a wide range of lengths (622 ± 555 residues (average length ± standard deviation) for disordered proteins and 569 ± 598 residues for folded proteins). Computational structural analyses revealed several unexpected features of the thermo

  6. Large-Scale, Ion-Current-Based Proteomic Investigation of the Rat Striatal Proteome in a Model of Short- and Long-Term Cocaine Withdrawal.

    PubMed

    Shen, Shichen; Jiang, Xiaosheng; Li, Jun; Straubinger, Robert M; Suarez, Mauricio; Tu, Chengjian; Duan, Xiaotao; Thompson, Alexis C; Qu, Jun

    2016-05-01

    Given the tremendous detriments of cocaine dependence, effective diagnosis and patient stratification are critical for successful intervention yet difficult to achieve due to the largely unknown molecular mechanisms involved. To obtain new insights into cocaine dependence and withdrawal, we employed a reproducible, reliable, and large-scale proteomics approach to investigate the striatal proteomes of rats (n = 40, 10 per group) subjected to chronic cocaine exposure, followed by either short- (WD1) or long- (WD22) term withdrawal. By implementing a surfactant-aided precipitation/on-pellet digestion procedure, a reproducible and sensitive nanoLC-Orbitrap MS analysis, and an optimized ion-current-based MS1 quantification pipeline, >2000 nonredundant proteins were quantified confidently without missing data in any replicate. Although cocaine was cleared from the body, 129/37 altered proteins were observed in WD1/WD22 that are implicated in several biological processes related closely to drug-induced neuroplasticity. Although many of these changes recapitulate the findings from independent studies reported over the last two decades, some novel insights were obtained and further validated by immunoassays. For example, significantly elevated striatal protein kinase C activity persisted over the 22 day cocaine withdrawal. Cofilin-1 activity was up-regulated in WD1 and down-regulated in WD22. These discoveries suggest potentially distinct structural plasticity after short- and long-term cocaine withdrawal. In addition, this study provides compelling evidence that blood vessel narrowing, a long-known effect of cocaine use, occurred after long-term but not short-term withdrawal. In summary, this work developed a well-optimized paradigm for ion-current-based quantitative proteomics in brain tissues and obtained novel insights into molecular alterations in the striatum following cocaine exposure and withdrawal. PMID:27018876

  7. Infrastructure for Large-Scale Quality-Improvement Projects: Early Lessons from North Carolina Improving Performance in Practice

    ERIC Educational Resources Information Center

    Newton, Warren P.; Lefebvre, Ann; Donahue, Katrina E.; Bacon, Thomas; Dobson, Allen

    2010-01-01

    Introduction: Little is known regarding how to accomplish large-scale health care improvement. Our goal is to improve the quality of chronic disease care in all primary care practices throughout North Carolina. Methods: Methods for improvement include (1) common quality measures and shared data system; (2) rapid cycle improvement principles; (3)…

  8. RichMind: A Tool for Improved Inference from Large-Scale Neuroimaging Results

    PubMed Central

    Maron-Katz, Adi; Amar, David; Simon, Eti Ben; Hendler, Talma; Shamir, Ron

    2016-01-01

    As the use of large-scale data-driven analysis becomes increasingly common, the need for robust methods for interpreting a large number of results increases. To date, neuroimaging attempts to interpret large-scale activity or connectivity results often turn to existing neural mapping based on previous literature. In case of a large number of results, manual selection or percent of overlap with existing maps is frequently used to facilitate interpretation, often without a clear statistical justification. Such methodology holds the risk of reporting false positive results and overlooking additional results. Here, we propose using enrichment analysis for improving the interpretation of large-scale neuroimaging results. We focus on two possible cases: position group analysis, where the identified results are a set of neural positions; and connection group analysis, where the identified results are a set of neural position-pairs (i.e. neural connections). We explore different models for detecting significant overrepresentation of known functional brain annotations using simulated and real data. We implemented our methods in a tool called RichMind, which provides both statistical significance reports and brain visualization. We demonstrate the abilities of RichMind by revisiting two previous fMRI studies. In both studies RichMind automatically highlighted most of the findings that were reported in the original studies as well as several additional findings that were overlooked. Hence, RichMind is a valuable new tool for rigorous inference from neuroimaging results. PMID:27455041

  9. Large-scale multi-configuration electromagnetic induction: a promising tool to improve hydrological models

    NASA Astrophysics Data System (ADS)

    von Hebel, Christian; Rudolph, Sebastian; Mester, Achim; Huisman, Johan A.; Montzka, Carsten; Weihermüller, Lutz; Vereecken, Harry; van der Kruk, Jan

    2015-04-01

    Large-scale multi-configuration electromagnetic induction (EMI) use different coil configurations, i.e., coil offsets and coil orientations, to sense coil specific depth volumes. The obtained apparent electrical conductivity (ECa) maps can be related to some soil properties such as clay content, soil water content, and pore water conductivity, which are important characteristics that influence hydrological processes. Here, we use large-scale EMI measurements to investigate changes in soil texture that drive the available water supply causing crop development patterns that were observed in leaf area index (LAI) maps obtained from RapidEye satellite images taken after a drought period. The 20 ha test site is situated within the Ellebach catchment (Germany) and consists of a sand-and-gravel dominated upper terrace (UT) and a loamy lower terrace (LT). The large-scale multi-configuration EMI measurements were calibrated using electrical resistivity tomography (ERT) measurements at selected transects and soil samples were taken at representative locations where changes in the electrical conductivity were observed and therefore changing soil properties were expected. By analyzing all the data, the observed LAI patterns could be attributed to buried paleo-river channel systems that contained a higher silt and clay content and provided a higher water holding capacity than the surrounding coarser material. Moreover, the measured EMI data showed highest correlation with LAI for the deepest sensing coil offset (up to 1.9 m), which indicates that the deeper subsoil is responsible for root water uptake especially under drought conditions. To obtain a layered subsurface electrical conductivity model that shows the subsurface structures more clearly, a novel EMI inversion scheme was applied to the field data. The obtained electrical conductivity distributions were validated with soil probes and ERT transects that confirmed the inverted lateral and vertical large-scale electrical

  10. Enablers and Barriers to Large-Scale Uptake of Improved Solid Fuel Stoves: A Systematic Review

    PubMed Central

    Puzzolo, Elisa; Stanistreet, Debbi; Pope, Daniel; Bruce, Nigel G.

    2013-01-01

    Background: Globally, 2.8 billion people rely on household solid fuels. Reducing the resulting adverse health, environmental, and development consequences will involve transitioning through a mix of clean fuels and improved solid fuel stoves (IS) of demonstrable effectiveness. To date, achieving uptake of IS has presented significant challenges. Objectives: We performed a systematic review of factors that enable or limit large-scale uptake of IS in low- and middle-income countries. Methods: We conducted systematic searches through multidisciplinary databases, specialist websites, and consulting experts. The review drew on qualitative, quantitative, and case studies and used standardized methods for screening, data extraction, critical appraisal, and synthesis. We summarized our findings as “factors” relating to one of seven domains—fuel and technology characteristics; household and setting characteristics; knowledge and perceptions; finance, tax, and subsidy aspects; market development; regulation, legislation, and standards; programmatic and policy mechanisms—and also recorded issues that impacted equity. Results: We identified 31 factors influencing uptake from 57 studies conducted in Asia, Africa, and Latin America. All domains matter. Although factors such as offering technologies that meet household needs and save fuel, user training and support, effective financing, and facilitative government action appear to be critical, none guarantee success: All factors can be influential, depending on context. The nature of available evidence did not permit further prioritization. Conclusions: Achieving adoption and sustained use of IS at a large scale requires that all factors, spanning household/community and program/societal levels, be assessed and supported by policy. We propose a planning tool that would aid this process and suggest further research to incorporate an evaluation of effectiveness. Citation: Rehfuess EA, Puzzolo E, Stanistreet D, Pope D, Bruce

  11. Highly Multiplexed and Reproducible Ion-Current-Based Strategy for Large-Scale Quantitative Proteomics and the Application to Protein Expression Dynamics Induced by Methylprednisolone in 60 Rats

    PubMed Central

    2015-01-01

    A proteome-level time-series study of drug effects (i.e., pharmacodynamics) is critical for understanding mechanisms of action and systems pharmacology, but is challenging, because of the requirement of a proteomics method for reliable quantification of many biological samples. Here, we describe a highly reproducible strategy, enabling a global, large-scale investigation of the expression dynamics of corticosteroid-regulated proteins in livers from adrenalectomized rats over 11 time points after drug dosing (0.5–66 h, N = 5/point). The analytical advances include (i) exhaustive tissue extraction with a Polytron/sonication procedure in a detergent cocktail buffer, and a cleanup/digestion procedure providing very consistent protein yields (relative standard deviation (RSD%) of 2.7%–6.4%) and peptide recoveries (4.1–9.0%) across the 60 animals; (ii) an ultrahigh-pressure nano-LC setup with substantially improved temperature stabilization, pump-noise suppression, and programmed interface cleaning, enabling excellent reproducibility for continuous analyses of numerous samples; (iii) separation on a 100-cm-long column (2-μm particles) with high reproducibility for days to enable both in-depth profiling and accurate peptide ion-current match; and (iv) well-controlled ion-current-based quantification. To obtain high-quality quantitative data necessary to describe the 11 time-points protein expression temporal profiles, strict criteria were used to define “quantifiable proteins”. A total of 323 drug-responsive proteins were revealed with confidence, and the time profiles of these proteins provided new insights into the diverse temporal changes of biological cascades associated with hepatic metabolism, response to hormone stimuli, gluconeogenesis, inflammatory responses, and protein translation processes. Most profile changes persisted well after the drug was eliminated. The developed strategy can also be broadly applied in preclinical and clinical research, where

  12. Improving Large-scale Storage System Performance via Topology-aware and Balanced Data Placement

    SciTech Connect

    Wang, Feiyi; Oral, H Sarp; Vazhkudai, Sudharshan S

    2014-01-01

    With the advent of big data, the I/O subsystems of large-scale compute clusters are becoming a center of focus, with more applications putting greater demands on end-to-end I/O performance. These subsystems are often complex in design. They comprise of multiple hardware and software layers to cope with the increasing capacity, capability and scalability requirements of data intensive applications. The sharing nature of storage resources and the intrinsic interactions across these layers make it to realize user-level, end-to-end performance gains a great challenge. We propose a topology-aware resource load balancing strategy to improve per-application I/O performance. We demonstrate the effectiveness of our algorithm on an extreme-scale compute cluster, Titan, at the Oak Ridge Leadership Computing Facility (OLCF). Our experiments with both synthetic benchmarks and a real-world application show that, even under congestion, our proposed algorithm can improve large-scale application I/O performance significantly, resulting in both the reduction of application run times and higher resolution simulation runs.

  13. Automatic large-scale classification of bird sounds is strongly improved by unsupervised feature learning

    PubMed Central

    Plumbley, Mark D.

    2014-01-01

    Automatic species classification of birds from their sound is a computational tool of increasing importance in ecology, conservation monitoring and vocal communication studies. To make classification useful in practice, it is crucial to improve its accuracy while ensuring that it can run at big data scales. Many approaches use acoustic measures based on spectrogram-type data, such as the Mel-frequency cepstral coefficient (MFCC) features which represent a manually-designed summary of spectral information. However, recent work in machine learning has demonstrated that features learnt automatically from data can often outperform manually-designed feature transforms. Feature learning can be performed at large scale and “unsupervised”, meaning it requires no manual data labelling, yet it can improve performance on “supervised” tasks such as classification. In this work we introduce a technique for feature learning from large volumes of bird sound recordings, inspired by techniques that have proven useful in other domains. We experimentally compare twelve different feature representations derived from the Mel spectrum (of which six use this technique), using four large and diverse databases of bird vocalisations, classified using a random forest classifier. We demonstrate that in our classification tasks, MFCCs can often lead to worse performance than the raw Mel spectral data from which they are derived. Conversely, we demonstrate that unsupervised feature learning provides a substantial boost over MFCCs and Mel spectra without adding computational complexity after the model has been trained. The boost is particularly notable for single-label classification tasks at large scale. The spectro-temporal activations learned through our procedure resemble spectro-temporal receptive fields calculated from avian primary auditory forebrain. However, for one of our datasets, which contains substantial audio data but few annotations, increased performance is not

  14. Automatic large-scale classification of bird sounds is strongly improved by unsupervised feature learning.

    PubMed

    Stowell, Dan; Plumbley, Mark D

    2014-01-01

    Automatic species classification of birds from their sound is a computational tool of increasing importance in ecology, conservation monitoring and vocal communication studies. To make classification useful in practice, it is crucial to improve its accuracy while ensuring that it can run at big data scales. Many approaches use acoustic measures based on spectrogram-type data, such as the Mel-frequency cepstral coefficient (MFCC) features which represent a manually-designed summary of spectral information. However, recent work in machine learning has demonstrated that features learnt automatically from data can often outperform manually-designed feature transforms. Feature learning can be performed at large scale and "unsupervised", meaning it requires no manual data labelling, yet it can improve performance on "supervised" tasks such as classification. In this work we introduce a technique for feature learning from large volumes of bird sound recordings, inspired by techniques that have proven useful in other domains. We experimentally compare twelve different feature representations derived from the Mel spectrum (of which six use this technique), using four large and diverse databases of bird vocalisations, classified using a random forest classifier. We demonstrate that in our classification tasks, MFCCs can often lead to worse performance than the raw Mel spectral data from which they are derived. Conversely, we demonstrate that unsupervised feature learning provides a substantial boost over MFCCs and Mel spectra without adding computational complexity after the model has been trained. The boost is particularly notable for single-label classification tasks at large scale. The spectro-temporal activations learned through our procedure resemble spectro-temporal receptive fields calculated from avian primary auditory forebrain. However, for one of our datasets, which contains substantial audio data but few annotations, increased performance is not discernible. We

  15. Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics

    PubMed Central

    Malmström, Erik; Kilsgård, Ola; Hauri, Simon; Smeds, Emanuel; Herwald, Heiko; Malmström, Lars; Malmström, Johan

    2016-01-01

    The plasma proteome is highly dynamic and variable, composed of proteins derived from surrounding tissues and cells. To investigate the complex processes that control the composition of the plasma proteome, we developed a mass spectrometry-based proteomics strategy to infer the origin of proteins detected in murine plasma. The strategy relies on the construction of a comprehensive protein tissue atlas from cells and highly vascularized organs using shotgun mass spectrometry. The protein tissue atlas was transformed to a spectral library for highly reproducible quantification of tissue-specific proteins directly in plasma using SWATH-like data-independent mass spectrometry analysis. We show that the method can determine drastic changes of tissue-specific protein profiles in blood plasma from mouse animal models with sepsis. The strategy can be extended to several other species advancing our understanding of the complex processes that contribute to the plasma proteome dynamics. PMID:26732734

  16. Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics.

    PubMed

    Malmström, Erik; Kilsgård, Ola; Hauri, Simon; Smeds, Emanuel; Herwald, Heiko; Malmström, Lars; Malmström, Johan

    2016-01-01

    The plasma proteome is highly dynamic and variable, composed of proteins derived from surrounding tissues and cells. To investigate the complex processes that control the composition of the plasma proteome, we developed a mass spectrometry-based proteomics strategy to infer the origin of proteins detected in murine plasma. The strategy relies on the construction of a comprehensive protein tissue atlas from cells and highly vascularized organs using shotgun mass spectrometry. The protein tissue atlas was transformed to a spectral library for highly reproducible quantification of tissue-specific proteins directly in plasma using SWATH-like data-independent mass spectrometry analysis. We show that the method can determine drastic changes of tissue-specific protein profiles in blood plasma from mouse animal models with sepsis. The strategy can be extended to several other species advancing our understanding of the complex processes that contribute to the plasma proteome dynamics. PMID:26732734

  17. Large-Scale Proteomics of the Cassava Storage Root and Identification of a Target Gene to Reduce Postharvest Deterioration.

    PubMed

    Vanderschuren, Hervé; Nyaboga, Evans; Poon, Jacquelyne S; Baerenfaller, Katja; Grossmann, Jonas; Hirsch-Hoffmann, Matthias; Kirchgessner, Norbert; Nanni, Paolo; Gruissem, Wilhelm

    2014-05-29

    Cassava (Manihot esculenta) is the most important root crop in the tropics, but rapid postharvest physiological deterioration (PPD) of the root is a major constraint to commercial cassava production. We established a reliable method for image-based PPD symptom quantification and used label-free quantitative proteomics to generate an extensive cassava root and PPD proteome. Over 2600 unique proteins were identified in the cassava root, and nearly 300 proteins showed significant abundance regulation during PPD. We identified protein abundance modulation in pathways associated with oxidative stress, phenylpropanoid biosynthesis (including scopoletin), the glutathione cycle, fatty acid α-oxidation, folate transformation, and the sulfate reduction II pathway. Increasing protein abundances and enzymatic activities of glutathione-associated enzymes, including glutathione reductases, glutaredoxins, and glutathione S-transferases, indicated a key role for ascorbate/glutathione cycles. Based on combined proteomics data, enzymatic activities, and lipid peroxidation assays, we identified glutathione peroxidase as a candidate for reducing PPD. Transgenic cassava overexpressing a cytosolic glutathione peroxidase in storage roots showed delayed PPD and reduced lipid peroxidation as well as decreased H2O2 accumulation. Quantitative proteomics data from ethene and phenylpropanoid pathways indicate additional gene candidates to further delay PPD. Cassava root proteomics data are available at www.pep2pro.ethz.ch for easy access and comparison with other proteomics data. PMID:24876255

  18. Getting It "Better": The Importance of Improving Background Questionnaires in International Large-Scale Assessment

    ERIC Educational Resources Information Center

    Rutkowski, Leslie; Rutkowski, David

    2010-01-01

    In addition to collecting achievement data, international large-scale assessment programmes gather auxiliary information from students and schools regarding the context of teaching and learning. In an effort to clarify some of the opacity surrounding international large-scale assessment programmes and the potential problems associated with less…

  19. Studying large-scale programmes to improve patient safety in whole care systems: challenges for research.

    PubMed

    Benn, Jonathan; Burnett, Susan; Parand, Anam; Pinto, Anna; Iskander, Sandra; Vincent, Charles

    2009-12-01

    Large-scale national and multi-institutional patient safety improvement programmes are being developed in the health care systems of several countries to address problems in the reliability of care delivered to patients. Drawing upon popular collaborative improvement models, these campaigns are ambitious in their aims to improve patient safety in macro-level systems such as whole health care organisations. This article considers the methodological issues involved in conducting research and evaluation of these programmes. Several specific research challenges are outlined, which result from the complexity of longitudinal, multi-level intervention programmes and the variable, highly sociotechnical care systems, with which they interact. Organisational-level improvement programmes are often underspecified due to local variations in context and organisational readiness for improvement work. The result is variable implementation patterns and local adaptations. Programme effects span levels and other boundaries within a system, vary dynamically or are cumulative over time and are problematic to understand in terms of cause and effect, where concurrent external influences exist and the impact upon study endpoints may be mediated by a range of organisational and social factors. We outline the methodological approach to research in the United Kingdom Safer Patients Initiative, to exemplify how some of the challenges for research in this area can be met through a multi-method, longitudinal research design. Specifically, effective research designs must be sensitive to complex variation, through employing multiple qualitative and quantitative measures, collect data over time to understand change and utilise descriptive techniques to capture specific interactions between programme and context for implementation. When considering the long-term, sustained impact of an improvement programme, researchers must consider how to define and measure the capability for continuous safe and

  20. The Proteomic Landscape of the Suprachiasmatic Nucleus Clock Reveals Large-Scale Coordination of Key Biological Processes

    PubMed Central

    Chiang, Cheng-Kang; Mehta, Neel; Patel, Abhilasha; Zhang, Peng; Ning, Zhibin; Mayne, Janice; Sun, Warren Y. L.

    2014-01-01

    The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry. Of the 2112 proteins that were accurately quantified, 20% (421 proteins) displayed a time-of-day-dependent expression profile. Within this time-of-day proteome, 11% (48 proteins) were further defined as circadian based on a sinusoidal expression pattern with a ∼24 h period. Nine circadianly expressed proteins exhibited 24 h rhythms at the transcript level, with an average time lag that exceeded 8 h. A substantial proportion of the time-of-day proteome exhibited abrupt fluctuations at the anticipated light-to-dark and dark-to-light transitions, and was enriched for proteins involved in several key biological pathways, most notably, mitochondrial oxidative phosphorylation. Additionally, predicted targets of miR-133ab were enriched in specific hierarchical clusters and were inversely correlated with miR133ab expression in the SCN. These insights into the proteomic landscape of the SCN will facilitate a more integrative understanding of cellular control within the SCN clock. PMID:25330117

  1. Vehicle impoundments improve drinking and driving licence suspension outcomes: Large-scale evidence from Ontario.

    PubMed

    Byrne, Patrick A; Ma, Tracey; Elzohairy, Yoassry

    2016-10-01

    Although vehicle impoundment has become a common sanction for various driving offences, large-scale evaluations of its effectiveness in preventing drinking and driving recidivism are almost non-existent in the peer-reviewed literature. One reason is that impoundment programs have typically been introduced simultaneously with other countermeasures, rendering it difficult to disentangle any observed effects. Previous studies of impoundment effectiveness conducted when such programs were implemented in isolation have typically been restricted to small jurisdictions, making high-quality evaluation difficult. In contrast, Ontario's "long-term" and "seven-day" impoundment programs were implemented in relative isolation, but with tight relationships to already existing drinking and driving suspensions. In this work, we used offence data produced by Ontario's population of over 9 million licensed drivers to perform interrupted time series analysis on drinking and driving recidivism and on rates of driving while suspended for drinking and driving. Our results demonstrate two key findings: (1) impoundment, or its threat, improves compliance with drinking and driving licence suspensions; and (2) addition of impoundment to suspension reduces drinking and driving recidivism, possibly through enhanced suspension compliance. PMID:27434801

  2. Large Scale Data Mining to Improve Usability of Data: An Intelligent Archive Testbed

    NASA Technical Reports Server (NTRS)

    Ramapriyan, Hampapuram; Isaac, David; Yang, Wenli; Morse, Steve

    2005-01-01

    Research in certain scientific disciplines - including Earth science, particle physics, and astrophysics - continually faces the challenge that the volume of data needed to perform valid scientific research can at times overwhelm even a sizable research community. The desire to improve utilization of this data gave rise to the Intelligent Archives project, which seeks to make data archives active participants in a knowledge building system capable of discovering events or patterns that represent new information or knowledge. Data mining can automatically discover patterns and events, but it is generally viewed as unsuited for large-scale use in disciplines like Earth science that routinely involve very high data volumes. Dozens of research projects have shown promising uses of data mining in Earth science, but all of these are based on experiments with data subsets of a few gigabytes or less, rather than the terabytes or petabytes typically encountered in operational systems. To bridge this gap, the Intelligent Archives project is establishing a testbed with the goal of demonstrating the use of data mining techniques in an operationally-relevant environment. This paper discusses the goals of the testbed and the design choices surrounding critical issues that arose during testbed implementation.

  3. Profiling and Improving I/O Performance of a Large-Scale Climate Scientific Application

    NASA Technical Reports Server (NTRS)

    Liu, Zhuo; Wang, Bin; Wang, Teng; Tian, Yuan; Xu, Cong; Wang, Yandong; Yu, Weikuan; Cruz, Carlos A.; Zhou, Shujia; Clune, Tom; Klasky, Scott

    2013-01-01

    Exascale computing systems are soon to emerge, which will pose great challenges on the huge gap between computing and I/O performance. Many large-scale scientific applications play an important role in our daily life. The huge amounts of data generated by such applications require highly parallel and efficient I/O management policies. In this paper, we adopt a mission-critical scientific application, GEOS-5, as a case to profile and analyze the communication and I/O issues that are preventing applications from fully utilizing the underlying parallel storage systems. Through in-detail architectural and experimental characterization, we observe that current legacy I/O schemes incur significant network communication overheads and are unable to fully parallelize the data access, thus degrading applications' I/O performance and scalability. To address these inefficiencies, we redesign its I/O framework along with a set of parallel I/O techniques to achieve high scalability and performance. Evaluation results on the NASA discover cluster show that our optimization of GEOS-5 with ADIOS has led to significant performance improvements compared to the original GEOS-5 implementation.

  4. An improved unified network protocol framework for large-scale wireless sensor networks

    NASA Astrophysics Data System (ADS)

    Ding, Jin; Sivalingam, Krishna M.

    2004-08-01

    Rapid technological advances in wireless communication have made it possible for networking sensor devices. Given the low computation and battery power capacities of these sensor nodes, the key design factors of network protocols are self-configuring, energy-efficient, adaptive, and scalable. We presented the multi-hop infrastructure network architecture (MINA) for a wireless sensor network consisting of a few hundred sensors that communicate data to a base station (BS). We designed a Unified Network Protocol Framework for MINA that encompasses network organization, medium access control (MAC) and routing protocols. In this paper, we improve it by adaptively varying transmission range to maintain network connectivity. It is a derivative-free optimization algorithm. The BS periodically evaluates the objective function, chooses the appropriate transmission range and broadcasts it to the sensor nodes that then update the transmission range. The advantages are: (i) Avoids the disconnectivity; (ii) Maximizes the number of nodes that can be connected to the BS, (iii) Minimizes the energyxdelay metric and (iv) Avoids the "hot-spot" nodes in the network. The performance in terms of delay, throughput, energy consumption and network lifetimes, is studied in detail using discrete-event simulation compared with other protocol. The results show that it is energy efficient in a large scale network.

  5. Improvement of Baltic proper water quality using large-scale ecological engineering.

    PubMed

    Stigebrandt, Anders; Gustafsson, Bo G

    2007-04-01

    Eutrophication of the Baltic proper has led to impaired water quality, demonstrated by, e.g., extensive blooming of cyanobacteria during the premium summer holiday season and severe oxygen deficit in the deepwater. Sustainable improvements in water quality by the reduction of phosphorus (P) supplies will take several decades before giving full effects because of large P storages both in soils in the watershed and in the water column and bottom sediments of the Baltic proper. In this article it is shown that drastically improved water quality may be obtained within a few years using large-scale ecological engineering methods. Natural variations in the Baltic proper during the last decades have demonstrated how rapid improvements may be achieved. The present article describes the basic dynamics of P, organic matter, and oxygen in the Baltic proper. It also briefly discusses the advantages and disadvantages of different classes of methods of ecological engineering aimed at restoring the Baltic proper from eutrophication effects. Preliminary computations show that the P content might be halved within a few years if about 100 kg O2 s(-1) are supplied to the upper deepwater. This would require 100 pump stations, each transporting about 100 m3 s(-1) of oxygen-rich so-called winter water from about 50 to 125 m depth where the water is released as a buoyant jet. Each pump station needs a power supply of 0.6 MW. Offshore wind power technology seems mature enough to provide the power needed by the pump stations. The cost to install 100 wind-powered pump stations, each with 0.6 MW power, at about 125-m depth is about 200 million Euros. PMID:17520945

  6. Improving urban streamflow forecasting using a high-resolution large scale modeling framework

    NASA Astrophysics Data System (ADS)

    Read, Laura; Hogue, Terri; Gochis, David; Salas, Fernando

    2016-04-01

    Urban flood forecasting is a critical component in effective water management, emergency response, regional planning, and disaster mitigation. As populations across the world continue to move to cities (~1.8% growth per year), and studies indicate that significant flood damages are occurring outside the floodplain in urban areas, the ability to model and forecast flow over the urban landscape becomes critical to maintaining infrastructure and society. In this work, we use the Weather Research and Forecasting- Hydrological (WRF-Hydro) modeling framework as a platform for testing improvements to representation of urban land cover, impervious surfaces, and urban infrastructure. The three improvements we evaluate include: updating the land cover to the latest 30-meter National Land Cover Dataset, routing flow over a high-resolution 30-meter grid, and testing a methodology for integrating an urban drainage network into the routing regime. We evaluate performance of these improvements in the WRF-Hydro model for specific flood events in the Denver-Metro Colorado domain, comparing to historic gaged streamflow for retrospective forecasts. Denver-Metro provides an interesting case study as it is a rapidly growing urban/peri-urban region with an active history of flooding events that have caused significant loss of life and property. Considering that the WRF-Hydro model will soon be implemented nationally in the U.S. to provide flow forecasts on the National Hydrography Dataset Plus river reaches - increasing capability from 3,600 forecast points to 2.7 million, we anticipate that this work will support validation of this service in urban areas for operational forecasting. Broadly, this research aims to provide guidance for integrating complex urban infrastructure with a large-scale, high resolution coupled land-surface and distributed hydrologic model.

  7. School Improvement Networks as a Strategy for Large-Scale Education Reform: The Role of Educational Environments

    ERIC Educational Resources Information Center

    Glazer, Joshua L.; Peurach, Donald J.

    2013-01-01

    The development and scale-up of school improvement networks is among the most important educational innovations of the last decade, and current federal, state, and district efforts attempt to use school improvement networks as a mechanism for supporting large-scale change. The potential of improvement networks, however, rests on the extent to…

  8. Improvement of methods for large scale sequencing; application to human Xq28

    SciTech Connect

    Gibbs, R.A.; Andersson, B.; Wentland, M.A.

    1994-09-01

    Sequencing of a one-metabase region of Xq28, spanning the FRAXA and IDS loci has been undertaken in order to investigate the practicality of the shotgun approach for large scale sequencing and as a platform to develop improved methods. The efficiency of several steps in the shotgun sequencing strategy has been increased using PCR-based approaches. An improved method for preparation of M13 libraries has been developed. This protocol combines a previously described adaptor-based protocol with the uracil DNA glycosylase (UDG)-cloning procedure. The efficiency of this procedure has been found to be up to 100-fold higher than that of previously used protocols. In addition the novel protocol is more reliable and thus easy to establish in a laboratory. The method has also been adapted for the simultaneous shotgun sequencing of multiple short fragments by concentrating them before library construction is presented. This protocol is suitable for rapid characterization of cDNA clones. A library was constructed from 15 PCR-amplified and concentrated human cDNA inserts, and the insert sequences could easily be identified as separate contigs during the assembly process and the sequence coverage was even along each fragment. Using this strategy, the fine structures of the FraxA and IDS loci have been revealed and several EST homologies indicating novel expressed sequences have been identified. Use of PCR to close repetitive regions that are difficult to clone was tested by determination of the sequence of a cosmid mapping DXS455 in Xq28, containing a polymorphic VNTR. The region containing the VNTR was not represented in the shotgun library, but by designing PCR primers in the sequences flanking the gap and by cloning and sequencing the PCR product, the fine structure of the VNTR has been determined. It was found to be an AT-rich VNTR with a repeated 25-mer at the center.

  9. Improving the local relevance of large scale water demand predictions: the way forward

    NASA Astrophysics Data System (ADS)

    Bernhard, Jeroen; Reynaud, Arnaud; de Roo, Ad

    2016-04-01

    use and water prices. Subsequently, econometric estimates allow us to make a monetary valuation of water and identify the dominant drivers of domestic and industrial water demand per country. Combined with socio-economic, demographic and climate scenarios we made predictions for future Europe. Since this is a first attempt we obtained mixed results between countries when it comes to data availability and therefore model uncertainty. For some countries we have been able to develop robust predictions based on vast amounts of data while some other countries proved more challenging. We do feel however, that large scale predictions based on regional data are the way forward to provide relevant scientific policy support. In order to improve on our work it is imperative to further expand our database of consistent regional data. We are looking forward to any kind of input and would be very interested in sharing our data to collaborate towards a better understanding of the water use system.

  10. Transcriptomic and proteomic responses of Serratia marcescens to spaceflight conditions involve large-scale changes in metabolic pathways

    NASA Astrophysics Data System (ADS)

    Wang, Yajuan; Yuan, Yanting; Liu, Jinwen; Su, Longxiang; Chang, De; Guo, Yinghua; Chen, Zhenhong; Fang, Xiangqun; Wang, Junfeng; Li, Tianzhi; Zhou, Lisha; Fang, Chengxiang; Yang, Ruifu; Liu, Changting

    2014-04-01

    The microgravity environment of spaceflight expeditions has been associated with altered microbial responses. This study explores the characterization of Serratia marcescensis grown in a spaceflight environment at the phenotypic, transcriptomic and proteomic levels. From November 1, 2011 to November 17, 2011, a strain of S. marcescensis was sent into space for 398 h on the Shenzhou VIII spacecraft, and ground simulation was performed as a control (LCT-SM213). After the flight, two mutant strains (LCT-SM166 and LCT-SM262) were selected for further analysis. Although no changes in the morphology, post-culture growth kinetics, hemolysis or antibiotic sensitivity were observed, the two mutant strains exhibited significant changes in their metabolic profiles after exposure to spaceflight. Enrichment analysis of the transcriptome showed that the differentially expressed genes of the two spaceflight strains and the ground control strain mainly included those involved in metabolism and degradation. The proteome revealed that changes at the protein level were also associated with metabolic functions, such as glycolysis/gluconeogenesis, pyruvate metabolism, arginine and proline metabolism and the degradation of valine, leucine and isoleucine. In summary S. marcescens showed alterations primarily in genes and proteins that were associated with metabolism under spaceflight conditions, which gave us valuable clues for future research.

  11. Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes.

    PubMed

    Ivarsson, Ylva; Arnold, Roland; McLaughlin, Megan; Nim, Satra; Joshi, Rakesh; Ray, Debashish; Liu, Bernard; Teyra, Joan; Pawson, Tony; Moffat, Jason; Li, Shawn Shun-Cheng; Sidhu, Sachdev S; Kim, Philip M

    2014-02-18

    The human proteome contains a plethora of short linear motifs (SLiMs) that serve as binding interfaces for modular protein domains. Such interactions are crucial for signaling and other cellular processes, but are difficult to detect because of their low to moderate affinities. Here we developed a dedicated approach, proteomic peptide-phage display (ProP-PD), to identify domain-SLiM interactions. Specifically, we generated phage libraries containing all human and viral C-terminal peptides using custom oligonucleotide microarrays. With these libraries we screened the nine PSD-95/Dlg/ZO-1 (PDZ) domains of human Densin-180, Erbin, Scribble, and Disks large homolog 1 for peptide ligands. We identified several known and putative interactions potentially relevant to cellular signaling pathways and confirmed interactions between full-length Scribble and the target proteins β-PIX, plakophilin-4, and guanylate cyclase soluble subunit α-2 using colocalization and coimmunoprecipitation experiments. The affinities of recombinant Scribble PDZ domains and the synthetic peptides representing the C termini of these proteins were in the 1- to 40-μM range. Furthermore, we identified several well-established host-virus protein-protein interactions, and confirmed that PDZ domains of Scribble interact with the C terminus of Tax-1 of human T-cell leukemia virus with micromolar affinity. Previously unknown putative viral protein ligands for the PDZ domains of Scribble and Erbin were also identified. Thus, we demonstrate that our ProP-PD libraries are useful tools for probing PDZ domain interactions. The method can be extended to interrogate all potential eukaryotic, bacterial, and viral SLiMs and we suggest it will be a highly valuable approach for studying cellular and pathogen-host protein-protein interactions. PMID:24550280

  12. Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains.

    PubMed

    Han, Mee-Jung; Kim, Jin Young; Kim, Jung A

    2014-04-01

    Escherichia coli typically secretes many proteins into the periplasmic space, and the periplasmic proteins have been used for the secretory production of various proteins by the biotechnology industry. However, the identity of all of the E. coli periplasmic proteins remains unknown. Here, high-resolution periplasmic proteome reference maps of the E. coli K-12 and B strains were constructed and compared. Of the 145 proteins identified by tandem mass spectrometry, 61 proteins were conserved in the two strains, whereas 11 and 12 strain-specific proteins were identified for the E. coli K-12 and B strains, respectively. In addition, 27 proteins exhibited differences in intensities greater than 2-fold between the K-12 and B strains. The periplasmic proteins MalE and OppA were the most abundant proteins in the two E. coli strains. Distinctive differences between the two strains included several proteins that were caused by genetic variations, such as CybC, FliC, FliY, KpsD, MglB, ModA, and Ybl119, hydrolytic enzymes, particularly phosphatases, glycosylases, and proteases, and many uncharacterized proteins. Compared to previous studies, the localization of many proteins, including 30 proteins for the K-12 strain and 53 proteins for the B strain, was newly identified as periplasmic. This study identifies the largest number of proteins in the E. coli periplasm as well as the dynamics of these proteins. Additionally, these findings are summarized as reference proteome maps that will be useful for studying protein secretion and may provide new strategies for the enhanced secretory production of recombinant proteins. PMID:24140104

  13. Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines.

    PubMed

    Yu, Wen; Taylor, J Alex; Davis, Michael T; Bonilla, Leo E; Lee, Kimberly A; Auger, Paul L; Farnsworth, Chris C; Welcher, Andrew A; Patterson, Scott D

    2010-03-01

    Despite recent advances in qualitative proteomics, the automatic identification of peptides with optimal sensitivity and accuracy remains a difficult goal. To address this deficiency, a novel algorithm, Multiple Search Engines, Normalization and Consensus is described. The method employs six search engines and a re-scoring engine to search MS/MS spectra against protein and decoy sequences. After the peptide hits from each engine are normalized to error rates estimated from the decoy hits, peptide assignments are then deduced using a minimum consensus model. These assignments are produced in a series of progressively relaxed false-discovery rates, thus enabling a comprehensive interpretation of the data set. Additionally, the estimated false-discovery rate was found to have good concordance with the observed false-positive rate calculated from known identities. Benchmarking against standard proteins data sets (ISBv1, sPRG2006) and their published analysis, demonstrated that the Multiple Search Engines, Normalization and Consensus algorithm consistently achieved significantly higher sensitivity in peptide identifications, which led to increased or more robust protein identifications in all data sets compared with prior methods. The sensitivity and the false-positive rate of peptide identification exhibit an inverse-proportional and linear relationship with the number of participating search engines. PMID:20101609

  14. Re-fraction: a machine learning approach for deterministic identification of protein homologues and splice variants in large-scale MS-based proteomics.

    PubMed

    Yang, Pengyi; Humphrey, Sean J; Fazakerley, Daniel J; Prior, Matthew J; Yang, Guang; James, David E; Yang, Jean Yee-Hwa

    2012-05-01

    A key step in the analysis of mass spectrometry (MS)-based proteomics data is the inference of proteins from identified peptide sequences. Here we describe Re-Fraction, a novel machine learning algorithm that enhances deterministic protein identification. Re-Fraction utilizes several protein physical properties to assign proteins to expected protein fractions that comprise large-scale MS-based proteomics data. This information is then used to appropriately assign peptides to specific proteins. This approach is sensitive, highly specific, and computationally efficient. We provide algorithms and source code for the current version of Re-Fraction, which accepts output tables from the MaxQuant environment. Nevertheless, the principles behind Re-Fraction can be applied to other protein identification pipelines where data are generated from samples fractionated at the protein level. We demonstrate the utility of this approach through reanalysis of data from a previously published study and generate lists of proteins deterministically identified by Re-Fraction that were previously only identified as members of a protein group. We find that this approach is particularly useful in resolving protein groups composed of splice variants and homologues, which are frequently expressed in a cell- or tissue-specific manner and may have important biological consequences. PMID:22428558

  15. Large-scale epigenome imputation improves data quality and disease variant enrichment

    PubMed Central

    Ernst, Jason; Kellis, Manolis

    2015-01-01

    With hundreds of epigenomic maps, the opportunity arises to exploit the correlated nature of epigenetic signals, across both marks and samples, for large-scale prediction of additional datasets. Here, we undertake epigenome imputation by leveraging such correlations through an ensemble of regression trees. We impute 4,315 high-resolution signal maps, of which 26% are also experimentally observed. Imputed signal tracks show overall similarity to observed signals, and surpass experimental datasets in consistency, recovery of gene annotations, and enrichment for disease-associated variants. We use the imputed data to detect low quality experimental datasets, to find genomic sites with unexpected epigenomic signals, to define high-priority marks for new experiments, and to delineate chromatin states in 127 reference epigenomes spanning diverse tissues and cell types. Our imputed datasets provide the most comprehensive human regulatory annotation to date, and our approach and the ChromImpute software constitute a useful complement to large-scale experimental mapping of epigenomic information. PMID:25690853

  16. Improved large-scale production of vitamin B12 by Pseudomonas denitrificans with betaine feeding.

    PubMed

    Li, Kun-Tai; Liu, Dong-Hong; Li, Yong-Liang; Chu, Ju; Wang, Yong-Hong; Zhuang, Ying-Ping; Zhang, Si-Liang

    2008-11-01

    The strategy of betaine control for vitamin B12 large-scale fermentation by Pseudomonas denitrificans was investigated in this paper. The results obtained in shake-flask experiments demonstrated that betaine could greatly stimulate vitamin B12 biosynthesis but had an inhibition to cell growth. Based on the influence of betaine on the fermentation of P. denitrificans, betaine feeding was a beneficial strategy to solve the inconsistency between cell growth and vitamin B12 production. As a result, an effective and economical strategy of betaine feeding was established for vitamin B12 fermentation in 120-m3 fermenter, in which betaine was continuously fed to maintain betaine concentration of the broth at the range of 5-7g/l during 50-140h of fermentation. PMID:18440227

  17. DeepMeSH: deep semantic representation for improving large-scale MeSH indexing

    PubMed Central

    Peng, Shengwen; You, Ronghui; Wang, Hongning; Zhai, Chengxiang; Mamitsuka, Hiroshi; Zhu, Shanfeng

    2016-01-01

    Motivation: Medical Subject Headings (MeSH) indexing, which is to assign a set of MeSH main headings to citations, is crucial for many important tasks in biomedical text mining and information retrieval. Large-scale MeSH indexing has two challenging aspects: the citation side and MeSH side. For the citation side, all existing methods, including Medical Text Indexer (MTI) by National Library of Medicine and the state-of-the-art method, MeSHLabeler, deal with text by bag-of-words, which cannot capture semantic and context-dependent information well. Methods: We propose DeepMeSH that incorporates deep semantic information for large-scale MeSH indexing. It addresses the two challenges in both citation and MeSH sides. The citation side challenge is solved by a new deep semantic representation, D2V-TFIDF, which concatenates both sparse and dense semantic representations. The MeSH side challenge is solved by using the ‘learning to rank’ framework of MeSHLabeler, which integrates various types of evidence generated from the new semantic representation. Results: DeepMeSH achieved a Micro F-measure of 0.6323, 2% higher than 0.6218 of MeSHLabeler and 12% higher than 0.5637 of MTI, for BioASQ3 challenge data with 6000 citations. Availability and Implementation: The software is available upon request. Contact: zhusf@fudan.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307646

  18. Improving irrigation efficiency in Italian apple orchards: A large-scale approach

    NASA Astrophysics Data System (ADS)

    Della Chiesa, Stefano; la Cecilia, Daniele; Niedrist, Georg; Hafner, Hansjörg; Thalheimer, Martin; Tappeiner, Ulrike

    2016-04-01

    Nord-Italian region South Tyrol is Europe's largest apple growing area. In order to enable an economically relevant fruit quality and quantity the relative dry climate of the region 450-700mm gets compensated by a large scale irrigation management which until now follows old, traditional rights. Due to ongoing climatic changes and rising public sensitivity toward sustainable usage of water resources, irrigation practices are more and more critically discussed. In order to establish an objective and quantitative base of information to optimise irrigation practice, 17 existing microclimatic stations were upgraded with soil moisture and soil water potential sensors. As a second information layer a data set of 20,000 soil analyses has been geo-referenced and spatialized using a modern geostatistical method. Finally, to assess whether the zones with shallow aquifer influence soil water availability, data of 70 groundwater depth measuring stations were retrieved. The preliminary results highlight that in many locations in particular in the valley bottoms irrigation largely exceeds plant water needs because either the shallow aquifer provides sufficient water supply by capillary rise processes into the root zone or irrigation is applied without accounting for the specific soil properties.

  19. Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an O-18-Labeled “Universal” Reference Sample

    SciTech Connect

    Qian, Weijun; Liu, Tao; Petyuk, Vladislav A.; Gritsenko, Marina A.; Petritis, Brianne O.; Polpitiya, Ashoka D.; Kaushal, Amit; Xiao, Wenzhong; Finnerty, Celeste C.; Jescheke, Marc G.; Jaitly, Navdeep; Monroe, Matthew E.; Moore, Ronald J.; Moldawer, Lyle L.; Davis, Ronald W.; Tompkins, Ronald G.; Hemdon, David N.; Camp, David G.; Smith, Richard D.

    2009-01-01

    Quantitative comparison of protein abundances across a relatively large number of patient samples is an important challenge for clinical proteomic applications. Herein we describe a dual-quantitation strategy that allows the simultaneous integration of complementary label-free and stable isotope labeling based approaches without increasing the number of LC-MS analyses. The approach utilizes a stable isotope 18O-labeled “universal” reference sample as a comprehensive set of internal standards spiked into each individually processed unlabeled patient sample. The quantitative data are based on both the direct 16O-MS intensities for label-free quantitation and the 16O/18O isotopic peptide pair ratios that compare each patient sample to the identical labeled reference. The effectiveness of this dual-quantitation approach for large scale quantitative proteomics is demonstrated by the application to a set of 38 clinical plasma samples from surviving and non-surviving severe burn patients. With the coupling of immunoaffinity depletion, cysteinyl-peptide enrichment based fractionation, high resolution LC-MS measurements, and the dual-quantitation approach, a total of 318 proteins were confidently quantified with at least two peptides and 263 proteins were quantified by both approaches. The strategy also enabled a direct comparison between the two approaches with the labeling approach showing significantly better precision in quantitation while the label-free approach resulted in more protein identifications. The relative abundance differences determined by the two approaches also show strong correlation. Finally, the dual-quantitation strategy allowed us to identify more candidate protein biomarkers, illustrating the complementary nature of the two quantitative methods.

  20. Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism.

    PubMed

    Zybailov, Boris; Friso, Giulia; Kim, Jitae; Rudella, Andrea; Rodríguez, Verenice Ramírez; Asakura, Yukari; Sun, Qi; van Wijk, Klaas J

    2009-08-01

    The clpr2-1 mutant is delayed in development due to reduction of the chloroplast ClpPR protease complex. To understand the role of Clp proteases in plastid biogenesis and homeostasis, leaf proteomes of young seedlings of clpr2-1 and wild type were compared using large scale mass spectrometry-based quantification using an LTQ-Orbitrap and spectral counting with significance determined by G-tests. Virtually only chloroplast-localized proteins were significantly affected, indicating that the molecular phenotype was confined to the chloroplast. A comparative chloroplast stromal proteome analysis of fully developed plants was used to complement the data set. Chloroplast unfoldase ClpB3 was strongly up-regulated in both young and mature leaves, suggesting widespread and persistent protein folding stress. The importance of ClpB3 in the clp2-1 mutant was demonstrated by the observation that a CLPR2 and CLPB3 double mutant was seedling-lethal. The observed up-regulation of chloroplast chaperones and protein sorting components further illustrated destabilization of protein homeostasis. Delayed rRNA processing and up-regulation of a chloroplast DEAD box RNA helicase and polynucleotide phosphorylase, but no significant change in accumulation of ribosomal subunits, suggested a bottleneck in ribosome assembly or RNA metabolism. Strong up-regulation of a chloroplast translational regulator TypA/BipA GTPase suggested a specific response in plastid gene expression to the distorted homeostasis. The stromal proteases PreP1,2 were up-regulated, likely constituting compensation for reduced Clp protease activity and possibly shared substrates between the ClpP and PreP protease systems. The thylakoid photosynthetic apparatus was decreased in the seedlings, whereas several structural thylakoid-associated plastoglobular proteins were strongly up-regulated. Two thylakoid-associated reductases involved in isoprenoid and chlorophyll synthesis were up-regulated reflecting feedback from rate

  1. Large Scale Comparative Proteomics of a Chloroplast Clp Protease Mutant Reveals Folding Stress, Altered Protein Homeostasis, and Feedback Regulation of Metabolism*

    PubMed Central

    Zybailov, Boris; Friso, Giulia; Kim, Jitae; Rudella, Andrea; Rodríguez, Verenice Ramírez; Asakura, Yukari; Sun, Qi; van Wijk, Klaas J.

    2009-01-01

    The clpr2-1 mutant is delayed in development due to reduction of the chloroplast ClpPR protease complex. To understand the role of Clp proteases in plastid biogenesis and homeostasis, leaf proteomes of young seedlings of clpr2-1 and wild type were compared using large scale mass spectrometry-based quantification using an LTQ-Orbitrap and spectral counting with significance determined by G-tests. Virtually only chloroplast-localized proteins were significantly affected, indicating that the molecular phenotype was confined to the chloroplast. A comparative chloroplast stromal proteome analysis of fully developed plants was used to complement the data set. Chloroplast unfoldase ClpB3 was strongly up-regulated in both young and mature leaves, suggesting widespread and persistent protein folding stress. The importance of ClpB3 in the clp2-1 mutant was demonstrated by the observation that a CLPR2 and CLPB3 double mutant was seedling-lethal. The observed up-regulation of chloroplast chaperones and protein sorting components further illustrated destabilization of protein homeostasis. Delayed rRNA processing and up-regulation of a chloroplast DEAD box RNA helicase and polynucleotide phosphorylase, but no significant change in accumulation of ribosomal subunits, suggested a bottleneck in ribosome assembly or RNA metabolism. Strong up-regulation of a chloroplast translational regulator TypA/BipA GTPase suggested a specific response in plastid gene expression to the distorted homeostasis. The stromal proteases PreP1,2 were up-regulated, likely constituting compensation for reduced Clp protease activity and possibly shared substrates between the ClpP and PreP protease systems. The thylakoid photosynthetic apparatus was decreased in the seedlings, whereas several structural thylakoid-associated plastoglobular proteins were strongly up-regulated. Two thylakoid-associated reductases involved in isoprenoid and chlorophyll synthesis were up-regulated reflecting feedback from rate

  2. Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an 18O-Labeled “Universal” Reference Sample

    PubMed Central

    Qian, Wei-Jun; Liu, Tao; Petyuk, Vladislav A.; Gritsenko, Marina A.; Petritis, Brianne O.; Polpitiya, Ashoka D.; Kaushal, Amit; Xiao, Wenzhong; Finnerty, Celeste C.; Jeschke, Marc G.; Jaitly, Navdeep; Monroe, Matthew E.; Moore, Ronald J.; Moldawer, Lyle L.; Davis, Ronald W.; Tompkins, Ronald G.; Herndon, David N.; Camp, David G.; Smith, Richard D.

    2009-01-01

    The quantitative comparison of protein abundances across a large number of biological or patient samples represents an important proteomics challenge that needs to be addressed for proteomics discovery applications. Herein, we describe a strategy that incorporates a stable isotope 18O-labeled ″universal″ reference sample as a comprehensive set of internal standards for analyzing large sample sets quantitatively. As a pooled sample, the 18O-labeled ″universal″ reference sample is spiked into each individually processed unlabeled biological sample and the peptide/protein abundances are quantified based on 16O/18O isotopic peptide pair abundance ratios that compare each unlabeled sample to the identical reference sample. This approach also allows for the direct application of label-free quantitation across the sample set simultaneously along with the labeling-approach (i.e., dual-quantitation) since each biological sample is unlabeled except for the labeled reference sample that is used as internal standards. The effectiveness of this approach for large-scale quantitative proteomics is demonstrated by its application to a set of 18 plasma samples from severe burn patients. When immunoaffinity depletion and cysteinyl-peptide enrichment-based fractionation with high resolution LC-MS measurements were combined, a total of 312 plasma proteins were confidently identified and quantified with a minimum of two unique peptides per protein. The isotope labeling data was directly compared with the label-free 16O-MS intensity data extracted from the same data sets. The results showed that the 18O reference-based labeling approach had significantly better quantitative precision compared to the label-free approach. The relative abundance differences determined by the two approaches also displayed strong correlation, illustrating the complementary nature of the two quantitative methods. The simplicity of including the 18O-reference for accurate quantitation makes this

  3. Improving Large-Scale Testing Capability by Modifying the 40- by 80-ft Wind Tunnel

    NASA Technical Reports Server (NTRS)

    Mort, Kenneth W.; Soderman, Paul T.; Eckert, William T.

    1979-01-01

    Interagency studies conducted during the last several years have indicated the need to Improve full-scale testing capabilities. The studies showed that the most effective trade between test capability and facility cost was provided by re-powering the existing Ames Research Center 40- by 80-ft Wind Tunnel to Increase the maximum speed from about 100 m/s (200 knots) lo about 150 m/s (300 knots) and by adding a new 24- by 37-m (80- by 120-ft) test section powered for about a 50-m/s (100-knot) maximum speed. This paper reviews the design of the facility, a few or its capabilities, and some of its unique features.

  4. Hydrological improvements for nutrient and pollutant emission modeling in large scale catchments

    NASA Astrophysics Data System (ADS)

    Höllering, S.; Ihringer, J.

    2012-04-01

    An estimation of emissions and loads of nutrients and pollutants into European water bodies with as much accuracy as possible depends largely on the knowledge about the spatially and temporally distributed hydrological runoff patterns. An improved hydrological water balance model for the pollutant emission model MoRE (Modeling of Regionalized Emissions) (IWG, 2011) has been introduced, that can form an adequate basis to simulate discharge in a hydrologically differentiated, land-use based way to subsequently provide the required distributed discharge components. First of all the hydrological model had to comply both with requirements of space and time in order to calculate sufficiently precise the water balance on the catchment scale spatially distributed in sub-catchments and with a higher temporal resolution. Aiming to reproduce seasonal dynamics and the characteristic hydrological regimes of river catchments a daily (instead of a yearly) time increment was applied allowing for a more process oriented simulation of discharge dynamics, volume and therefore water balance. The enhancement of the hydrological model became also necessary to potentially account for the hydrological functioning of catchments in regard to scenarios of e.g. a changing climate or alterations of land use. As a deterministic, partly physically based, conceptual hydrological watershed and water balance model the Precipitation Runoff Modeling System (PRMS) (USGS, 2009) was selected to improve the hydrological input for MoRE. In PRMS the spatial discretization is implemented with sub-catchments and so called hydrologic response units (HRUs) which are the hydrotropic, distributed, finite modeling entities each having a homogeneous runoff reaction due to hydro-meteorological events. Spatial structures and heterogeneities in sub-catchments e.g. urbanity, land use and soil types were identified to derive hydrological similarities and classify in different urban and rural HRUs. In this way the

  5. Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

    PubMed Central

    Hoinka, Jan; Berezhnoy, Alexey; Dao, Phuong; Sauna, Zuben E.; Gilboa, Eli; Przytycka, Teresa M.

    2015-01-01

    High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. This emerging technology provides data for a global analysis of the selection process and for simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for their analysis. To close this gap, we developed novel in-silico methods to analyze HT-SELEX data and utilized them to study the emergence of polymerase errors during HT-SELEX. Rather than considering these errors as a nuisance, we demonstrated their utility for guiding aptamer discovery. Our approach builds on two main advancements in aptamer analysis: AptaMut—a novel technique allowing for the identification of polymerase errors conferring an improved binding affinity relative to the ‘parent’ sequence and AptaCluster—an aptamer clustering algorithm which is to our best knowledge, the only currently available tool capable of efficiently clustering entire aptamer pools. We applied these methods to an HT-SELEX experiment developing aptamers against Interleukin 10 receptor alpha chain (IL-10RA) and experimentally confirmed our predictions thus validating our computational methods. PMID:25870409

  6. Social Aspects of Photobooks: Improving Photobook Authoring from Large-Scale Multimedia Analysis

    NASA Astrophysics Data System (ADS)

    Sandhaus, Philipp; Boll, Susanne

    With photo albums we aim to capture personal events such as weddings, vacations, and parties of family and friends. By arranging photo prints, captions and paper souvenirs such as tickets over the pages of a photobook we tell a story to capture and share our memories. The photo memories captured in such a photobook tell us much about the content and the relevance of the photos for the user. The way in which we select photos and arrange them in the photo album reveal a lot about the events, persons and places on the photos: captions describe content, closeness and arrangement of photos express relations between photos and their content and especially about the social relations of the author and the persons present in the album. Nowadays the process of photo album authoring has become digital, photos and texts can be arranged and laid out with the help of authoring tools in a digital photo album which can be printed as a physical photobook. In this chapter we present results of the analysis of a large repository of digitally mastered photobooks to learn about their social aspects. We explore to which degree a social aspect can be identified and how expressive and vivid different classes of photobooks are. The photobooks are anonymized, real world photobooks from customers of our industry partner CeWe Color. The knowledge gained from this social photobook analysis is meant both to better understand how people author their photobooks and to improve the automatic selection of and layout of photobooks.

  7. An improved method to characterise the modulation of small-scale turbulent by large-scale structures

    NASA Astrophysics Data System (ADS)

    Agostini, Lionel; Leschziner, Michael; Gaitonde, Datta

    2015-11-01

    A key aspect of turbulent boundary layer dynamics is ``modulation,'' which refers to degree to which the intensity of coherent large-scale structures (LS) cause an amplification or attenuation of the intensity of the small-scale structures (SS) through large-scale-linkage. In order to identify the variation of the amplitude of the SS motion, the envelope of the fluctuations needs to be determined. Mathis et al. (2009) proposed to define this latter by low-pass filtering the modulus of the analytic signal built from the Hilbert transform of SS. The validity of this definition, as a basis for quantifying the modulated SS signal, is re-examined on the basis of DNS data for a channel flow. The analysis shows that the modulus of the analytic signal is very sensitive to the skewness of its PDF, which is dependent, in turn, on the sign of the LS fluctuation and thus of whether these fluctuations are associated with sweeps or ejections. The conclusion is that generating an envelope by use of a low-pass filtering step leads to an important loss of information associated with the effects of the local skewness of the PDF of the SS on the modulation process. An improved Hilbert-transform-based method is proposed to characterize the modulation of SS turbulence by LS structures

  8. Mutual coupling of hydrologic and hydrodynamic models - a viable approach for improved large-scale inundation estimates?

    NASA Astrophysics Data System (ADS)

    Hoch, Jannis; Winsemius, Hessel; van Beek, Ludovicus; Haag, Arjen; Bierkens, Marc

    2016-04-01

    Due to their increasing occurrence rate and associated economic costs, fluvial floods are large-scale and cross-border phenomena that need to be well understood. Sound information about temporal and spatial variations of flood hazard is essential for adequate flood risk management and climate change adaption measures. While progress has been made in assessments of flood hazard and risk on the global scale, studies to date have made compromises between spatial resolution on the one hand and local detail that influences their temporal characteristics (rate of rise, duration) on the other. Moreover, global models cannot realistically model flood wave propagation due to a lack of detail in channel and floodplain geometry, and the representation of hydrologic processes influencing the surface water balance such as open water evaporation from inundated water and re-infiltration of water in river banks. To overcome these restrictions and to obtain a better understanding of flood propagation including its spatio-temporal variations at the large scale, yet at a sufficiently high resolution, the present study aims to develop a large-scale modeling tool by coupling the global hydrologic model PCR-GLOBWB and the recently developed hydrodynamic model DELFT3D-FM. The first computes surface water volumes which are routed by the latter, solving the full Saint-Venant equations. With DELFT3D FM being capable of representing the model domain as a flexible mesh, model accuracy is only improved at relevant locations (river and adjacent floodplain) and the computation time is not unnecessarily increased. This efficiency is very advantageous for large-scale modelling approaches. The model domain is thereby schematized by 2D floodplains, being derived from global data sets (HydroSHEDS and G3WBM, respectively). Since a previous study with 1way-coupling showed good model performance (J.M. Hoch et al., in prep.), this approach was extended to 2way-coupling to fully represent evaporation

  9. Improved Proteome Coverage by Using High Efficiency Cysteinyl-peptide Enrichment: The Human Mammary Epithelial Cell Proteome

    SciTech Connect

    Liu, Tao; Qian, Weijun; Chen, Wan-Nan U.; Jacobs, Jon M.; Moore, Ronald J.; Anderson, David J.; Gritsenko, Marina A.; Monroe, Matthew E.; Thrall, Brian D.; Camp, David G.; Smith, Richard D.

    2005-04-05

    Automated multidimensional capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been increasingly applied in various large scale proteome profiling efforts. However, comprehensive global proteome analysis remains technically challenging due to issues associated with sample complexity and dynamic range of protein abundances, which is particularly apparent in mammalian biological systems. We report here the application of a high efficiency cysteinyl-peptide enrichment (CPE) approach to the global proteome analysis of human mammary epithelial cells (HMECs) which significantly improved both sequence coverage of protein identifications and the overall proteome coverage. The cysteinyl-peptides were specifically enriched by using a thiol-specific covalent resin, fractionated by strong cation exchange chromatography, and subsequently analyzed by reversed-phase capillary LC-MS/MS. An HMEC tryptic digest without CPE was also fractionated and analyzed under the same conditions for comparison. The combined analyses of HMEC tryptic digests with and without CPE resulted in a total of 14,416 confidently identified peptides covering 4,294 different proteins with an estimated 10% gene coverage of the human geome. By using the high efficiency CPE, an additional 1,096 relatively low abundance proteins were identified, resulting in 34.3% increase in proteome coverage; 1,390 proteomes were observed with increased sequence coverage. Comparative protein distribution analyses revealed that the CPE method is not biased by protein molecular weight, pI, gene location, cellular location, or biological functions. These results demonstrate that the use of the CPE approach provides improved efficiency in comprehensive proteome-wide analyses of highly complex mammalian biological systems.

  10. High-throughput database search and large-scale negative polarity liquid chromatography-tandem mass spectrometry with ultraviolet photodissociation for complex proteomic samples.

    PubMed

    Madsen, James A; Xu, Hua; Robinson, Michelle R; Horton, Andrew P; Shaw, Jared B; Giles, David K; Kaoud, Tamer S; Dalby, Kevin N; Trent, M Stephen; Brodbelt, Jennifer S

    2013-09-01

    The use of ultraviolet photodissociation (UVPD) for the activation and dissociation of peptide anions is evaluated for broader coverage of the proteome. To facilitate interpretation and assignment of the resulting UVPD mass spectra of peptide anions, the MassMatrix database search algorithm was modified to allow automated analysis of negative polarity MS/MS spectra. The new UVPD algorithms were developed based on the MassMatrix database search engine by adding specific fragmentation pathways for UVPD. The new UVPD fragmentation pathways in MassMatrix were rigorously and statistically optimized using two large data sets with high mass accuracy and high mass resolution for both MS(1) and MS(2) data acquired on an Orbitrap mass spectrometer for complex Halobacterium and HeLa proteome samples. Negative mode UVPD led to the identification of 3663 and 2350 peptides for the Halo and HeLa tryptic digests, respectively, corresponding to 655 and 645 peptides that were unique when compared with electron transfer dissociation (ETD), higher energy collision-induced dissociation, and collision-induced dissociation results for the same digests analyzed in the positive mode. In sum, 805 and 619 proteins were identified via UVPD for the Halobacterium and HeLa samples, respectively, with 49 and 50 unique proteins identified in contrast to the more conventional MS/MS methods. The algorithm also features automated charge determination for low mass accuracy data, precursor filtering (including intact charge-reduced peaks), and the ability to combine both positive and negative MS/MS spectra into a single search, and it is freely open to the public. The accuracy and specificity of the MassMatrix UVPD search algorithm was also assessed for low resolution, low mass accuracy data on a linear ion trap. Analysis of a known mixture of three mitogen-activated kinases yielded similar sequence coverage percentages for UVPD of peptide anions versus conventional collision-induced dissociation of

  11. High-throughput Database Search and Large-scale Negative Polarity Liquid Chromatography–Tandem Mass Spectrometry with Ultraviolet Photodissociation for Complex Proteomic Samples*

    PubMed Central

    Madsen, James A.; Xu, Hua; Robinson, Michelle R.; Horton, Andrew P.; Shaw, Jared B.; Giles, David K.; Kaoud, Tamer S.; Dalby, Kevin N.; Trent, M. Stephen; Brodbelt, Jennifer S.

    2013-01-01

    The use of ultraviolet photodissociation (UVPD) for the activation and dissociation of peptide anions is evaluated for broader coverage of the proteome. To facilitate interpretation and assignment of the resulting UVPD mass spectra of peptide anions, the MassMatrix database search algorithm was modified to allow automated analysis of negative polarity MS/MS spectra. The new UVPD algorithms were developed based on the MassMatrix database search engine by adding specific fragmentation pathways for UVPD. The new UVPD fragmentation pathways in MassMatrix were rigorously and statistically optimized using two large data sets with high mass accuracy and high mass resolution for both MS1 and MS2 data acquired on an Orbitrap mass spectrometer for complex Halobacterium and HeLa proteome samples. Negative mode UVPD led to the identification of 3663 and 2350 peptides for the Halo and HeLa tryptic digests, respectively, corresponding to 655 and 645 peptides that were unique when compared with electron transfer dissociation (ETD), higher energy collision-induced dissociation, and collision-induced dissociation results for the same digests analyzed in the positive mode. In sum, 805 and 619 proteins were identified via UVPD for the Halobacterium and HeLa samples, respectively, with 49 and 50 unique proteins identified in contrast to the more conventional MS/MS methods. The algorithm also features automated charge determination for low mass accuracy data, precursor filtering (including intact charge-reduced peaks), and the ability to combine both positive and negative MS/MS spectra into a single search, and it is freely open to the public. The accuracy and specificity of the MassMatrix UVPD search algorithm was also assessed for low resolution, low mass accuracy data on a linear ion trap. Analysis of a known mixture of three mitogen-activated kinases yielded similar sequence coverage percentages for UVPD of peptide anions versus conventional collision-induced dissociation of

  12. Proteomics: a biotechnology tool for crop improvement

    PubMed Central

    Eldakak, Moustafa; Milad, Sanaa I. M.; Nawar, Ali I.; Rohila, Jai S.

    2013-01-01

    A sharp decline in the availability of arable land and sufficient supply of irrigation water along with a continuous steep increase in food demands have exerted a pressure on farmers to produce more with fewer resources. A viable solution to release this pressure is to speed up the plant breeding process by employing biotechnology in breeding programs. The majority of biotechnological applications rely on information generated from various -omic technologies. The latest outstanding improvements in proteomic platforms and many other but related advances in plant biotechnology techniques offer various new ways to encourage the usage of these technologies by plant scientists for crop improvement programs. A combinatorial approach of accelerated gene discovery through genomics, proteomics, and other associated -omic branches of biotechnology, as an applied approach, is proving to be an effective way to speed up the crop improvement programs worldwide. In the near future, swift improvements in -omic databases are becoming critical and demand immediate attention for the effective utilization of these techniques to produce next-generation crops for the progressive farmers. Here, we have reviewed the recent advances in proteomics, as tools of biotechnology, which are offering great promise and leading the path toward crop improvement for sustainable agriculture. PMID:23450788

  13. Proteomics: a biotechnology tool for crop improvement.

    PubMed

    Eldakak, Moustafa; Milad, Sanaa I M; Nawar, Ali I; Rohila, Jai S

    2013-01-01

    A sharp decline in the availability of arable land and sufficient supply of irrigation water along with a continuous steep increase in food demands have exerted a pressure on farmers to produce more with fewer resources. A viable solution to release this pressure is to speed up the plant breeding process by employing biotechnology in breeding programs. The majority of biotechnological applications rely on information generated from various -omic technologies. The latest outstanding improvements in proteomic platforms and many other but related advances in plant biotechnology techniques offer various new ways to encourage the usage of these technologies by plant scientists for crop improvement programs. A combinatorial approach of accelerated gene discovery through genomics, proteomics, and other associated -omic branches of biotechnology, as an applied approach, is proving to be an effective way to speed up the crop improvement programs worldwide. In the near future, swift improvements in -omic databases are becoming critical and demand immediate attention for the effective utilization of these techniques to produce next-generation crops for the progressive farmers. Here, we have reviewed the recent advances in proteomics, as tools of biotechnology, which are offering great promise and leading the path toward crop improvement for sustainable agriculture. PMID:23450788

  14. NAEP Validity Studies: Improving the Information Value of Performance Items in Large Scale Assessments. Working Paper No. 2003-08

    ERIC Educational Resources Information Center

    Pearson, P. David; Garavaglia, Diane R.

    2003-01-01

    The purpose of this essay is to explore both what is known and what needs to be learned about the information value of performance items "when they are used in large scale assessments." Within the context of the National Assessment of Educational Progress (NAEP), there is substantial motivation for answering these questions. Over the…

  15. Improving predictions of large scale soil carbon dynamics: Integration of fine-scale hydrological and biogeochemical processes, scaling, and benchmarking

    NASA Astrophysics Data System (ADS)

    Riley, W. J.; Dwivedi, D.; Ghimire, B.; Hoffman, F. M.; Pau, G. S. H.; Randerson, J. T.; Shen, C.; Tang, J.; Zhu, Q.

    2015-12-01

    Numerical model representations of decadal- to centennial-scale soil-carbon dynamics are a dominant cause of uncertainty in climate change predictions. Recent attempts by some Earth System Model (ESM) teams to integrate previously unrepresented soil processes (e.g., explicit microbial processes, abiotic interactions with mineral surfaces, vertical transport), poor performance of many ESM land models against large-scale and experimental manipulation observations, and complexities associated with spatial heterogeneity highlight the nascent nature of our community's ability to accurately predict future soil carbon dynamics. I will present recent work from our group to develop a modeling framework to integrate pore-, column-, watershed-, and global-scale soil process representations into an ESM (ACME), and apply the International Land Model Benchmarking (ILAMB) package for evaluation. At the column scale and across a wide range of sites, observed depth-resolved carbon stocks and their 14C derived turnover times can be explained by a model with explicit representation of two microbial populations, a simple representation of mineralogy, and vertical transport. Integrating soil and plant dynamics requires a 'process-scaling' approach, since all aspects of the multi-nutrient system cannot be explicitly resolved at ESM scales. I will show that one approach, the Equilibrium Chemistry Approximation, improves predictions of forest nitrogen and phosphorus experimental manipulations and leads to very different global soil carbon predictions. Translating model representations from the site- to ESM-scale requires a spatial scaling approach that either explicitly resolves the relevant processes, or more practically, accounts for fine-resolution dynamics at coarser scales. To that end, I will present recent watershed-scale modeling work that applies reduced order model methods to accurately scale fine-resolution soil carbon dynamics to coarse-resolution simulations. Finally, we

  16. Leveraging Genomics Software to Improve Proteomics Results

    SciTech Connect

    Fodor, I K; Nelson, D O

    2005-09-06

    Rigorous data analysis techniques are essential in quantifying the differential expression of proteins in biological samples of interest. Statistical methods from the microarray literature were applied to the analysis of two-dimensional difference gel electrophoresis (2-D DIGE) proteomics experiments, in the context of technical variability studies involving human plasma. Protein expression measurements were corrected to account for observed intensity-dependent biases within gels, and normalized to mitigate observed gel to gel variations. The methods improved upon the results achieved using the best currently available 2-D DIGE proteomics software. The spot-wise protein variance was reduced by 10% and the number of apparently differentially expressed proteins was reduced by over 50%.

  17. Toward system-level understanding of baculovirus–host cell interactions: from molecular fundamental studies to large-scale proteomics approaches

    PubMed Central

    Monteiro, Francisca; Carinhas, Nuno; Carrondo, Manuel J. T.; Bernal, Vicente; Alves, Paula M.

    2012-01-01

    Baculoviruses are insect viruses extensively exploited as eukaryotic protein expression vectors. Molecular biology studies have provided exciting discoveries on virus–host interactions, but the application of omic high-throughput techniques on the baculovirus–insect cell system has been hampered by the lack of host genome sequencing. While a broader, systems-level analysis of biological responses to infection is urgently needed, recent advances on proteomic studies have yielded new insights on the impact of infection on the host cell. These works are reviewed and critically assessed in the light of current biological knowledge of the molecular biology of baculoviruses and insect cells. PMID:23162544

  18. Large scale tracking algorithms.

    SciTech Connect

    Hansen, Ross L.; Love, Joshua Alan; Melgaard, David Kennett; Karelitz, David B.; Pitts, Todd Alan; Zollweg, Joshua David; Anderson, Dylan Z.; Nandy, Prabal; Whitlow, Gary L.; Bender, Daniel A.; Byrne, Raymond Harry

    2015-01-01

    Low signal-to-noise data processing algorithms for improved detection, tracking, discrimination and situational threat assessment are a key research challenge. As sensor technologies progress, the number of pixels will increase signi cantly. This will result in increased resolution, which could improve object discrimination, but unfortunately, will also result in a significant increase in the number of potential targets to track. Many tracking techniques, like multi-hypothesis trackers, suffer from a combinatorial explosion as the number of potential targets increase. As the resolution increases, the phenomenology applied towards detection algorithms also changes. For low resolution sensors, "blob" tracking is the norm. For higher resolution data, additional information may be employed in the detection and classfication steps. The most challenging scenarios are those where the targets cannot be fully resolved, yet must be tracked and distinguished for neighboring closely spaced objects. Tracking vehicles in an urban environment is an example of such a challenging scenario. This report evaluates several potential tracking algorithms for large-scale tracking in an urban environment.

  19. Large scale dynamic systems

    NASA Technical Reports Server (NTRS)

    Doolin, B. F.

    1975-01-01

    Classes of large scale dynamic systems were discussed in the context of modern control theory. Specific examples discussed were in the technical fields of aeronautics, water resources and electric power.

  20. Large-scale proteome analysis of abscisic acid and ABSCISIC ACID INSENSITIVE3-dependent proteins related to desiccation tolerance in Physcomitrella patens.

    PubMed

    Yotsui, Izumi; Serada, Satoshi; Naka, Tetsuji; Saruhashi, Masashi; Taji, Teruaki; Hayashi, Takahisa; Quatrano, Ralph S; Sakata, Yoichi

    2016-03-18

    Desiccation tolerance is an ancestral feature of land plants and is still retained in non-vascular plants such as bryophytes and some vascular plants. However, except for seeds and spores, this trait is absent in vegetative tissues of vascular plants. Although many studies have focused on understanding the molecular basis underlying desiccation tolerance using transcriptome and proteome approaches, the critical molecular differences between desiccation tolerant plants and non-desiccation plants are still not clear. The moss Physcomitrella patens cannot survive rapid desiccation under laboratory conditions, but if cells of the protonemata are treated by the phytohormone abscisic acid (ABA) prior to desiccation, it can survive 24 h exposure to desiccation and regrow after rehydration. The desiccation tolerance induced by ABA (AiDT) is specific to this hormone, but also depends on a plant transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3). Here we report the comparative proteomic analysis of AiDT between wild type and ABI3 deleted mutant (Δabi3) of P. patens using iTRAQ (Isobaric Tags for Relative and Absolute Quantification). From a total of 1980 unique proteins that we identified, only 16 proteins are significantly altered in Δabi3 compared to wild type after desiccation following ABA treatment. Among this group, three of the four proteins that were severely affected in Δabi3 tissue were Arabidopsis orthologous genes, which were expressed in maturing seeds under the regulation of ABI3. These included a Group 1 late embryogenesis abundant (LEA) protein, a short-chain dehydrogenase, and a desiccation-related protein. Our results suggest that at least three of these proteins expressed in desiccation tolerant cells of both Arabidopsis and the moss are very likely to play important roles in acquisition of desiccation tolerance in land plants. Furthermore, our results suggest that the regulatory machinery of ABA- and ABI3-mediated gene expression for desiccation

  1. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome.

    PubMed

    Peng, Junmin; Elias, Joshua E; Thoreen, Carson C; Licklider, Larry J; Gygi, Steven P

    2003-01-01

    Highly complex protein mixtures can be directly analyzed after proteolysis by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). In this paper, we have utilized the combination of strong cation exchange (SCX) and reversed-phase (RP) chromatography to achieve two-dimensional separation prior to MS/MS. One milligram of whole yeast protein was proteolyzed and separated by SCX chromatography (2.1 mm i.d.) with fraction collection every minute during an 80-min elution. Eighty fractions were reduced in volume and then re-injected via an autosampler in an automated fashion using a vented-column (100 microm i.d.) approach for RP-LC-MS/MS analysis. More than 162,000 MS/MS spectra were collected with 26,815 matched to yeast peptides (7,537 unique peptides). A total of 1,504 yeast proteins were unambiguously identified in this single analysis. We present a comparison of this experiment with a previously published yeast proteome analysis by Yates and colleagues (Washburn, M. P.; Wolters, D.; Yates, J. R., III. Nat. Biotechnol. 2001, 19, 242-7). In addition, we report an in-depth analysis of the false-positive rates associated with peptide identification using the Sequest algorithm and a reversed yeast protein database. New criteria are proposed to decrease false-positives to less than 1% and to greatly reduce the need for manual interpretation while permitting more proteins to be identified. PMID:12643542

  2. Atomistic Origin of Brittle Failure of Boron Carbide from Large-Scale Reactive Dynamics Simulations: Suggestions toward Improved Ductility

    NASA Astrophysics Data System (ADS)

    An, Qi; Goddard, William A.

    2015-09-01

    Ceramics are strong, but their low fracture toughness prevents extended engineering applications. In particular, boron carbide (B4C ), the third hardest material in nature, has not been incorporated into many commercial applications because it exhibits anomalous failure when subjected to hypervelocity impact. To determine the atomistic origin of this brittle failure, we performed large-scale (˜200 000 atoms /cell ) reactive-molecular-dynamics simulations of shear deformations of B4C , using the quantum-mechanics-derived reactive force field simulation. We examined the (0001 )/⟨10 1 ¯ 0 ⟩ slip system related to deformation twinning and the (01 1 ¯ 1 ¯ )/⟨1 ¯ 101 ⟩ slip system related to amorphous band formation. We find that brittle failure in B4C arises from formation of higher density amorphous bands due to fracture of the icosahedra, a unique feature of these boron based materials. This leads to negative pressure and cavitation resulting in crack opening. Thus, to design ductile materials based on B4C we propose alloying aimed at promoting shear relaxation through intericosahedral slip that avoids icosahedral fracture.

  3. Large-scale preparation of shape controlled SnO and improved capacitance for supercapacitors: from nanoclusters to square microplates

    NASA Astrophysics Data System (ADS)

    Wang, Lu; Ji, Hongmei; Zhu, Feng; Chen, Zhi; Yang, Yang; Jiang, Xuefan; Pinto, João; Yang, Gang

    2013-07-01

    Here, we first provide a facile ultrasonic-assisted synthesis of SnO using SnCl2 and the organic solvent of ethanolamine (ETA). The moderate alkalinity of ETA and ultrasound play very important roles in the synthesis of SnO. After the hydrolysis of the intermediate of ETA-Sn(ii), the as-synthesized SnO nanoclusters undergo assembly, amalgamation, and preferential growth to microplates in hydrothermal treatment. The as-synthesized SnO was characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), ultraviolet-visible absorption spectroscopy (UV-vis) and X-ray diffraction (XRD). To explore its potential applications in energy storage, SnO was fabricated into a supercapacitor electrode and characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and galvanostatic charge-discharge measurements. The as-synthesized SnO exhibits remarkable pseudocapacitive activity including high specific capacitance (208.9 F g-1 at 0.1 A g-1), good rate capability (65.8 F g-1 at 40 A g-1), and excellent cycling stability (retention 119.3% after 10 000 cycles) for application in supercapacitors. The capacitive behavior of SnO with various crystal morphologies was observed by fitted EIS using an equivalent circuit. The novel synthetic route for SnO is a convenient and potential way to large-scale production of microplates which is expected to be applicable in the synthesis of other metal oxide nanoparticles.Here, we first provide a facile ultrasonic-assisted synthesis of SnO using SnCl2 and the organic solvent of ethanolamine (ETA). The moderate alkalinity of ETA and ultrasound play very important roles in the synthesis of SnO. After the hydrolysis of the intermediate of ETA-Sn(ii), the as-synthesized SnO nanoclusters undergo assembly, amalgamation, and preferential growth to microplates in hydrothermal treatment. The as-synthesized SnO was characterized by scanning

  4. Large-scale preparation of shape controlled SnO and improved capacitance for supercapacitors: from nanoclusters to square microplates.

    PubMed

    Wang, Lu; Ji, Hongmei; Zhu, Feng; Chen, Zhi; Yang, Yang; Jiang, Xuefan; Pinto, João; Yang, Gang

    2013-08-21

    Here, we first provide a facile ultrasonic-assisted synthesis of SnO using SnCl2 and the organic solvent of ethanolamine (ETA). The moderate alkalinity of ETA and ultrasound play very important roles in the synthesis of SnO. After the hydrolysis of the intermediate of ETA-Sn(II), the as-synthesized SnO nanoclusters undergo assembly, amalgamation, and preferential growth to microplates in hydrothermal treatment. The as-synthesized SnO was characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), ultraviolet-visible absorption spectroscopy (UV-vis) and X-ray diffraction (XRD). To explore its potential applications in energy storage, SnO was fabricated into a supercapacitor electrode and characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and galvanostatic charge-discharge measurements. The as-synthesized SnO exhibits remarkable pseudocapacitive activity including high specific capacitance (208.9 F g(-1) at 0.1 A g(-1)), good rate capability (65.8 F g(-1) at 40 A g(-1)), and excellent cycling stability (retention 119.3% after 10,000 cycles) for application in supercapacitors. The capacitive behavior of SnO with various crystal morphologies was observed by fitted EIS using an equivalent circuit. The novel synthetic route for SnO is a convenient and potential way to large-scale production of microplates which is expected to be applicable in the synthesis of other metal oxide nanoparticles. PMID:23842544

  5. Improving Large-scale Biomass Burning Carbon Consumption and Emissions Estimates in the Former Soviet Union based on Fire Weather

    NASA Astrophysics Data System (ADS)

    Westberg, D. J.; Soja, A. J.; Tchebakova, N.; Parfenova, E. I.; Kukavskaya, E.; de Groot, B.; McRae, D.; Conard, S. G.; Stackhouse, P. W., Jr.

    2012-12-01

    Estimating the amount of biomass burned during fire events is challenging, particularly in remote and diverse regions, like those of the Former Soviet Union (FSU). Historically, we have typically assumed 25 tons of carbon per hectare (tC/ha) is emitted, however depending on the ecosystem and severity, biomass burning emissions can range from 2 to 75 tC/ha. Ecosystems in the FSU span from the tundra through the taiga to the forest-steppe, steppe and desserts and include the extensive West Siberian lowlands, permafrost-lain forests and agricultural lands. Excluding this landscape disparity results in inaccurate emissions estimates and incorrect assumptions in the transport of these emissions. In this work, we present emissions based on a hybrid ecosystem map and explicit estimates of fuel that consider the depth of burning based on the Canadian Forest Fire Weather Index System. Specifically, the ecosystem map is a fusion of satellite-based data, a detailed ecosystem map and Alexeyev and Birdsey carbon storage data, which is used to build carbon databases that include the forest overstory and understory, litter, peatlands and soil organic material for the FSU. We provide a range of potential carbon consumption estimates for low- to high-severity fires across the FSU that can be used with fire weather indices to more accurately estimate fire emissions. These data can be incorporated at ecoregion and administrative territory scales and are optimized for use in large-scale Chemical Transport Models. Additionally, paired with future climate scenarios and ecoregion cover, these carbon consumption data can be used to estimate potential emissions.

  6. Large Scale Computing

    NASA Astrophysics Data System (ADS)

    Capiluppi, Paolo

    2005-04-01

    Large Scale Computing is acquiring an important role in the field of data analysis and treatment for many Sciences and also for some Social activities. The present paper discusses the characteristics of Computing when it becomes "Large Scale" and the current state of the art for some particular application needing such a large distributed resources and organization. High Energy Particle Physics (HEP) Experiments are discussed in this respect; in particular the Large Hadron Collider (LHC) Experiments are analyzed. The Computing Models of LHC Experiments represent the current prototype implementation of Large Scale Computing and describe the level of maturity of the possible deployment solutions. Some of the most recent results on the measurements of the performances and functionalities of the LHC Experiments' testing are discussed.

  7. Large-Scale Disasters

    NASA Astrophysics Data System (ADS)

    Gad-El-Hak, Mohamed

    "Extreme" events - including climatic events, such as hurricanes, tornadoes, and drought - can cause massive disruption to society, including large death tolls and property damage in the billions of dollars. Events in recent years have shown the importance of being prepared and that countries need to work together to help alleviate the resulting pain and suffering. This volume presents a review of the broad research field of large-scale disasters. It establishes a common framework for predicting, controlling and managing both manmade and natural disasters. There is a particular focus on events caused by weather and climate change. Other topics include air pollution, tsunamis, disaster modeling, the use of remote sensing and the logistics of disaster management. It will appeal to scientists, engineers, first responders and health-care professionals, in addition to graduate students and researchers who have an interest in the prediction, prevention or mitigation of large-scale disasters.

  8. 30 Days Wild: Development and Evaluation of a Large-Scale Nature Engagement Campaign to Improve Well-Being

    PubMed Central

    Richardson, Miles; Cormack, Adam; McRobert, Lucy; Underhill, Ralph

    2016-01-01

    There is a need to increase people’s engagement with and connection to nature, both for human well-being and the conservation of nature itself. In order to suggest ways for people to engage with nature and create a wider social context to normalise nature engagement, The Wildlife Trusts developed a mass engagement campaign, 30 Days Wild. The campaign asked people to engage with nature every day for a month. 12,400 people signed up for 30 Days Wild via an online sign-up with an estimated 18,500 taking part overall, resulting in an estimated 300,000 engagements with nature by participants. Samples of those taking part were found to have sustained increases in happiness, health, connection to nature and pro-nature behaviours. With the improvement in health being predicted by the improvement in happiness, this relationship was mediated by the change in connection to nature. PMID:26890891

  9. Improved large-scale hydrological modelling through the assimilation of streamflow and downscaled satellite soil moisture observations

    NASA Astrophysics Data System (ADS)

    López López, Patricia; Wanders, Niko; Schellekens, Jaap; Renzullo, Luigi J.; Sutanudjaja, Edwin H.; Bierkens, Marc F. P.

    2016-07-01

    The coarse spatial resolution of global hydrological models (typically >  0.25°) limits their ability to resolve key water balance processes for many river basins and thus compromises their suitability for water resources management, especially when compared to locally tuned river models. A possible solution to the problem may be to drive the coarse-resolution models with locally available high-spatial-resolution meteorological data as well as to assimilate ground-based and remotely sensed observations of key water cycle variables. While this would improve the resolution of the global model, the impact of prediction accuracy remains largely an open question. In this study, we investigate the impact of assimilating streamflow and satellite soil moisture observations on the accuracy of global hydrological model estimations, when driven by either coarse- or high-resolution meteorological observations in the Murrumbidgee River basin in Australia. To this end, a 0.08° resolution version of the PCR-GLOBWB global hydrological model is forced with downscaled global meteorological data (downscaled from 0.5° to 0.08° resolution) obtained from the WATCH Forcing Data methodology applied to ERA-Interim (WFDEI) and a local high-resolution, gauging-station-based gridded data set (0.05°). Downscaled satellite-derived soil moisture (downscaled from ˜  0.5° to 0.08° resolution) from the remote observation system AMSR-E and streamflow observations collected from 23 gauging stations are assimilated using an ensemble Kalman filter. Several scenarios are analysed to explore the added value of data assimilation considering both local and global meteorological data. Results show that the assimilation of soil moisture observations results in the largest improvement of the model estimates of streamflow. The joint assimilation of both streamflow and downscaled soil moisture observations leads to further improvement in streamflow simulations (20 % reduction in RMSE

  10. Improved large-scale hydrological modelling through the assimilation of streamflow and downscaled satellite soil moisture observations

    NASA Astrophysics Data System (ADS)

    Lopez Lopez, P.; Wanders, N.; Schellekens, J.; Renzullo, L. J.; Sutanudjaja, E. H.; Bierkens, M. F. P.

    2015-10-01

    The coarse spatial resolution of global hydrological models (typically > 0.25°) limits their ability to resolve key water balance processes for many river basins and thus compromises their suitability for water resources management, especially when compared to locally-tuned river models. A possible solution to the problem may be to drive the coarse resolution models with locally available high spatial resolution meteorological data as well as to assimilate ground-based and remotely-sensed observations of key water cycle variables. While this would improve the resolution of the global model, the impact of prediction accuracy remains largely an open question. In this study we investigate the impact of assimilating streamflow and satellite soil moisture observations on the accuracy of global hydrological model estimations, when driven by either coarse- or high-resolution meteorological observations in the Murrumbidgee river basin in Australia. To this end, a 0.08° resolution version of the PCR-GLOBWB global hydrological model is forced with downscaled global meteorological data (from 0.5° downscaled to 0.08° resolution) obtained from the WATCH Forcing Data methodology applied to ERA-Interim (WFDEI) and a local high resolution gauging station based gridded dataset (0.05°). Downscaled satellite derived soil moisture (from approx. 0.5° downscaled to 0.08° resolution) from AMSR-E and streamflow observations collected from 23 gauging stations are assimilated using an ensemble Kalman filter. Several scenarios are analysed to explore the added value of data assimilation considering both local and global meteorological data. Results show that the assimilation of soil moisture observations results in the largest improvement of the model estimates of streamflow. The joint assimilation of both streamflow and downscaled soil moisture observations leads to further improvement in streamflow simulations (20 % reduction in RMSE). Furthermore, results show that the added

  11. Improved large-scale hydrological modelling through the assimilation of streamflow and downscaled satellite soil moisture observations.

    NASA Astrophysics Data System (ADS)

    López López, Patricia; Wanders, Niko; Sutanudjaja, Edwin; Renzullo, Luigi; Sterk, Geert; Schellekens, Jaap; Bierkens, Marc

    2015-04-01

    The coarse spatial resolution of global hydrological models (typically > 0.25o) often limits their ability to resolve key water balance processes for many river basins and thus compromises their suitability for water resources management, especially when compared to locally-tunes river models. A possible solution to the problem may be to drive the coarse resolution models with high-resolution meteorological data as well as to assimilate ground-based and remotely-sensed observations of key water cycle variables. While this would improve the modelling resolution of the global model, the impact of prediction accuracy remains largely an open question. In this study we investigated the impact that assimilating streamflow and satellite soil moisture observations have on global hydrological model estimation, driven by coarse- and high-resolution meteorological observations, for the Murrumbidgee river basin in Australia. The PCR-GLOBWB global hydrological model is forced with downscaled global climatological data (from 0.5o downscaled to 0.1o resolution) obtained from the WATCH Forcing Data (WFDEI) and local high resolution gauging station based gridded datasets (0.05o), sourced from the Australian Bureau of Meteorology. Downscaled satellite derived soil moisture (from 0.5o downscaled to 0.1o resolution) from AMSR-E and streamflow observations collected from 25 gauging stations are assimilated using an ensemble Kalman filter. Several scenarios are analysed to explore the added value of data assimilation considering both local and global climatological data. Results show that the assimilation of streamflow observations result in the largest improvement of the model estimates. The joint assimilation of both streamflow and downscaled soil moisture observations leads to further improved in streamflow simulations (10% reduction in RMSE), mainly in the headwater catchments (up to 10,000 km2). Results also show that the added contribution of data assimilation, for both soil

  12. Improved Redirection with Distractors: A Large-Scale-Real-Walking Locomotion Interface and its Effect on Navigation in Virtual Environments

    PubMed Central

    Peck, Tabitha C.; Fuchs, Henry; Whitton, Mary C.

    2014-01-01

    Users in virtual environments often find navigation more difficult than in the real world. Our new locomotion interface, Improved Redirection with Distractors (IRD), enables users to walk in larger-than-tracked space VEs without predefined waypoints. We compared IRD to the current best interface, really walking, by conducting a user study measuring navigational ability. Our results show that IRD users can really walk through VEs that are larger than the tracked space and can point to targets and complete maps of VEs no worse than when really walking. PMID:25429369

  13. An approach to improve kernel-based Protein-Protein Interaction extraction by learning from large-scale network data.

    PubMed

    Li, Lishuang; Guo, Rui; Jiang, Zhenchao; Huang, Degen

    2015-07-15

    Protein-Protein Interaction extraction (PPIe) from biomedical literatures is an important task in biomedical text mining and has achieved desirable results on the annotated datasets. However, the traditional machine learning methods on PPIe suffer badly from vocabulary gap and data sparseness, which weakens classification performance. In this work, an approach capturing external information from the web-based data is introduced to address these problems and boost the existing methods. The approach involves three kinds of word representation techniques: distributed representation, vector clustering and Brown clusters. Experimental results show that our method outperforms the state-of-the-art methods on five publicly available corpora. Our code and data are available at: http://chaoslog.com/improving-kernel-based-protein-protein-interaction-extraction-by-unsupervised-word-representation-codes-and-data.html. PMID:25864936

  14. Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments.

    PubMed

    Sastry, Madhavi; Lowrie, Jeffrey F; Dixon, Steven L; Sherman, Woody

    2010-05-24

    A systematic virtual screening study on 11 pharmaceutically relevant targets has been conducted to investigate the interrelation between 8 two-dimensional (2D) fingerprinting methods, 13 atom-typing schemes, 13 bit scaling rules, and 12 similarity metrics using the new cheminformatics package Canvas. In total, 157 872 virtual screens were performed to assess the ability of each combination of parameters to identify actives in a database screen. In general, fingerprint methods, such as MOLPRINT2D, Radial, and Dendritic that encode information about local environment beyond simple linear paths outperformed other fingerprint methods. Atom-typing schemes with more specific information, such as Daylight, Mol2, and Carhart were generally superior to more generic atom-typing schemes. Enrichment factors across all targets were improved considerably with the best settings, although no single set of parameters performed optimally on all targets. The size of the addressable bit space for the fingerprints was also explored, and it was found to have a substantial impact on enrichments. Small bit spaces, such as 1024, resulted in many collisions and in a significant degradation in enrichments compared to larger bit spaces that avoid collisions. PMID:20450209

  15. Large-scale Manufacturing of Nanoparticulate-based Lubrication Additives for Improved Energy Efficiency and Reduced Emissions

    SciTech Connect

    Erdemir, Ali

    2013-09-26

    This project was funded under the Department of Energy (DOE) Lab Call on Nanomanufacturing for Energy Efficiency and was directed toward the development of novel boron-based nanocolloidal lubrication additives for improving the friction and wear performance of machine components in a wide range of industrial and transportation applications. Argonne's research team concentrated on the scientific and technical aspects of the project, using a range of state-of-the art analytical and tribological test facilities. Argonne has extensive past experience and expertise in working with boron-based solid and liquid lubrication additives, and has intellectual property ownership of several. There were two industrial collaborators in this project: Ashland Oil (represented by its Valvoline subsidiary) and Primet Precision Materials, Inc. (a leading nanomaterials company). There was also a sub-contract with the University of Arkansas. The major objectives of the project were to develop novel boron-based nanocolloidal lubrication additives and to optimize and verify their performance under boundary-lubricated sliding conditions. The project also tackled problems related to colloidal dispersion, larger-scale manufacturing and blending of nano-additives with base carrier oils. Other important issues dealt with in the project were determination of the optimum size and concentration of the particles and compatibility with various base fluids and/or additives. Boron-based particulate additives considered in this project included boric acid (H{sub 3}BO{sub 3}), hexagonal boron nitride (h-BN), boron oxide, and borax. As part of this project, we also explored a hybrid MoS{sub 2} + boric acid formulation approach for more effective lubrication and reported the results. The major motivation behind this work was to reduce energy losses related to friction and wear in a wide spectrum of mechanical systems and thereby reduce our dependence on imported oil. Growing concern over greenhouse gas

  16. Improved Large-Scale Inundation Modelling by 1D-2D Coupling and Consideration of Hydrologic and Hydrodynamic Processes - a Case Study in the Amazon

    NASA Astrophysics Data System (ADS)

    Hoch, J. M.; Bierkens, M. F.; Van Beek, R.; Winsemius, H.; Haag, A.

    2015-12-01

    Understanding the dynamics of fluvial floods is paramount to accurate flood hazard and risk modeling. Currently, economic losses due to flooding constitute about one third of all damage resulting from natural hazards. Given future projections of climate change, the anticipated increase in the World's population and the associated implications, sound knowledge of flood hazard and related risk is crucial. Fluvial floods are cross-border phenomena that need to be addressed accordingly. Yet, only few studies model floods at the large-scale which is preferable to tiling the output of small-scale models. Most models cannot realistically model flood wave propagation due to a lack of either detailed channel and floodplain geometry or the absence of hydrologic processes. This study aims to develop a large-scale modeling tool that accounts for both hydrologic and hydrodynamic processes, to find and understand possible sources of errors and improvements and to assess how the added hydrodynamics affect flood wave propagation. Flood wave propagation is simulated by DELFT3D-FM (FM), a hydrodynamic model using a flexible mesh to schematize the study area. It is coupled to PCR-GLOBWB (PCR), a macro-scale hydrological model, that has its own simpler 1D routing scheme (DynRout) which has already been used for global inundation modeling and flood risk assessments (GLOFRIS; Winsemius et al., 2013). A number of model set-ups are compared and benchmarked for the simulation period 1986-1996: (0) PCR with DynRout; (1) using a FM 2D flexible mesh forced with PCR output and (2) as in (1) but discriminating between 1D channels and 2D floodplains, and, for comparison, (3) and (4) the same set-ups as (1) and (2) but forced with observed GRDC discharge values. Outputs are subsequently validated against observed GRDC data at Óbidos and flood extent maps from the Dartmouth Flood Observatory. The present research constitutes a first step into a globally applicable approach to fully couple

  17. Improved L-BFGS diagonal preconditioners for a large-scale 4D-Var inversion system: application to CO2 flux constraints and analysis error calculation

    NASA Astrophysics Data System (ADS)

    Bousserez, Nicolas; Henze, Daven; Bowman, Kevin; Liu, Junjie; Jones, Dylan; Keller, Martin; Deng, Feng

    2013-04-01

    This work presents improved analysis error estimates for 4D-Var systems. From operational NWP models to top-down constraints on trace gas emissions, many of today's data assimilation and inversion systems in atmospheric science rely on variational approaches. This success is due to both the mathematical clarity of these formulations and the availability of computationally efficient minimization algorithms. However, unlike Kalman Filter-based algorithms, these methods do not provide an estimate of the analysis or forecast error covariance matrices, these error statistics being propagated only implicitly by the system. From both a practical (cycling assimilation) and scientific perspective, assessing uncertainties in the solution of the variational problem is critical. For large-scale linear systems, deterministic or randomization approaches can be considered based on the equivalence between the inverse Hessian of the cost function and the covariance matrix of analysis error. For perfectly quadratic systems, like incremental 4D-Var, Lanczos/Conjugate-Gradient algorithms have proven to be most efficient in generating low-rank approximations of the Hessian matrix during the minimization. For weakly non-linear systems though, the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS), a quasi-Newton descent algorithm, is usually considered the best method for the minimization. Suitable for large-scale optimization, this method allows one to generate an approximation to the inverse Hessian using the latest m vector/gradient pairs generated during the minimization, m depending upon the available core memory. At each iteration, an initial low-rank approximation to the inverse Hessian has to be provided, which is called preconditioning. The ability of the preconditioner to retain useful information from previous iterations largely determines the efficiency of the algorithm. Here we assess the performance of different preconditioners to estimate the inverse Hessian of a

  18. Conformational and Thermal Stability Improvements for the Large-Scale Production of Yeast-Derived Rabbit Hemorrhagic Disease Virus-Like Particles as Multipurpose Vaccine

    PubMed Central

    Méndez, Lídice; González, Nemecio; Parra, Francisco; Martín-Alonso, José M.; Limonta, Miladys; Sánchez, Kosara; Cabrales, Ania; Estrada, Mario P.; Rodríguez-Mallón, Alina; Farnós, Omar

    2013-01-01

    Recombinant virus-like particles (VLP) antigenically similar to rabbit hemorrhagic disease virus (RHDV) were recently expressed at high levels inside Pichia pastoris cells. Based on the potential of RHDV VLP as platform for diverse vaccination purposes we undertook the design, development and scale-up of a production process. Conformational and stability issues were addressed to improve process control and optimization. Analyses on the structure, morphology and antigenicity of these multimers were carried out at different pH values during cell disruption and purification by size-exclusion chromatography. Process steps and environmental stresses in which aggregation or conformational instability can be detected were included. These analyses revealed higher stability and recoveries of properly assembled high-purity capsids at acidic and neutral pH in phosphate buffer. The use of stabilizers during long-term storage in solution showed that sucrose, sorbitol, trehalose and glycerol acted as useful aggregation-reducing agents. The VLP emulsified in an oil-based adjuvant were subjected to accelerated thermal stress treatments. None to slight variations were detected in the stability of formulations and in the structure of recovered capsids. A comprehensive analysis on scale-up strategies was accomplished and a nine steps large-scale production process was established. VLP produced after chromatographic separation protected rabbits against a lethal challenge. The minimum protective dose was identified. Stabilized particles were ultimately assayed as carriers of a foreign viral epitope from another pathogen affecting a larger animal species. For that purpose, a linear protective B-cell epitope from Classical Swine Fever Virus (CSFV) E2 envelope protein was chemically coupled to RHDV VLP. Conjugates were able to present the E2 peptide fragment for immune recognition and significantly enhanced the peptide-specific antibody response in vaccinated pigs. Overall these results

  19. Large-scale combining signals from both biomedical literature and the FDA Adverse Event Reporting System (FAERS) to improve post-marketing drug safety signal detection

    PubMed Central

    2014-01-01

    Background Independent data sources can be used to augment post-marketing drug safety signal detection. The vast amount of publicly available biomedical literature contains rich side effect information for drugs at all clinical stages. In this study, we present a large-scale signal boosting approach that combines over 4 million records in the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) and over 21 million biomedical articles. Results The datasets are comprised of 4,285,097 records from FAERS and 21,354,075 MEDLINE articles. We first extracted all drug-side effect (SE) pairs from FAERS. Our study implemented a total of seven signal ranking algorithms. We then compared these different ranking algorithms before and after they were boosted with signals from MEDLINE sentences or abstracts. Finally, we manually curated all drug-cardiovascular (CV) pairs that appeared in both data sources and investigated whether our approach can detect many true signals that have not been included in FDA drug labels. We extracted a total of 2,787,797 drug-SE pairs from FAERS with a low initial precision of 0.025. The ranking algorithm combined signals from both FAERS and MEDLINE, significantly improving the precision from 0.025 to 0.371 for top-ranked pairs, representing a 13.8 fold elevation in precision. We showed by manual curation that drug-SE pairs that appeared in both data sources were highly enriched with true signals, many of which have not yet been included in FDA drug labels. Conclusions We have developed an efficient and effective drug safety signal ranking and strengthening approach We demonstrate that large-scale combining information from FAERS and biomedical literature can significantly contribute to drug safety surveillance. PMID:24428898

  20. Large scale traffic simulations

    SciTech Connect

    Nagel, K.; Barrett, C.L.; Rickert, M.

    1997-04-01

    Large scale microscopic (i.e. vehicle-based) traffic simulations pose high demands on computational speed in at least two application areas: (i) real-time traffic forecasting, and (ii) long-term planning applications (where repeated {open_quotes}looping{close_quotes} between the microsimulation and the simulated planning of individual person`s behavior is necessary). As a rough number, a real-time simulation of an area such as Los Angeles (ca. 1 million travellers) will need a computational speed of much higher than 1 million {open_quotes}particle{close_quotes} (= vehicle) updates per second. This paper reviews how this problem is approached in different projects and how these approaches are dependent both on the specific questions and on the prospective user community. The approaches reach from highly parallel and vectorizable, single-bit implementations on parallel supercomputers for Statistical Physics questions, via more realistic implementations on coupled workstations, to more complicated driving dynamics implemented again on parallel supercomputers. 45 refs., 9 figs., 1 tab.

  1. Evaluating a Large-Scale Community-Based Intervention to Improve Pregnancy and Newborn Health Among the Rural Poor in India.

    PubMed

    Acharya, Arnab; Lalwani, Tanya; Dutta, Rahul; Rajaratnam, Julie Knoll; Ruducha, Jenny; Varkey, Leila Caleb; Wunnava, Sita; Menezes, Lysander; Taylor, Catharine; Bernson, Jeff

    2015-01-01

    Objectives. We evaluated the effectiveness of the Sure Start project, which was implemented in 7 districts of Uttar Pradesh, India, to improve maternal and newborn health. Methods. Interventions were implemented at 2 randomly assigned levels of intensity. Forty percent of the areas received a more intense intervention, including community-level meetings with expectant mothers. A baseline survey consisted of 12 000 women who completed pregnancy in 2007; a follow-up survey was conducted for women in 2010 in the same villages. Our quantitative analyses provide an account of the project's impact. Results. We observed significant health improvements in both intervention areas over time; in the more intensive intervention areas, we found greater improvements in care-seeking and healthy behaviors. The more intensive intervention areas did not experience a significantly greater decline in neonatal mortality. Conclusions. This study demonstrates that community-based efforts, especially mothers' group meetings designed to increase care-seeking and healthy behaviors, are effective and can be implemented at large scale. PMID:25393175

  2. Health risks from large-scale water pollution: Current trends and implications for improving drinking water quality in the lower Amu Darya drainage basin, Uzbekistan

    NASA Astrophysics Data System (ADS)

    Törnqvist, Rebecka; Jarsjö, Jerker

    2010-05-01

    Safe drinking water is a primary prerequisite to human health, well being and development. Yet, there are roughly one billion people around the world that lack access to safe drinking water supply. Health risk assessments are effective for evaluating the suitability of using various water sources as drinking water supply. Additionally, knowledge of pollutant transport processes on relatively large scales is needed to identify effective management strategies for improving water resources of poor quality. The lower Amu Darya drainage basin close to the Aral Sea in Uzbekistan suffers from physical water scarcity and poor water quality. This is mainly due to the intensive agriculture production in the region, which requires extensive freshwater withdrawals and use of fertilizers and pesticides. In addition, recurrent droughts in the region affect the surface water availability. On average 20% of the population in rural areas in Uzbekistan lack access to improved drinking water sources, and the situation is even more severe in the lower Amu Darya basin. In this study, we consider health risks related to water-borne contaminants by dividing measured substance concentrations with health-risk based guideline values from the World Health Organisation (WHO). In particular, we analyse novel results of water quality measurements performed in 2007 and 2008 in the Mejdurechye Reservoir (located in the downstream part of the Amu Darya river basin). We furthermore identify large-scale trends by comparing the Mejdurechye results to reported water quality results from a considerable stretch of the Amu Darya river basin, including drainage water, river water and groundwater. The results show that concentrations of cadmium and nitrite exceed the WHO health-risk based guideline values in Mejdurechye Reservoir. Furthermore, concentrations of the since long ago banned and highly toxic pesticides dichlorodiphenyltrichloroethane (DDT) and γ-hexachlorocyclohexane (γ-HCH) were detected in

  3. Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT

    PubMed Central

    Fonslow, Bryan R.; Carvalho, Paulo C.; Academia, Katrina; Freeby, Steve; Xu, Tao; Nakorchevsky, Aleksey; Paulus, Aran; Yates, John R.

    2011-01-01

    Ideally shotgun proteomics would facilitate the identification of an entire proteome with 100% protein sequence coverage. In reality, the large dynamic range and complexity of cellular proteomes results in oversampling of abundant proteins, while peptides from low abundance proteins are undersampled or remain undetected. We tested the proteome equalization technology, ProteoMiner, in conjunction with Multidimensional Protein Identification Technology (MudPIT) to determine how the equalization of protein dynamic range could improve shotgun proteomics methods for the analysis of cellular proteomes. Our results suggest low abundance protein identifications were improved by two mechanisms: (1) depletion of high abundance proteins freed ion trap sampling space usually occupied by high abundance peptides and (2) enrichment of low abundance proteins increased the probability of sampling their corresponding more abundant peptides. Both mechanisms also contributed to dramatic increases in the quantity of peptides identified and the quality of MS/MS spectra acquired due to increases in precursor intensity of peptides from low abundance proteins. From our large data set of identified proteins, we categorized the dominant physicochemical factors which facilitate proteome equalization with a hexapeptide library. These results illustrate that equalization of the dynamic range of the cellular proteome is a promising methodology to improve low abundance protein identification confidence, reproducibility, and sequence coverage in shotgun proteomics experiments, opening a new avenue of research for improving proteome coverage. PMID:21702434

  4. A Large-Scale Screen for Artificial Selection in Maize Identifies Candidate Agronomic Loci for Domestication and Crop ImprovementW⃞

    PubMed Central

    Yamasaki, Masanori; Tenaillon, Maud I.; Vroh Bi, Irie; Schroeder, Steve G.; Sanchez-Villeda, Hector; Doebley, John F.; Gaut, Brandon S.; McMullen, Michael D.

    2005-01-01

    Maize (Zea mays subsp mays) was domesticated from teosinte (Z. mays subsp parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties, which were spread throughout the Americas by Native Americans and adapted to a wide range of environmental conditions. Starting with landraces, 20th century plant breeders selected inbred lines of maize for use in hybrid maize production. Both domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. Here, we sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero sequence diversity as potential targets of selection. These 35 genes were then sequenced in a sample of diverse maize landraces and teosintes and tested for selection. Using two statistical tests, we identified eight candidate genes. Extended gene sequencing of these eight candidate loci confirmed that six were selected throughout the gene, and the remaining two exhibited evidence of selection in the 3′ portion of each gene. The selected genes have functions consistent with agronomic selection for nutritional quality, maturity, and productivity. Our large-scale screen for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown. PMID:16227451

  5. Challenges for Large Scale Simulations

    NASA Astrophysics Data System (ADS)

    Troyer, Matthias

    2010-03-01

    With computational approaches becoming ubiquitous the growing impact of large scale computing on research influences both theoretical and experimental work. I will review a few examples in condensed matter physics and quantum optics, including the impact of computer simulations in the search for supersolidity, thermometry in ultracold quantum gases, and the challenging search for novel phases in strongly correlated electron systems. While only a decade ago such simulations needed the fastest supercomputers, many simulations can now be performed on small workstation clusters or even a laptop: what was previously restricted to a few experts can now potentially be used by many. Only part of the gain in computational capabilities is due to Moore's law and improvement in hardware. Equally impressive is the performance gain due to new algorithms - as I will illustrate using some recently developed algorithms. At the same time modern peta-scale supercomputers offer unprecedented computational power and allow us to tackle new problems and address questions that were impossible to solve numerically only a few years ago. While there is a roadmap for future hardware developments to exascale and beyond, the main challenges are on the algorithmic and software infrastructure side. Among the problems that face the computational physicist are: the development of new algorithms that scale to thousands of cores and beyond, a software infrastructure that lifts code development to a higher level and speeds up the development of new simulation programs for large scale computing machines, tools to analyze the large volume of data obtained from such simulations, and as an emerging field provenance-aware software that aims for reproducibility of the complete computational workflow from model parameters to the final figures. Interdisciplinary collaborations and collective efforts will be required, in contrast to the cottage-industry culture currently present in many areas of computational

  6. Working with Secondary School Leadership in a Large-Scale Reform in London, UK: Consultants' Perspectives of Their Role as Agents of School Change and Improvement

    ERIC Educational Resources Information Center

    Cameron, David Hagen

    2010-01-01

    This article uses a cultural and political theoretical framework to examine the relationship between consultants and secondary school leaders within a large-scale consultancy-based reform, the Secondary National Strategy (SNS), in London UK. The SNS follows a cascade model of implementation, in which nationally created initiatives are introduced…

  7. The Use of Qualitative Methods in Large-Scale Evaluation: Improving the Quality of the Evaluation and the Meaningfulness of the Findings

    ERIC Educational Resources Information Center

    Slayton, Julie; Llosa, Lorena

    2005-01-01

    In light of the current debate over the meaning of "scientifically based research", we argue that qualitative methods should be an essential part of large-scale program evaluations if program effectiveness is to be determined and understood. This article chronicles the challenges involved in incorporating qualitative methods into the large-scale…

  8. Assessment and improvement of statistical tools for comparative proteomics analysis of sparse data sets with few experimental replicates.

    PubMed

    Schwämmle, Veit; León, Ileana Rodríguez; Jensen, Ole Nørregaard

    2013-09-01

    Large-scale quantitative analyses of biological systems are often performed with few replicate experiments, leading to multiple nonidentical data sets due to missing values. For example, mass spectrometry driven proteomics experiments are frequently performed with few biological or technical replicates due to sample-scarcity or due to duty-cycle or sensitivity constraints, or limited capacity of the available instrumentation, leading to incomplete results where detection of significant feature changes becomes a challenge. This problem is further exacerbated for the detection of significant changes on the peptide level, for example, in phospho-proteomics experiments. In order to assess the extent of this problem and the implications for large-scale proteome analysis, we investigated and optimized the performance of three statistical approaches by using simulated and experimental data sets with varying numbers of missing values. We applied three tools, including standard t test, moderated t test, also known as limma, and rank products for the detection of significantly changing features in simulated and experimental proteomics data sets with missing values. The rank product method was improved to work with data sets containing missing values. Extensive analysis of simulated and experimental data sets revealed that the performance of the statistical analysis tools depended on simple properties of the data sets. High-confidence results were obtained by using the limma and rank products methods for analyses of triplicate data sets that exhibited more than 1000 features and more than 50% missing values. The maximum number of differentially represented features was identified by using limma and rank products methods in a complementary manner. We therefore recommend combined usage of these methods as a novel and optimal way to detect significantly changing features in these data sets. This approach is suitable for large quantitative data sets from stable isotope labeling

  9. Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource

    PubMed Central

    Druce, Megan; Hulo, Chantal; Masson, Patrick; Sommer, Paula; Xenarios, Ioannis; Le Mercier, Philippe; De Oliveira, Tulio

    2016-01-01

    The Human Immunodeficiency Virus (HIV) is one of the pathogens that cause the greatest global concern, with approximately 35 million people currently infected with HIV. Extensive HIV research has been performed, generating a large amount of HIV and host genomic data. However, no effective vaccine that protects the host from HIV infection is available and HIV is still spreading at an alarming rate, despite effective antiretroviral (ARV) treatment. In order to develop effective therapies, we need to expand our knowledge of the interaction between HIV and host proteins. In contrast to virus proteins, which often rapidly evolve drug resistance mutations, the host proteins are essentially invariant within all humans. Thus, if we can identify the host proteins needed for virus replication, such as those involved in transporting viral proteins to the cell surface, we have a chance of interrupting viral replication. There is no proteome resource that summarizes this interaction, making research on this subject a difficult enterprise. In order to fill this gap in knowledge, we curated a resource presents detailed annotation on the interaction between the HIV proteome and host proteins. Our resource was produced in collaboration with ViralZone and used manual curation techniques developed by UniProtKB/Swiss-Prot. Our new website also used previous annotations of the BioAfrica HIV-1 Proteome Resource, which has been accessed by approximately 10 000 unique users a year since its inception in 2005. The novel features include a dedicated new page for each HIV protein, a graphic display of its function and a section on its interaction with host proteins. Our new webpages also add information on the genomic location of each HIV protein and the position of ARV drug resistance mutations. Our improved BioAfrica HIV-1 Proteome Resource fills a gap in the current knowledge of biocuration. Database URL: http://www.bioafrica.net/proteomics/HIVproteome.html PMID:27087306

  10. Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource.

    PubMed

    Druce, Megan; Hulo, Chantal; Masson, Patrick; Sommer, Paula; Xenarios, Ioannis; Le Mercier, Philippe; De Oliveira, Tulio

    2016-01-01

    The Human Immunodeficiency Virus (HIV) is one of the pathogens that cause the greatest global concern, with approximately 35 million people currently infected with HIV. Extensive HIV research has been performed, generating a large amount of HIV and host genomic data. However, no effective vaccine that protects the host from HIV infection is available and HIV is still spreading at an alarming rate, despite effective antiretroviral (ARV) treatment. In order to develop effective therapies, we need to expand our knowledge of the interaction between HIV and host proteins. In contrast to virus proteins, which often rapidly evolve drug resistance mutations, the host proteins are essentially invariant within all humans. Thus, if we can identify the host proteins needed for virus replication, such as those involved in transporting viral proteins to the cell surface, we have a chance of interrupting viral replication. There is no proteome resource that summarizes this interaction, making research on this subject a difficult enterprise. In order to fill this gap in knowledge, we curated a resource presents detailed annotation on the interaction between the HIV proteome and host proteins. Our resource was produced in collaboration with ViralZone and used manual curation techniques developed by UniProtKB/Swiss-Prot. Our new website also used previous annotations of the BioAfrica HIV-1 Proteome Resource, which has been accessed by approximately 10 000 unique users a year since its inception in 2005. The novel features include a dedicated new page for each HIV protein, a graphic display of its function and a section on its interaction with host proteins. Our new webpages also add information on the genomic location of each HIV protein and the position of ARV drug resistance mutations. Our improved BioAfrica HIV-1 Proteome Resource fills a gap in the current knowledge of biocuration.Database URL:http://www.bioafrica.net/proteomics/HIVproteome.html. PMID:27087306

  11. How does large-scale nudging in a regional climate model contribute to improving the simulation of weather regimes and seasonal extremes over North America?

    NASA Astrophysics Data System (ADS)

    Lucas-Picher, Philippe; Cattiaux, Julien; Bougie, Alexandre; Laprise, René

    2016-02-01

    To determine the extent to which regional climate models (RCMs) preserve the large-scale atmospheric circulation of their driving fields, we investigate the ability of two RCM simulations to reproduce weather regimes over North America. Each RCM simulation is driven at its lateral boundaries by the ERA-Interim reanalysis, but one of them uses additional large-scale nudging (LSN) in the domain interior. Four weather regimes describing the variability of the large-scale atmospheric dynamics over North America are identified in winter and in summer. The analysis shows that for both seasons, the mean frequency of occurrence and persistence of the four weather regimes for the two RCM simulations are comparable to those of ERA-Interim. However, the frequency of false daily attributions of a specific regime on day-to-day and seasonal bases is significantly high, especially in summer, for the classic lateral-boundary driven simulation. Those false attributions are largely corrected with LSN. Using composite means for each weather regimes, substantial 2-m air temperature and precipitation anomalies associated to the large-scale atmospheric circulation are found. These anomalies are larger in winter than in summer. The validation of the simulations reveals that the 2-m air temperature bias is dependent on the weather regimes, especially in summer. Conversely, the precipitation bias varies significantly from one regime to another, especially in winter. Overall, the results suggest that a classic RCM simulates the mean statistics of the weather regimes well, but that LSN is necessary to reproduce daily weather regimes and seasonal anomalies that match with the driving field.

  12. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database.

    PubMed

    Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L; Markley, John L; Akutsu, Hideo; Fujiwara, Toshimichi

    2012-08-01

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including (1)H, (13)C and (15)N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001-2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies. PMID:22689068

  13. USING PROTEOMICS TO IMPROVE RISK ASSESSMENT OF HUMAN EXPOSURE TO ENVIRONMENTAL AGENTS

    EPA Science Inventory

    Using Proteomics to Improve Risk Assessment of Human Exposure to Environmental Agents.
    Authors: Witold M. Winnik
    Key Words (4): Proteomics, LC/MS, Western Blots, 1D and 2D gel electrophoresis, toxicity

    The goal of this project is to use proteomics for the character...

  14. Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement

    PubMed Central

    Ramalingam, Abirami; Kudapa, Himabindu; Pazhamala, Lekha T.; Weckwerth, Wolfram; Varshney, Rajeev K.

    2015-01-01

    The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several

  15. Large Scale Chemical Cross-linking Mass Spectrometry Perspectives

    PubMed Central

    Zybailov, Boris L.; Glazko, Galina V.; Jaiswal, Mihir; Raney, Kevin D.

    2014-01-01

    The spectacular heterogeneity of a complex protein mixture from biological samples becomes even more difficult to tackle when one’s attention is shifted towards different protein complex topologies, transient interactions, or localization of PPIs. Meticulous protein-by-protein affinity pull-downs and yeast-two-hybrid screens are the two approaches currently used to decipher proteome-wide interaction networks. Another method is to employ chemical cross-linking, which gives not only identities of interactors, but could also provide information on the sites of interactions and interaction interfaces. Despite significant advances in mass spectrometry instrumentation over the last decade, mapping Protein-Protein Interactions (PPIs) using chemical cross-linking remains time consuming and requires substantial expertise, even in the simplest of systems. While robust methodologies and software exist for the analysis of binary PPIs and also for the single protein structure refinement using cross-linking-derived constraints, undertaking a proteome-wide cross-linking study is highly complex. Difficulties include i) identifying cross-linkers of the right length and selectivity that could capture interactions of interest; ii) enrichment of the cross-linked species; iii) identification and validation of the cross-linked peptides and cross-linked sites. In this review we examine existing literature aimed at the large-scale protein cross-linking and discuss possible paths for improvement. We also discuss short-length cross-linkers of broad specificity such as formaldehyde and diazirine-based photo-cross-linkers. These cross-linkers could potentially capture many types of interactions, without strict requirement for a particular amino-acid to be present at a given protein-protein interface. How these shortlength, broad specificity cross-linkers be applied to proteome-wide studies? We will suggest specific advances in methodology, instrumentation and software that are needed to

  16. Galaxy clustering on large scales.

    PubMed

    Efstathiou, G

    1993-06-01

    I describe some recent observations of large-scale structure in the galaxy distribution. The best constraints come from two-dimensional galaxy surveys and studies of angular correlation functions. Results from galaxy redshift surveys are much less precise but are consistent with the angular correlations, provided the distortions in mapping between real-space and redshift-space are relatively weak. The galaxy two-point correlation function, rich-cluster two-point correlation function, and galaxy-cluster cross-correlation function are all well described on large scales ( greater, similar 20h-1 Mpc, where the Hubble constant, H0 = 100h km.s-1.Mpc; 1 pc = 3.09 x 10(16) m) by the power spectrum of an initially scale-invariant, adiabatic, cold-dark-matter Universe with Gamma = Omegah approximately 0.2. I discuss how this fits in with the Cosmic Background Explorer (COBE) satellite detection of large-scale anisotropies in the microwave background radiation and other measures of large-scale structure in the Universe. PMID:11607400

  17. Very Large Scale Integration (VLSI).

    ERIC Educational Resources Information Center

    Yeaman, Andrew R. J.

    Very Large Scale Integration (VLSI), the state-of-the-art production techniques for computer chips, promises such powerful, inexpensive computing that, in the future, people will be able to communicate with computer devices in natural language or even speech. However, before full-scale VLSI implementation can occur, certain salient factors must be…

  18. Improving the TFold test for differential shotgun proteomics

    PubMed Central

    Carvalho, Paulo C.; Yates, John R.; Barbosa, Valmir C.

    2012-01-01

    Summary: We present an updated version of the TFold software for pinpointing differentially expressed proteins in shotgun proteomics experiments. Given an FDR bound, the updated approach uses a theoretical FDR estimator to maximize the number of identifications that satisfy both a fold-change cutoff that varies with the t-test P-value as a power law and a stringency criterion that aims to detect lowly abundant proteins. The new version has yielded significant improvements in sensitivity over the previous one. Availability: Freely available for academic use at http://pcarvalho.com/patternlab. Contact: paulo@pcarvalho.com PMID:22539673

  19. Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry*

    PubMed Central

    Olsen, Jesper V.; Mann, Matthias

    2013-01-01

    Cellular function can be controlled through the gene expression program, but often protein post-translational modifications (PTMs) provide a more precise and elegant mechanism. Key functional roles of specific modification events—for instance, during the cell cycle—have been known for decades, but only in the past 10 years has mass-spectrometry-(MS)-based proteomics begun to reveal the true extent of the PTM universe. In this overview for the special PTM issue of Molecular and Cellular Proteomics, we take stock of where MS-based proteomics stands in the large-scale analysis of protein modifications. For many PTMs, including phosphorylation, ubiquitination, glycosylation, and acetylation, tens of thousands of sites can now be confidently identified and localized in the sequence of the protein. The quantification of PTM levels between different cellular states is likewise established, with label-free methods showing particular promise. It is also becoming possible to determine the absolute occupancy or stoichiometry of PTM sites on a large scale. Powerful software for the bioinformatic analysis of thousands of PTM sites has been developed. However, a complete inventory of sites has not been established for any PTM, and this situation will persist into the foreseeable future. Furthermore, although PTM coverage by MS-based methods is impressive, it still needs to be improved, especially in tissues and in clinically relevant systems. The central challenge for the field is to develop streamlined methods for determining biological functions for the myriad of modifications now known to exist. PMID:24187339

  20. Microfluidic large-scale integration.

    PubMed

    Thorsen, Todd; Maerkl, Sebastian J; Quake, Stephen R

    2002-10-18

    We developed high-density microfluidic chips that contain plumbing networks with thousands of micromechanical valves and hundreds of individually addressable chambers. These fluidic devices are analogous to electronic integrated circuits fabricated using large-scale integration. A key component of these networks is the fluidic multiplexor, which is a combinatorial array of binary valve patterns that exponentially increases the processing power of a network by allowing complex fluid manipulations with a minimal number of inputs. We used these integrated microfluidic networks to construct the microfluidic analog of a comparator array and a microfluidic memory storage device whose behavior resembles random-access memory. PMID:12351675

  1. In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models.

    PubMed

    Lyutvinskiy, Yaroslav; Yang, Hongqian; Rutishauser, Dorothea; Zubarev, Roman A

    2013-08-01

    In the analysis of proteome changes arising during the early stages of a biological process (e.g. disease or drug treatment) or from the indirect influence of an important factor, the biological variations of interest are often small (∼10%). The corresponding requirements for the precision of proteomics analysis are high, and this often poses a challenge, especially when employing label-free quantification. One of the main contributors to the inaccuracy of label-free proteomics experiments is the variability of the instrumental response during LC-MS/MS runs. Such variability might include fluctuations in the electrospray current, transmission efficiency from the air-vacuum interface to the detector, and detection sensitivity. We have developed an in silico post-processing method of reducing these variations, and have thus significantly improved the precision of label-free proteomics analysis. For abundant blood plasma proteins, a coefficient of variation of approximately 1% was achieved, which allowed for sex differentiation in pooled samples and ≈90% accurate differentiation of individual samples by means of a single LC-MS/MS analysis. This method improves the precision of measurements and increases the accuracy of predictive models based on the measurements. The post-acquisition nature of the correction technique and its generality promise its widespread application in LC-MS/MS-based methods such as proteomics and metabolomics. PMID:23589346

  2. Large scale topography of Io

    NASA Technical Reports Server (NTRS)

    Gaskell, R. W.; Synnott, S. P.

    1987-01-01

    To investigate the large scale topography of the Jovian satellite Io, both limb observations and stereographic techniques applied to landmarks are used. The raw data for this study consists of Voyager 1 images of Io, 800x800 arrays of picture elements each of which can take on 256 possible brightness values. In analyzing this data it was necessary to identify and locate landmarks and limb points on the raw images, remove the image distortions caused by the camera electronics and translate the corrected locations into positions relative to a reference geoid. Minimizing the uncertainty in the corrected locations is crucial to the success of this project. In the highest resolution frames, an error of a tenth of a pixel in image space location can lead to a 300 m error in true location. In the lowest resolution frames, the same error can lead to an uncertainty of several km.

  3. Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Datta, Susmita; Payne, Samuel H.; Kang, Jiyun; Bramer, Lisa M.; Nicora, Carrie D.; Shukla, Anil K.; Metz, Thomas O.; Rodland, Karin D.; Smith, Richard D.; Tardiff, Mark F.; McDermott, Jason E.; Pounds, Joel G.; Waters, Katrina M.

    2014-12-01

    As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally-driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab ® and R packages at https://github.com/PNNL-Comp-Mass-Spec/BP-Quant.

  4. Dynameomics: Data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction

    PubMed Central

    Rysavy, Steven J; Beck, David AC; Daggett, Valerie

    2014-01-01

    Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼25–75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. PMID:25142412

  5. Neutrinos and large-scale structure

    SciTech Connect

    Eisenstein, Daniel J.

    2015-07-15

    I review the use of cosmological large-scale structure to measure properties of neutrinos and other relic populations of light relativistic particles. With experiments to measure the anisotropies of the cosmic microwave anisotropies and the clustering of matter at low redshift, we now have securely measured a relativistic background with density appropriate to the cosmic neutrino background. Our limits on the mass of the neutrino continue to shrink. Experiments coming in the next decade will greatly improve the available precision on searches for the energy density of novel relativistic backgrounds and the mass of neutrinos.

  6. Integrating Remote Sensing Information Into A Distributed Hydrological Model for Improving Water Budget Predictions in Large-scale Basins through Data Assimilation

    PubMed Central

    Qin, Changbo; Jia, Yangwen; Su, Z.(Bob); Zhou, Zuhao; Qiu, Yaqin; Suhui, Shen

    2008-01-01

    This paper investigates whether remote sensing evapotranspiration estimates can be integrated by means of data assimilation into a distributed hydrological model for improving the predictions of spatial water distribution over a large river basin with an area of 317,800 km2. A series of available MODIS satellite images over the Haihe River basin in China are used for the year 2005. Evapotranspiration is retrieved from these 1×1 km resolution images using the SEBS (Surface Energy Balance System) algorithm. The physically-based distributed model WEP-L (Water and Energy transfer Process in Large river basins) is used to compute the water balance of the Haihe River basin in the same year. Comparison between model-derived and remote sensing retrieval basin-averaged evapotranspiration estimates shows a good piecewise linear relationship, but their spatial distribution within the Haihe basin is different. The remote sensing derived evapotranspiration shows variability at finer scales. An extended Kalman filter (EKF) data assimilation algorithm, suitable for non-linear problems, is used. Assimilation results indicate that remote sensing observations have a potentially important role in providing spatial information to the assimilation system for the spatially optical hydrological parameterization of the model. This is especially important for large basins, such as the Haihe River basin in this study. Combining and integrating the capabilities of and information from model simulation and remote sensing techniques may provide the best spatial and temporal characteristics for hydrological states/fluxes, and would be both appealing and necessary for improving our knowledge of fundamental hydrological processes and for addressing important water resource management problems.

  7. Large Scale Homing in Honeybees

    PubMed Central

    Pahl, Mario; Zhu, Hong; Tautz, Jürgen; Zhang, Shaowu

    2011-01-01

    Honeybee foragers frequently fly several kilometres to and from vital resources, and communicate those locations to their nest mates by a symbolic dance language. Research has shown that they achieve this feat by memorizing landmarks and the skyline panorama, using the sun and polarized skylight as compasses and by integrating their outbound flight paths. In order to investigate the capacity of the honeybees' homing abilities, we artificially displaced foragers to novel release spots at various distances up to 13 km in the four cardinal directions. Returning bees were individually registered by a radio frequency identification (RFID) system at the hive entrance. We found that homing rate, homing speed and the maximum homing distance depend on the release direction. Bees released in the east were more likely to find their way back home, and returned faster than bees released in any other direction, due to the familiarity of global landmarks seen from the hive. Our findings suggest that such large scale homing is facilitated by global landmarks acting as beacons, and possibly the entire skyline panorama. PMID:21602920

  8. Large-scale hydrological modeling for calculating water stress indices: implications of improved spatiotemporal resolution, surface-groundwater differentiation, and uncertainty characterization.

    PubMed

    Scherer, Laura; Venkatesh, Aranya; Karuppiah, Ramkumar; Pfister, Stephan

    2015-04-21

    Physical water scarcities can be described by water stress indices. These are often determined at an annual scale and a watershed level; however, such scales mask seasonal fluctuations and spatial heterogeneity within a watershed. In order to account for this level of detail, first and foremost, water availability estimates must be improved and refined. State-of-the-art global hydrological models such as WaterGAP and UNH/GRDC have previously been unable to reliably reflect water availability at the subbasin scale. In this study, the Soil and Water Assessment Tool (SWAT) was tested as an alternative to global models, using the case study of the Mississippi watershed. While SWAT clearly outperformed the global models at the scale of a large watershed, it was judged to be unsuitable for global scale simulations due to the high calibration efforts required. The results obtained in this study show that global assessments miss out on key aspects related to upstream/downstream relations and monthly fluctuations, which are important both for the characterization of water scarcity in the Mississippi watershed and for water footprints. Especially in arid regions, where scarcity is high, these models provide unsatisfying results. PMID:25822378

  9. Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

    PubMed

    Ley, A C; Hardy, O J

    2013-04-01

    AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species. PMID:23398575

  10. Molecular Biologist's Guide to Proteomics

    PubMed Central

    Graves, Paul R.; Haystead, Timothy A. J.

    2002-01-01

    The emergence of proteomics, the large-scale analysis of proteins, has been inspired by the realization that the final product of a gene is inherently more complex and closer to function than the gene itself. Shortfalls in the ability of bioinformatics to predict both the existence and function of genes have also illustrated the need for protein analysis. Moreover, only through the study of proteins can posttranslational modifications be determined, which can profoundly affect protein function. Proteomics has been enabled by the accumulation of both DNA and protein sequence databases, improvements in mass spectrometry, and the development of computer algorithms for database searching. In this review, we describe why proteomics is important, how it is conducted, and how it can be applied to complement other existing technologies. We conclude that currently, the most practical application of proteomics is the analysis of target proteins as opposed to entire proteomes. This type of proteomics, referred to as functional proteomics, is always driven by a specific biological question. In this way, protein identification and characterization has a meaningful outcome. We discuss some of the advantages of a functional proteomics approach and provide examples of how different methodologies can be utilized to address a wide variety of biological problems. PMID:11875127

  11. Large Scale Nanolaminate Deformable Mirror

    SciTech Connect

    Papavasiliou, A; Olivier, S; Barbee, T; Miles, R; Chang, K

    2005-11-30

    This work concerns the development of a technology that uses Nanolaminate foils to form light-weight, deformable mirrors that are scalable over a wide range of mirror sizes. While MEMS-based deformable mirrors and spatial light modulators have considerably reduced the cost and increased the capabilities of adaptive optic systems, there has not been a way to utilize the advantages of lithography and batch-fabrication to produce large-scale deformable mirrors. This technology is made scalable by using fabrication techniques and lithography that are not limited to the sizes of conventional MEMS devices. Like many MEMS devices, these mirrors use parallel plate electrostatic actuators. This technology replicates that functionality by suspending a horizontal piece of nanolaminate foil over an electrode by electroplated nickel posts. This actuator is attached, with another post, to another nanolaminate foil that acts as the mirror surface. Most MEMS devices are produced with integrated circuit lithography techniques that are capable of very small line widths, but are not scalable to large sizes. This technology is very tolerant of lithography errors and can use coarser, printed circuit board lithography techniques that can be scaled to very large sizes. These mirrors use small, lithographically defined actuators and thin nanolaminate foils allowing them to produce deformations over a large area while minimizing weight. This paper will describe a staged program to develop this technology. First-principles models were developed to determine design parameters. Three stages of fabrication will be described starting with a 3 x 3 device using conventional metal foils and epoxy to a 10-across all-metal device with nanolaminate mirror surfaces.

  12. Large-Scale Information Systems

    SciTech Connect

    D. M. Nicol; H. R. Ammerlahn; M. E. Goldsby; M. M. Johnson; D. E. Rhodes; A. S. Yoshimura

    2000-12-01

    Large enterprises are ever more dependent on their Large-Scale Information Systems (LSLS), computer systems that are distinguished architecturally by distributed components--data sources, networks, computing engines, simulations, human-in-the-loop control and remote access stations. These systems provide such capabilities as workflow, data fusion and distributed database access. The Nuclear Weapons Complex (NWC) contains many examples of LSIS components, a fact that motivates this research. However, most LSIS in use grew up from collections of separate subsystems that were not designed to be components of an integrated system. For this reason, they are often difficult to analyze and control. The problem is made more difficult by the size of a typical system, its diversity of information sources, and the institutional complexities associated with its geographic distribution across the enterprise. Moreover, there is no integrated approach for analyzing or managing such systems. Indeed, integrated development of LSIS is an active area of academic research. This work developed such an approach by simulating the various components of the LSIS and allowing the simulated components to interact with real LSIS subsystems. This research demonstrated two benefits. First, applying it to a particular LSIS provided a thorough understanding of the interfaces between the system's components. Second, it demonstrated how more rapid and detailed answers could be obtained to questions significant to the enterprise by interacting with the relevant LSIS subsystems through simulated components designed with those questions in mind. In a final, added phase of the project, investigations were made on extending this research to wireless communication networks in support of telemetry applications.

  13. Advances in plant proteomics toward improvement of crop productivity and stress resistancex

    PubMed Central

    Hu, Junjie; Rampitsch, Christof; Bykova, Natalia V.

    2015-01-01

    Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein–protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed. PMID:25926838

  14. Engineering management of large scale systems

    NASA Technical Reports Server (NTRS)

    Sanders, Serita; Gill, Tepper L.; Paul, Arthur S.

    1989-01-01

    The organization of high technology and engineering problem solving, has given rise to an emerging concept. Reasoning principles for integrating traditional engineering problem solving with system theory, management sciences, behavioral decision theory, and planning and design approaches can be incorporated into a methodological approach to solving problems with a long range perspective. Long range planning has a great potential to improve productivity by using a systematic and organized approach. Thus, efficiency and cost effectiveness are the driving forces in promoting the organization of engineering problems. Aspects of systems engineering that provide an understanding of management of large scale systems are broadly covered here. Due to the focus and application of research, other significant factors (e.g., human behavior, decision making, etc.) are not emphasized but are considered.

  15. Characterization of quinoa seed proteome combining different protein precipitation techniques: Improvement of knowledge of nonmodel plant proteomics.

    PubMed

    Capriotti, Anna Laura; Cavaliere, Chiara; Piovesana, Susy; Stampachiacchiere, Serena; Ventura, Salvatore; Zenezini Chiozzi, Riccardo; Laganà, Aldo

    2015-03-01

    A shotgun proteomics approach was used to characterize the quinoa seed proteome. To obtain comprehensive proteomic data from quinoa seeds three different precipitation procedures were employed: MeOH/CHCl3 /double-distilled H2 O, acetone either alone or with trichloroacetic acid; the isolated proteins were then in-solution digested and the resulting peptides were analyzed by nano-liquid chromatography coupled to tandem mass spectrometry. However, since quinoa is a nonmodel plant species, only a few protein sequences are included in the most widely known protein sequence databases. To improve the data reliability a UniProt subdatabase, containing only proteins of Caryophillales order, was used. A total of 352 proteins were identified and evaluated both from a qualitative and quantitative point of view. This combined approach is certainly useful to increase the final number of identifications, but no particular class of proteins was extracted and identified in spite of the different chemistries and the different precipitation protocols. However, with respect to the other two procedures, from the relative quantitative analysis, based on the number of spectral counts, the trichloroacetic acid/acetone protocol was the best procedure for sample handling and quantitative protein extraction. This study could pave the way to further high-throughput studies on Chenopodium Quinoa. PMID:25580831

  16. Supporting large-scale computational science

    SciTech Connect

    Musick, R., LLNL

    1998-02-19

    Business needs have driven the development of commercial database systems since their inception. As a result, there has been a strong focus on supporting many users, minimizing the potential corruption or loss of data, and maximizing performance metrics like transactions per second, or TPC-C and TPC-D results. It turns out that these optimizations have little to do with the needs of the scientific community, and in particular have little impact on improving the management and use of large-scale high-dimensional data. At the same time, there is an unanswered need in the scientific community for many of the benefits offered by a robust DBMS. For example, tying an ad-hoc query language such as SQL together with a visualization toolkit would be a powerful enhancement to current capabilities. Unfortunately, there has been little emphasis or discussion in the VLDB community on this mismatch over the last decade. The goal of the paper is to identify the specific issues that need to be resolved before large-scale scientific applications can make use of DBMS products. This topic is addressed in the context of an evaluation of commercial DBMS technology applied to the exploration of data generated by the Department of Energy`s Accelerated Strategic Computing Initiative (ASCI). The paper describes the data being generated for ASCI as well as current capabilities for interacting with and exploring this data. The attraction of applying standard DBMS technology to this domain is discussed, as well as the technical and business issues that currently make this an infeasible solution.

  17. Large-Scale Reform Comes of Age

    ERIC Educational Resources Information Center

    Fullan, Michael

    2009-01-01

    This article reviews the history of large-scale education reform and makes the case that large-scale or whole system reform policies and strategies are becoming increasingly evident. The review briefly addresses the pre 1997 period concluding that while the pressure for reform was mounting that there were very few examples of deliberate or…

  18. Large-scale infrared scene projectors

    NASA Astrophysics Data System (ADS)

    Murray, Darin A.

    1999-07-01

    Large-scale infrared scene projectors, typically have unique opto-mechanical characteristics associated to their application. This paper outlines two large-scale zoom lens assemblies with different environmental and package constraints. Various challenges and their respective solutions are discussed and presented.

  19. An improved protocol to study the plant cell wall proteome

    PubMed Central

    Printz, Bruno; Dos Santos Morais, Raphaël; Wienkoop, Stefanie; Sergeant, Kjell; Lutts, Stanley; Hausman, Jean-Francois; Renaut, Jenny

    2015-01-01

    Cell wall proteins were extracted from alfalfa stems according to a three-steps extraction procedure using sequentially CaCl2, EGTA, and LiCl-complemented buffers. The efficiency of this protocol for extracting cell wall proteins was compared with the two previously published methods optimized for alfalfa stem cell wall protein analysis. Following LC-MS/MS analysis the three-steps extraction procedure resulted in the identification of the highest number of cell wall proteins (242 NCBInr identifiers) and gave the lowest percentage of non-cell wall proteins (about 30%). However, the three protocols are rather complementary than substitutive since 43% of the identified proteins were specific to one protocol. This three-step protocol was therefore selected for a more detailed proteomic characterization using 2D-gel electrophoresis. With this technique, 75% of the identified proteins were shown to be fraction-specific and 72.7% were predicted as belonging to the cell wall compartment. Although, being less sensitive than LC-MS/MS approaches in detecting and identifying low-abundant proteins, gel-based approaches are valuable tools for the differentiation and relative quantification of protein isoforms and/or modified proteins. In particular isoforms, having variations in their amino-acid sequence and/or carrying different N-linked glycan chains were detected and characterized. This study highlights how the extracting protocols as well as the analytical techniques devoted to the study of the plant cell wall proteome are complementary and how they may be combined to elucidate the dynamism of the plant cell wall proteome in biological studies. Data are available via ProteomeXchange with identifier PXD001927. PMID:25914713

  20. Functional Module Search in Protein Networks based on Semantic Similarity Improves the Analysis of Proteomics Data*

    PubMed Central

    Boyanova, Desislava; Nilla, Santosh; Klau, Gunnar W.; Dandekar, Thomas; Müller, Tobias; Dittrich, Marcus

    2014-01-01

    The continuously evolving field of proteomics produces increasing amounts of data while improving the quality of protein identifications. Albeit quantitative measurements are becoming more popular, many proteomic studies are still based on non-quantitative methods for protein identification. These studies result in potentially large sets of identified proteins, where the biological interpretation of proteins can be challenging. Systems biology develops innovative network-based methods, which allow an integrated analysis of these data. Here we present a novel approach, which combines prior knowledge of protein-protein interactions (PPI) with proteomics data using functional similarity measurements of interacting proteins. This integrated network analysis exactly identifies network modules with a maximal consistent functional similarity reflecting biological processes of the investigated cells. We validated our approach on small (H9N2 virus-infected gastric cells) and large (blood constituents) proteomic data sets. Using this novel algorithm, we identified characteristic functional modules in virus-infected cells, comprising key signaling proteins (e.g. the stress-related kinase RAF1) and demonstrate that this method allows a module-based functional characterization of cell types. Analysis of a large proteome data set of blood constituents resulted in clear separation of blood cells according to their developmental origin. A detailed investigation of the T-cell proteome further illustrates how the algorithm partitions large networks into functional subnetworks each representing specific cellular functions. These results demonstrate that the integrated network approach not only allows a detailed analysis of proteome networks but also yields a functional decomposition of complex proteomic data sets and thereby provides deeper insights into the underlying cellular processes of the investigated system. PMID:24807868

  1. Synthesis of small and large scale dynamos

    NASA Astrophysics Data System (ADS)

    Subramanian, Kandaswamy

    Using a closure model for the evolution of magnetic correlations, we uncover an interesting plausible saturated state of the small-scale fluctuation dynamo (SSD) and a novel analogy between quantum mechanical tunnelling and the generation of large-scale fields. Large scale fields develop via the α-effect, but as magnetic helicity can only change on a resistive timescale, the time it takes to organize the field into large scales increases with magnetic Reynolds number. This is very similar to the results which obtain from simulations using the full MHD equations.

  2. Large-scale regions of antimatter

    SciTech Connect

    Grobov, A. V. Rubin, S. G.

    2015-07-15

    Amodified mechanism of the formation of large-scale antimatter regions is proposed. Antimatter appears owing to fluctuations of a complex scalar field that carries a baryon charge in the inflation era.

  3. Food appropriation through large scale land acquisitions

    NASA Astrophysics Data System (ADS)

    Rulli, Maria Cristina; D'Odorico, Paolo

    2014-05-01

    The increasing demand for agricultural products and the uncertainty of international food markets has recently drawn the attention of governments and agribusiness firms toward investments in productive agricultural land, mostly in the developing world. The targeted countries are typically located in regions that have remained only marginally utilized because of lack of modern technology. It is expected that in the long run large scale land acquisitions (LSLAs) for commercial farming will bring the technology required to close the existing crops yield gaps. While the extent of the acquired land and the associated appropriation of freshwater resources have been investigated in detail, the amount of food this land can produce and the number of people it could feed still need to be quantified. Here we use a unique dataset of land deals to provide a global quantitative assessment of the rates of crop and food appropriation potentially associated with LSLAs. We show how up to 300-550 million people could be fed by crops grown in the acquired land, should these investments in agriculture improve crop production and close the yield gap. In contrast, about 190-370 million people could be supported by this land without closing of the yield gap. These numbers raise some concern because the food produced in the acquired land is typically exported to other regions, while the target countries exhibit high levels of malnourishment. Conversely, if used for domestic consumption, the crops harvested in the acquired land could ensure food security to the local populations.

  4. Challenges, current status and future perspectives of proteomics in improving understanding, diagnosis and treatment of vascular disease

    PubMed Central

    Moxon, Joseph V.; Padula, Matthew P.; Herbert, Ben R.; Golledge, Jonathan

    2009-01-01

    Technical advances have seen the rapid adoption of genomics and multiplex genetic polymorphism identification to research on vascular diseases. The utilization of proteomics for the study of vascular diseases has been limited by comparison. In this review we outline currently available proteomics techniques, the challenges to using these approaches and modifications which may improve the utilization of proteomics in the study of vascular diseases. PMID:19541510

  5. Newton iterative methods for large scale nonlinear systems

    SciTech Connect

    Walker, H.F.; Turner, K.

    1993-01-01

    Objective is to develop robust, efficient Newton iterative methods for general large scale problems well suited for discretizations of partial differential equations, integral equations, and other continuous problems. A concomitant objective is to develop improved iterative linear algebra methods. We first outline research on Newton iterative methods and then review work on iterative linear algebra methods. (DLC)

  6. Large-scale inhomogeneities and galaxy statistics

    NASA Technical Reports Server (NTRS)

    Schaeffer, R.; Silk, J.

    1984-01-01

    The density fluctuations associated with the formation of large-scale cosmic pancake-like and filamentary structures are evaluated using the Zel'dovich approximation for the evolution of nonlinear inhomogeneities in the expanding universe. It is shown that the large-scale nonlinear density fluctuations in the galaxy distribution due to pancakes modify the standard scale-invariant correlation function xi(r) at scales comparable to the coherence length of adiabatic fluctuations. The typical contribution of pancakes and filaments to the J3 integral, and more generally to the moments of galaxy counts in a volume of approximately (15-40 per h Mpc)exp 3, provides a statistical test for the existence of large scale inhomogeneities. An application to several recent three dimensional data sets shows that despite large observational uncertainties over the relevant scales characteristic features may be present that can be attributed to pancakes in most, but not all, of the various galaxy samples.

  7. Survey on large scale system control methods

    NASA Technical Reports Server (NTRS)

    Mercadal, Mathieu

    1987-01-01

    The problem inherent to large scale systems such as power network, communication network and economic or ecological systems were studied. The increase in size and flexibility of future spacecraft has put those dynamical systems into the category of large scale systems, and tools specific to the class of large systems are being sought to design control systems that can guarantee more stability and better performance. Among several survey papers, reference was found to a thorough investigation on decentralized control methods. Especially helpful was the classification made of the different existing approaches to deal with large scale systems. A very similar classification is used, even though the papers surveyed are somehow different from the ones reviewed in other papers. Special attention is brought to the applicability of the existing methods to controlling large mechanical systems like large space structures. Some recent developments are added to this survey.

  8. Sensitivity technologies for large scale simulation.

    SciTech Connect

    Collis, Samuel Scott; Bartlett, Roscoe Ainsworth; Smith, Thomas Michael; Heinkenschloss, Matthias; Wilcox, Lucas C.; Hill, Judith C.; Ghattas, Omar; Berggren, Martin Olof; Akcelik, Volkan; Ober, Curtis Curry; van Bloemen Waanders, Bart Gustaaf; Keiter, Eric Richard

    2005-01-01

    Sensitivity analysis is critically important to numerous analysis algorithms, including large scale optimization, uncertainty quantification,reduced order modeling, and error estimation. Our research focused on developing tools, algorithms and standard interfaces to facilitate the implementation of sensitivity type analysis into existing code and equally important, the work was focused on ways to increase the visibility of sensitivity analysis. We attempt to accomplish the first objective through the development of hybrid automatic differentiation tools, standard linear algebra interfaces for numerical algorithms, time domain decomposition algorithms and two level Newton methods. We attempt to accomplish the second goal by presenting the results of several case studies in which direct sensitivities and adjoint methods have been effectively applied, in addition to an investigation of h-p adaptivity using adjoint based a posteriori error estimation. A mathematical overview is provided of direct sensitivities and adjoint methods for both steady state and transient simulations. Two case studies are presented to demonstrate the utility of these methods. A direct sensitivity method is implemented to solve a source inversion problem for steady state internal flows subject to convection diffusion. Real time performance is achieved using novel decomposition into offline and online calculations. Adjoint methods are used to reconstruct initial conditions of a contamination event in an external flow. We demonstrate an adjoint based transient solution. In addition, we investigated time domain decomposition algorithms in an attempt to improve the efficiency of transient simulations. Because derivative calculations are at the root of sensitivity calculations, we have developed hybrid automatic differentiation methods and implemented this approach for shape optimization for gas dynamics using the Euler equations. The hybrid automatic differentiation method was applied to a first

  9. International space station. Large scale integration approach

    NASA Astrophysics Data System (ADS)

    Cohen, Brad

    The International Space Station is the most complex large scale integration program in development today. The approach developed for specification, subsystem development, and verification lay a firm basis on which future programs of this nature can be based. International Space Station is composed of many critical items, hardware and software, built by numerous International Partners, NASA Institutions, and U.S. Contractors and is launched over a period of five years. Each launch creates a unique configuration that must be safe, survivable, operable, and support ongoing assembly (assemblable) to arrive at the assembly complete configuration in 2003. The approaches to integrating each of the modules into a viable spacecraft and continue the assembly is a challenge in itself. Added to this challenge are the severe schedule constraints and lack of an "Iron Bird", which prevents assembly and checkout of each on-orbit configuration prior to launch. This paper will focus on the following areas: 1) Specification development process explaining how the requirements and specifications were derived using a modular concept driven by launch vehicle capability. Each module is composed of components of subsystems versus completed subsystems. 2) Approach to stage (each stage consists of the launched module added to the current on-orbit spacecraft) specifications. Specifically, how each launched module and stage ensures support of the current and future elements of the assembly. 3) Verification approach, due to the schedule constraints, is primarily analysis supported by testing. Specifically, how are the interfaces ensured to mate and function on-orbit when they cannot be mated before launch. 4) Lessons learned. Where can we improve this complex system design and integration task?

  10. The large-scale distribution of galaxies

    NASA Technical Reports Server (NTRS)

    Geller, Margaret J.

    1989-01-01

    The spatial distribution of galaxies in the universe is characterized on the basis of the six completed strips of the Harvard-Smithsonian Center for Astrophysics redshift-survey extension. The design of the survey is briefly reviewed, and the results are presented graphically. Vast low-density voids similar to the void in Bootes are found, almost completely surrounded by thin sheets of galaxies. Also discussed are the implications of the results for the survey sampling problem, the two-point correlation function of the galaxy distribution, the possibility of detecting large-scale coherent flows, theoretical models of large-scale structure, and the identification of groups and clusters of galaxies.

  11. Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity

    PubMed Central

    Chandramouli, Kondethimmanahalli; Qian, Pei-Yuan

    2009-01-01

    Proteomics is the large-scale study of the structure and function of proteins in complex biological sample. Such an approach has the potential value to understand the complex nature of the organism. Current proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. Advances in protein fractionation and labeling techniques have improved protein identification to include the least abundant proteins. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. However, the major limitation of proteomic investigations remains the complexity of biological structures and physiological processes, rendering the path of exploration paved with various difficulties and pitfalls. The quantity of data that is acquired with new techniques places new challenges on data processing and analysis. This article provides a brief overview of currently available proteomic techniques and their applications, followed by detailed description of advantages and technical challenges. Some solutions to circumvent technical difficulties are proposed. PMID:20948568

  12. Large Scale Commodity Clusters for Lattice QCD

    SciTech Connect

    A. Pochinsky; W. Akers; R. Brower; J. Chen; P. Dreher; R. Edwards; S. Gottlieb; D. Holmgren; P. Mackenzie; J. Negele; D. Richards; J. Simone; W. Watson

    2002-06-01

    We describe the construction of large scale clusters for lattice QCD computing being developed under the umbrella of the U.S. DoE SciDAC initiative. We discuss the study of floating point and network performance that drove the design of the cluster, and present our plans for future multi-Terascale facilities.

  13. Management of large-scale technology

    NASA Technical Reports Server (NTRS)

    Levine, A.

    1985-01-01

    Two major themes are addressed in this assessment of the management of large-scale NASA programs: (1) how a high technology agency was a decade marked by a rapid expansion of funds and manpower in the first half and almost as rapid contraction in the second; and (2) how NASA combined central planning and control with decentralized project execution.

  14. A Large Scale Computer Terminal Output Controller.

    ERIC Educational Resources Information Center

    Tucker, Paul Thomas

    This paper describes the design and implementation of a large scale computer terminal output controller which supervises the transfer of information from a Control Data 6400 Computer to a PLATO IV data network. It discusses the cost considerations leading to the selection of educational television channels rather than telephone lines for…

  15. Large-scale CFB combustion demonstration project

    SciTech Connect

    Nielsen, P.T.; Hebb, J.L.; Aquino, R.

    1998-07-01

    The Jacksonville Electric Authority's large-scale CFB demonstration project is described. Given the early stage of project development, the paper focuses on the project organizational structure, its role within the Department of Energy's Clean Coal Technology Demonstration Program, and the projected environmental performance. A description of the CFB combustion process in included.

  16. Large-scale CFB combustion demonstration project

    SciTech Connect

    Nielsen, P.T.; Hebb, J.L.; Aquino, R.

    1998-04-01

    The Jacksonville Electric Authority`s large-scale CFB demonstration project is described. Given the early stage of project development, the paper focuses on the project organizational structure, its role within the Department of Energy`s Clean Coal Technology Demonstration Program, and the projected environmental performance. A description of the CFB combustion process is included.

  17. Evaluating Large-Scale Interactive Radio Programmes

    ERIC Educational Resources Information Center

    Potter, Charles; Naidoo, Gordon

    2009-01-01

    This article focuses on the challenges involved in conducting evaluations of interactive radio programmes in South Africa with large numbers of schools, teachers, and learners. It focuses on the role such large-scale evaluation has played during the South African radio learning programme's development stage, as well as during its subsequent…

  18. ARPACK: Solving large scale eigenvalue problems

    NASA Astrophysics Data System (ADS)

    Lehoucq, Rich; Maschhoff, Kristi; Sorensen, Danny; Yang, Chao

    2013-11-01

    ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. The package is designed to compute a few eigenvalues and corresponding eigenvectors of a general n by n matrix A. It is most appropriate for large sparse or structured matrices A where structured means that a matrix-vector product w

  19. Proteomic insights into floral biology.

    PubMed

    Li, Xiaobai; Jackson, Aaron; Xie, Ming; Wu, Dianxing; Tsai, Wen-Chieh; Zhang, Sheng

    2016-08-01

    The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:26945514

  20. Moon-based Earth Observation for Large Scale Geoscience Phenomena

    NASA Astrophysics Data System (ADS)

    Guo, Huadong; Liu, Guang; Ding, Yixing

    2016-07-01

    The capability of Earth observation for large-global-scale natural phenomena needs to be improved and new observing platform are expected. We have studied the concept of Moon as an Earth observation in these years. Comparing with manmade satellite platform, Moon-based Earth observation can obtain multi-spherical, full-band, active and passive information,which is of following advantages: large observation range, variable view angle, long-term continuous observation, extra-long life cycle, with the characteristics of longevity ,consistency, integrity, stability and uniqueness. Moon-based Earth observation is suitable for monitoring the large scale geoscience phenomena including large scale atmosphere change, large scale ocean change,large scale land surface dynamic change,solid earth dynamic change,etc. For the purpose of establishing a Moon-based Earth observation platform, we already have a plan to study the five aspects as follows: mechanism and models of moon-based observing earth sciences macroscopic phenomena; sensors' parameters optimization and methods of moon-based Earth observation; site selection and environment of moon-based Earth observation; Moon-based Earth observation platform; and Moon-based Earth observation fundamental scientific framework.

  1. Over-driven control for large-scale MR dampers

    NASA Astrophysics Data System (ADS)

    Friedman, A. J.; Dyke, S. J.; Phillips, B. M.

    2013-04-01

    As semi-active electro-mechanical control devices increase in scale for use in real-world civil engineering applications, their dynamics become increasingly complicated. Control designs that are able to take these characteristics into account will be more effective in achieving good performance. Large-scale magnetorheological (MR) dampers exhibit a significant time lag in their force-response to voltage inputs, reducing the efficacy of typical controllers designed for smaller scale devices where the lag is negligible. A new control algorithm is presented for large-scale MR devices that uses over-driving and back-driving of the commands to overcome the challenges associated with the dynamics of these large-scale MR dampers. An illustrative numerical example is considered to demonstrate the controller performance. Via simulations of the structure using several seismic ground motions, the merits of the proposed control strategy to achieve reductions in various response parameters are examined and compared against several accepted control algorithms. Experimental evidence is provided to validate the improved capabilities of the proposed controller in achieving the desired control force levels. Through real-time hybrid simulation (RTHS), the proposed controllers are also examined and experimentally evaluated in terms of their efficacy and robust performance. The results demonstrate that the proposed control strategy has superior performance over typical control algorithms when paired with a large-scale MR damper, and is robust for structural control applications.

  2. Decomposition and coordination of large-scale operations optimization

    NASA Astrophysics Data System (ADS)

    Cheng, Ruoyu

    Nowadays, highly integrated manufacturing has resulted in more and more large-scale industrial operations. As one of the most effective strategies to ensure high-level operations in modern industry, large-scale engineering optimization has garnered a great amount of interest from academic scholars and industrial practitioners. Large-scale optimization problems frequently occur in industrial applications, and many of them naturally present special structure or can be transformed to taking special structure. Some decomposition and coordination methods have the potential to solve these problems at a reasonable speed. This thesis focuses on three classes of large-scale optimization problems: linear programming, quadratic programming, and mixed-integer programming problems. The main contributions include the design of structural complexity analysis for investigating scaling behavior and computational efficiency of decomposition strategies, novel coordination techniques and algorithms to improve the convergence behavior of decomposition and coordination methods, as well as the development of a decentralized optimization framework which embeds the decomposition strategies in a distributed computing environment. The complexity study can provide fundamental guidelines to practical applications of the decomposition and coordination methods. In this thesis, several case studies imply the viability of the proposed decentralized optimization techniques for real industrial applications. A pulp mill benchmark problem is used to investigate the applicability of the LP/QP decentralized optimization strategies, while a truck allocation problem in the decision support of mining operations is used to study the MILP decentralized optimization strategies.

  3. Fractals and cosmological large-scale structure

    NASA Technical Reports Server (NTRS)

    Luo, Xiaochun; Schramm, David N.

    1992-01-01

    Observations of galaxy-galaxy and cluster-cluster correlations as well as other large-scale structure can be fit with a 'limited' fractal with dimension D of about 1.2. This is not a 'pure' fractal out to the horizon: the distribution shifts from power law to random behavior at some large scale. If the observed patterns and structures are formed through an aggregation growth process, the fractal dimension D can serve as an interesting constraint on the properties of the stochastic motion responsible for limiting the fractal structure. In particular, it is found that the observed fractal should have grown from two-dimensional sheetlike objects such as pancakes, domain walls, or string wakes. This result is generic and does not depend on the details of the growth process.

  4. Condition Monitoring of Large-Scale Facilities

    NASA Technical Reports Server (NTRS)

    Hall, David L.

    1999-01-01

    This document provides a summary of the research conducted for the NASA Ames Research Center under grant NAG2-1182 (Condition-Based Monitoring of Large-Scale Facilities). The information includes copies of view graphs presented at NASA Ames in the final Workshop (held during December of 1998), as well as a copy of a technical report provided to the COTR (Dr. Anne Patterson-Hine) subsequent to the workshop. The material describes the experimental design, collection of data, and analysis results associated with monitoring the health of large-scale facilities. In addition to this material, a copy of the Pennsylvania State University Applied Research Laboratory data fusion visual programming tool kit was also provided to NASA Ames researchers.

  5. Large scale processes in the solar nebula.

    NASA Astrophysics Data System (ADS)

    Boss, A. P.

    Most proposed chondrule formation mechanisms involve processes occurring inside the solar nebula, so the large scale (roughly 1 to 10 AU) structure of the nebula is of general interest for any chrondrule-forming mechanism. Chondrules and Ca, Al-rich inclusions (CAIs) might also have been formed as a direct result of the large scale structure of the nebula, such as passage of material through high temperature regions. While recent nebula models do predict the existence of relatively hot regions, the maximum temperatures in the inner planet region may not be high enough to account for chondrule or CAI thermal processing, unless the disk mass is considerably greater than the minimum mass necessary to restore the planets to solar composition. Furthermore, it does not seem to be possible to achieve both rapid heating and rapid cooling of grain assemblages in such a large scale furnace. However, if the accretion flow onto the nebula surface is clumpy, as suggested by observations of variability in young stars, then clump-disk impacts might be energetic enough to launch shock waves which could propagate through the nebula to the midplane, thermally processing any grain aggregates they encounter, and leaving behind a trail of chondrules.

  6. Large-scale extraction of proteins.

    PubMed

    Cunha, Teresa; Aires-Barros, Raquel

    2002-01-01

    The production of foreign proteins using selected host with the necessary posttranslational modifications is one of the key successes in modern biotechnology. This methodology allows the industrial production of proteins that otherwise are produced in small quantities. However, the separation and purification of these proteins from the fermentation media constitutes a major bottleneck for the widespread commercialization of recombinant proteins. The major production costs (50-90%) for typical biological product resides in the purification strategy. There is a need for efficient, effective, and economic large-scale bioseparation techniques, to achieve high purity and high recovery, while maintaining the biological activity of the molecule. Aqueous two-phase systems (ATPS) allow process integration as simultaneously separation and concentration of the target protein is achieved, with posterior removal and recycle of the polymer. The ease of scale-up combined with the high partition coefficients obtained allow its potential application in large-scale downstream processing of proteins produced by fermentation. The equipment and the methodology for aqueous two-phase extraction of proteins on a large scale using mixer-settlerand column contractors are described. The operation of the columns, either stagewise or differential, are summarized. A brief description of the methods used to account for mass transfer coefficients, hydrodynamics parameters of hold-up, drop size, and velocity, back mixing in the phases, and flooding performance, required for column design, is also provided. PMID:11876297

  7. MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments*

    PubMed Central

    Rardin, Matthew J.; Schilling, Birgit; Cheng, Lin-Yang; MacLean, Brendan X.; Sorensen, Dylan J.; Sahu, Alexandria K.; MacCoss, Michael J.; Vitek, Olga; Gibson, Bradford W.

    2015-01-01

    Quantitative analysis of discovery-based proteomic workflows now relies on high-throughput large-scale methods for identification and quantitation of proteins and post-translational modifications. Advancements in label-free quantitative techniques, using either data-dependent or data-independent mass spectrometric acquisitions, have coincided with improved instrumentation featuring greater precision, increased mass accuracy, and faster scan speeds. We recently reported on a new quantitative method called MS1 Filtering (Schilling et al. (2012) Mol. Cell. Proteomics 11, 202–214) for processing data-independent MS1 ion intensity chromatograms from peptide analytes using the Skyline software platform. In contrast, data-independent acquisitions from MS2 scans, or SWATH, can quantify all fragment ion intensities when reference spectra are available. As each SWATH acquisition cycle typically contains an MS1 scan, these two independent label-free quantitative approaches can be acquired in a single experiment. Here, we have expanded the capability of Skyline to extract both MS1 and MS2 ion intensity chromatograms from a single SWATH data-independent acquisition in an Integrated Dual Scan Analysis approach. The performance of both MS1 and MS2 data was examined in simple and complex samples using standard concentration curves. Cases of interferences in MS1 and MS2 ion intensity data were assessed, as were the differentiation and quantitation of phosphopeptide isomers in MS2 scan data. In addition, we demonstrated an approach for optimization of SWATH m/z window sizes to reduce interferences using MS1 scans as a guide. Finally, a correlation analysis was performed on both MS1 and MS2 ion intensity data obtained from SWATH acquisitions on a complex mixture using a linear model that automatically removes signals containing interferences. This work demonstrates the practical advantages of properly acquiring and processing MS1 precursor data in addition to MS2 fragment ion

  8. Toward Increasing Fairness in Score Scale Calibrations Employed in International Large-Scale Assessments

    ERIC Educational Resources Information Center

    Oliveri, Maria Elena; von Davier, Matthias

    2014-01-01

    In this article, we investigate the creation of comparable score scales across countries in international assessments. We examine potential improvements to current score scale calibration procedures used in international large-scale assessments. Our approach seeks to improve fairness in scoring international large-scale assessments, which often…

  9. Nanoscale Proteomics

    SciTech Connect

    Shen, Yufeng; Tolic, Nikola; Masselon, Christophe D.; Pasa-Tolic, Liljiana; Camp, David G.; Anderson, Gordon A.; Smith, Richard D.; Lipton, Mary S.

    2004-02-01

    This paper describes efforts to develop a liquid chromatography (LC)/mass spectrometry (MS) technology for ultra-sensitive proteomics studies, i.e. nanoscale proteomics. The approach combines high-efficiency nano-scale LC with advanced MS, including high sensitivity and high resolution Fourier transform ion cyclotron resonance (FTICR) MS, to perform both single-stage MS and tandem MS (MS/MS) proteomic analyses. The technology developed enables large-scale protein identification from nanogram size proteomic samples and characterization of more abundant proteins from sub-picogram size complex samples. Protein identification in such studies using MS is feasible from <75 zeptomole of a protein, and the average proteome measurement throughput is >200 proteins/h and ~3 h/sample. Higher throughput (>1000 proteins/h) and more sensitive detection limits can be obtained using a “accurate mass and time” tag approach developed at our laboratory. These capabilities lay the foundation for studies from single or limited numbers of cells.

  10. Proteomics Improves the Prediction of Burns Mortality: Results from Regression Spline Modeling

    PubMed Central

    Finnerty, Celeste C.; Ju, Hyunsu; Spratt, Heidi; Victor, Sundar; Jeschke, Marc G.; Hegde, Sachin; Bhavnani, Suresh K.; Luxon, Bruce A.; Brasier, Allan R.; Herndon, David N.

    2012-01-01

    Prediction of mortality in severely burned patients remains unreliable. Although clinical covariates and plasma protein abundance have been used with varying degrees of success, the triad of burn size, inhalation injury, and age remains the most reliable predictor. We investigated the effect of combining proteomics variables with these three clinical covariates on prediction of mortality in burned children. Serum samples were collected from 330 burned children (burns covering >25% of the total body surface area) between admission and the time of the first operation for clinical chemistry analyses and proteomic assays of cytokines. Principal component analysis revealed that serum protein abundance and the clinical covariates each provided independent information regarding patient survival. To determine whether combining proteomics with clinical variables improves prediction of patient mortality, we used multivariate adaptive regression splines, since the relationships between analytes and mortality were not linear. Combining these factors increased overall outcome prediction accuracy from 52% to 81% and area under the receiver operating characteristic curve from 0.82 to 0.95. Thus, the predictive accuracy of burns mortality is substantially improved by combining protein abundance information with clinical covariates in a multivariate adaptive regression splines classifier, a model currently being validated in a prospective study. PMID:22686201

  11. Differential Proteomics Analysis of Bacillus amyloliquefaciens and Its Genome-Shuffled Mutant for Improving Surfactin Production

    PubMed Central

    Zhao, Junfeng; Cao, Lin; Zhang, Chong; Zhong, Lei; Lu, Jing; Lu, Zhaoxin

    2014-01-01

    Genome shuffling technology was used as a novel whole-genome engineering approach to rapidly improve the antimicrobial lipopeptide yield of Bacillus amyloliquefaciens. Comparative proteomic analysis of the parental ES-2-4 and genome-shuffled FMB38 strains was conducted to examine the differentially expressed proteins. The proteome was separated by 2-DE (two dimensional electrophoresis) and analyzed by MS (mass spectrum). In the shuffled strain FMB38, 51 differentially expressed protein spots with higher than two-fold spot density were detected by gel image comparison. Forty-six protein spots were detectable by silver staining and further MS analysis. The results demonstrated that among the 46 protein spots expressed particularly induced in the genome-shuffled mutant, 15 were related to metabolism, five to DNA replication, recombination and repair, six to translation and post-translational modifications, one to cell secretion and signal transduction mechanisms, three to surfactin synthesis, two to energy production and conversion, and 14 to others. All these indicated that the metabolic capability of the mutant was improved by the genome shuffling. The study will enable future detailed investigation of gene expression and function linked with surfactin synthesis. The results of proteome analysis may provide information for metabolic engineering of Bacillus amyloliquefaciens for overproduction of surfactin. PMID:25365175

  12. Large-Scale PV Integration Study

    SciTech Connect

    Lu, Shuai; Etingov, Pavel V.; Diao, Ruisheng; Ma, Jian; Samaan, Nader A.; Makarov, Yuri V.; Guo, Xinxin; Hafen, Ryan P.; Jin, Chunlian; Kirkham, Harold; Shlatz, Eugene; Frantzis, Lisa; McClive, Timothy; Karlson, Gregory; Acharya, Dhruv; Ellis, Abraham; Stein, Joshua; Hansen, Clifford; Chadliev, Vladimir; Smart, Michael; Salgo, Richard; Sorensen, Rahn; Allen, Barbara; Idelchik, Boris

    2011-07-29

    This research effort evaluates the impact of large-scale photovoltaic (PV) and distributed generation (DG) output on NV Energy’s electric grid system in southern Nevada. It analyzes the ability of NV Energy’s generation to accommodate increasing amounts of utility-scale PV and DG, and the resulting cost of integrating variable renewable resources. The study was jointly funded by the United States Department of Energy and NV Energy, and conducted by a project team comprised of industry experts and research scientists from Navigant Consulting Inc., Sandia National Laboratories, Pacific Northwest National Laboratory and NV Energy.

  13. Large-scale planar lightwave circuits

    NASA Astrophysics Data System (ADS)

    Bidnyk, Serge; Zhang, Hua; Pearson, Matt; Balakrishnan, Ashok

    2011-01-01

    By leveraging advanced wafer processing and flip-chip bonding techniques, we have succeeded in hybrid integrating a myriad of active optical components, including photodetectors and laser diodes, with our planar lightwave circuit (PLC) platform. We have combined hybrid integration of active components with monolithic integration of other critical functions, such as diffraction gratings, on-chip mirrors, mode-converters, and thermo-optic elements. Further process development has led to the integration of polarization controlling functionality. Most recently, all these technological advancements have been combined to create large-scale planar lightwave circuits that comprise hundreds of optical elements integrated on chips less than a square inch in size.

  14. Experimental Simulations of Large-Scale Collisions

    NASA Technical Reports Server (NTRS)

    Housen, Kevin R.

    2002-01-01

    This report summarizes research on the effects of target porosity on the mechanics of impact cratering. Impact experiments conducted on a centrifuge provide direct simulations of large-scale cratering on porous asteroids. The experiments show that large craters in porous materials form mostly by compaction, with essentially no deposition of material into the ejecta blanket that is a signature of cratering in less-porous materials. The ratio of ejecta mass to crater mass is shown to decrease with increasing crater size or target porosity. These results are consistent with the observation that large closely-packed craters on asteroid Mathilde appear to have formed without degradation to earlier craters.

  15. Colloquium: Large scale simulations on GPU clusters

    NASA Astrophysics Data System (ADS)

    Bernaschi, Massimo; Bisson, Mauro; Fatica, Massimiliano

    2015-06-01

    Graphics processing units (GPU) are currently used as a cost-effective platform for computer simulations and big-data processing. Large scale applications require that multiple GPUs work together but the efficiency obtained with cluster of GPUs is, at times, sub-optimal because the GPU features are not exploited at their best. We describe how it is possible to achieve an excellent efficiency for applications in statistical mechanics, particle dynamics and networks analysis by using suitable memory access patterns and mechanisms like CUDA streams, profiling tools, etc. Similar concepts and techniques may be applied also to other problems like the solution of Partial Differential Equations.

  16. Nonthermal Components in the Large Scale Structure

    NASA Astrophysics Data System (ADS)

    Miniati, Francesco

    2004-12-01

    I address the issue of nonthermal processes in the large scale structure of the universe. After reviewing the properties of cosmic shocks and their role as particle accelerators, I discuss the main observational results, from radio to γ-ray and describe the processes that are thought be responsible for the observed nonthermal emissions. Finally, I emphasize the important role of γ-ray astronomy for the progress in the field. Non detections at these photon energies have already allowed us important conclusions. Future observations will tell us more about the physics of the intracluster medium, shocks dissipation and CR acceleration.

  17. Large scale phononic metamaterials for seismic isolation

    SciTech Connect

    Aravantinos-Zafiris, N.; Sigalas, M. M.

    2015-08-14

    In this work, we numerically examine structures that could be characterized as large scale phononic metamaterials. These novel structures could have band gaps in the frequency spectrum of seismic waves when their dimensions are chosen appropriately, thus raising the belief that they could be serious candidates for seismic isolation structures. Different and easy to fabricate structures were examined made from construction materials such as concrete and steel. The well-known finite difference time domain method is used in our calculations in order to calculate the band structures of the proposed metamaterials.

  18. Systems proteomics of liver mitochondria function.

    PubMed

    Williams, Evan G; Wu, Yibo; Jha, Pooja; Dubuis, Sébastien; Blattmann, Peter; Argmann, Carmen A; Houten, Sander M; Amariuta, Tiffany; Wolski, Witold; Zamboni, Nicola; Aebersold, Ruedi; Auwerx, Johan

    2016-06-10

    Recent improvements in quantitative proteomics approaches, including Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS), permit reproducible large-scale protein measurements across diverse cohorts. Together with genomics, transcriptomics, and other technologies, transomic data sets can be generated that permit detailed analyses across broad molecular interaction networks. Here, we examine mitochondrial links to liver metabolism through the genome, transcriptome, proteome, and metabolome of 386 individuals in the BXD mouse reference population. Several links were validated between genetic variants toward transcripts, proteins, metabolites, and phenotypes. Among these, sequence variants in Cox7a2l alter its protein's activity, which in turn leads to downstream differences in mitochondrial supercomplex formation. This data set demonstrates that the proteome can now be quantified comprehensively, serving as a key complement to transcriptomics, genomics, and metabolomics--a combination moving us forward in complex trait analysis. PMID:27284200

  19. The Phoenix series large scale LNG pool fire experiments.

    SciTech Connect

    Simpson, Richard B.; Jensen, Richard Pearson; Demosthenous, Byron; Luketa, Anay Josephine; Ricks, Allen Joseph; Hightower, Marion Michael; Blanchat, Thomas K.; Helmick, Paul H.; Tieszen, Sheldon Robert; Deola, Regina Anne; Mercier, Jeffrey Alan; Suo-Anttila, Jill Marie; Miller, Timothy J.

    2010-12-01

    The increasing demand for natural gas could increase the number and frequency of Liquefied Natural Gas (LNG) tanker deliveries to ports across the United States. Because of the increasing number of shipments and the number of possible new facilities, concerns about the potential safety of the public and property from an accidental, and even more importantly intentional spills, have increased. While improvements have been made over the past decade in assessing hazards from LNG spills, the existing experimental data is much smaller in size and scale than many postulated large accidental and intentional spills. Since the physics and hazards from a fire change with fire size, there are concerns about the adequacy of current hazard prediction techniques for large LNG spills and fires. To address these concerns, Congress funded the Department of Energy (DOE) in 2008 to conduct a series of laboratory and large-scale LNG pool fire experiments at Sandia National Laboratories (Sandia) in Albuquerque, New Mexico. This report presents the test data and results of both sets of fire experiments. A series of five reduced-scale (gas burner) tests (yielding 27 sets of data) were conducted in 2007 and 2008 at Sandia's Thermal Test Complex (TTC) to assess flame height to fire diameter ratios as a function of nondimensional heat release rates for extrapolation to large-scale LNG fires. The large-scale LNG pool fire experiments were conducted in a 120 m diameter pond specially designed and constructed in Sandia's Area III large-scale test complex. Two fire tests of LNG spills of 21 and 81 m in diameter were conducted in 2009 to improve the understanding of flame height, smoke production, and burn rate and therefore the physics and hazards of large LNG spills and fires.

  20. Large-scale Globally Propagating Coronal Waves

    NASA Astrophysics Data System (ADS)

    Warmuth, Alexander

    2015-09-01

    Large-scale, globally propagating wave-like disturbances have been observed in the solar chromosphere and by inference in the corona since the 1960s. However, detailed analysis of these phenomena has only been conducted since the late 1990s. This was prompted by the availability of high-cadence coronal imaging data from numerous spaced-based instruments, which routinely show spectacular globally propagating bright fronts. Coronal waves, as these perturbations are usually referred to, have now been observed in a wide range of spectral channels, yielding a wealth of information. Many findings have supported the "classical" interpretation of the disturbances: fast-mode MHD waves or shocks that are propagating in the solar corona. However, observations that seemed inconsistent with this picture have stimulated the development of alternative models in which "pseudo waves" are generated by magnetic reconfiguration in the framework of an expanding coronal mass ejection. This has resulted in a vigorous debate on the physical nature of these disturbances. This review focuses on demonstrating how the numerous observational findings of the last one and a half decades can be used to constrain our models of large-scale coronal waves, and how a coherent physical understanding of these disturbances is finally emerging.

  1. Local gravity and large-scale structure

    NASA Technical Reports Server (NTRS)

    Juszkiewicz, Roman; Vittorio, Nicola; Wyse, Rosemary F. G.

    1990-01-01

    The magnitude and direction of the observed dipole anisotropy of the galaxy distribution can in principle constrain the amount of large-scale power present in the spectrum of primordial density fluctuations. This paper confronts the data, provided by a recent redshift survey of galaxies detected by the IRAS satellite, with the predictions of two cosmological models with very different levels of large-scale power: the biased Cold Dark Matter dominated model (CDM) and a baryon-dominated model (BDM) with isocurvature initial conditions. Model predictions are investigated for the Local Group peculiar velocity, v(R), induced by mass inhomogeneities distributed out to a given radius, R, for R less than about 10,000 km/s. Several convergence measures for v(R) are developed, which can become powerful cosmological tests when deep enough samples become available. For the present data sets, the CDM and BDM predictions are indistinguishable at the 2 sigma level and both are consistent with observations. A promising discriminant between cosmological models is the misalignment angle between v(R) and the apex of the dipole anisotropy of the microwave background.

  2. Improved metabolites of pharmaceutical ingredient grade Ginkgo biloba and the correlated proteomics analysis.

    PubMed

    Zheng, Wen; Li, Ximin; Zhang, Lin; Zhang, Yanzhen; Lu, Xiaoping; Tian, Jingkui

    2015-06-01

    Ginkgo biloba is an attractive and traditional medicinal plant, and has been widely used as a phytomedicine in the prevention and treatment of cardiovascular and cerebrovascular diseases. Flavonoids and terpene lactones are the major bioactive components of Ginkgo, whereas the ginkgolic acids (GAs) with strong allergenic properties are strictly controlled. In this study, we tested the content of flavonoids and GAs under ultraviolet-B (UV-B) treatment and performed comparative proteomic analyses to determine the differential proteins that occur upon UV-B radiation. That might play a crucial role in producing flavonoids and GAs. Our phytochemical analyses demonstrated that UV-B irradiation significantly increased the content of active flavonoids, and decreased the content of toxic GAs. We conducted comparative proteomic analysis of both whole leaf and chloroplasts proteins. In total, 27 differential proteins in the whole leaf and 43 differential proteins in the chloroplast were positively identified and functionally annotated. The proteomic data suggested that enhanced UV-B radiation exposure activated antioxidants and stress-responsive proteins as well as reduced the rate of photosynthesis. We demonstrate that UV-B irradiation pharmaceutically improved the metabolic ingredients of Ginkgo, particularly in terms of reducing GAs. With high UV absorption properties, and antioxidant activities, the flavonoids were likely highly induced as protective molecules following UV-B irradiation. PMID:25604066

  3. Reliability assessment for components of large scale photovoltaic systems

    NASA Astrophysics Data System (ADS)

    Ahadi, Amir; Ghadimi, Noradin; Mirabbasi, Davar

    2014-10-01

    Photovoltaic (PV) systems have significantly shifted from independent power generation systems to a large-scale grid-connected generation systems in recent years. The power output of PV systems is affected by the reliability of various components in the system. This study proposes an analytical approach to evaluate the reliability of large-scale, grid-connected PV systems. The fault tree method with an exponential probability distribution function is used to analyze the components of large-scale PV systems. The system is considered in the various sequential and parallel fault combinations in order to find all realistic ways in which the top or undesired events can occur. Additionally, it can identify areas that the planned maintenance should focus on. By monitoring the critical components of a PV system, it is possible not only to improve the reliability of the system, but also to optimize the maintenance costs. The latter is achieved by informing the operators about the system component's status. This approach can be used to ensure secure operation of the system by its flexibility in monitoring system applications. The implementation demonstrates that the proposed method is effective and efficient and can conveniently incorporate more system maintenance plans and diagnostic strategies.

  4. Robust regression for large-scale neuroimaging studies.

    PubMed

    Fritsch, Virgile; Da Mota, Benoit; Loth, Eva; Varoquaux, Gaël; Banaschewski, Tobias; Barker, Gareth J; Bokde, Arun L W; Brühl, Rüdiger; Butzek, Brigitte; Conrod, Patricia; Flor, Herta; Garavan, Hugh; Lemaitre, Hervé; Mann, Karl; Nees, Frauke; Paus, Tomas; Schad, Daniel J; Schümann, Gunter; Frouin, Vincent; Poline, Jean-Baptiste; Thirion, Bertrand

    2015-05-01

    Multi-subject datasets used in neuroimaging group studies have a complex structure, as they exhibit non-stationary statistical properties across regions and display various artifacts. While studies with small sample sizes can rarely be shown to deviate from standard hypotheses (such as the normality of the residuals) due to the poor sensitivity of normality tests with low degrees of freedom, large-scale studies (e.g. >100 subjects) exhibit more obvious deviations from these hypotheses and call for more refined models for statistical inference. Here, we demonstrate the benefits of robust regression as a tool for analyzing large neuroimaging cohorts. First, we use an analytic test based on robust parameter estimates; based on simulations, this procedure is shown to provide an accurate statistical control without resorting to permutations. Second, we show that robust regression yields more detections than standard algorithms using as an example an imaging genetics study with 392 subjects. Third, we show that robust regression can avoid false positives in a large-scale analysis of brain-behavior relationships with over 1500 subjects. Finally we embed robust regression in the Randomized Parcellation Based Inference (RPBI) method and demonstrate that this combination further improves the sensitivity of tests carried out across the whole brain. Altogether, our results show that robust procedures provide important advantages in large-scale neuroimaging group studies. PMID:25731989

  5. Geospatial Optimization of Siting Large-Scale Solar Projects

    SciTech Connect

    Macknick, J.; Quinby, T.; Caulfield, E.; Gerritsen, M.; Diffendorfer, J.; Haines, S.

    2014-03-01

    Recent policy and economic conditions have encouraged a renewed interest in developing large-scale solar projects in the U.S. Southwest. However, siting large-scale solar projects is complex. In addition to the quality of the solar resource, solar developers must take into consideration many environmental, social, and economic factors when evaluating a potential site. This report describes a proof-of-concept, Web-based Geographical Information Systems (GIS) tool that evaluates multiple user-defined criteria in an optimization algorithm to inform discussions and decisions regarding the locations of utility-scale solar projects. Existing siting recommendations for large-scale solar projects from governmental and non-governmental organizations are not consistent with each other, are often not transparent in methods, and do not take into consideration the differing priorities of stakeholders. The siting assistance GIS tool we have developed improves upon the existing siting guidelines by being user-driven, transparent, interactive, capable of incorporating multiple criteria, and flexible. This work provides the foundation for a dynamic siting assistance tool that can greatly facilitate siting decisions among multiple stakeholders.

  6. Lateral stirring of large-scale tracer fields by altimetry

    NASA Astrophysics Data System (ADS)

    Dencausse, Guillaume; Morrow, Rosemary; Rogé, Marine; Fleury, Sara

    2014-01-01

    Ocean surface fronts and filaments have a strong impact on the global ocean circulation and biogeochemistry. Surface Lagrangian advection with time-evolving altimetric geostrophic velocities can be used to simulate the submesoscale front and filament structures in large-scale tracer fields. We study this technique in the Southern Ocean region south of Tasmania, a domain marked by strong meso- to submesoscale features such as the fronts of the Antarctic Circumpolar Current (ACC). Starting with large-scale surface tracer fields that we stir with altimetric velocities, we determine `advected' fields which compare well with high-resolution in situ or satellite tracer data. We find that fine scales are best represented in a statistical sense after an optimal advection time of ˜2 weeks, with enhanced signatures of the ACC fronts and better spectral energy. The technique works best in moderate to high EKE regions where lateral advection dominates. This technique may be used to infer the distribution of unresolved small scales in any physical or biogeochemical surface tracer that is dominated by lateral advection. Submesoscale dynamics also impact the subsurface of the ocean, and the Lagrangian advection at depth shows promising results. Finally, we show that climatological tracer fields computed from the advected large-scale fields display improved fine-scale mean features, such as the ACC fronts, which can be useful in the context of ocean modelling.

  7. Multiresolution comparison of precipitation datasets for large-scale models

    NASA Astrophysics Data System (ADS)

    Chun, K. P.; Sapriza Azuri, G.; Davison, B.; DeBeer, C. M.; Wheater, H. S.

    2014-12-01

    Gridded precipitation datasets are crucial for driving large-scale models which are related to weather forecast and climate research. However, the quality of precipitation products is usually validated individually. Comparisons between gridded precipitation products along with ground observations provide another avenue for investigating how the precipitation uncertainty would affect the performance of large-scale models. In this study, using data from a set of precipitation gauges over British Columbia and Alberta, we evaluate several widely used North America gridded products including the Canadian Gridded Precipitation Anomalies (CANGRD), the National Center for Environmental Prediction (NCEP) reanalysis, the Water and Global Change (WATCH) project, the thin plate spline smoothing algorithms (ANUSPLIN) and Canadian Precipitation Analysis (CaPA). Based on verification criteria for various temporal and spatial scales, results provide an assessment of possible applications for various precipitation datasets. For long-term climate variation studies (~100 years), CANGRD, NCEP, WATCH and ANUSPLIN have different comparative advantages in terms of their resolution and accuracy. For synoptic and mesoscale precipitation patterns, CaPA provides appealing performance of spatial coherence. In addition to the products comparison, various downscaling methods are also surveyed to explore new verification and bias-reduction methods for improving gridded precipitation outputs for large-scale models.

  8. Large scale water lens for solar concentration.

    PubMed

    Mondol, A S; Vogel, B; Bastian, G

    2015-06-01

    Properties of large scale water lenses for solar concentration were investigated. These lenses were built from readily available materials, normal tap water and hyper-elastic linear low density polyethylene foil. Exposed to sunlight, the focal lengths and light intensities in the focal spot were measured and calculated. Their optical properties were modeled with a raytracing software based on the lens shape. We have achieved a good match of experimental and theoretical data by considering wavelength dependent concentration factor, absorption and focal length. The change in light concentration as a function of water volume was examined via the resulting load on the foil and the corresponding change of shape. The latter was extracted from images and modeled by a finite element simulation. PMID:26072893

  9. Large Scale Quantum Simulations of Nuclear Pasta

    NASA Astrophysics Data System (ADS)

    Fattoyev, Farrukh J.; Horowitz, Charles J.; Schuetrumpf, Bastian

    2016-03-01

    Complex and exotic nuclear geometries collectively referred to as ``nuclear pasta'' are expected to naturally exist in the crust of neutron stars and in supernovae matter. Using a set of self-consistent microscopic nuclear energy density functionals we present the first results of large scale quantum simulations of pasta phases at baryon densities 0 . 03 < ρ < 0 . 10 fm-3, proton fractions 0 . 05

  10. Large-scale simulations of reionization

    SciTech Connect

    Kohler, Katharina; Gnedin, Nickolay Y.; Hamilton, Andrew J.S.; /JILA, Boulder

    2005-11-01

    We use cosmological simulations to explore the large-scale effects of reionization. Since reionization is a process that involves a large dynamic range--from galaxies to rare bright quasars--we need to be able to cover a significant volume of the universe in our simulation without losing the important small scale effects from galaxies. Here we have taken an approach that uses clumping factors derived from small scale simulations to approximate the radiative transfer on the sub-cell scales. Using this technique, we can cover a simulation size up to 1280h{sup -1} Mpc with 10h{sup -1} Mpc cells. This allows us to construct synthetic spectra of quasars similar to observed spectra of SDSS quasars at high redshifts and compare them to the observational data. These spectra can then be analyzed for HII region sizes, the presence of the Gunn-Peterson trough, and the Lyman-{alpha} forest.

  11. Large-scale databases of proper names.

    PubMed

    Conley, P; Burgess, C; Hage, D

    1999-05-01

    Few tools for research in proper names have been available--specifically, there is no large-scale corpus of proper names. Two corpora of proper names were constructed, one based on U.S. phone book listings, the other derived from a database of Usenet text. Name frequencies from both corpora were compared with human subjects' reaction times (RTs) to the proper names in a naming task. Regression analysis showed that the Usenet frequencies contributed to predictions of human RT, whereas phone book frequencies did not. In addition, semantic neighborhood density measures derived from the HAL corpus were compared with the subjects' RTs and found to be a better predictor of RT than was frequency in either corpus. These new corpora are freely available on line for download. Potentials for these corpora range from using the names as stimuli in experiments to using the corpus data in software applications. PMID:10495803

  12. Estimation of large-scale dimension densities.

    PubMed

    Raab, C; Kurths, J

    2001-07-01

    We propose a technique to calculate large-scale dimension densities in both higher-dimensional spatio-temporal systems and low-dimensional systems from only a few data points, where known methods usually have an unsatisfactory scaling behavior. This is mainly due to boundary and finite-size effects. With our rather simple method, we normalize boundary effects and get a significant correction of the dimension estimate. This straightforward approach is based on rather general assumptions. So even weak coherent structures obtained from small spatial couplings can be detected with this method, which is impossible by using the Lyapunov-dimension density. We demonstrate the efficiency of our technique for coupled logistic maps, coupled tent maps, the Lorenz attractor, and the Roessler attractor. PMID:11461376

  13. The challenge of large-scale structure

    NASA Astrophysics Data System (ADS)

    Gregory, S. A.

    1996-03-01

    The tasks that I have assumed for myself in this presentation include three separate parts. The first, appropriate to the particular setting of this meeting, is to review the basic work of the founding of this field; the appropriateness comes from the fact that W. G. Tifft made immense contributions that are not often realized by the astronomical community. The second task is to outline the general tone of the observational evidence for large scale structures. (Here, in particular, I cannot claim to be complete. I beg forgiveness from any workers who are left out by my oversight for lack of space and time.) The third task is to point out some of the major aspects of the field that may represent the clues by which some brilliant sleuth will ultimately figure out how galaxies formed.

  14. Large scale cryogenic fluid systems testing

    NASA Technical Reports Server (NTRS)

    1992-01-01

    NASA Lewis Research Center's Cryogenic Fluid Systems Branch (CFSB) within the Space Propulsion Technology Division (SPTD) has the ultimate goal of enabling the long term storage and in-space fueling/resupply operations for spacecraft and reusable vehicles in support of space exploration. Using analytical modeling, ground based testing, and on-orbit experimentation, the CFSB is studying three primary categories of fluid technology: storage, supply, and transfer. The CFSB is also investigating fluid handling, advanced instrumentation, and tank structures and materials. Ground based testing of large-scale systems is done using liquid hydrogen as a test fluid at the Cryogenic Propellant Tank Facility (K-site) at Lewis' Plum Brook Station in Sandusky, Ohio. A general overview of tests involving liquid transfer, thermal control, pressure control, and pressurization is given.

  15. Batteries for Large Scale Energy Storage

    SciTech Connect

    Soloveichik, Grigorii L.

    2011-07-15

    In recent years, with the deployment of renewable energy sources, advances in electrified transportation, and development in smart grids, the markets for large-scale stationary energy storage have grown rapidly. Electrochemical energy storage methods are strong candidate solutions due to their high energy density, flexibility, and scalability. This review provides an overview of mature and emerging technologies for secondary and redox flow batteries. New developments in the chemistry of secondary and flow batteries as well as regenerative fuel cells are also considered. Advantages and disadvantages of current and prospective electrochemical energy storage options are discussed. The most promising technologies in the short term are high-temperature sodium batteries with β”-alumina electrolyte, lithium-ion batteries, and flow batteries. Regenerative fuel cells and lithium metal batteries with high energy density require further research to become practical.

  16. Grid sensitivity capability for large scale structures

    NASA Technical Reports Server (NTRS)

    Nagendra, Gopal K.; Wallerstein, David V.

    1989-01-01

    The considerations and the resultant approach used to implement design sensitivity capability for grids into a large scale, general purpose finite element system (MSC/NASTRAN) are presented. The design variables are grid perturbations with a rather general linking capability. Moreover, shape and sizing variables may be linked together. The design is general enough to facilitate geometric modeling techniques for generating design variable linking schemes in an easy and straightforward manner. Test cases have been run and validated by comparison with the overall finite difference method. The linking of a design sensitivity capability for shape variables in MSC/NASTRAN with an optimizer would give designers a powerful, automated tool to carry out practical optimization design of real life, complicated structures.

  17. Large-Scale Astrophysical Visualization on Smartphones

    NASA Astrophysics Data System (ADS)

    Becciani, U.; Massimino, P.; Costa, A.; Gheller, C.; Grillo, A.; Krokos, M.; Petta, C.

    2011-07-01

    Nowadays digital sky surveys and long-duration, high-resolution numerical simulations using high performance computing and grid systems produce multidimensional astrophysical datasets in the order of several Petabytes. Sharing visualizations of such datasets within communities and collaborating research groups is of paramount importance for disseminating results and advancing astrophysical research. Moreover educational and public outreach programs can benefit greatly from novel ways of presenting these datasets by promoting understanding of complex astrophysical processes, e.g., formation of stars and galaxies. We have previously developed VisIVO Server, a grid-enabled platform for high-performance large-scale astrophysical visualization. This article reviews the latest developments on VisIVO Web, a custom designed web portal wrapped around VisIVO Server, then introduces VisIVO Smartphone, a gateway connecting VisIVO Web and data repositories for mobile astrophysical visualization. We discuss current work and summarize future developments.

  18. The XMM Large Scale Structure Survey

    NASA Astrophysics Data System (ADS)

    Pierre, Marguerite

    2005-10-01

    We propose to complete, by an additional 5 deg2, the XMM-LSS Survey region overlying the Spitzer/SWIRE field. This field already has CFHTLS and Integral coverage, and will encompass about 10 deg2. The resulting multi-wavelength medium-depth survey, which complements XMM and Chandra deep surveys, will provide a unique view of large-scale structure over a wide range of redshift, and will show active galaxies in the full range of environments. The complete coverage by optical and IR surveys provides high-quality photometric redshifts, so that cosmological results can quickly be extracted. In the spirit of a Legacy survey, we will make the raw X-ray data immediately public. Multi-band catalogues and images will also be made available on short time scales.

  19. Estimation of large-scale dimension densities

    NASA Astrophysics Data System (ADS)

    Raab, Corinna; Kurths, Jürgen

    2001-07-01

    We propose a technique to calculate large-scale dimension densities in both higher-dimensional spatio-temporal systems and low-dimensional systems from only a few data points, where known methods usually have an unsatisfactory scaling behavior. This is mainly due to boundary and finite-size effects. With our rather simple method, we normalize boundary effects and get a significant correction of the dimension estimate. This straightforward approach is based on rather general assumptions. So even weak coherent structures obtained from small spatial couplings can be detected with this method, which is impossible by using the Lyapunov-dimension density. We demonstrate the efficiency of our technique for coupled logistic maps, coupled tent maps, the Lorenz attractor, and the Roessler attractor.

  20. Large-Scale Organization of Glycosylation Networks

    NASA Astrophysics Data System (ADS)

    Kim, Pan-Jun; Lee, Dong-Yup; Jeong, Hawoong

    2009-03-01

    Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are frequently attached to proteins and lipids. Glycans participate in fundamental biological processes including molecular trafficking and clearance, cell proliferation and apoptosis, developmental biology, immune response, and pathogenesis. N-linked glycans found on proteins are formed by sequential attachments of monosaccharides with the help of a relatively small number of enzymes. Many of these enzymes can accept multiple N-linked glycans as substrates, thus generating a large number of glycan intermediates and their intermingled pathways. Motivated by the quantitative methods developed in complex network research, we investigate the large-scale organization of such N-glycosylation pathways in a mammalian cell. The uncovered results give the experimentally-testable predictions for glycosylation process, and can be applied to the engineering of therapeutic glycoproteins.

  1. Proteomics of Saccharomyces cerevisiae Organelles*

    PubMed Central

    Wiederhold, Elena; Veenhoff, Liesbeth M.; Poolman, Bert; Slotboom, Dirk Jan

    2010-01-01

    Knowledge of the subcellular localization of proteins is indispensable to understand their physiological roles. In the past decade, 18 studies have been performed to analyze the protein content of isolated organelles from Saccharomyces cerevisiae. Here, we integrate the data sets and compare them with other large scale studies on protein localization and abundance. We evaluate the completeness and reliability of the organelle proteomics studies. Reliability depends on the purity of the organelle preparations, which unavoidably contain (small) amounts of contaminants from different locations. Quantitative proteomics methods can be used to distinguish between true organellar constituents and contaminants. Completeness is compromised when loosely or dynamically associated proteins are lost during organelle preparation and also depends on the sensitivity of the analytical methods for protein detection. There is a clear trend in the data from the 18 organelle proteomics studies showing that proteins of low abundance frequently escape detection. Proteins with unknown function or cellular abundance are also infrequently detected, indicating that these proteins may not be expressed under the conditions used. We discuss that the yeast organelle proteomics studies provide powerful lead data for further detailed studies and that methodological advances in organelle preparation and in protein detection may help to improve the completeness and reliability of the data. PMID:19955081

  2. Large-scale sequential quadratic programming algorithms

    SciTech Connect

    Eldersveld, S.K.

    1992-09-01

    The problem addressed is the general nonlinear programming problem: finding a local minimizer for a nonlinear function subject to a mixture of nonlinear equality and inequality constraints. The methods studied are in the class of sequential quadratic programming (SQP) algorithms, which have previously proved successful for problems of moderate size. Our goal is to devise an SQP algorithm that is applicable to large-scale optimization problems, using sparse data structures and storing less curvature information but maintaining the property of superlinear convergence. The main features are: 1. The use of a quasi-Newton approximation to the reduced Hessian of the Lagrangian function. Only an estimate of the reduced Hessian matrix is required by our algorithm. The impact of not having available the full Hessian approximation is studied and alternative estimates are constructed. 2. The use of a transformation matrix Q. This allows the QP gradient to be computed easily when only the reduced Hessian approximation is maintained. 3. The use of a reduced-gradient form of the basis for the null space of the working set. This choice of basis is more practical than an orthogonal null-space basis for large-scale problems. The continuity condition for this choice is proven. 4. The use of incomplete solutions of quadratic programming subproblems. Certain iterates generated by an active-set method for the QP subproblem are used in place of the QP minimizer to define the search direction for the nonlinear problem. An implementation of the new algorithm has been obtained by modifying the code MINOS. Results and comparisons with MINOS and NPSOL are given for the new algorithm on a set of 92 test problems.

  3. Supporting large-scale computational science

    SciTech Connect

    Musick, R

    1998-10-01

    A study has been carried out to determine the feasibility of using commercial database management systems (DBMSs) to support large-scale computational science. Conventional wisdom in the past has been that DBMSs are too slow for such data. Several events over the past few years have muddied the clarity of this mindset: 1. 2. 3. 4. Several commercial DBMS systems have demonstrated storage and ad-hoc quer access to Terabyte data sets. Several large-scale science teams, such as EOSDIS [NAS91], high energy physics [MM97] and human genome [Kin93] have adopted (or make frequent use of) commercial DBMS systems as the central part of their data management scheme. Several major DBMS vendors have introduced their first object-relational products (ORDBMSs), which have the potential to support large, array-oriented data. In some cases, performance is a moot issue. This is true in particular if the performance of legacy applications is not reduced while new, albeit slow, capabilities are added to the system. The basic assessment is still that DBMSs do not scale to large computational data. However, many of the reasons have changed, and there is an expiration date attached to that prognosis. This document expands on this conclusion, identifies the advantages and disadvantages of various commercial approaches, and describes the studies carried out in exploring this area. The document is meant to be brief, technical and informative, rather than a motivational pitch. The conclusions within are very likely to become outdated within the next 5-7 years, as market forces will have a significant impact on the state of the art in scientific data management over the next decade.

  4. Introducing Large-Scale Innovation in Schools

    NASA Astrophysics Data System (ADS)

    Sotiriou, Sofoklis; Riviou, Katherina; Cherouvis, Stephanos; Chelioti, Eleni; Bogner, Franz X.

    2016-08-01

    Education reform initiatives tend to promise higher effectiveness in classrooms especially when emphasis is given to e-learning and digital resources. Practical changes in classroom realities or school organization, however, are lacking. A major European initiative entitled Open Discovery Space (ODS) examined the challenge of modernizing school education via a large-scale implementation of an open-scale methodology in using technology-supported innovation. The present paper describes this innovation scheme which involved schools and teachers all over Europe, embedded technology-enhanced learning into wider school environments and provided training to teachers. Our implementation scheme consisted of three phases: (1) stimulating interest, (2) incorporating the innovation into school settings and (3) accelerating the implementation of the innovation. The scheme's impact was monitored for a school year using five indicators: leadership and vision building, ICT in the curriculum, development of ICT culture, professional development support, and school resources and infrastructure. Based on about 400 schools, our study produced four results: (1) The growth in digital maturity was substantial, even for previously high scoring schools. This was even more important for indicators such as vision and leadership" and "professional development." (2) The evolution of networking is presented graphically, showing the gradual growth of connections achieved. (3) These communities became core nodes, involving numerous teachers in sharing educational content and experiences: One out of three registered users (36 %) has shared his/her educational resources in at least one community. (4) Satisfaction scores ranged from 76 % (offer of useful support through teacher academies) to 87 % (good environment to exchange best practices). Initiatives such as ODS add substantial value to schools on a large scale.

  5. Introducing Large-Scale Innovation in Schools

    NASA Astrophysics Data System (ADS)

    Sotiriou, Sofoklis; Riviou, Katherina; Cherouvis, Stephanos; Chelioti, Eleni; Bogner, Franz X.

    2016-02-01

    Education reform initiatives tend to promise higher effectiveness in classrooms especially when emphasis is given to e-learning and digital resources. Practical changes in classroom realities or school organization, however, are lacking. A major European initiative entitled Open Discovery Space (ODS) examined the challenge of modernizing school education via a large-scale implementation of an open-scale methodology in using technology-supported innovation. The present paper describes this innovation scheme which involved schools and teachers all over Europe, embedded technology-enhanced learning into wider school environments and provided training to teachers. Our implementation scheme consisted of three phases: (1) stimulating interest, (2) incorporating the innovation into school settings and (3) accelerating the implementation of the innovation. The scheme's impact was monitored for a school year using five indicators: leadership and vision building, ICT in the curriculum, development of ICT culture, professional development support, and school resources and infrastructure. Based on about 400 schools, our study produced four results: (1) The growth in digital maturity was substantial, even for previously high scoring schools. This was even more important for indicators such as vision and leadership" and "professional development." (2) The evolution of networking is presented graphically, showing the gradual growth of connections achieved. (3) These communities became core nodes, involving numerous teachers in sharing educational content and experiences: One out of three registered users (36 %) has shared his/her educational resources in at least one community. (4) Satisfaction scores ranged from 76 % (offer of useful support through teacher academies) to 87 % (good environment to exchange best practices). Initiatives such as ODS add substantial value to schools on a large scale.

  6. Improved Proteomic Analysis Following Trichloroacetic Acid Extraction of Bacillus anthracis Spore Proteins

    SciTech Connect

    Kaiser, Brooke LD; Wunschel, David S.; Sydor, Michael A.; Warner, Marvin G.; Wahl, Karen L.; Hutchison, Janine R.

    2015-08-07

    Proteomic analysis of bacterial samples provides valuable information about cellular responses and functions under different environmental pressures. Proteomic analysis is dependent upon efficient extraction of proteins from bacterial samples without introducing bias toward extraction of particular protein classes. While no single method can recover 100% of the bacterial proteins, selected protocols can improve overall protein isolation, peptide recovery, or enrich for certain classes of proteins. The method presented here is technically simple and does not require specialized equipment such as a mechanical disrupter. Our data reveal that for particularly challenging samples, such as B. anthracis Sterne spores, trichloroacetic acid extraction improved the number of proteins identified within a sample compared to bead beating (714 vs 660, respectively). Further, TCA extraction enriched for 103 known spore specific proteins whereas bead beating resulted in 49 unique proteins. Analysis of C. botulinum samples grown to 5 days, composed of vegetative biomass and spores, showed a similar trend with improved protein yields and identification using our method compared to bead beating. Interestingly, easily lysed samples, such as B. anthracis vegetative cells, were equally as effectively processed via TCA and bead beating, but TCA extraction remains the easiest and most cost effective option. As with all assays, supplemental methods such as implementation of an alternative preparation method may provide additional insight to the protein biology of the bacteria being studied.

  7. Gravity and large-scale nonlocal bias

    NASA Astrophysics Data System (ADS)

    Chan, Kwan Chuen; Scoccimarro, Román; Sheth, Ravi K.

    2012-04-01

    For Gaussian primordial fluctuations the relationship between galaxy and matter overdensities, bias, is most often assumed to be local at the time of observation in the large-scale limit. This hypothesis is however unstable under time evolution, we provide proofs under several (increasingly more realistic) sets of assumptions. In the simplest toy model galaxies are created locally and linearly biased at a single formation time, and subsequently move with the dark matter (no velocity bias) conserving their comoving number density (no merging). We show that, after this formation time, the bias becomes unavoidably nonlocal and nonlinear at large scales. We identify the nonlocal gravitationally induced fields in which the galaxy overdensity can be expanded, showing that they can be constructed out of the invariants of the deformation tensor (Galileons), the main signature of which is a quadrupole field in second-order perturbation theory. In addition, we show that this result persists if we include an arbitrary evolution of the comoving number density of tracers. We then include velocity bias, and show that new contributions appear; these are related to the breaking of Galilean invariance of the bias relation, a dipole field being the signature at second order. We test these predictions by studying the dependence of halo overdensities in cells of fixed dark matter density: measurements in simulations show that departures from the mean bias relation are strongly correlated with the nonlocal gravitationally induced fields identified by our formalism, suggesting that the halo distribution at the present time is indeed more closely related to the mass distribution at an earlier rather than present time. However, the nonlocality seen in the simulations is not fully captured by assuming local bias in Lagrangian space. The effects on nonlocal bias seen in the simulations are most important for the most biased halos, as expected from our predictions. Accounting for these

  8. Large-Scale Statistics for Cu Electromigration

    NASA Astrophysics Data System (ADS)

    Hauschildt, M.; Gall, M.; Hernandez, R.

    2009-06-01

    Even after the successful introduction of Cu-based metallization, the electromigration failure risk has remained one of the important reliability concerns for advanced process technologies. The observation of strong bimodality for the electron up-flow direction in dual-inlaid Cu interconnects has added complexity, but is now widely accepted. The failure voids can occur both within the via ("early" mode) or within the trench ("late" mode). More recently, bimodality has been reported also in down-flow electromigration, leading to very short lifetimes due to small, slit-shaped voids under vias. For a more thorough investigation of these early failure phenomena, specific test structures were designed based on the Wheatstone Bridge technique. The use of these structures enabled an increase of the tested sample size close to 675000, allowing a direct analysis of electromigration failure mechanisms at the single-digit ppm regime. Results indicate that down-flow electromigration exhibits bimodality at very small percentage levels, not readily identifiable with standard testing methods. The activation energy for the down-flow early failure mechanism was determined to be 0.83±0.02 eV. Within the small error bounds of this large-scale statistical experiment, this value is deemed to be significantly lower than the usually reported activation energy of 0.90 eV for electromigration-induced diffusion along Cu/SiCN interfaces. Due to the advantages of the Wheatstone Bridge technique, we were also able to expand the experimental temperature range down to 150° C, coming quite close to typical operating conditions up to 125° C. As a result of the lowered activation energy, we conclude that the down-flow early failure mode may control the chip lifetime at operating conditions. The slit-like character of the early failure void morphology also raises concerns about the validity of the Blech-effect for this mechanism. A very small amount of Cu depletion may cause failure even before a

  9. Implementation of Large Scale Integrated (LSI) circuit design software

    NASA Technical Reports Server (NTRS)

    Kuehlthau, R. L.; Pitts, E. R.

    1976-01-01

    Portions of the Computer Aided Design and Test system, a collection of Large Scale Integrated (LSI) circuit design programs were modified and upgraded. Major modifications were made to the Mask Analysis Program in the form of additional operating commands and file processing options. Modifications were also made to the Artwork Interactive Design System to correct some deficiencies in the original program as well as to add several new command features related to improving the response of AIDS when dealing with large files. The remaining work was concerned with updating various programs within CADAT to incorporate the silicon on sapphire silicon gate technology.

  10. A multilevel optimization of large-scale dynamic systems

    NASA Technical Reports Server (NTRS)

    Siljak, D. D.; Sundareshan, M. K.

    1976-01-01

    A multilevel feedback control scheme is proposed for optimization of large-scale systems composed of a number of (not necessarily weakly coupled) subsystems. Local controllers are used to optimize each subsystem, ignoring the interconnections. Then, a global controller may be applied to minimize the effect of interconnections and improve the performance of the overall system. At the cost of suboptimal performance, this optimization strategy ensures invariance of suboptimality and stability of the systems under structural perturbations whereby subsystems are disconnected and again connected during operation.

  11. Urine proteomics for discovery of improved diagnostic markers of Kawasaki disease

    PubMed Central

    Kentsis, Alex; Shulman, Andrew; Ahmed, Saima; Brennan, Eileen; Monuteaux, Michael C; Lee, Young-Ho; Lipsett, Susan; Paulo, Joao A; Dedeoglu, Fatma; Fuhlbrigge, Robert; Bachur, Richard; Bradwin, Gary; Arditi, Moshe; Sundel, Robert P; Newburger, Jane W; Steen, Hanno; Kim, Susan

    2013-01-01

    Kawasaki disease (KD) is a systemic vasculitis of unknown etiology. Absence of definitive diagnostic markers limits the accuracy of clinical evaluations of suspected KD with significant increases in morbidity. In turn, incomplete understanding of its molecular pathogenesis hinders the identification of rational targets needed to improve therapy. We used high-accuracy mass spectrometry proteomics to analyse over 2000 unique proteins in clinical urine specimens of patients with KD. We discovered that urine proteomes of patients with KD, but not those with mimicking conditions, were enriched for markers of cellular injury such as filamin and talin, immune regulators such as complement regulator CSMD3, immune pattern recognition receptor muclin, and immune cytokine protease meprin A. Significant elevations of filamin C and meprin A were detected in both the serum and urine in two independent cohorts of patients with KD, comprised of a total of 236 patients. Meprin A and filamin C exhibited superior diagnostic performance as compared to currently used markers of disease in a blinded case-control study of 107 patients with suspected KD, with receiver operating characteristic areas under the curve of 0.98 (95% confidence intervals [CI] of 0.97–1 and 0.95–1, respectively). Notably, meprin A was enriched in the coronary artery lesions of a mouse model of KD. In all, urine proteome profiles revealed novel candidate molecular markers of KD, including filamin C and meprin A that exhibit excellent diagnostic performance. These disease markers may improve the diagnostic accuracy of clinical evaluations of children with suspected KD, lead to the identification of novel therapeutic targets, and allow the development of a biological classification of Kawasaki disease. PMID:23281308

  12. Curvature constraints from large scale structure

    NASA Astrophysics Data System (ADS)

    Di Dio, Enea; Montanari, Francesco; Raccanelli, Alvise; Durrer, Ruth; Kamionkowski, Marc; Lesgourgues, Julien

    2016-06-01

    We modified the CLASS code in order to include relativistic galaxy number counts in spatially curved geometries; we present the formalism and study the effect of relativistic corrections on spatial curvature. The new version of the code is now publicly available. Using a Fisher matrix analysis, we investigate how measurements of the spatial curvature parameter ΩK with future galaxy surveys are affected by relativistic effects, which influence observations of the large scale galaxy distribution. These effects include contributions from cosmic magnification, Doppler terms and terms involving the gravitational potential. As an application, we consider angle and redshift dependent power spectra, which are especially well suited for model independent cosmological constraints. We compute our results for a representative deep, wide and spectroscopic survey, and our results show the impact of relativistic corrections on spatial curvature parameter estimation. We show that constraints on the curvature parameter may be strongly biased if, in particular, cosmic magnification is not included in the analysis. Other relativistic effects turn out to be subdominant in the studied configuration. We analyze how the shift in the estimated best-fit value for the curvature and other cosmological parameters depends on the magnification bias parameter, and find that significant biases are to be expected if this term is not properly considered in the analysis.

  13. Large scale digital atlases in neuroscience

    NASA Astrophysics Data System (ADS)

    Hawrylycz, M.; Feng, D.; Lau, C.; Kuan, C.; Miller, J.; Dang, C.; Ng, L.

    2014-03-01

    Imaging in neuroscience has revolutionized our current understanding of brain structure, architecture and increasingly its function. Many characteristics of morphology, cell type, and neuronal circuitry have been elucidated through methods of neuroimaging. Combining this data in a meaningful, standardized, and accessible manner is the scope and goal of the digital brain atlas. Digital brain atlases are used today in neuroscience to characterize the spatial organization of neuronal structures, for planning and guidance during neurosurgery, and as a reference for interpreting other data modalities such as gene expression and connectivity data. The field of digital atlases is extensive and in addition to atlases of the human includes high quality brain atlases of the mouse, rat, rhesus macaque, and other model organisms. Using techniques based on histology, structural and functional magnetic resonance imaging as well as gene expression data, modern digital atlases use probabilistic and multimodal techniques, as well as sophisticated visualization software to form an integrated product. Toward this goal, brain atlases form a common coordinate framework for summarizing, accessing, and organizing this knowledge and will undoubtedly remain a key technology in neuroscience in the future. Since the development of its flagship project of a genome wide image-based atlas of the mouse brain, the Allen Institute for Brain Science has used imaging as a primary data modality for many of its large scale atlas projects. We present an overview of Allen Institute digital atlases in neuroscience, with a focus on the challenges and opportunities for image processing and computation.

  14. Large-scale carbon fiber tests

    NASA Technical Reports Server (NTRS)

    Pride, R. A.

    1980-01-01

    A realistic release of carbon fibers was established by burning a minimum of 45 kg of carbon fiber composite aircraft structural components in each of five large scale, outdoor aviation jet fuel fire tests. This release was quantified by several independent assessments with various instruments developed specifically for these tests. The most likely values for the mass of single carbon fibers released ranged from 0.2 percent of the initial mass of carbon fiber for the source tests (zero wind velocity) to a maximum of 0.6 percent of the initial carbon fiber mass for dissemination tests (5 to 6 m/s wind velocity). Mean fiber lengths for fibers greater than 1 mm in length ranged from 2.5 to 3.5 mm. Mean diameters ranged from 3.6 to 5.3 micrometers which was indicative of significant oxidation. Footprints of downwind dissemination of the fire released fibers were measured to 19.1 km from the fire.

  15. Large-scale wind turbine structures

    NASA Technical Reports Server (NTRS)

    Spera, David A.

    1988-01-01

    The purpose of this presentation is to show how structural technology was applied in the design of modern wind turbines, which were recently brought to an advanced stage of development as sources of renewable power. Wind turbine structures present many difficult problems because they are relatively slender and flexible; subject to vibration and aeroelastic instabilities; acted upon by loads which are often nondeterministic; operated continuously with little maintenance in all weather; and dominated by life-cycle cost considerations. Progress in horizontal-axis wind turbines (HAWT) development was paced by progress in the understanding of structural loads, modeling of structural dynamic response, and designing of innovative structural response. During the past 15 years a series of large HAWTs was developed. This has culminated in the recent completion of the world's largest operating wind turbine, the 3.2 MW Mod-5B power plane installed on the island of Oahu, Hawaii. Some of the applications of structures technology to wind turbine will be illustrated by referring to the Mod-5B design. First, a video overview will be presented to provide familiarization with the Mod-5B project and the important components of the wind turbine system. Next, the structural requirements for large-scale wind turbines will be discussed, emphasizing the difficult fatigue-life requirements. Finally, the procedures used to design the structure will be presented, including the use of the fracture mechanics approach for determining allowable fatigue stresses.

  16. Large-scale wind turbine structures

    NASA Astrophysics Data System (ADS)

    Spera, David A.

    1988-05-01

    The purpose of this presentation is to show how structural technology was applied in the design of modern wind turbines, which were recently brought to an advanced stage of development as sources of renewable power. Wind turbine structures present many difficult problems because they are relatively slender and flexible; subject to vibration and aeroelastic instabilities; acted upon by loads which are often nondeterministic; operated continuously with little maintenance in all weather; and dominated by life-cycle cost considerations. Progress in horizontal-axis wind turbines (HAWT) development was paced by progress in the understanding of structural loads, modeling of structural dynamic response, and designing of innovative structural response. During the past 15 years a series of large HAWTs was developed. This has culminated in the recent completion of the world's largest operating wind turbine, the 3.2 MW Mod-5B power plane installed on the island of Oahu, Hawaii. Some of the applications of structures technology to wind turbine will be illustrated by referring to the Mod-5B design. First, a video overview will be presented to provide familiarization with the Mod-5B project and the important components of the wind turbine system. Next, the structural requirements for large-scale wind turbines will be discussed, emphasizing the difficult fatigue-life requirements. Finally, the procedures used to design the structure will be presented, including the use of the fracture mechanics approach for determining allowable fatigue stresses.

  17. Large Scale Computer Simulation of Erthocyte Membranes

    NASA Astrophysics Data System (ADS)

    Harvey, Cameron; Revalee, Joel; Laradji, Mohamed

    2007-11-01

    The cell membrane is crucial to the life of the cell. Apart from partitioning the inner and outer environment of the cell, they also act as a support of complex and specialized molecular machinery, important for both the mechanical integrity of the cell, and its multitude of physiological functions. Due to its relative simplicity, the red blood cell has been a favorite experimental prototype for investigations of the structural and functional properties of the cell membrane. The erythrocyte membrane is a composite quasi two-dimensional structure composed essentially of a self-assembled fluid lipid bilayer and a polymerized protein meshwork, referred to as the cytoskeleton or membrane skeleton. In the case of the erythrocyte, the polymer meshwork is mainly composed of spectrin, anchored to the bilayer through specialized proteins. Using a coarse-grained model, recently developed by us, of self-assembled lipid membranes with implicit solvent and using soft-core potentials, we simulated large scale red-blood-cells bilayers with dimensions ˜ 10-1 μm^2, with explicit cytoskeleton. Our aim is to investigate the renormalization of the elastic properties of the bilayer due to the underlying spectrin meshwork.

  18. Silicone/graphite coating for on-target desalting and improved peptide mapping performance of matrix-assisted laser desorption/ionization-mass spectrometry targets in proteomic experiments.

    PubMed

    Li, Xinping; Wilm, Matthias; Franz, Thomas

    2005-04-01

    In two-dimensional gel electrophoresis-based proteomic experiments matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) peptide mass fingerprinting is often the technique of choice in identifying proteins. Here, we present a novel surface coating technique for MALDI-MS targets that improves manual and automatic sample analysis. A mixture of silicone and graphite is spread in the form of a thin layer over the target. Due to the hydrophobicity of the coating, aqueous solutions can be applied to relatively small spots very precisely using a robotic system. At least four times more liquid can be concentrated on the same area compared to uncoated steel targets. alpha-cyano-4-hydrocinnamic acid crystallizes in form of very small crystals evenly distributed over the surface. The search for "hot spots" during the analysis is not necessary, which supports the automatic acquisition of data. The homogeneous crystal layer can be very effectively washed on-target without encountering major sample losses. This efficient washing and the focused application of aqueous samples replace expensive and time-consuming reversed phase micro column based sample clean-ups. When analyzing peptide mixtures, the signal intensities are up to five times higher than with preparations of the same un-desalted samples on steel targets, since four times more sample can be loaded. The mass resolution remains unaffected by the surface coating. After usage the coating can be removed, followed by a new coating avoiding any carry-over of sample to the next analysis. All these properties make the precoating of MALDI-MS targets with a silicone/graphite layer an ideal technique for routine analysis in large-scale proteomic experiments. PMID:15838907

  19. An informal paper on large-scale dynamic systems

    NASA Technical Reports Server (NTRS)

    Ho, Y. C.

    1975-01-01

    Large scale systems are defined as systems requiring more than one decision maker to control the system. Decentralized control and decomposition are discussed for large scale dynamic systems. Information and many-person decision problems are analyzed.

  20. Analysis and Management of Large-Scale Activities Based on Interface

    NASA Astrophysics Data System (ADS)

    Yang, Shaofan; Ji, Jingwei; Lu, Ligang; Wang, Zhiyi

    Based on the concepts of system safety engineering, life-cycle and interface that comes from American system safety standard MIL-STD-882E, and apply them to the process of risk analysis and management of large-scale activities. Identify the involved personnel, departments, funds and other contents throughout the life cycle of large-scale activities. Recognize and classify the ultimate risk sources of people, objects and environment of large-scale activities from the perspective of interface. Put forward the accident cause analysis model according to the previous large-scale activities' accidents and combine with the analysis of the risk source interface. Analyze the risks of each interface and summary various types of risks the large-scale activities faced. Come up with the risk management consciousness, policies and regulations, risk control and supervision departments improvement ideas.

  1. Large Scale Flame Spread Environmental Characterization Testing

    NASA Technical Reports Server (NTRS)

    Clayman, Lauren K.; Olson, Sandra L.; Gokoghi, Suleyman A.; Brooker, John E.; Ferkul, Paul V.; Kacher, Henry F.

    2013-01-01

    Under the Advanced Exploration Systems (AES) Spacecraft Fire Safety Demonstration Project (SFSDP), as a risk mitigation activity in support of the development of a large-scale fire demonstration experiment in microgravity, flame-spread tests were conducted in normal gravity on thin, cellulose-based fuels in a sealed chamber. The primary objective of the tests was to measure pressure rise in a chamber as sample material, burning direction (upward/downward), total heat release, heat release rate, and heat loss mechanisms were varied between tests. A Design of Experiments (DOE) method was imposed to produce an array of tests from a fixed set of constraints and a coupled response model was developed. Supplementary tests were run without experimental design to additionally vary select parameters such as initial chamber pressure. The starting chamber pressure for each test was set below atmospheric to prevent chamber overpressure. Bottom ignition, or upward propagating burns, produced rapid acceleratory turbulent flame spread. Pressure rise in the chamber increases as the amount of fuel burned increases mainly because of the larger amount of heat generation and, to a much smaller extent, due to the increase in gaseous number of moles. Top ignition, or downward propagating burns, produced a steady flame spread with a very small flat flame across the burning edge. Steady-state pressure is achieved during downward flame spread as the pressure rises and plateaus. This indicates that the heat generation by the flame matches the heat loss to surroundings during the longer, slower downward burns. One heat loss mechanism included mounting a heat exchanger directly above the burning sample in the path of the plume to act as a heat sink and more efficiently dissipate the heat due to the combustion event. This proved an effective means for chamber overpressure mitigation for those tests producing the most total heat release and thusly was determined to be a feasible mitigation

  2. Synchronization of coupled large-scale Boolean networks

    SciTech Connect

    Li, Fangfei

    2014-03-15

    This paper investigates the complete synchronization and partial synchronization of two large-scale Boolean networks. First, the aggregation algorithm towards large-scale Boolean network is reviewed. Second, the aggregation algorithm is applied to study the complete synchronization and partial synchronization of large-scale Boolean networks. Finally, an illustrative example is presented to show the efficiency of the proposed results.

  3. Why large-scale seasonal streamflow forecasts are feasible

    NASA Astrophysics Data System (ADS)

    Bierkens, M. F.; Candogan Yossef, N.; Van Beek, L. P.

    2011-12-01

    -based skill scores. In conclusion, the inertia of large-scale hydrological systems and a focus on anomalous flows make seasonal streamflow forecasts feasible and useful. To further improve on the current skill, investment is required in better state estimation, which can be achieved with better hydrological models (including better past forcing, i.e. analysis, products) and improved hydrological data-assimilation.

  4. Ecohydrological modeling for large-scale environmental impact assessment.

    PubMed

    Woznicki, Sean A; Nejadhashemi, A Pouyan; Abouali, Mohammad; Herman, Matthew R; Esfahanian, Elaheh; Hamaamin, Yaseen A; Zhang, Zhen

    2016-02-01

    Ecohydrological models are frequently used to assess the biological integrity of unsampled streams. These models vary in complexity and scale, and their utility depends on their final application. Tradeoffs are usually made in model scale, where large-scale models are useful for determining broad impacts of human activities on biological conditions, and regional-scale (e.g. watershed or ecoregion) models provide stakeholders greater detail at the individual stream reach level. Given these tradeoffs, the objective of this study was to develop large-scale stream health models with reach level accuracy similar to regional-scale models thereby allowing for impacts assessments and improved decision-making capabilities. To accomplish this, four measures of biological integrity (Ephemeroptera, Plecoptera, and Trichoptera taxa (EPT), Family Index of Biotic Integrity (FIBI), Hilsenhoff Biotic Index (HBI), and fish Index of Biotic Integrity (IBI)) were modeled based on four thermal classes (cold, cold-transitional, cool, and warm) of streams that broadly dictate the distribution of aquatic biota in Michigan. The Soil and Water Assessment Tool (SWAT) was used to simulate streamflow and water quality in seven watersheds and the Hydrologic Index Tool was used to calculate 171 ecologically relevant flow regime variables. Unique variables were selected for each thermal class using a Bayesian variable selection method. The variables were then used in development of adaptive neuro-fuzzy inference systems (ANFIS) models of EPT, FIBI, HBI, and IBI. ANFIS model accuracy improved when accounting for stream thermal class rather than developing a global model. PMID:26595397

  5. Exact-Differential Large-Scale Traffic Simulation

    SciTech Connect

    Hanai, Masatoshi; Suzumura, Toyotaro; Theodoropoulos, Georgios; Perumalla, Kalyan S

    2015-01-01

    Analyzing large-scale traffics by simulation needs repeating execution many times with various patterns of scenarios or parameters. Such repeating execution brings about big redundancy because the change from a prior scenario to a later scenario is very minor in most cases, for example, blocking only one of roads or changing the speed limit of several roads. In this paper, we propose a new redundancy reduction technique, called exact-differential simulation, which enables to simulate only changing scenarios in later execution while keeping exactly same results as in the case of whole simulation. The paper consists of two main efforts: (i) a key idea and algorithm of the exact-differential simulation, (ii) a method to build large-scale traffic simulation on the top of the exact-differential simulation. In experiments of Tokyo traffic simulation, the exact-differential simulation shows 7.26 times as much elapsed time improvement in average and 2.26 times improvement even in the worst case as the whole simulation.

  6. Large-Scale Spacecraft Fire Safety Tests

    NASA Technical Reports Server (NTRS)

    Urban, David; Ruff, Gary A.; Ferkul, Paul V.; Olson, Sandra; Fernandez-Pello, A. Carlos; T'ien, James S.; Torero, Jose L.; Cowlard, Adam J.; Rouvreau, Sebastien; Minster, Olivier; Toth, Balazs; Legros, Guillaume; Eigenbrod, Christian; Smirnov, Nickolay; Fujita, Osamu; Jomaas, Grunde

    2014-01-01

    An international collaborative program is underway to address open issues in spacecraft fire safety. Because of limited access to long-term low-gravity conditions and the small volume generally allotted for these experiments, there have been relatively few experiments that directly study spacecraft fire safety under low-gravity conditions. Furthermore, none of these experiments have studied sample sizes and environment conditions typical of those expected in a spacecraft fire. The major constraint has been the size of the sample, with prior experiments limited to samples of the order of 10 cm in length and width or smaller. This lack of experimental data forces spacecraft designers to base their designs and safety precautions on 1-g understanding of flame spread, fire detection, and suppression. However, low-gravity combustion research has demonstrated substantial differences in flame behavior in low-gravity. This, combined with the differences caused by the confined spacecraft environment, necessitates practical scale spacecraft fire safety research to mitigate risks for future space missions. To address this issue, a large-scale spacecraft fire experiment is under development by NASA and an international team of investigators. This poster presents the objectives, status, and concept of this collaborative international project (Saffire). The project plan is to conduct fire safety experiments on three sequential flights of an unmanned ISS re-supply spacecraft (the Orbital Cygnus vehicle) after they have completed their delivery of cargo to the ISS and have begun their return journeys to earth. On two flights (Saffire-1 and Saffire-3), the experiment will consist of a flame spread test involving a meter-scale sample ignited in the pressurized volume of the spacecraft and allowed to burn to completion while measurements are made. On one of the flights (Saffire-2), 9 smaller (5 x 30 cm) samples will be tested to evaluate NASAs material flammability screening tests

  7. High-Throughput Proteomics

    NASA Astrophysics Data System (ADS)

    Zhang, Zhaorui; Wu, Si; Stenoien, David L.; Paša-Tolić, Ljiljana

    2014-06-01

    Mass spectrometry (MS)-based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.

  8. IP over optical multicasting for large-scale video delivery

    NASA Astrophysics Data System (ADS)

    Jin, Yaohui; Hu, Weisheng; Sun, Weiqiang; Guo, Wei

    2007-11-01

    In the IPTV systems, multicasting will play a crucial role in the delivery of high-quality video services, which can significantly improve bandwidth efficiency. However, the scalability and the signal quality of current IPTV can barely compete with the existing broadcast digital TV systems since it is difficult to implement large-scale multicasting with end-to-end guaranteed quality of service (QoS) in packet-switched IP network. China 3TNet project aimed to build a high performance broadband trial network to support large-scale concurrent streaming media and interactive multimedia services. The innovative idea of 3TNet is that an automatic switched optical networks (ASON) with the capability of dynamic point-to-multipoint (P2MP) connections replaces the conventional IP multicasting network in the transport core, while the edge remains an IP multicasting network. In this paper, we will introduce the network architecture and discuss challenges in such IP over Optical multicasting for video delivery.

  9. A First Look at the Head Start CARES Demonstration: Large-Scale Implementation of Programs to Improve Children's Social-Emotional Competence. OPRE Report 2013-47

    ERIC Educational Resources Information Center

    Mattera, Shira Kolnik; Lloyd, Chrishana M.; Fishman, Mike; Bangser, Michael

    2013-01-01

    Low-income preschool children face many risks to their social-emotional development that can affect their school experience and social outcomes for years to come. Although there are some promising approaches to improving young children's social-emotional competence, the evidence base is limited, particularly on the effectiveness of these…

  10. Large-scale assembly of colloidal particles

    NASA Astrophysics Data System (ADS)

    Yang, Hongta

    This study reports a simple, roll-to-roll compatible coating technology for producing three-dimensional highly ordered colloidal crystal-polymer composites, colloidal crystals, and macroporous polymer membranes. A vertically beveled doctor blade is utilized to shear align silica microsphere-monomer suspensions to form large-area composites in a single step. The polymer matrix and the silica microspheres can be selectively removed to create colloidal crystals and self-standing macroporous polymer membranes. The thickness of the shear-aligned crystal is correlated with the viscosity of the colloidal suspension and the coating speed, and the correlations can be qualitatively explained by adapting the mechanisms developed for conventional doctor blade coating. Five important research topics related to the application of large-scale three-dimensional highly ordered macroporous films by doctor blade coating are covered in this study. The first topic describes the invention in large area and low cost color reflective displays. This invention is inspired by the heat pipe technology. The self-standing macroporous polymer films exhibit brilliant colors which originate from the Bragg diffractive of visible light form the three-dimensional highly ordered air cavities. The colors can be easily changed by tuning the size of the air cavities to cover the whole visible spectrum. When the air cavities are filled with a solvent which has the same refractive index as that of the polymer, the macroporous polymer films become completely transparent due to the index matching. When the solvent trapped in the cavities is evaporated by in-situ heating, the sample color changes back to brilliant color. This process is highly reversible and reproducible for thousands of cycles. The second topic reports the achievement of rapid and reversible vapor detection by using 3-D macroporous photonic crystals. Capillary condensation of a condensable vapor in the interconnected macropores leads to the

  11. Population generation for large-scale simulation

    NASA Astrophysics Data System (ADS)

    Hannon, Andrew C.; King, Gary; Morrison, Clayton; Galstyan, Aram; Cohen, Paul

    2005-05-01

    Computer simulation is used to research phenomena ranging from the structure of the space-time continuum to population genetics and future combat.1-3 Multi-agent simulations in particular are now commonplace in many fields.4, 5 By modeling populations whose complex behavior emerges from individual interactions, these simulations help to answer questions about effects where closed form solutions are difficult to solve or impossible to derive.6 To be useful, simulations must accurately model the relevant aspects of the underlying domain. In multi-agent simulation, this means that the modeling must include both the agents and their relationships. Typically, each agent can be modeled as a set of attributes drawn from various distributions (e.g., height, morale, intelligence and so forth). Though these can interact - for example, agent height is related to agent weight - they are usually independent. Modeling relations between agents, on the other hand, adds a new layer of complexity, and tools from graph theory and social network analysis are finding increasing application.7, 8 Recognizing the role and proper use of these techniques, however, remains the subject of ongoing research. We recently encountered these complexities while building large scale social simulations.9-11 One of these, the Hats Simulator, is designed to be a lightweight proxy for intelligence analysis problems. Hats models a "society in a box" consisting of many simple agents, called hats. Hats gets its name from the classic spaghetti western, in which the heroes and villains are known by the color of the hats they wear. The Hats society also has its heroes and villains, but the challenge is to identify which color hat they should be wearing based on how they behave. There are three types of hats: benign hats, known terrorists, and covert terrorists. Covert terrorists look just like benign hats but act like terrorists. Population structure can make covert hat identification significantly more

  12. Application of an improved proteomics method for abundant protein cleanup: molecular and genomic mechanisms study in plant defense.

    PubMed

    Zhang, Yixiang; Gao, Peng; Xing, Zhuo; Jin, Shumei; Chen, Zhide; Liu, Lantao; Constantino, Nasie; Wang, Xinwang; Shi, Weibing; Yuan, Joshua S; Dai, Susie Y

    2013-11-01

    High abundance proteins like ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) impose a consistent challenge for the whole proteome characterization using shot-gun proteomics. To address this challenge, we developed and evaluated Polyethyleneimine Assisted Rubisco Cleanup (PARC) as a new method by combining both abundant protein removal and fractionation. The new approach was applied to a plant insect interaction study to validate the platform and investigate mechanisms for plant defense against herbivorous insects. Our results indicated that PARC can effectively remove Rubisco, improve the protein identification, and discover almost three times more differentially regulated proteins. The significantly enhanced shot-gun proteomics performance was translated into in-depth proteomic and molecular mechanisms for plant insect interaction, where carbon re-distribution was used to play an essential role. Moreover, the transcriptomic validation also confirmed the reliability of PARC analysis. Finally, functional studies were carried out for two differentially regulated genes as revealed by PARC analysis. Insect resistance was induced by over-expressing either jacalin-like or cupin-like genes in rice. The results further highlighted that PARC can serve as an effective strategy for proteomics analysis and gene discovery. PMID:23943779

  13. Application of an Improved Proteomics Method for Abundant Protein Cleanup: Molecular and Genomic Mechanisms Study in Plant Defense*

    PubMed Central

    Zhang, Yixiang; Gao, Peng; Xing, Zhuo; Jin, Shumei; Chen, Zhide; Liu, Lantao; Constantino, Nasie; Wang, Xinwang; Shi, Weibing; Yuan, Joshua S.; Dai, Susie Y.

    2013-01-01

    High abundance proteins like ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) impose a consistent challenge for the whole proteome characterization using shot-gun proteomics. To address this challenge, we developed and evaluated Polyethyleneimine Assisted Rubisco Cleanup (PARC) as a new method by combining both abundant protein removal and fractionation. The new approach was applied to a plant insect interaction study to validate the platform and investigate mechanisms for plant defense against herbivorous insects. Our results indicated that PARC can effectively remove Rubisco, improve the protein identification, and discover almost three times more differentially regulated proteins. The significantly enhanced shot-gun proteomics performance was translated into in-depth proteomic and molecular mechanisms for plant insect interaction, where carbon re-distribution was used to play an essential role. Moreover, the transcriptomic validation also confirmed the reliability of PARC analysis. Finally, functional studies were carried out for two differentially regulated genes as revealed by PARC analysis. Insect resistance was induced by over-expressing either jacalin-like or cupin-like genes in rice. The results further highlighted that PARC can serve as an effective strategy for proteomics analysis and gene discovery. PMID:23943779

  14. From Correlation to Causality: Statistical Approaches to Learning Regulatory Relationships in Large-Scale Biomolecular Investigations.

    PubMed

    Ness, Robert O; Sachs, Karen; Vitek, Olga

    2016-03-01

    Causal inference, the task of uncovering regulatory relationships between components of biomolecular pathways and networks, is a primary goal of many high-throughput investigations. Statistical associations between observed protein concentrations can suggest an enticing number of hypotheses regarding the underlying causal interactions, but when do such associations reflect the underlying causal biomolecular mechanisms? The goal of this perspective is to provide suggestions for causal inference in large-scale experiments, which utilize high-throughput technologies such as mass-spectrometry-based proteomics. We describe in nontechnical terms the pitfalls of inference in large data sets and suggest methods to overcome these pitfalls and reliably find regulatory associations. PMID:26731284

  15. Multitree Algorithms for Large-Scale Astrostatistics

    NASA Astrophysics Data System (ADS)

    March, William B.; Ozakin, Arkadas; Lee, Dongryeol; Riegel, Ryan; Gray, Alexander G.

    2012-03-01

    this number every week, resulting in billions of objects. At such scales, even linear-time analysis operations present challenges, particularly since statistical analyses are inherently interactive processes, requiring that computations complete within some reasonable human attention span. The quadratic (or worse) runtimes of straightforward implementations become quickly unbearable. Examples of applications. These analysis subroutines occur ubiquitously in astrostatistical work. We list just a few examples. The need to cross-match objects across different catalogs has led to various algorithms, which at some point perform an AllNN computation. 2-point and higher-order spatial correlations for the basis of spatial statistics, and are utilized in astronomy to compare the spatial structures of two datasets, such as an observed sample and a theoretical sample, for example, forming the basis for two-sample hypothesis testing. Friends-of-friends clustering is often used to identify halos in data from astrophysical simulations. Minimum spanning tree properties have also been proposed as statistics of large-scale structure. Comparison of the distributions of different kinds of objects requires accurate density estimation, for which KDE is the overall statistical method of choice. The prediction of redshifts from optical data requires accurate regression, for which kernel regression is a powerful method. The identification of objects of various types in astronomy, such as stars versus galaxies, requires accurate classification, for which KDA is a powerful method. Overview. In this chapter, we will briefly sketch the main ideas behind recent fast algorithms which achieve, for example, linear runtimes for pairwise-distance problems, or similarly dramatic reductions in computational growth. In some cases, the runtime orders for these algorithms are mathematically provable statements, while in others we have only conjectures backed by experimental observations for the time being

  16. A large-scale evaluation of computational protein function prediction

    PubMed Central

    Radivojac, Predrag; Clark, Wyatt T; Ronnen Oron, Tal; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kassner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Böhm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-01-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based Critical Assessment of protein Function Annotation (CAFA) experiment. Fifty-four methods representing the state-of-the-art for protein function prediction were evaluated on a target set of 866 proteins from eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed widely-used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is significant need for improvement of currently available tools. PMID:23353650

  17. Large Scale Bacterial Colony Screening of Diversified FRET Biosensors

    PubMed Central

    Litzlbauer, Julia; Schifferer, Martina; Ng, David; Fabritius, Arne; Thestrup, Thomas; Griesbeck, Oliver

    2015-01-01

    Biosensors based on Förster Resonance Energy Transfer (FRET) between fluorescent protein mutants have started to revolutionize physiology and biochemistry. However, many types of FRET biosensors show relatively small FRET changes, making measurements with these probes challenging when used under sub-optimal experimental conditions. Thus, a major effort in the field currently lies in designing new optimization strategies for these types of sensors. Here we describe procedures for optimizing FRET changes by large scale screening of mutant biosensor libraries in bacterial colonies. We describe optimization of biosensor expression, permeabilization of bacteria, software tools for analysis, and screening conditions. The procedures reported here may help in improving FRET changes in multiple suitable classes of biosensors. PMID:26061878

  18. Large scale rigidity-based flexibility analysis of biomolecules

    PubMed Central

    Streinu, Ileana

    2016-01-01

    KINematics And RIgidity (KINARI) is an on-going project for in silico flexibility analysis of proteins. The new version of the software, Kinari-2, extends the functionality of our free web server KinariWeb, incorporates advanced web technologies, emphasizes the reproducibility of its experiments, and makes substantially improved tools available to the user. It is designed specifically for large scale experiments, in particular, for (a) very large molecules, including bioassemblies with high degree of symmetry such as viruses and crystals, (b) large collections of related biomolecules, such as those obtained through simulated dilutions, mutations, or conformational changes from various types of dynamics simulations, and (c) is intended to work as seemlessly as possible on the large, idiosyncratic, publicly available repository of biomolecules, the Protein Data Bank. We describe the system design, along with the main data processing, computational, mathematical, and validation challenges underlying this phase of the KINARI project. PMID:26958583

  19. A large-scale evaluation of computational protein function prediction.

    PubMed

    Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kaßner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Boehm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas A; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-03-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools. PMID:23353650

  20. Galaxy clustering and the origin of large-scale flows

    NASA Technical Reports Server (NTRS)

    Juszkiewicz, R.; Yahil, A.

    1989-01-01

    Peebles's 'cosmic virial theorem' is extended from its original range of validity at small separations, where hydrostatic equilibrium holds, to large separations, in which linear gravitational stability theory applies. The rms pairwise velocity difference at separation r is shown to depend on the spatial galaxy correlation function xi(x) only for x less than r. Gravitational instability theory can therefore be tested by comparing the two up to the maximum separation for which both can reliably be determined, and there is no dependence on the poorly known large-scale density and velocity fields. With the expected improvement in the data over the next few years, however, this method should yield a reliable determination of omega.

  1. Probes of large-scale structure in the universe

    NASA Technical Reports Server (NTRS)

    Suto, Yasushi; Gorski, Krzysztof; Juszkiewicz, Roman; Silk, Joseph

    1988-01-01

    A general formalism is developed which shows that the gravitational instability theory for the origin of the large-scale structure of the universe is now capable of critically confronting observational results on cosmic background radiation angular anisotropies, large-scale bulk motions, and large-scale clumpiness in the galaxy counts. The results indicate that presently advocated cosmological models will have considerable difficulty in simultaneously explaining the observational results.

  2. Superconducting materials for large scale applications

    SciTech Connect

    Scanlan, Ronald M.; Malozemoff, Alexis P.; Larbalestier, David C.

    2004-05-06

    Significant improvements in the properties ofsuperconducting materials have occurred recently. These improvements arebeing incorporated into the latest generation of wires, cables, and tapesthat are being used in a broad range of prototype devices. These devicesinclude new, high field accelerator and NMR magnets, magnets for fusionpower experiments, motors, generators, and power transmission lines.These prototype magnets are joining a wide array of existing applicationsthat utilize the unique capabilities of superconducting magnets:accelerators such as the Large Hadron Collider, fusion experiments suchas ITER, 930 MHz NMR, and 4 Tesla MRI. In addition, promising newmaterials such as MgB2 have been discovered and are being studied inorder to assess their potential for new applications. In this paper, wewill review the key developments that are leading to these newapplications for superconducting materials. In some cases, the key factoris improved understanding or development of materials with significantlyimproved properties. An example of the former is the development of Nb3Snfor use in high field magnets for accelerators. In other cases, thedevelopment is being driven by the application. The aggressive effort todevelop HTS tapes is being driven primarily by the need for materialsthat can operate at temperatures of 50 K and higher. The implications ofthese two drivers for further developments will be discussed. Finally, wewill discuss the areas where further improvements are needed in order fornew applications to be realized.

  3. Evaluation of drought propagation in an ensemble mean of large-scale hydrological models

    NASA Astrophysics Data System (ADS)

    Van Loon, A. F.; Van Huijgevoort, M. H. J.; Van Lanen, H. A. J.

    2012-07-01

    snow-related droughts. Furthermore, almost no composite droughts were simulated for slowly responding areas, while many multi-year drought events were expected in these systems. We conclude that drought propagation processes are reasonably well reproduced by the ensemble mean of large-scale models in contrasting catchments in Europe and that some challenges remain in catchments with cold and semi-arid climates and catchments with large storage in aquifers or lakes. Improvement of drought simulation in large-scale models should focus on a better representation of hydrological processes that are important for drought development, such as evapotranspiration, snow accumulation and melt, and especially storage. Besides the more explicit inclusion of storage (e.g. aquifers) in large-scale models, also parametrisation of storage processes requires attention, for example through a global scale dataset on aquifer characteristics.

  4. "Cosmological Parameters from Large Scale Structure"

    NASA Technical Reports Server (NTRS)

    Hamilton, A. J. S.

    2005-01-01

    This grant has provided primary support for graduate student Mark Neyrinck, and some support for the PI and for colleague Nick Gnedin, who helped co-supervise Neyrinck. This award had two major goals. First, to continue to develop and apply methods for measuring galaxy power spectra on large, linear scales, with a view to constraining cosmological parameters. And second, to begin try to understand galaxy clustering at smaller. nonlinear scales well enough to constrain cosmology from those scales also. Under this grant, the PI and collaborators, notably Max Tegmark. continued to improve their technology for measuring power spectra from galaxy surveys at large, linear scales. and to apply the technology to surveys as the data become available. We believe that our methods are best in the world. These measurements become the foundation from which we and other groups measure cosmological parameters.

  5. INTERNATIONAL WORKSHOP ON LARGE-SCALE REFORESTATION: PROCEEDINGS

    EPA Science Inventory

    The purpose of the workshop was to identify major operational and ecological considerations needed to successfully conduct large-scale reforestation projects throughout the forested regions of the world. Large-scale" for this workshop means projects where, by human effort, approx...

  6. Using Large-Scale Assessment Scores to Determine Student Grades

    ERIC Educational Resources Information Center

    Miller, Tess

    2013-01-01

    Many Canadian provinces provide guidelines for teachers to determine students' final grades by combining a percentage of students' scores from provincial large-scale assessments with their term scores. This practice is thought to hold students accountable by motivating them to put effort into completing the large-scale assessment, thereby…

  7. Large-scale Stratospheric Transport Processes

    NASA Technical Reports Server (NTRS)

    Plumb, R. Alan

    2003-01-01

    The PI has undertaken a theoretical analysis of the existence and nature of compact tracer-tracer relationships of the kind observed in the stratosphere, augmented with three-dimensional model simulations of stratospheric tracers (the latter being an extension of modeling work the group did during the SOLVE experiment). This work achieves a rigorous theoretical basis for the existence and shape of these relationships, as well as a quantitative theory of their width and evolution, in terms of the joint tracer-tracer PDF distribution. A paper on this work is almost complete and will soon be submitted to Rev. Geophys. We have analyzed lower stratospheric water in simulations with an isentropic-coordinate version of the MATCH transport model which we recently helped to develop. The three-dimensional structure of lower stratospheric water, in particular, attracted our attention: dry air is, below about 400K potential temperature, localized in the regions of the west Pacific and equatorial South America. We have been analyzing air trajectories to determine how air passes through the tropopause cold trap. This work is now being completed, and a paper will be submitted to Geophys. Res. Lett. before the end of summer. We are continuing to perform experiments with the 'MATCH' CTM, in both sigma- and entropy-coordinate forms. We earlier found (in collaboration with Dr Natalie Mahowald, and as part of an NSF-funded project) that switching to isentropic coordinates made a substantial improvement to the simulation of the age of stratospheric air. We are now running experiments with near-tropopause sources in both versions of the model, to see if and to what extent the simulation of stratosphere-troposphere transport is dependent on the model coordinate. Personnel Research is supervised by the PI, Prof. Alan Plumb. Mr William Heres conducts the tracer modeling work and performs other modeling tasks. Two graduate students, Ms Irene Lee and Mr Michael Ring, have been participating

  8. Improving Peptide Identification Sensitivity in Shotgun Proteomics by Stratification of Search Space

    PubMed Central

    Alves, Gelio; Yu, Yi-Kuo

    2013-01-01

    Due to its high specificity, trypsin is the enzyme of choice in shotgun proteomics. Nonetheless, several publications do report the identification of semi-tryptic and non-tryptic peptides. Many of these peptides are conjectured to be signaling peptides or to have formed during sample preparation. It is known that only a small fraction of tandem mass spectra from a trypsin-digested protein mixture can be confidently matched to tryptic peptides. Leaving aside other possibilities such as post-translational modifications and single amino acid polymorphisms, this suggests that many unidentified spectra originate from semi-tryptic and non-tryptic peptides. To include them in database searches, however, may not improve overall peptide identification due to possible sensitivity reduction from search space expansion. To circumvent this issue for E-value based search methods, we have designed a scheme that categorizes qualified peptides ( i.e., peptides whose molecular weight differences from the parent ion are within a specified error tolerance) into three tiers: tryptic, semi-tryptic and non-tryptic. This classification allows peptides belonging to different tiers to have different Bonferroni correction factors. Our results show that this scheme can significantly improve retrieval performance when compared to search strategies that assign equal Bonferroni correction factors to all qualified peptides. PMID:23668635

  9. Improvements to the Percolator algorithm for peptide identification from shotgun proteomics data sets

    PubMed Central

    Spivak, Marina; Weston, Jason; Bottou, Léon; Käll, Lukas; Noble, William Stafford

    2009-01-01

    Shotgun proteomics coupled with database search software allows the identification of a large number of peptides in a single experiment. However, some existing search algorithms, such as SEQUEST, use score functions that are designed primarily to identify the best peptide for a given spectrum. Consequently, when comparing identifications across spectra, the SEQUEST score function Xcorr fails to discriminate accurately between correct and incorrect peptide identifications. Several machine learning methods have been proposed to address the resulting classification task of distinguishing between correct and incorrect peptide-spectrum matches (PSMs). A recent example is Percolator, which uses semi-supervised learning and a decoy database search strategy to learn to distinguish between correct and incorrect PSMs identified by a database search algorithm. The current work describes three improvements to Percolator. (1) Percolator’s heuristic optimization is replaced with a clear objective function, with intuitive reasons behind its choice. (2) Tractable nonlinear models are used instead of linear models, leading to improved accuracy over the original Percolator. (3) A method, Q-ranker, for directly optimizing the number of identified spectra at a specified q value is proposed, which achieves further gains. PMID:19385687

  10. The use of time-resolved fluorescence in gel-based proteomics for improved biomarker discovery

    NASA Astrophysics Data System (ADS)

    Sandberg, AnnSofi; Buschmann, Volker; Kapusta, Peter; Erdmann, Rainer; Wheelock, Åsa M.

    2010-02-01

    This paper describes a new platform for quantitative intact proteomics, entitled Cumulative Time-resolved Emission 2-Dimensional Gel Electrophoresis (CuTEDGE). The CuTEDGE technology utilizes differences in fluorescent lifetimes to subtract the confounding background fluorescence during in-gel detection and quantification of proteins, resulting in a drastic improvement in both sensitivity and dynamic range compared to existing technology. The platform is primarily designed for image acquisition in 2-dimensional gel electrophoresis (2-DE), but is also applicable to 1-dimensional gel electrophoresis (1-DE), and proteins electroblotted to membranes. In a set of proof-of-principle measurements, we have evaluated the performance of the novel technology using the MicroTime 100 instrument (PicoQuant GmbH) in conjunction with the CyDye minimal labeling fluorochromes (GE Healthcare, Uppsala, Sweden) to perform differential gel electrophoresis (DIGE) analyses. The results indicate that the CuTEDGE technology provides an improvement in the dynamic range and sensitivity of detection of 3 orders of magnitude as compared to current state-of-the-art image acquisition instrumentation available for 2-DE (Typhoon 9410, GE Healthcare). Given the potential dynamic range of 7-8 orders of magnitude and sensitivities in the attomol range, the described invention represents a technological leap in detection of low abundance cellular proteins, which is desperately needed in the field of biomarker discovery.

  11. Applications of Proteomic Technologies to Toxicology

    EPA Science Inventory

    Proteomics is the large-scale study of gene expression at the protein level. This cutting edge technology has been extensively applied to toxicology research recently. The up-to-date development of proteomics has presented the toxicology community with an unprecedented opportunit...

  12. Optimal Wind Energy Integration in Large-Scale Electric Grids

    NASA Astrophysics Data System (ADS)

    Albaijat, Mohammad H.

    The major concern in electric grid operation is operating under the most economical and reliable fashion to ensure affordability and continuity of electricity supply. This dissertation investigates the effects of such challenges, which affect electric grid reliability and economic operations. These challenges are: 1. Congestion of transmission lines, 2. Transmission lines expansion, 3. Large-scale wind energy integration, and 4. Phaser Measurement Units (PMUs) optimal placement for highest electric grid observability. Performing congestion analysis aids in evaluating the required increase of transmission line capacity in electric grids. However, it is necessary to evaluate expansion of transmission line capacity on methods to ensure optimal electric grid operation. Therefore, the expansion of transmission line capacity must enable grid operators to provide low-cost electricity while maintaining reliable operation of the electric grid. Because congestion affects the reliability of delivering power and increases its cost, the congestion analysis in electric grid networks is an important subject. Consequently, next-generation electric grids require novel methodologies for studying and managing congestion in electric grids. We suggest a novel method of long-term congestion management in large-scale electric grids. Owing to the complication and size of transmission line systems and the competitive nature of current grid operation, it is important for electric grid operators to determine how many transmission lines capacity to add. Traditional questions requiring answers are "Where" to add, "How much of transmission line capacity" to add, and "Which voltage level". Because of electric grid deregulation, transmission lines expansion is more complicated as it is now open to investors, whose main interest is to generate revenue, to build new transmission lines. Adding a new transmission capacity will help the system to relieve the transmission system congestion, create

  13. Integrative analysis of extracellular and intracellular bladder cancer cell line proteome with transcriptome: improving coverage and validity of -omics findings.

    PubMed

    Latosinska, Agnieszka; Makridakis, Manousos; Frantzi, Maria; Borràs, Daniel M; Janssen, Bart; Mullen, William; Zoidakis, Jerome; Merseburger, Axel S; Jankowski, Vera; Mischak, Harald; Vlahou, Antonia

    2016-01-01

    Characterization of disease-associated proteins improves our understanding of disease pathophysiology. Obtaining a comprehensive coverage of the proteome is challenging, mainly due to limited statistical power and an inability to verify hundreds of putative biomarkers. In an effort to address these issues, we investigated the value of parallel analysis of compartment-specific proteomes with an assessment of findings by cross-strategy and cross-omics (proteomics-transcriptomics) agreement. The validity of the individual datasets and of a "verified" dataset based on cross-strategy/omics agreement was defined following their comparison with published literature. The proteomic analysis of the cell extract, Endoplasmic Reticulum/Golgi apparatus and conditioned medium of T24 vs. its metastatic subclone T24M bladder cancer cells allowed the identification of 253, 217 and 256 significant changes, respectively. Integration of these findings with transcriptomics resulted in 253 "verified" proteins based on the agreement of at least 2 strategies. This approach revealed findings of higher validity, as supported by a higher level of agreement in the literature data than those of individual datasets. As an example, the coverage and shortlisting of targets in the IL-8 signalling pathway are discussed. Collectively, an integrative analysis appears a safer way to evaluate -omics datasets and ultimately generate models from valid observations. PMID:27167498

  14. The role of large-scale, extratropical dynamics in climate change

    SciTech Connect

    Shepherd, T.G.

    1994-02-01

    The climate modeling community has focused recently on improving our understanding of certain processes, such as cloud feedbacks and ocean circulation, that are deemed critical to climate-change prediction. Although attention to such processes is warranted, emphasis on these areas has diminished a general appreciation of the role played by the large-scale dynamics of the extratropical atmosphere. Lack of interest in extratropical dynamics may reflect the assumption that these dynamical processes are a non-problem as far as climate modeling is concerned, since general circulation models (GCMs) calculate motions on this scale from first principles. Nevertheless, serious shortcomings in our ability to understand and simulate large-scale dynamics exist. Partly due to a paucity of standard GCM diagnostic calculations of large-scale motions and their transports of heat, momentum, potential vorticity, and moisture, a comprehensive understanding of the role of large-scale dynamics in GCM climate simulations has not been developed. Uncertainties remain in our understanding and simulation of large-scale extratropical dynamics and their interaction with other climatic processes, such as cloud feedbacks, large-scale ocean circulation, moist convection, air-sea interaction and land-surface processes. To address some of these issues, the 17th Stanstead Seminar was convened at Bishop`s University in Lennoxville, Quebec. The purpose of the Seminar was to promote discussion of the role of large-scale extratropical dynamics in global climate change. Abstracts of the talks are included in this volume. On the basis of these talks, several key issues emerged concerning large-scale extratropical dynamics and their climatic role. Individual records are indexed separately for the database.

  15. Distribution probability of large-scale landslides in central Nepal

    NASA Astrophysics Data System (ADS)

    Timilsina, Manita; Bhandary, Netra P.; Dahal, Ranjan Kumar; Yatabe, Ryuichi

    2014-12-01

    Large-scale landslides in the Himalaya are defined as huge, deep-seated landslide masses that occurred in the geological past. They are widely distributed in the Nepal Himalaya. The steep topography and high local relief provide high potential for such failures, whereas the dynamic geology and adverse climatic conditions play a key role in the occurrence and reactivation of such landslides. The major geoscientific problems related with such large-scale landslides are 1) difficulties in their identification and delineation, 2) sources of small-scale failures, and 3) reactivation. Only a few scientific publications have been published concerning large-scale landslides in Nepal. In this context, the identification and quantification of large-scale landslides and their potential distribution are crucial. Therefore, this study explores the distribution of large-scale landslides in the Lesser Himalaya. It provides simple guidelines to identify large-scale landslides based on their typical characteristics and using a 3D schematic diagram. Based on the spatial distribution of landslides, geomorphological/geological parameters and logistic regression, an equation of large-scale landslide distribution is also derived. The equation is validated by applying it to another area. For the new area, the area under the receiver operating curve of the landslide distribution probability in the new area is 0.699, and a distribution probability value could explain > 65% of existing landslides. Therefore, the regression equation can be applied to areas of the Lesser Himalaya of central Nepal with similar geological and geomorphological conditions.

  16. The Status of Large-Scale Assessment in the Pacific Region. REL Technical Brief. REL 2008-No. 003

    ERIC Educational Resources Information Center

    Ryan, Jennifer; Keir, Scott

    2008-01-01

    This technical brief describes the large-scale assessment measures and practices used in the jurisdictions served by the Pacific Regional Educational Laboratory. The need for effective large-scale assessment was identified as a major priority for improving student achievement in the Pacific Region jurisdictions: American Samoa, Guam, Hawaii, the…

  17. Status of the development of solid polymer electrolyte water electrolysis for large scale hydrogen generation

    NASA Astrophysics Data System (ADS)

    Russell, J. H.

    1982-02-01

    Solid polymer electrolyte water electrolysis for large scale hydrogen generation is reported. The program was aimed at performance improvement. Reductions in cell impedance were demonstrated which improve cell performance by over 100 mV. A prototype 500 SCFH system for field evaluation was developed.

  18. A large-scale electrophoresis- and chromatography-based determination of gene expression profiles in bovine brain capillary endothelial cells after the re-induction of blood-brain barrier properties

    PubMed Central

    2010-01-01

    Background Brain capillary endothelial cells (BCECs) form the physiological basis of the blood-brain barrier (BBB). The barrier function is (at least in part) due to well-known proteins such as transporters, tight junctions and metabolic barrier proteins (e.g. monoamine oxidase, gamma glutamyltranspeptidase and P-glycoprotein). Our previous 2-dimensional gel proteome analysis had identified a large number of proteins and revealed the major role of dynamic cytoskeletal remodelling in the differentiation of bovine BCECs. The aim of the present study was to elaborate a reference proteome of Triton X-100-soluble species from bovine BCECs cultured in the well-established in vitro BBB model developed in our laboratory. Results A total of 215 protein spots (corresponding to 130 distinct proteins) were identified by 2-dimensional gel electrophoresis, whereas over 350 proteins were identified by a shotgun approach. We classified around 430 distinct proteins expressed by bovine BCECs. Our large-scale gene expression analysis enabled the correction of mistakes referenced into protein databases (e.g. bovine vinculin) and constitutes valuable evidence for predictions based on genome annotation. Conclusions Elaboration of a reference proteome constitutes the first step in creating a gene expression database dedicated to capillary endothelial cells displaying BBB characteristics. It improves of our knowledge of the BBB and the key proteins in cell structures, cytoskeleton organization, metabolism, detoxification and drug resistance. Moreover, our results emphasize the need for both appropriate experimental design and correct interpretation of proteome datasets. PMID:21078152

  19. A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum

    PubMed Central

    Krishna, Ritesh; Xia, Dong; Sanderson, Sanya; Shanmugasundram, Achchuthan; Vermont, Sarah; Bernal, Axel; Daniel-Naguib, Gianluca; Ghali, Fawaz; Brunk, Brian P; Roos, David S; Wastling, Jonathan M; Jones, Andrew R

    2015-01-01

    Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large-scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta-analysis. We identified a total of 201 996 and 39 953 peptide-spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein-level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA-Seq-derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA-Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes. The findings of this study have been integrated into the EuPathDB. The data have been deposited to the ProteomeXchange with identifiers PXD000297and PXD000298. PMID:25867681

  20. Needs, opportunities, and options for large scale systems research

    SciTech Connect

    Thompson, G.L.

    1984-10-01

    The Office of Energy Research was recently asked to perform a study of Large Scale Systems in order to facilitate the development of a true large systems theory. It was decided to ask experts in the fields of electrical engineering, chemical engineering and manufacturing/operations research for their ideas concerning large scale systems research. The author was asked to distribute a questionnaire among these experts to find out their opinions concerning recent accomplishments and future research directions in large scale systems research. He was also requested to convene a conference which included three experts in each area as panel members to discuss the general area of large scale systems research. The conference was held on March 26--27, 1984 in Pittsburgh with nine panel members, and 15 other attendees. The present report is a summary of the ideas presented and the recommendations proposed by the attendees.

  1. Interpretation of large-scale deviations from the Hubble flow

    NASA Astrophysics Data System (ADS)

    Grinstein, B.; Politzer, H. David; Rey, S.-J.; Wise, Mark B.

    1987-03-01

    The theoretical expectation for large-scale streaming velocities relative to the Hubble flow is expressed in terms of statistical correlation functions. Only for objects that trace the mass would these velocities have a simple cosmological interpretation. If some biasing effects the objects' formation, then nonlinear gravitational evolution is essential to predicting the expected large-scale velocities, which also depend on the nature of the biasing.

  2. Large scale suppression of scalar power on a spatial condensation

    NASA Astrophysics Data System (ADS)

    Kouwn, Seyen; Kwon, O.-Kab; Oh, Phillial

    2015-03-01

    We consider a deformed single-field inflation model in terms of three SO(3) symmetric moduli fields. We find that spatially linear solutions for the moduli fields induce a phase transition during the early stage of the inflation and the suppression of scalar power spectrum at large scales. This suppression can be an origin of anomalies for large-scale perturbation modes in the cosmological observation.

  3. Evaluation of drought propagation in an ensemble mean of large-scale hydrological models

    NASA Astrophysics Data System (ADS)

    Van Loon, A. F.; Van Huijgevoort, M. H. J.; Van Lanen, H. A. J.

    2012-11-01

    snow-related droughts. Furthermore, almost no composite droughts were simulated for slowly responding areas, while many multi-year drought events were expected in these systems. We conclude that most drought propagation processes are reasonably well reproduced by the ensemble mean of large-scale models in contrasting catchments in Europe. Challenges, however, remain in catchments with cold and semi-arid climates and catchments with large storage in aquifers or lakes. This leads to a high uncertainty in hydrological drought simulation at large scales. Improvement of drought simulation in large-scale models should focus on a better representation of hydrological processes that are important for drought development, such as evapotranspiration, snow accumulation and melt, and especially storage. Besides the more explicit inclusion of storage in large-scale models, also parametrisation of storage processes requires attention, for example through a global-scale dataset on aquifer characteristics, improved large-scale datasets on other land characteristics (e.g. soils, land cover), and calibration/evaluation of the models against observations of storage (e.g. in snow, groundwater).

  4. Large-scale motions in a plane wall jet

    NASA Astrophysics Data System (ADS)

    Gnanamanickam, Ebenezer; Jonathan, Latim; Shibani, Bhatt

    2015-11-01

    The dynamic significance of large-scale motions in turbulent boundary layers have been the focus of several recent studies, primarily focussing on canonical flows - zero pressure gradient boundary layers, flows within pipes and channels. This work presents an investigation into the large-scale motions in a boundary layer that is used as the prototypical flow field for flows with large-scale mixing and reactions, the plane wall jet. An experimental investigation is carried out in a plane wall jet facility designed to operate at friction Reynolds numbers Reτ > 1000 , which allows for the development of a significant logarithmic region. The streamwise turbulent intensity across the boundary layer is decomposed into small-scale (less than one integral length-scale δ) and large-scale components. The small-scale energy has a peak in the near-wall region associated with the near-wall turbulent cycle as in canonical boundary layers. However, eddies of large-scales are the dominating eddies having significantly higher energy, than the small-scales across almost the entire boundary layer even at the low to moderate Reynolds numbers under consideration. The large-scales also appear to amplitude and frequency modulate the smaller scales across the entire boundary layer.

  5. Large-Scale Spray Releases: Additional Aerosol Test Results

    SciTech Connect

    Daniel, Richard C.; Gauglitz, Phillip A.; Burns, Carolyn A.; Fountain, Matthew S.; Shimskey, Rick W.; Billing, Justin M.; Bontha, Jagannadha R.; Kurath, Dean E.; Jenks, Jeromy WJ; MacFarlan, Paul J.; Mahoney, Lenna A.

    2013-08-01

    One of the events postulated in the hazard analysis for the Waste Treatment and Immobilization Plant (WTP) and other U.S. Department of Energy (DOE) nuclear facilities is a breach in process piping that produces aerosols with droplet sizes in the respirable range. The current approach for predicting the size and concentration of aerosols produced in a spray leak event involves extrapolating from correlations reported in the literature. These correlations are based on results obtained from small engineered spray nozzles using pure liquids that behave as a Newtonian fluid. The narrow ranges of physical properties on which the correlations are based do not cover the wide range of slurries and viscous materials that will be processed in the WTP and in processing facilities across the DOE complex. To expand the data set upon which the WTP accident and safety analyses were based, an aerosol spray leak testing program was conducted by Pacific Northwest National Laboratory (PNNL). PNNL’s test program addressed two key technical areas to improve the WTP methodology (Larson and Allen 2010). The first technical area was to quantify the role of slurry particles in small breaches where slurry particles may plug the hole and prevent high-pressure sprays. The results from an effort to address this first technical area can be found in Mahoney et al. (2012a). The second technical area was to determine aerosol droplet size distribution and total droplet volume from prototypic breaches and fluids, including sprays from larger breaches and sprays of slurries for which literature data are mostly absent. To address the second technical area, the testing program collected aerosol generation data at two scales, commonly referred to as small-scale and large-scale testing. The small-scale testing and resultant data are described in Mahoney et al. (2012b), and the large-scale testing and resultant data are presented in Schonewill et al. (2012). In tests at both scales, simulants were used

  6. Large-scale simulations of layered double hydroxide nanocomposite materials

    NASA Astrophysics Data System (ADS)

    Thyveetil, Mary-Ann

    Layered double hydroxides (LDHs) have the ability to intercalate a multitude of anionic species. Atomistic simulation techniques such as molecular dynamics have provided considerable insight into the behaviour of these materials. We review these techniques and recent algorithmic advances which considerably improve the performance of MD applications. In particular, we discuss how the advent of high performance computing and computational grids has allowed us to explore large scale models with considerable ease. Our simulations have been heavily reliant on computational resources on the UK's NGS (National Grid Service), the US TeraGrid and the Distributed European Infrastructure for Supercomputing Applications (DEISA). In order to utilise computational grids we rely on grid middleware to launch, computationally steer and visualise our simulations. We have integrated the RealityGrid steering library into the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) 1 . which has enabled us to perform re mote computational steering and visualisation of molecular dynamics simulations on grid infrastruc tures. We also use the Application Hosting Environment (AHE) 2 in order to launch simulations on remote supercomputing resources and we show that data transfer rates between local clusters and super- computing resources can be considerably enhanced by using optically switched networks. We perform large scale molecular dynamics simulations of MgiAl-LDHs intercalated with either chloride ions or a mixture of DNA and chloride ions. The systems exhibit undulatory modes, which are suppressed in smaller scale simulations, caused by the collective thermal motion of atoms in the LDH layers. Thermal undulations provide elastic properties of the system including the bending modulus, Young's moduli and Poisson's ratios. To explore the interaction between LDHs and DNA. we use molecular dynamics techniques to per form simulations of double stranded, linear and plasmid DNA up

  7. Fast large-scale object retrieval with binary quantization

    NASA Astrophysics Data System (ADS)

    Zhou, Shifu; Zeng, Dan; Shen, Wei; Zhang, Zhijiang; Tian, Qi

    2015-11-01

    The objective of large-scale object retrieval systems is to search for images that contain the target object in an image database. Where state-of-the-art approaches rely on global image representations to conduct searches, we consider many boxes per image as candidates to search locally in a picture. In this paper, a feature quantization algorithm called binary quantization is proposed. In binary quantization, a scale-invariant feature transform (SIFT) feature is quantized into a descriptive and discriminative bit-vector, which allows itself to adapt to the classic inverted file structure for box indexing. The inverted file, which stores the bit-vector and box ID where the SIFT feature is located inside, is compact and can be loaded into the main memory for efficient box indexing. We evaluate our approach on available object retrieval datasets. Experimental results demonstrate that the proposed approach is fast and achieves excellent search quality. Therefore, the proposed approach is an improvement over state-of-the-art approaches for object retrieval.

  8. Large-Scale Advanced Prop-Fan (LAP)

    NASA Technical Reports Server (NTRS)

    Degeorge, C. L.

    1988-01-01

    In recent years, considerable attention has been directed toward improving aircraft fuel efficiency. Analytical studies and research with wind tunnel models have demonstrated that the high inherent efficiency of low speed turboprop propulsion systems may now be extended to the Mach .8 flight regime of today's commercial airliners. This can be accomplished with a propeller, employing a large number of thin highly swept blades. The term Prop-Fan has been coined to describe such a propulsion system. In 1983 the NASA-Lewis Research Center contracted with Hamilton Standard to design, build and test a near full scale Prop-Fan, designated the Large Scale Advanced Prop-Fan (LAP). This report provides a detailed description of the LAP program. The assumptions and analytical procedures used in the design of Prop-Fan system components are discussed in detail. The manufacturing techniques used in the fabrication of the Prop-Fan are presented. Each of the tests run during the course of the program are also discussed and the major conclusions derived from them stated.

  9. Implicit solvers for large-scale nonlinear problems

    SciTech Connect

    Keyes, D E; Reynolds, D; Woodward, C S

    2006-07-13

    Computational scientists are grappling with increasingly complex, multi-rate applications that couple such physical phenomena as fluid dynamics, electromagnetics, radiation transport, chemical and nuclear reactions, and wave and material propagation in inhomogeneous media. Parallel computers with large storage capacities are paving the way for high-resolution simulations of coupled problems; however, hardware improvements alone will not prove enough to enable simulations based on brute-force algorithmic approaches. To accurately capture nonlinear couplings between dynamically relevant phenomena, often while stepping over rapid adjustments to quasi-equilibria, simulation scientists are increasingly turning to implicit formulations that require a discrete nonlinear system to be solved for each time step or steady state solution. Recent advances in iterative methods have made fully implicit formulations a viable option for solution of these large-scale problems. In this paper, we overview one of the most effective iterative methods, Newton-Krylov, for nonlinear systems and point to software packages with its implementation. We illustrate the method with an example from magnetically confined plasma fusion and briefly survey other areas in which implicit methods have bestowed important advantages, such as allowing high-order temporal integration and providing a pathway to sensitivity analyses and optimization. Lastly, we overview algorithm extensions under development motivated by current SciDAC applications.

  10. Large-Scale NMR Measurements in Porous Media

    NASA Astrophysics Data System (ADS)

    Legchenko, Anatoly; Vouillamoz, Jean-Michel

    2011-03-01

    The large-scale Nuclear Magnetic Resonance measurements in the Earth's magnetic field (Surface NMR method) is a geophysical technique that allows non-invasive investigations of water-saturated rocks. The measuring setup consists of a wire loop on the surface that is energized by one or two pulses of oscillating current. After the pulses are cut off, the free induction decay (FID) and/or the spin echo (SE) signal from groundwater could be measured. SNMR results are averaged over the investigated volume that depends on the loop size and typically varies from 20x20x20 to 100x100x100 cubic meters. The maximum depth of groundwater detection can vary from 45 to 150 m depending on measurement conditions, although an average depth of investigation is generally considered to be about 100 m. Our recent results show that combination of FID and SE allows rendering the SNMR less dependent on the geological conditions. Because of different scales, use of rock samples for calibration of the SNMR-estimate of the water content is difficult or impossible. Thus, for interpretation of experimental data we use a mathematical model that allows computing the theoretical signal generated by groundwater. The processing of SNMR data can provide the depth, thickness and water content of investigated aquifers. For improving accuracy of the SNMR results we use calibration based on borehole pumping test data. Based on the water content and the relaxation time provided by MRS it is possible to estimate the aquifer's hydrodynamic properties.

  11. Characterizing unknown systematics in large scale structure surveys

    SciTech Connect

    Agarwal, Nishant; Ho, Shirley; Myers, Adam D.; Seo, Hee-Jong; Ross, Ashley J.; Bahcall, Neta; Brinkmann, Jonathan; Eisenstein, Daniel J.; Muna, Demitri; Palanque-Delabrouille, Nathalie; Yèche, Christophe; Petitjean, Patrick; Schneider, Donald P.; Streblyanska, Alina; Weaver, Benjamin A.

    2014-04-01

    Photometric large scale structure (LSS) surveys probe the largest volumes in the Universe, but are inevitably limited by systematic uncertainties. Imperfect photometric calibration leads to biases in our measurements of the density fields of LSS tracers such as galaxies and quasars, and as a result in cosmological parameter estimation. Earlier studies have proposed using cross-correlations between different redshift slices or cross-correlations between different surveys to reduce the effects of such systematics. In this paper we develop a method to characterize unknown systematics. We demonstrate that while we do not have sufficient information to correct for unknown systematics in the data, we can obtain an estimate of their magnitude. We define a parameter to estimate contamination from unknown systematics using cross-correlations between different redshift slices and propose discarding bins in the angular power spectrum that lie outside a certain contamination tolerance level. We show that this method improves estimates of the bias using simulated data and further apply it to photometric luminous red galaxies in the Sloan Digital Sky Survey as a case study.

  12. Locating inefficient links in a large-scale transportation network

    NASA Astrophysics Data System (ADS)

    Sun, Li; Liu, Like; Xu, Zhongzhi; Jie, Yang; Wei, Dong; Wang, Pu

    2015-02-01

    Based on data from geographical information system (GIS) and daily commuting origin destination (OD) matrices, we estimated the distribution of traffic flow in the San Francisco road network and studied Braess's paradox in a large-scale transportation network with realistic travel demand. We measured the variation of total travel time Δ T when a road segment is closed, and found that | Δ T | follows a power-law distribution if Δ T < 0 or Δ T > 0. This implies that most roads have a negligible effect on the efficiency of the road network, while the failure of a few crucial links would result in severe travel delays, and closure of a few inefficient links would counter-intuitively reduce travel costs considerably. Generating three theoretical networks, we discovered that the heterogeneously distributed travel demand may be the origin of the observed power-law distributions of | Δ T | . Finally, a genetic algorithm was used to pinpoint inefficient link clusters in the road network. We found that closing specific road clusters would further improve the transportation efficiency.

  13. Assessing large-scale wildlife responses to human infrastructure development.

    PubMed

    Torres, Aurora; Jaeger, Jochen A G; Alonso, Juan Carlos

    2016-07-26

    Habitat loss and deterioration represent the main threats to wildlife species, and are closely linked to the expansion of roads and human settlements. Unfortunately, large-scale effects of these structures remain generally overlooked. Here, we analyzed the European transportation infrastructure network and found that 50% of the continent is within 1.5 km of transportation infrastructure. We present a method for assessing the impacts from infrastructure on wildlife, based on functional response curves describing density reductions in birds and mammals (e.g., road-effect zones), and apply it to Spain as a case study. The imprint of infrastructure extends over most of the country (55.5% in the case of birds and 97.9% for mammals), with moderate declines predicted for birds (22.6% of individuals) and severe declines predicted for mammals (46.6%). Despite certain limitations, we suggest the approach proposed is widely applicable to the evaluation of effects of planned infrastructure developments under multiple scenarios, and propose an internationally coordinated strategy to update and improve it in the future. PMID:27402749

  14. Scalable NIC-based reduction on large-scale clusters

    SciTech Connect

    Moody, A.; Fernández, J. C.; Petrini, F.; Panda, Dhabaleswar K.

    2003-01-01

    Many parallel algorithms require effiaent support for reduction mllectives. Over the years, researchers have developed optimal reduction algonduns by taking inm account system size, dam size, and complexities of reduction operations. However, all of these algorithm have assumed the faa that the reduction precessing takes place on the host CPU. Modem Network Interface Cards (NICs) sport programmable processors with substantial memory and thus introduce a fresh variable into the equation This raises the following intersting challenge: Can we take advantage of modern NICs to implementJost redudion operations? In this paper, we take on this challenge in the context of large-scale clusters. Through experiments on the 960-node, 1920-processor or ASCI Linux Cluster (ALC) located at the Lawrence Livermore National Laboratory, we show that NIC-based reductions indeed perform with reduced latency and immed consistency over host-based aleorithms for the wmmon case and that these benefits scale as the system grows. In the largest configuration tested--1812 processors-- our NIC-based algorithm can sum a single element vector in 73 ps with 32-bi integers and in 118 with Mbit floating-point numnbers. These results represent an improvement, respeaively, of 121% and 39% with resvect w the {approx}roductionle vel MPI library

  15. Determining Environmental Impacts of Large Scale Irrigation in Turkey

    NASA Astrophysics Data System (ADS)

    Simpson, K.; Douglas, E. M.; Limbrunner, J. F.; Ozertan, G.

    2010-12-01

    In 1989, the Turkish government launched their most comprehensive regional development plan in history entitled the Southeastern Anatolia Project (SAP) which focuses on improving the quality of life and income level within the most underdeveloped region in Turkey. This project aims to integrate sustainable human development through agriculture, industry, transportation, education, health and rural and urban infrastructure building. In May 2008, a new action plan was announced for the region which includes the designation of almost 800,000 hectares of previously unirrigated land to be open for irrigation within the next five years. If not done in a sustainable manner, such a large-scale irrigation project could cause severe environmental impacts. The first objective of our research is to use computer simulations to reproduce the observed environmental impacts of irrigated agriculture in this arid region, primarily by simulating the effects of soil salinization. The second objective of our research is to estimate soil salinization that could result from expanded irrigation and suggest sustainable strategies for the newly irrigated land in Turkey in order to minimize these environmental impacts.

  16. Scalable pattern recognition for large-scale scientific data mining

    SciTech Connect

    Kamath, C.; Musick, R.

    1998-03-23

    Our ability to generate data far outstrips our ability to explore and understand it. The true value of this data lies not in its final size or complexity, but rather in our ability to exploit the data to achieve scientific goals. The data generated by programs such as ASCI have such a large scale that it is impractical to manually analyze, explore, and understand it. As a result, useful information is overlooked, and the potential benefits of increased computational and data gathering capabilities are only partially realized. The difficulties that will be faced by ASCI applications in the near future are foreshadowed by the challenges currently facing astrophysicists in making full use of the data they have collected over the years. For example, among other difficulties, astrophysicists have expressed concern that the sheer size of their data restricts them to looking at very small, narrow portions at any one time. This narrow focus has resulted in the loss of ``serendipitous`` discoveries which have been so vital to progress in the area in the past. To solve this problem, a new generation of computational tools and techniques is needed to help automate the exploration and management of large scientific data. This whitepaper proposes applying and extending ideas from the area of data mining, in particular pattern recognition, to improve the way in which scientists interact with large, multi-dimensional, time-varying data.

  17. State of the Art in Large-Scale Soil Moisture Monitoring

    NASA Technical Reports Server (NTRS)

    Ochsner, Tyson E.; Cosh, Michael Harold; Cuenca, Richard H.; Dorigo, Wouter; Draper, Clara S.; Hagimoto, Yutaka; Kerr, Yan H.; Larson, Kristine M.; Njoku, Eni Gerald; Small, Eric E.; Zreda, Marek G.

    2013-01-01

    Soil moisture is an essential climate variable influencing land atmosphere interactions, an essential hydrologic variable impacting rainfall runoff processes, an essential ecological variable regulating net ecosystem exchange, and an essential agricultural variable constraining food security. Large-scale soil moisture monitoring has advanced in recent years creating opportunities to transform scientific understanding of soil moisture and related processes. These advances are being driven by researchers from a broad range of disciplines, but this complicates collaboration and communication. For some applications, the science required to utilize large-scale soil moisture data is poorly developed. In this review, we describe the state of the art in large-scale soil moisture monitoring and identify some critical needs for research to optimize the use of increasingly available soil moisture data. We review representative examples of 1) emerging in situ and proximal sensing techniques, 2) dedicated soil moisture remote sensing missions, 3) soil moisture monitoring networks, and 4) applications of large-scale soil moisture measurements. Significant near-term progress seems possible in the use of large-scale soil moisture data for drought monitoring. Assimilation of soil moisture data for meteorological or hydrologic forecasting also shows promise, but significant challenges related to model structures and model errors remain. Little progress has been made yet in the use of large-scale soil moisture observations within the context of ecological or agricultural modeling. Opportunities abound to advance the science and practice of large-scale soil moisture monitoring for the sake of improved Earth system monitoring, modeling, and forecasting.

  18. Proteomic profiling of Plasmodium falciparum through improved, semiquantitative two-dimensional gel electrophoresis.

    PubMed

    Smit, Salome; Stoychev, Stoyan; Louw, Abraham I; Birkholtz, Lyn-Marie

    2010-05-01

    Two-dimensional gel electrophoresis (2-DE) is one of the most commonly used technologies to obtain a snapshot of the proteome at any specific time. However, its application to study the Plasmodial (malaria parasite) proteome is still limited due to inefficient extraction and detection methods and the extraordinarily large size of some proteins. Here, we report an optimized protein extraction method, the most appropriate methods for Plasmodial protein quantification and 2-DE detection, and finally protein identification by mass spectrometry (MS). Linear detection of Plasmodial proteins in a optimized lysis buffer was only possible with the 2-D Quant kit, and of the four stains investigated, Flamingo Pink was superior regarding sensitivity, linearity, and excellent MS-compatibility. 2-DE analyses of the Plasmodial proteome using this methodology resulted in the reliable detection of 349 spots and a 95% success rate in MS/MS identification. Subsequent application to the analyses of the Plasmodial ring and trophozoite proteomes ultimately resulted in the identification of 125 protein spots, which constituted 57 and 49 proteins from the Plasmodial ring and trophozoite stages, respectively. This study additionally highlights the presence of various isoforms within the Plasmodial proteome, which is of significant biological importance within the Plasmodial parasite during development in the intraerythrocytic developmental cycle. PMID:20218691

  19. The large-scale landslide risk classification in catchment scale

    NASA Astrophysics Data System (ADS)

    Liu, Che-Hsin; Wu, Tingyeh; Chen, Lien-Kuang; Lin, Sheng-Chi

    2013-04-01

    The landslide disasters caused heavy casualties during Typhoon Morakot, 2009. This disaster is defined as largescale landslide due to the casualty numbers. This event also reflects the survey on large-scale landslide potential is so far insufficient and significant. The large-scale landslide potential analysis provides information about where should be focused on even though it is very difficult to distinguish. Accordingly, the authors intend to investigate the methods used by different countries, such as Hong Kong, Italy, Japan and Switzerland to clarify the assessment methodology. The objects include the place with susceptibility of rock slide and dip slope and the major landslide areas defined from historical records. Three different levels of scales are confirmed necessarily from country to slopeland, which are basin, catchment, and slope scales. Totally ten spots were classified with high large-scale landslide potential in the basin scale. The authors therefore focused on the catchment scale and employ risk matrix to classify the potential in this paper. The protected objects and large-scale landslide susceptibility ratio are two main indexes to classify the large-scale landslide risk. The protected objects are the constructions and transportation facilities. The large-scale landslide susceptibility ratio is based on the data of major landslide area and dip slope and rock slide areas. Totally 1,040 catchments are concerned and are classified into three levels, which are high, medium, and low levels. The proportions of high, medium, and low levels are 11%, 51%, and 38%, individually. This result represents the catchments with high proportion of protected objects or large-scale landslide susceptibility. The conclusion is made and it be the base material for the slopeland authorities when considering slopeland management and the further investigation.

  20. A Topology Visualization Early Warning Distribution Algorithm for Large-Scale Network Security Incidents

    PubMed Central

    He, Hui; Fan, Guotao; Ye, Jianwei; Zhang, Weizhe

    2013-01-01

    It is of great significance to research the early warning system for large-scale network security incidents. It can improve the network system's emergency response capabilities, alleviate the cyber attacks' damage, and strengthen the system's counterattack ability. A comprehensive early warning system is presented in this paper, which combines active measurement and anomaly detection. The key visualization algorithm and technology of the system are mainly discussed. The large-scale network system's plane visualization is realized based on the divide and conquer thought. First, the topology of the large-scale network is divided into some small-scale networks by the MLkP/CR algorithm. Second, the sub graph plane visualization algorithm is applied to each small-scale network. Finally, the small-scale networks' topologies are combined into a topology based on the automatic distribution algorithm of force analysis. As the algorithm transforms the large-scale network topology plane visualization problem into a series of small-scale network topology plane visualization and distribution problems, it has higher parallelism and is able to handle the display of ultra-large-scale network topology. PMID:24191145

  1. A global review of large-scale experimental manipulations of streamflow

    NASA Astrophysics Data System (ADS)

    Konrad, C. P.; Olden, J. D.

    2010-12-01

    Ecological objectives have been integrated increasingly into the operation of water resources systems including dams, diversions, and pumps. In some cases, streamflow has been manipulated as a large-scale experiment aimed at both learning and improving river, floodplain, and estuarine resources. Our working group at the National Center for Ecological Analysis and Synthesis has conducted a global review of large-scale flow experiments to assess how these efforts can be effective both scientifically and socially. Rivers, floodplains, and estuaries are particularly challenging subjects for large-scale experiments because they are open systems with strong longitudinal connectivity and heterogeneity. These systems rarely can be isolated from their social context, thus stakeholders and water managers must be involved in experimental planning and implementation. Large-scale flow experiments have been effective for learning and informing management decisions when 1) treatments can be applied discretely - separate from other management interventions - and repeated, 2) directly measured responses have mechanistic links to broader resource objectives, and 3) there is institutional support for investigations and adoption of new information into operating policies. In focused applications with a clear nexus to decision-making, large-scale flow experiments complement longer term monitoring of aquatic ecosystems and evaluation of operations in adaptive management of water resources.

  2. A topology visualization early warning distribution algorithm for large-scale network security incidents.

    PubMed

    He, Hui; Fan, Guotao; Ye, Jianwei; Zhang, Weizhe

    2013-01-01

    It is of great significance to research the early warning system for large-scale network security incidents. It can improve the network system's emergency response capabilities, alleviate the cyber attacks' damage, and strengthen the system's counterattack ability. A comprehensive early warning system is presented in this paper, which combines active measurement and anomaly detection. The key visualization algorithm and technology of the system are mainly discussed. The large-scale network system's plane visualization is realized based on the divide and conquer thought. First, the topology of the large-scale network is divided into some small-scale networks by the MLkP/CR algorithm. Second, the sub graph plane visualization algorithm is applied to each small-scale network. Finally, the small-scale networks' topologies are combined into a topology based on the automatic distribution algorithm of force analysis. As the algorithm transforms the large-scale network topology plane visualization problem into a series of small-scale network topology plane visualization and distribution problems, it has higher parallelism and is able to handle the display of ultra-large-scale network topology. PMID:24191145

  3. Fast Computation of Wideband Beam Pattern for Designing Large-Scale 2-D Arrays.

    PubMed

    Chi, Cheng; Li, Zhaohui

    2016-06-01

    For real-time and high-resolution 3-D ultrasound imaging, the design of sparse distribution and weights of elements of a large-scale wideband 2-D array is needed to reduce hardware cost and achieve better directivity. However, due to the high time consumption of computing the wideband beam pattern, the design methods that need massive iterations have rarely been applied to design large-scale wideband 2-D arrays by directly computing the wideband beam pattern. In this paper, a fast method is proposed to realize the computation of a wideband beam pattern of arbitrary 2-D arrays in the far field in order to design large-scale wideband 2-D arrays. The proposed fast method exploits two important techniques: 1) nonuniform fast Fourier transform (FFT) and 2) short inverse FFT. Compared with the commonly used ultrasound simulator Field II, two orders of magnitude improvement in computation speed is achieved with comparable accuracy. The proposed fast method enables massive iterations of direct wideband beam pattern computation of arbitrary large-scale 2-D arrays. A design example in this paper demonstrates that the proposed fast method can help achieve better performance in designing large-scale wideband 2-D arrays. PMID:27046870

  4. Combining p-values in large-scale genomics experiments.

    PubMed

    Zaykin, Dmitri V; Zhivotovsky, Lev A; Czika, Wendy; Shao, Susan; Wolfinger, Russell D

    2007-01-01

    In large-scale genomics experiments involving thousands of statistical tests, such as association scans and microarray expression experiments, a key question is: Which of the L tests represent true associations (TAs)? The traditional way to control false findings is via individual adjustments. In the presence of multiple TAs, p-value combination methods offer certain advantages. Both Fisher's and Lancaster's combination methods use an inverse gamma transformation. We identify the relation of the shape parameter of that distribution to the implicit threshold value; p-values below that threshold are favored by the inverse gamma method (GM). We explore this feature to improve power over Fisher's method when L is large and the number of TAs is moderate. However, the improvement in power provided by combination methods is at the expense of a weaker claim made upon rejection of the null hypothesis - that there are some TAs among the L tests. Thus, GM remains a global test. To allow a stronger claim about a subset of p-values that is smaller than L, we investigate two methods with an explicit truncation: the rank truncated product method (RTP) that combines the first K-ordered p-values, and the truncated product method (TPM) that combines p-values that are smaller than a specified threshold. We conclude that TPM allows claims to be made about subsets of p-values, while the claim of the RTP is, like GM, more appropriately about all L tests. GM gives somewhat higher power than TPM, RTP, Fisher, and Simes methods across a range of simulations. PMID:17879330

  5. Combining p-values in large scale genomics experiments

    PubMed Central

    Zaykin, Dmitri V.; Zhivotovsky, Lev A.; Czika, Wendy; Shao, Susan; Wolfinger, Russell D.

    2008-01-01

    Summary In large-scale genomics experiments involving thousands of statistical tests, such as association scans and microarray expression experiments, a key question is: Which of the L tests represent true associations (TAs)? The traditional way to control false findings is via individual adjustments. In the presence of multiple TAs, p-value combination methods offer certain advantages. Both Fisher’s and Lancaster’s combination methods use an inverse gamma transformation. We identify the relation of the shape parameter of that distribution to the implicit threshold value; p-values below that threshold are favored by the inverse gamma method (GM). We explore this feature to improve power over Fisher’s method when L is large and the number of TAs is moderate. However, the improvement in power provided by combination methods is at the expense of a weaker claim made upon rejection of the null hypothesis – that there are some TAs among the L tests. Thus, GM remains a global test. To allow a stronger claim about a subset of p-values that is smaller than L, we investigate two methods with an explicit truncation: the rank truncated product method (RTP) that combines the first K ordered p-values, and the truncated product method (TPM) that combines p-values that are smaller than a specified threshold. We conclude that TPM allows claims to be made about subsets of p-values, while the claim of the RTP is, like GM, more appropriately about all L tests. GM gives somewhat higher power than TPM, RTP, Fisher, and Simes methods across a range of simulations. PMID:17879330

  6. Ultra-Fast Sample Preparation for High-Throughput Proteomics

    SciTech Connect

    Lopez-Ferrer, Daniel; Hixson, Kim K.; Belov, Mikhail E.; Smith, Richard D.

    2011-06-21

    Sample preparation oftentimes can be the Achilles Heel of any analytical process and in the field of proteomics, preparing samples for mass spectrometric analysis is no exception. Current goals, concerning proteomic sample preparation on a large scale, include efforts toward improving reproducibility, reducing the time of processing and ultimately the automation of the entire workflow. This chapter reviews an array of recent approaches applied to bottom-up proteomics sample preparation to reduce the processing time down from hours to minutes. The current state-of-the-art in the field uses different energy inputs like microwave, ultrasound or pressure to perform the four basic steps in sample preparation: protein extraction, denaturation, reduction and alkylation, and digestion. No single energy input for enhancement of proteome sample preparation has become the universal gold standard. Instead, a combination of different energy inputs tend to produce the best results. This chapter further describes the future trends in the field such as the hyphenation of sample preparation with downstream detection and analysis systems. Finally, a detailed protocol describing the combined use of both pressure cycling technology and ultrasonic energy inputs to hasten proteomic sample preparation is presented.

  7. Using the High-Level Based Program Interface to Facilitate the Large Scale Scientific Computing

    PubMed Central

    Shang, Yizi; Shang, Ling; Gao, Chuanchang; Lu, Guiming; Ye, Yuntao; Jia, Dongdong

    2014-01-01

    This paper is to make further research on facilitating the large-scale scientific computing on the grid and the desktop grid platform. The related issues include the programming method, the overhead of the high-level program interface based middleware, and the data anticipate migration. The block based Gauss Jordan algorithm as a real example of large-scale scientific computing is used to evaluate those issues presented above. The results show that the high-level based program interface makes the complex scientific applications on large-scale scientific platform easier, though a little overhead is unavoidable. Also, the data anticipation migration mechanism can improve the efficiency of the platform which needs to process big data based scientific applications. PMID:24574931

  8. Building a Large-Scale Computational Model of a Cortical Neuronal Network

    NASA Astrophysics Data System (ADS)

    Zemanová, Lucia; Zhou, Changsong; Kurths, Jürgen

    We introduce the general framework of the large-scale neuronal model used in the 5th Helmholtz Summer School — Complex Brain Networks. The main aim is to build a universal large-scale model of a cortical neuronal network, structured as a network of networks, which is flexible enough to implement different kinds of topology and neuronal models and which exhibits behavior in various dynamical regimes. First, we describe important biological aspects of brain topology and use them in the construction of a large-scale cortical network. Second, the general dynamical model is presented together with explanations of the major dynamical properties of neurons. Finally, we discuss the implementation of the model into parallel code and its possible modifications and improvements.

  9. Advancing Cell Biology Through Proteomics in Space and Time (PROSPECTS)*

    PubMed Central

    Lamond, Angus I.; Uhlen, Mathias; Horning, Stevan; Makarov, Alexander; Robinson, Carol V.; Serrano, Luis; Hartl, F. Ulrich; Baumeister, Wolfgang; Werenskiold, Anne Katrin; Andersen, Jens S.; Vorm, Ole; Linial, Michal; Aebersold, Ruedi; Mann, Matthias

    2012-01-01

    The term “proteomics” encompasses the large-scale detection and analysis of proteins and their post-translational modifications. Driven by major improvements in mass spectrometric instrumentation, methodology, and data analysis, the proteomics field has burgeoned in recent years. It now provides a range of sensitive and quantitative approaches for measuring protein structures and dynamics that promise to revolutionize our understanding of cell biology and molecular mechanisms in both human cells and model organisms. The Proteomics Specification in Time and Space (PROSPECTS) Network is a unique EU-funded project that brings together leading European research groups, spanning from instrumentation to biomedicine, in a collaborative five year initiative to develop new methods and applications for the functional analysis of cellular proteins. This special issue of Molecular and Cellular Proteomics presents 16 research papers reporting major recent progress by the PROSPECTS groups, including improvements to the resolution and sensitivity of the Orbitrap family of mass spectrometers, systematic detection of proteins using highly characterized antibody collections, and new methods for absolute as well as relative quantification of protein levels. Manuscripts in this issue exemplify approaches for performing quantitative measurements of cell proteomes and for studying their dynamic responses to perturbation, both during normal cellular responses and in disease mechanisms. Here we present a perspective on how the proteomics field is moving beyond simply identifying proteins with high sensitivity toward providing a powerful and versatile set of assay systems for characterizing proteome dynamics and thereby creating a new “third generation” proteomics strategy that offers an indispensible tool for cell biology and molecular medicine. PMID:22311636

  10. Newton iterative methods for large scale nonlinear systems. Progress report, 1992--1993

    SciTech Connect

    Walker, H.F.; Turner, K.

    1993-06-01

    Objective is to develop robust, efficient Newton iterative methods for general large scale problems well suited for discretizations of partial differential equations, integral equations, and other continuous problems. A concomitant objective is to develop improved iterative linear algebra methods. We first outline research on Newton iterative methods and then review work on iterative linear algebra methods. (DLC)

  11. Reflections on the Increasing Relevance of Large-Scale Professional Development

    ERIC Educational Resources Information Center

    Krainer, Konrad

    2015-01-01

    This paper focuses on commonalities and differences of three approaches to large-scale professional development (PD) in mathematics education, based on two studies from Germany and one from the United States of America. All three initiatives break new ground in improving PD targeted at educating "multipliers", and in all three cases…

  12. Inquiry-Based Educational Design for Large-Scale High School Astronomy Projects Using Real Telescopes

    ERIC Educational Resources Information Center

    Fitzgerald, Michael; McKinnon, David H.; Danaia, Lena

    2015-01-01

    In this paper, we outline the theory behind the educational design used to implement a large-scale high school astronomy education project. This design was created in response to the realization of ineffective educational design in the initial early stages of the project. The new design follows an iterative improvement model where the materials…

  13. Unsaturated Hydraulic Conductivity for Evaporation in Large scale Heterogeneous Soils

    NASA Astrophysics Data System (ADS)

    Sun, D.; Zhu, J.

    2014-12-01

    In this study we aim to provide some practical guidelines of how the commonly used simple averaging schemes (arithmetic, geometric, or harmonic mean) perform in simulating large scale evaporation in a large scale heterogeneous landscape. Previous studies on hydraulic property upscaling focusing on steady state flux exchanges illustrated that an effective hydraulic property is usually more difficult to define for evaporation. This study focuses on upscaling hydraulic properties of large scale transient evaporation dynamics using the idea of the stream tube approach. Specifically, the two main objectives are: (1) if the three simple averaging schemes (i.e., arithmetic, geometric and harmonic means) of hydraulic parameters are appropriate in representing large scale evaporation processes, and (2) how the applicability of these simple averaging schemes depends on the time scale of evaporation processes in heterogeneous soils. Multiple realizations of local evaporation processes are carried out using HYDRUS-1D computational code (Simunek et al, 1998). The three averaging schemes of soil hydraulic parameters were used to simulate the cumulative flux exchange, which is then compared with the large scale average cumulative flux. The sensitivity of the relative errors to the time frame of evaporation processes is also discussed.

  14. EINSTEIN'S SIGNATURE IN COSMOLOGICAL LARGE-SCALE STRUCTURE

    SciTech Connect

    Bruni, Marco; Hidalgo, Juan Carlos; Wands, David

    2014-10-10

    We show how the nonlinearity of general relativity generates a characteristic nonGaussian signal in cosmological large-scale structure that we calculate at all perturbative orders in a large-scale limit. Newtonian gravity and general relativity provide complementary theoretical frameworks for modeling large-scale structure in ΛCDM cosmology; a relativistic approach is essential to determine initial conditions, which can then be used in Newtonian simulations studying the nonlinear evolution of the matter density. Most inflationary models in the very early universe predict an almost Gaussian distribution for the primordial metric perturbation, ζ. However, we argue that it is the Ricci curvature of comoving-orthogonal spatial hypersurfaces, R, that drives structure formation at large scales. We show how the nonlinear relation between the spatial curvature, R, and the metric perturbation, ζ, translates into a specific nonGaussian contribution to the initial comoving matter density that we calculate for the simple case of an initially Gaussian ζ. Our analysis shows the nonlinear signature of Einstein's gravity in large-scale structure.

  15. Report of the Workshop on Petascale Systems Integration for LargeScale Facilities

    SciTech Connect

    Kramer, William T.C.; Walter, Howard; New, Gary; Engle, Tom; Pennington, Rob; Comes, Brad; Bland, Buddy; Tomlison, Bob; Kasdorf, Jim; Skinner, David; Regimbal, Kevin

    2007-10-01

    There are significant issues regarding Large Scale System integration that are not being addressed in other forums such as current research portfolios or vendor user groups. Unfortunately, the issues in the area of large-scale system integration often fall into a netherworld; not research, not facilities, not procurement, not operations, not user services. Taken together, these issues along with the impact of sub-optimal integration technology means the time required to deploy, integrate and stabilize large scale system may consume up to 20 percent of the useful life of such systems. Improving the state of the art for large scale systems integration has potential to increase the scientific productivity of these systems. Sites have significant expertise, but there are no easy ways to leverage this expertise among them . Many issues inhibit the sharing of information, including available time and effort, as well as issues with sharing proprietary information. Vendors also benefit in the long run from the solutions to issues detected during site testing and integration. There is a great deal of enthusiasm for making large scale system integration a full-fledged partner along with the other major thrusts supported by funding agencies in the definition, design, and use of a petascale systems. Integration technology and issues should have a full 'seat at the table' as petascale and exascale initiatives and programs are planned. The workshop attendees identified a wide range of issues and suggested paths forward. Pursuing these with funding opportunities and innovation offers the opportunity to dramatically improve the state of large scale system integration.

  16. Understanding the Physical Properties that Control Protein Crystallization by Analysis of Large-Scale Experimental Data

    SciTech Connect

    Price, W.; Chen, Y; Handelman, S; Neely, H; Manor, P; Karlin, R; Nair, R; Montelione, G; Hunt, J; et. al.

    2008-01-01

    Crystallization is the most serious bottleneck in high-throughput protein-structure determination by diffraction methods. We have used data mining of the large-scale experimental results of the Northeast Structural Genomics Consortium and experimental folding studies to characterize the biophysical properties that control protein crystallization. This analysis leads to the conclusion that crystallization propensity depends primarily on the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. We identify specific sequence features that correlate with crystallization propensity and that can be used to estimate the crystallization probability of a given construct. Analyses of entire predicted proteomes demonstrate substantial differences in the amino acid-sequence properties of human versus eubacterial proteins, which likely reflect differences in biophysical properties, including crystallization propensity. Our thermodynamic measurements do not generally support previous claims regarding correlations between sequence properties and protein stability.

  17. Acoustic Studies of the Large Scale Ocean Circulation

    NASA Technical Reports Server (NTRS)

    Menemenlis, Dimitris

    1999-01-01

    Detailed knowledge of ocean circulation and its transport properties is prerequisite to an understanding of the earth's climate and of important biological and chemical cycles. Results from two recent experiments, THETIS-2 in the Western Mediterranean and ATOC in the North Pacific, illustrate the use of ocean acoustic tomography for studies of the large scale circulation. The attraction of acoustic tomography is its ability to sample and average the large-scale oceanic thermal structure, synoptically, along several sections, and at regular intervals. In both studies, the acoustic data are compared to, and then combined with, general circulation models, meteorological analyses, satellite altimetry, and direct measurements from ships. Both studies provide complete regional descriptions of the time-evolving, three-dimensional, large scale circulation, albeit with large uncertainties. The studies raise serious issues about existing ocean observing capability and provide guidelines for future efforts.

  18. A relativistic signature in large-scale structure

    NASA Astrophysics Data System (ADS)

    Bartolo, Nicola; Bertacca, Daniele; Bruni, Marco; Koyama, Kazuya; Maartens, Roy; Matarrese, Sabino; Sasaki, Misao; Verde, Licia; Wands, David

    2016-09-01

    In General Relativity, the constraint equation relating metric and density perturbations is inherently nonlinear, leading to an effective non-Gaussianity in the dark matter density field on large scales-even if the primordial metric perturbation is Gaussian. Intrinsic non-Gaussianity in the large-scale dark matter overdensity in GR is real and physical. However, the variance smoothed on a local physical scale is not correlated with the large-scale curvature perturbation, so that there is no relativistic signature in the galaxy bias when using the simplest model of bias. It is an open question whether the observable mass proxies such as luminosity or weak lensing correspond directly to the physical mass in the simple halo bias model. If not, there may be observables that encode this relativistic signature.

  19. Coupling between convection and large-scale circulation

    NASA Astrophysics Data System (ADS)

    Becker, T.; Stevens, B. B.; Hohenegger, C.

    2014-12-01

    The ultimate drivers of convection - radiation, tropospheric humidity and surface fluxes - are altered both by the large-scale circulation and by convection itself. A quantity to which all drivers of convection contribute is moist static energy, or gross moist stability, respectively. Therefore, a variance analysis of the moist static energy budget in radiative-convective equilibrium helps understanding the interaction of precipitating convection and the large-scale environment. In addition, this method provides insights concerning the impact of convective aggregation on this coupling. As a starting point, the interaction is analyzed with a general circulation model, but a model intercomparison study using a hierarchy of models is planned. Effective coupling parameters will be derived from cloud resolving models and these will in turn be related to assumptions used to parameterize convection in large-scale models.

  20. Large-scale current systems in the dayside Venus ionosphere

    NASA Technical Reports Server (NTRS)

    Luhmann, J. G.; Elphic, R. C.; Brace, L. H.

    1981-01-01

    The occasional observation of large-scale horizontal magnetic fields within the dayside ionosphere of Venus by the flux gate magnetometer on the Pioneer Venus orbiter suggests the presence of large-scale current systems. Using the measured altitude profiles of the magnetic field and the electron density and temperature, together with the previously reported neutral atmosphere density and composition, it is found that the local ionosphere can be described at these times by a simple steady state model which treats the unobserved quantities, such as the electric field, as parameters. When the model is appropriate, the altitude profiles of the ion and electron velocities and the currents along the satellite trajectory can be inferred. These results elucidate the configurations and sources of the ionospheric current systems which produce the observed large-scale magnetic fields, and in particular illustrate the effect of ion-neutral coupling in the determination of the current system at low altitudes.

  1. Do Large-Scale Topological Features Correlate with Flare Properties?

    NASA Astrophysics Data System (ADS)

    DeRosa, Marc L.; Barnes, Graham

    2016-05-01

    In this study, we aim to identify whether the presence or absence of particular topological features in the large-scale coronal magnetic field are correlated with whether a flare is confined or eruptive. To this end, we first determine the locations of null points, spine lines, and separatrix surfaces within the potential fields associated with the locations of several strong flares from the current and previous sunspot cycles. We then validate the topological skeletons against large-scale features in observations, such as the locations of streamers and pseudostreamers in coronagraph images. Finally, we characterize the topological environment in the vicinity of the flaring active regions and identify the trends involving their large-scale topologies and the properties of the associated flares.

  2. Comparative proteomics in acute myeloid leukemia

    PubMed Central

    Luczak, Magdalena; Kaźmierczak, Maciej; Hadschuh, Luiza; Lewandowski, Krzysztof; Komarnicki, Mieczysław

    2012-01-01

    The term proteomics was used for the first time in 1995 to describe large-scale protein analyses. At the same time proteomics was distinguished as a new domain of the life sciences. The major object of proteomic studies is the proteome, i.e. the set of all proteins accumulating in a given cell, tissue or organ. During the last years several new methods and techniques have been developed to increase the fidelity and efficacy of proteomic analyses. The most widely used are two-dimensional electrophoresis (2DE) and mass spectrometry (MS). In the past decade proteomic analyses have also been successfully applied in biomedical research. They allow one to determine how various diseases affect the pattern of protein accumulation. In this paper, we attempt to summarize the results of the proteomic analyses of acute myeloid leukemia (AML) cells. They have increased our knowledge on the mechanisms underlying AML development and contributed to progress in AML diagnostics and treatment. PMID:23788862

  3. Magnetic Helicity and Large Scale Magnetic Fields: A Primer

    NASA Astrophysics Data System (ADS)

    Blackman, Eric G.

    2015-05-01

    Magnetic fields of laboratory, planetary, stellar, and galactic plasmas commonly exhibit significant order on large temporal or spatial scales compared to the otherwise random motions within the hosting system. Such ordered fields can be measured in the case of planets, stars, and galaxies, or inferred indirectly by the action of their dynamical influence, such as jets. Whether large scale fields are amplified in situ or a remnant from previous stages of an object's history is often debated for objects without a definitive magnetic activity cycle. Magnetic helicity, a measure of twist and linkage of magnetic field lines, is a unifying tool for understanding large scale field evolution for both mechanisms of origin. Its importance stems from its two basic properties: (1) magnetic helicity is typically better conserved than magnetic energy; and (2) the magnetic energy associated with a fixed amount of magnetic helicity is minimized when the system relaxes this helical structure to the largest scale available. Here I discuss how magnetic helicity has come to help us understand the saturation of and sustenance of large scale dynamos, the need for either local or global helicity fluxes to avoid dynamo quenching, and the associated observational consequences. I also discuss how magnetic helicity acts as a hindrance to turbulent diffusion of large scale fields, and thus a helper for fossil remnant large scale field origin models in some contexts. I briefly discuss the connection between large scale fields and accretion disk theory as well. The goal here is to provide a conceptual primer to help the reader efficiently penetrate the literature.

  4. Large Scale Electronic Structure Calculations using Quantum Chemistry Methods

    NASA Astrophysics Data System (ADS)

    Scuseria, Gustavo E.

    1998-03-01

    This talk will address our recent efforts in developing fast, linear scaling electronic structure methods for large scale applications. Of special importance is our fast multipole method( M. C. Strain, G. E. Scuseria, and M. J. Frisch, Science 271), 51 (1996). (FMM) for achieving linear scaling for the quantum Coulomb problem (GvFMM), the traditional bottleneck in quantum chemistry calculations based on Gaussian orbitals. Fast quadratures(R. E. Stratmann, G. E. Scuseria, and M. J. Frisch, Chem. Phys. Lett. 257), 213 (1996). combined with methods that avoid the Hamiltonian diagonalization( J. M. Millam and G. E. Scuseria, J. Chem. Phys. 106), 5569 (1997) have resulted in density functional theory (DFT) programs that can be applied to systems containing many hundreds of atoms and ---depending on computational resources or level of theory-- to many thousands of atoms.( A. D. Daniels, J. M. Millam and G. E. Scuseria, J. Chem. Phys. 107), 425 (1997). Three solutions for the diagonalization bottleneck will be analyzed and compared: a conjugate gradient density matrix search (CGDMS), a Hamiltonian polynomial expansion of the density matrix, and a pseudo-diagonalization method. Besides DFT, our near-field exchange method( J. C. Burant, G. E. Scuseria, and M. J. Frisch, J. Chem. Phys. 105), 8969 (1996). for linear scaling Hartree-Fock calculations will be discussed. Based on these improved capabilities, we have also developed programs to obtain vibrational frequencies (via analytic energy second derivatives) and excitation energies (through time-dependent DFT) of large molecules like porphyn or C_70. Our GvFMM has been extended to periodic systems( K. N. Kudin and G. E. Scuseria, Chem. Phys. Lett., in press.) and progress towards a Gaussian-based DFT and HF program for polymers and solids will be reported. Last, we will discuss our progress on a Laplace-transformed \\cal O(N^2) second-order pertubation theory (MP2) method.

  5. Survey Design for Large-Scale, Unstructured Resistivity Surveys

    NASA Astrophysics Data System (ADS)

    Labrecque, D. J.; Casale, D.

    2009-12-01

    In this paper, we discuss the issues in designing data collection strategies for large-scale, poorly structured resistivity surveys. Existing or proposed applications for these types of surveys include carbon sequestration, enhanced oil recovery monitoring, monitoring of leachate from working or abandoned mines, and mineral surveys. Electrode locations are generally chosen by land access, utilities, roads, existing wells etc. Classical arrays such as the Wenner array or dipole-dipole arrays are not applicable if the electrodes cannot be placed in quasi-regular lines or grids. A new, far more generalized strategy is needed for building data collection schemes. Following the approach of earlier two-dimensional (2-D) survey designs, the proposed method begins by defining a base array. In (2-D) design, this base array is often a standard dipole-dipole array. For unstructured three-dimensional (3-D) design, determining this base array is a multi-step process. The first step is to determine a set of base dipoles with similar characteristics. For example, the base dipoles may consist of electrode pairs trending within 30 degrees of north and with a length between 100 and 250 m in length. These dipoles are then combined into a trial set of arrays. This trial set of arrays is reduced by applying a series of filters based on criteria such as separation between the dipoles. Using the base array set, additional arrays are added and tested to determine the overall improvement in resolution and to determine an optimal set of arrays. Examples of the design process are shown for a proposed carbon sequestration monitoring system.

  6. Numerical Technology for Large-Scale Computational Electromagnetics

    SciTech Connect

    Sharpe, R; Champagne, N; White, D; Stowell, M; Adams, R

    2003-01-30

    The key bottleneck of implicit computational electromagnetics tools for large complex geometries is the solution of the resulting linear system of equations. The goal of this effort was to research and develop critical numerical technology that alleviates this bottleneck for large-scale computational electromagnetics (CEM). The mathematical operators and numerical formulations used in this arena of CEM yield linear equations that are complex valued, unstructured, and indefinite. Also, simultaneously applying multiple mathematical modeling formulations to different portions of a complex problem (hybrid formulations) results in a mixed structure linear system, further increasing the computational difficulty. Typically, these hybrid linear systems are solved using a direct solution method, which was acceptable for Cray-class machines but does not scale adequately for ASCI-class machines. Additionally, LLNL's previously existing linear solvers were not well suited for the linear systems that are created by hybrid implicit CEM codes. Hence, a new approach was required to make effective use of ASCI-class computing platforms and to enable the next generation design capabilities. Multiple approaches were investigated, including the latest sparse-direct methods developed by our ASCI collaborators. In addition, approaches that combine domain decomposition (or matrix partitioning) with general-purpose iterative methods and special purpose pre-conditioners were investigated. Special-purpose pre-conditioners that take advantage of the structure of the matrix were adapted and developed based on intimate knowledge of the matrix properties. Finally, new operator formulations were developed that radically improve the conditioning of the resulting linear systems thus greatly reducing solution time. The goal was to enable the solution of CEM problems that are 10 to 100 times larger than our previous capability.

  7. From Systematic Errors to Cosmology Using Large-Scale Structure

    NASA Astrophysics Data System (ADS)

    Hunterer, Dragan

    We propose to carry out a two-pronged program to significantly improve links between galaxy surveys and constraints on primordial cosmology and fundamental physics. We will first develop the methodology to self-calibrate the survey, that is, determine the large-angle calibration systematics internally from the survey. We will use this information to correct biases that propagate from the largest to smaller angular scales. Our approach for tackling the systematics is very complementary to existing ones, in particular in the sense that it does not assume knowledge of specific systematic maps or templates. It is timely to undertake these analyses, since none of the currently known methods addresses the multiplicative effects of large-angle calibration errors that contaminate the small-scale signal and present one of the most significant sources of error in the large-scale structure. The second part of the proposal is to precisely quantify the statistical and systematic errors in the reconstruction of the Integrated Sachs-Wolfe (ISW) contribution to the cosmic microwave background (CMB) sky map using information from galaxy surveys. Unlike the ISW contributions to CMB power, the ISW map reconstruction has not been studied in detail to date. We will create a nimble plug-and-play pipeline to ascertain how reliably a map from an arbitrary LSS survey can be used to separate the late-time and early-time contributions to CMB anisotropy at large angular scales. We will pay particular attention to partial sky coverage, incomplete redshift information, finite redshift range, and imperfect knowledge of the selection function for the galaxy survey. Our work should serve as the departure point for a variety of implications in cosmology, including the physical origin of the large-angle CMB "anomalies".

  8. Large-Scale Data Challenges in Future Power Grids

    SciTech Connect

    Yin, Jian; Sharma, Poorva; Gorton, Ian; Akyol, Bora A.

    2013-03-25

    This paper describes technical challenges in supporting large-scale real-time data analysis for future power grid systems and discusses various design options to address these challenges. Even though the existing U.S. power grid has served the nation remarkably well over the last 120 years, big changes are in the horizon. The widespread deployment of renewable generation, smart grid controls, energy storage, plug-in hybrids, and new conducting materials will require fundamental changes in the operational concepts and principal components. The whole system becomes highly dynamic and needs constant adjustments based on real time data. Even though millions of sensors such as phase measurement units (PMUs) and smart meters are being widely deployed, a data layer that can support this amount of data in real time is needed. Unlike the data fabric in cloud services, the data layer for smart grids must address some unique challenges. This layer must be scalable to support millions of sensors and a large number of diverse applications and still provide real time guarantees. Moreover, the system needs to be highly reliable and highly secure because the power grid is a critical piece of infrastructure. No existing systems can satisfy all the requirements at the same time. We examine various design options. In particular, we explore the special characteristics of power grid data to meet both scalability and quality of service requirements. Our initial prototype can improve performance by orders of magnitude over existing general-purpose systems. The prototype was demonstrated with several use cases from PNNL’s FPGI and was shown to be able to integrate huge amount of data from a large number of sensors and a diverse set of applications.

  9. Coupled binary embedding for large-scale image retrieval.

    PubMed

    Zheng, Liang; Wang, Shengjin; Tian, Qi

    2014-08-01

    Visual matching is a crucial step in image retrieval based on the bag-of-words (BoW) model. In the baseline method, two keypoints are considered as a matching pair if their SIFT descriptors are quantized to the same visual word. However, the SIFT visual word has two limitations. First, it loses most of its discriminative power during quantization. Second, SIFT only describes the local texture feature. Both drawbacks impair the discriminative power of the BoW model and lead to false positive matches. To tackle this problem, this paper proposes to embed multiple binary features at indexing level. To model correlation between features, a multi-IDF scheme is introduced, through which different binary features are coupled into the inverted file. We show that matching verification methods based on binary features, such as Hamming embedding, can be effectively incorporated in our framework. As an extension, we explore the fusion of binary color feature into image retrieval. The joint integration of the SIFT visual word and binary features greatly enhances the precision of visual matching, reducing the impact of false positive matches. Our method is evaluated through extensive experiments on four benchmark datasets (Ukbench, Holidays, DupImage, and MIR Flickr 1M). We show that our method significantly improves the baseline approach. In addition, large-scale experiments indicate that the proposed method requires acceptable memory usage and query time compared with other approaches. Further, when global color feature is integrated, our method yields competitive performance with the state-of-the-arts. PMID:24951697

  10. Developments in large-scale coastal flood hazard mapping

    NASA Astrophysics Data System (ADS)

    Vousdoukas, Michalis I.; Voukouvalas, Evangelos; Mentaschi, Lorenzo; Dottori, Francesco; Giardino, Alessio; Bouziotas, Dimitrios; Bianchi, Alessandra; Salamon, Peter; Feyen, Luc

    2016-08-01

    Coastal flooding related to marine extreme events has severe socioeconomic impacts, and even though the latter are projected to increase under the changing climate, there is a clear deficit of information and predictive capacity related to coastal flood mapping. The present contribution reports on efforts towards a new methodology for mapping coastal flood hazard at European scale, combining (i) the contribution of waves to the total water level; (ii) improved inundation modeling; and (iii) an open, physics-based framework which can be constantly upgraded, whenever new and more accurate data become available. Four inundation approaches of gradually increasing complexity and computational costs were evaluated in terms of their applicability to large-scale coastal flooding mapping: static inundation (SM); a semi-dynamic method, considering the water volume discharge over the dykes (VD); the flood intensity index approach (Iw); and the model LISFLOOD-FP (LFP). A validation test performed against observed flood extents during the Xynthia storm event showed that SM and VD can lead to an overestimation of flood extents by 232 and 209 %, while Iw and LFP showed satisfactory predictive skill. Application at pan-European scale for the present-day 100-year event confirmed that static approaches can overestimate flood extents by 56 % compared to LFP; however, Iw can deliver results of reasonable accuracy in cases when reduced computational costs are a priority. Moreover, omitting the wave contribution in the extreme total water level (TWL) can result in a ˜ 60 % underestimation of the flooded area. The present findings have implications for impact assessment studies, since combination of the estimated inundation maps with population exposure maps revealed differences in the estimated number of people affected within the 20-70 % range.

  11. The Evolution of Baryons in Cosmic Large Scale Structure

    NASA Astrophysics Data System (ADS)

    Snedden, Ali; Arielle Phillips, Lara; Mathews, Grant James; Coughlin, Jared; Suh, In-Saeng; Bhattacharya, Aparna

    2015-01-01

    The environments of galaxies play a critical role in their formation and evolution. We study these environments using cosmological simulations with star formation and supernova feedback included. From these simulations, we parse the large scale structure into clusters, filaments and voids using a segmentation algorithm adapted from medical imaging. We trace the star formation history, gas phase and metal evolution of the baryons in the intergalactic medium as function of structure. We find that our algorithm reproduces the baryon fraction in the intracluster medium and that the majority of star formation occurs in cold, dense filaments. We present the consequences this large scale environment has for galactic halos and galaxy evolution.

  12. Corridors Increase Plant Species Richness at Large Scales

    SciTech Connect

    Damschen, Ellen I.; Haddad, Nick M.; Orrock,John L.; Tewksbury, Joshua J.; Levey, Douglas J.

    2006-09-01

    Habitat fragmentation is one of the largest threats to biodiversity. Landscape corridors, which are hypothesized to reduce the negative consequences of fragmentation, have become common features of ecological management plans worldwide. Despite their popularity, there is little evidence documenting the effectiveness of corridors in preserving biodiversity at large scales. Using a large-scale replicated experiment, we showed that habitat patches connected by corridors retain more native plant species than do isolated patches, that this difference increases over time, and that corridors do not promote invasion by exotic species. Our results support the use of corridors in biodiversity conservation.

  13. Large-scale ER-damper for seismic protection

    NASA Astrophysics Data System (ADS)

    McMahon, Scott; Makris, Nicos

    1997-05-01

    A large scale electrorheological (ER) damper has been designed, constructed, and tested. The damper consists of a main cylinder and a piston rod that pushes an ER-fluid through a number of stationary annular ducts. This damper is a scaled- up version of a prototype ER-damper which has been developed and extensively studied in the past. In this paper, results from comprehensive testing of the large-scale damper are presented, and the proposed theory developed for predicting the damper response is validated.

  14. Survey of decentralized control methods. [for large scale dynamic systems

    NASA Technical Reports Server (NTRS)

    Athans, M.

    1975-01-01

    An overview is presented of the types of problems that are being considered by control theorists in the area of dynamic large scale systems with emphasis on decentralized control strategies. Approaches that deal directly with decentralized decision making for large scale systems are discussed. It is shown that future advances in decentralized system theory are intimately connected with advances in the stochastic control problem with nonclassical information pattern. The basic assumptions and mathematical tools associated with the latter are summarized, and recommendations concerning future research are presented.

  15. Clearing and Labeling Techniques for Large-Scale Biological Tissues

    PubMed Central

    Seo, Jinyoung; Choe, Minjin; Kim, Sung-Yon

    2016-01-01

    Clearing and labeling techniques for large-scale biological tissues enable simultaneous extraction of molecular and structural information with minimal disassembly of the sample, facilitating the integration of molecular, cellular and systems biology across different scales. Recent years have witnessed an explosive increase in the number of such methods and their applications, reflecting heightened interest in organ-wide clearing and labeling across many fields of biology and medicine. In this review, we provide an overview and comparison of existing clearing and labeling techniques and discuss challenges and opportunities in the investigations of large-scale biological systems. PMID:27239813

  16. Large-scale liquid scintillation detectors for solar neutrinos

    NASA Astrophysics Data System (ADS)

    Benziger, Jay B.; Calaprice, Frank P.

    2016-04-01

    Large-scale liquid scintillation detectors are capable of providing spectral yields of the low energy solar neutrinos. These detectors require > 100 tons of liquid scintillator with high optical and radiopurity. In this paper requirements for low-energy neutrino detection by liquid scintillation are specified and the procedures to achieve low backgrounds in large-scale liquid scintillation detectors for solar neutrinos are reviewed. The designs, operations and achievements of Borexino, KamLAND and SNO+ in measuring the low-energy solar neutrino fluxes are reviewed.

  17. Contribution of peculiar shear motions to large-scale structure

    NASA Technical Reports Server (NTRS)

    Mueler, Hans-Reinhard; Treumann, Rudolf A.

    1994-01-01

    Self-gravitating shear flow instability simulations in a cold dark matter-dominated expanding Einstein-de Sitter universe have been performed. When the shear flow speed exceeds a certain threshold, self-gravitating Kelvin-Helmoholtz instability occurs, forming density voids and excesses along the shear flow layer which serve as seeds for large-scale structure formation. A possible mechanism for generating shear peculiar motions are velocity fluctuations induced by the density perturbations of the postinflation era. In this scenario, short scales grow earlier than large scales. A model of this kind may contribute to the cellular structure of the luminous mass distribution in the universe.

  18. Clearing and Labeling Techniques for Large-Scale Biological Tissues.

    PubMed

    Seo, Jinyoung; Choe, Minjin; Kim, Sung-Yon

    2016-06-30

    Clearing and labeling techniques for large-scale biological tissues enable simultaneous extraction of molecular and structural information with minimal disassembly of the sample, facilitating the integration of molecular, cellular and systems biology across different scales. Recent years have witnessed an explosive increase in the number of such methods and their applications, reflecting heightened interest in organ-wide clearing and labeling across many fields of biology and medicine. In this review, we provide an overview and comparison of existing clearing and labeling techniques and discuss challenges and opportunities in the investigations of large-scale biological systems. PMID:27239813

  19. Use of Time-Resolved Fluorescence To Improve Sensitivity and Dynamic Range of Gel-Based Proteomics.

    PubMed

    Sandberg, AnnSofi; Buschmann, Volker; Kapusta, Peter; Erdmann, Rainer; Wheelock, Åsa M

    2016-03-15

    Limitations in the sensitivity and dynamic range of two-dimensional gel electrophoresis (2-DE) are currently hampering its utility in global proteomics and biomarker discovery applications. In the current study, we present proof-of-concept analyses showing that introducing time-resolved fluorescence in the image acquisition step of in-gel protein quantification provides a sensitive and accurate method for subtracting confounding background fluorescence at the photon level. In-gel protein detection using the minimal difference gel electrophoresis workflow showed improvements in lowest limit of quantification in terms of CyDye molecules per pixel of 330-fold in the blue-green region (Cy2) and 8000-fold in the red region (Cy5) over conventional state-of-the-art image acquisition instrumentation, here represented by the Typhoon 9400 instrument. These improvements make possible the detection of low-abundance proteins present at sub-attomolar levels, thereby representing a quantum leap for the use of gel-based proteomics in biomarker discovery. These improvements were achieved using significantly lower laser powers and overall excitation times, thereby drastically decreasing photobleaching during repeated scanning. The single-fluorochrome detection limits achieved by the cumulative time-resolved emission two-dimensional electrophoresis (CuTEDGE) technology facilitates in-depth proteomics characterization of very scarce samples, for example, primary human tissue materials collected in clinical studies. The unique information provided by high-sensitivity 2-DE, including positional shifts due to post-translational modifications, may increase the chance to detect biomarker signatures of relevance for identification of disease subphenotypes. PMID:26854653

  20. Large-Scale Spray Releases: Initial Aerosol Test Results

    SciTech Connect

    Schonewill, Philip P.; Gauglitz, Phillip A.; Bontha, Jagannadha R.; Daniel, Richard C.; Kurath, Dean E.; Adkins, Harold E.; Billing, Justin M.; Burns, Carolyn A.; Davis, James M.; Enderlin, Carl W.; Fischer, Christopher M.; Jenks, Jeromy WJ; Lukins, Craig D.; MacFarlan, Paul J.; Shutthanandan, Janani I.; Smith, Dennese M.

    2012-12-01

    One of the events postulated in the hazard analysis at the Waste Treatment and Immobilization Plant (WTP) and other U.S. Department of Energy (DOE) nuclear facilities is a breach in process piping that produces aerosols with droplet sizes in the respirable range. The current approach for predicting the size and concentration of aerosols produced in a spray leak involves extrapolating from correlations reported in the literature. These correlations are based on results obtained from small engineered spray nozzles using pure liquids with Newtonian fluid behavior. The narrow ranges of physical properties on which the correlations are based do not cover the wide range of slurries and viscous materials that will be processed in the WTP and across processing facilities in the DOE complex. Two key technical areas were identified where testing results were needed to improve the technical basis by reducing the uncertainty due to extrapolating existing literature results. The first technical need was to quantify the role of slurry particles in small breaches where the slurry particles may plug and result in substantially reduced, or even negligible, respirable fraction formed by high-pressure sprays. The second technical need was to determine the aerosol droplet size distribution and volume from prototypic breaches and fluids, specifically including sprays from larger breaches with slurries where data from the literature are scarce. To address these technical areas, small- and large-scale test stands were constructed and operated with simulants to determine aerosol release fractions and generation rates from a range of breach sizes and geometries. The properties of the simulants represented the range of properties expected in the WTP process streams and included water, sodium salt solutions, slurries containing boehmite or gibbsite, and a hazardous chemical simulant. The effect of anti-foam agents was assessed with most of the simulants. Orifices included round holes and

  1. Assuring Quality in Large-Scale Online Course Development

    ERIC Educational Resources Information Center

    Parscal, Tina; Riemer, Deborah

    2010-01-01

    Student demand for online education requires colleges and universities to rapidly expand the number of courses and programs offered online while maintaining high quality. This paper outlines two universities respective processes to assure quality in large-scale online programs that integrate instructional design, eBook custom publishing, Quality…

  2. Large-scale search for dark-matter axions

    SciTech Connect

    Hagmann, C.A., LLNL; Kinion, D.; Stoeffl, W.; Van Bibber, K.; Daw, E.J.; McBride, J.; Peng, H.; Rosenberg, L.J.; Xin, H.; Laveigne, J.; Sikivie, P.; Sullivan, N.S.; Tanner, D.B.; Moltz, D.M.; Powell, J.; Clarke, J.; Nezrick, F.A.; Turner, M.S.; Golubev, N.A.; Kravchuk, L.V.

    1998-01-01

    Early results from a large-scale search for dark matter axions are presented. In this experiment, axions constituting our dark-matter halo may be resonantly converted to monochromatic microwave photons in a high-Q microwave cavity permeated by a strong magnetic field. Sensitivity at the level of one important axion model (KSVZ) has been demonstrated.

  3. DESIGN OF LARGE-SCALE AIR MONITORING NETWORKS

    EPA Science Inventory

    The potential effects of air pollution on human health have received much attention in recent years. In the U.S. and other countries, there are extensive large-scale monitoring networks designed to collect data to inform the public of exposure risks to air pollution. A major crit...

  4. Large-scale search for dark-matter axions

    SciTech Connect

    Kinion, D; van Bibber, K

    2000-08-30

    We review the status of two ongoing large-scale searches for axions which may constitute the dark matter of our Milky Way halo. The experiments are based on the microwave cavity technique proposed by Sikivie, and marks a ''second-generation'' to the original experiments performed by the Rochester-Brookhaven-Fermilab collaboration, and the University of Florida group.

  5. Large-Scale Innovation and Change in UK Higher Education

    ERIC Educational Resources Information Center

    Brown, Stephen

    2013-01-01

    This paper reflects on challenges universities face as they respond to change. It reviews current theories and models of change management, discusses why universities are particularly difficult environments in which to achieve large scale, lasting change and reports on a recent attempt by the UK JISC to enable a range of UK universities to employ…

  6. Global smoothing and continuation for large-scale molecular optimization

    SciTech Connect

    More, J.J.; Wu, Zhijun

    1995-10-01

    We discuss the formulation of optimization problems that arise in the study of distance geometry, ionic systems, and molecular clusters. We show that continuation techniques based on global smoothing are applicable to these molecular optimization problems, and we outline the issues that must be resolved in the solution of large-scale molecular optimization problems.

  7. The Large-Scale Structure of Scientific Method

    ERIC Educational Resources Information Center

    Kosso, Peter

    2009-01-01

    The standard textbook description of the nature of science describes the proposal, testing, and acceptance of a theoretical idea almost entirely in isolation from other theories. The resulting model of science is a kind of piecemeal empiricism that misses the important network structure of scientific knowledge. Only the large-scale description of…

  8. Individual Skill Differences and Large-Scale Environmental Learning

    ERIC Educational Resources Information Center

    Fields, Alexa W.; Shelton, Amy L.

    2006-01-01

    Spatial skills are known to vary widely among normal individuals. This project was designed to address whether these individual differences are differentially related to large-scale environmental learning from route (ground-level) and survey (aerial) perspectives. Participants learned two virtual environments (route and survey) with limited…

  9. Mixing Metaphors: Building Infrastructure for Large Scale School Turnaround

    ERIC Educational Resources Information Center

    Peurach, Donald J.; Neumerski, Christine M.

    2015-01-01

    The purpose of this analysis is to increase understanding of the possibilities and challenges of building educational infrastructure--the basic, foundational structures, systems, and resources--to support large-scale school turnaround. Building educational infrastructure often exceeds the capacity of schools, districts, and state education…

  10. Large-scale drift and Rossby wave turbulence

    NASA Astrophysics Data System (ADS)

    Harper, K. L.; Nazarenko, S. V.

    2016-08-01

    We study drift/Rossby wave turbulence described by the large-scale limit of the Charney–Hasegawa–Mima equation. We define the zonal and meridional regions as Z:= \\{{k} :| {k}y| \\gt \\sqrt{3}{k}x\\} and M:= \\{{k} :| {k}y| \\lt \\sqrt{3}{k}x\\} respectively, where {k}=({k}x,{k}y) is in a plane perpendicular to the magnetic field such that k x is along the isopycnals and k y is along the plasma density gradient. We prove that the only types of resonant triads allowed are M≤ftrightarrow M+Z and Z≤ftrightarrow Z+Z. Therefore, if the spectrum of weak large-scale drift/Rossby turbulence is initially in Z it will remain in Z indefinitely. We present a generalised Fjørtoft’s argument to find transfer directions for the quadratic invariants in the two-dimensional {k}-space. Using direct numerical simulations, we test and confirm our theoretical predictions for weak large-scale drift/Rossby turbulence, and establish qualitative differences with cases when turbulence is strong. We demonstrate that the qualitative features of the large-scale limit survive when the typical turbulent scale is only moderately greater than the Larmor/Rossby radius.

  11. Large Scale Field Campaign Contributions to Soil Moisture Remote Sensing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Large-scale field experiments have been an essential component of soil moisture remote sensing for over two decades. They have provided test beds for both the technology and science necessary to develop and refine satellite mission concepts. The high degree of spatial variability of soil moisture an...

  12. Large-scale V/STOL testing. [in wind tunnels

    NASA Technical Reports Server (NTRS)

    Koenig, D. G.; Aiken, T. N.; Aoyagi, K.; Falarski, M. D.

    1977-01-01

    Several facets of large-scale testing of V/STOL aircraft configurations are discussed with particular emphasis on test experience in the Ames 40- by 80-foot wind tunnel. Examples of powered-lift test programs are presented in order to illustrate tradeoffs confronting the planner of V/STOL test programs. It is indicated that large-scale V/STOL wind-tunnel testing can sometimes compete with small-scale testing in the effort required (overall test time) and program costs because of the possibility of conducting a number of different tests with a single large-scale model where several small-scale models would be required. The benefits of both high- and full-scale Reynolds numbers, more detailed configuration simulation, and number and type of onboard measurements increase rapidly with scale. Planning must be more detailed at large scale in order to balance the trade-offs between the increased costs, as number of measurements and model configuration variables increase and the benefits of larger amounts of information coming out of one test.

  13. Current Scientific Issues in Large Scale Atmospheric Dynamics

    NASA Technical Reports Server (NTRS)

    Miller, T. L. (Compiler)

    1986-01-01

    Topics in large scale atmospheric dynamics are discussed. Aspects of atmospheric blocking, the influence of transient baroclinic eddies on planetary-scale waves, cyclogenesis, the effects of orography on planetary scale flow, small scale frontal structure, and simulations of gravity waves in frontal zones are discussed.

  14. Large-Scale Machine Learning for Classification and Search

    ERIC Educational Resources Information Center

    Liu, Wei

    2012-01-01

    With the rapid development of the Internet, nowadays tremendous amounts of data including images and videos, up to millions or billions, can be collected for training machine learning models. Inspired by this trend, this thesis is dedicated to developing large-scale machine learning techniques for the purpose of making classification and nearest…

  15. Considerations for Managing Large-Scale Clinical Trials.

    ERIC Educational Resources Information Center

    Tuttle, Waneta C.; And Others

    1989-01-01

    Research management strategies used effectively in a large-scale clinical trial to determine the health effects of exposure to Agent Orange in Vietnam are discussed, including pre-project planning, organization according to strategy, attention to scheduling, a team approach, emphasis on guest relations, cross-training of personnel, and preparing…

  16. Ecosystem resilience despite large-scale altered hydro climatic conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Climate change is predicted to increase both drought frequency and duration, and when coupled with substantial warming, will establish a new hydroclimatological paradigm for many regions. Large-scale, warm droughts have recently impacted North America, Africa, Europe, Amazonia, and Australia result...

  17. Lessons from Large-Scale Renewable Energy Integration Studies: Preprint

    SciTech Connect

    Bird, L.; Milligan, M.

    2012-06-01

    In general, large-scale integration studies in Europe and the United States find that high penetrations of renewable generation are technically feasible with operational changes and increased access to transmission. This paper describes other key findings such as the need for fast markets, large balancing areas, system flexibility, and the use of advanced forecasting.

  18. Probabilistic Cuing in Large-Scale Environmental Search

    ERIC Educational Resources Information Center

    Smith, Alastair D.; Hood, Bruce M.; Gilchrist, Iain D.

    2010-01-01

    Finding an object in our environment is an important human ability that also represents a critical component of human foraging behavior. One type of information that aids efficient large-scale search is the likelihood of the object being in one location over another. In this study we investigated the conditions under which individuals respond to…

  19. Extracting Useful Semantic Information from Large Scale Corpora of Text

    ERIC Educational Resources Information Center

    Mendoza, Ray Padilla, Jr.

    2012-01-01

    Extracting and representing semantic information from large scale corpora is at the crux of computer-assisted knowledge generation. Semantic information depends on collocation extraction methods, mathematical models used to represent distributional information, and weighting functions which transform the space. This dissertation provides a…

  20. Efficient On-Demand Operations in Large-Scale Infrastructures

    ERIC Educational Resources Information Center

    Ko, Steven Y.

    2009-01-01

    In large-scale distributed infrastructures such as clouds, Grids, peer-to-peer systems, and wide-area testbeds, users and administrators typically desire to perform "on-demand operations" that deal with the most up-to-date state of the infrastructure. However, the scale and dynamism present in the operating environment make it challenging to…

  1. Large-Scale Environmental Influences on Aquatic Animal Health

    EPA Science Inventory

    In the latter portion of the 20th century, North America experienced numerous large-scale mortality events affecting a broad diversity of aquatic animals. Short-term forensic investigations of these events have sometimes characterized a causative agent or condition, but have rare...

  2. Implicit solution of large-scale radiation diffusion problems

    SciTech Connect

    Brown, P N; Graziani, F; Otero, I; Woodward, C S

    2001-01-04

    In this paper, we present an efficient solution approach for fully implicit, large-scale, nonlinear radiation diffusion problems. The fully implicit approach is compared to a semi-implicit solution method. Accuracy and efficiency are shown to be better for the fully implicit method on both one- and three-dimensional problems with tabular opacities taken from the LEOS opacity library.

  3. Resilience of Florida Keys coral communities following large scale disturbances

    EPA Science Inventory

    The decline of coral reefs in the Caribbean over the last 40 years has been attributed to multiple chronic stressors and episodic large-scale disturbances. This study assessed the resilience of coral communities in two different regions of the Florida Keys reef system between 199...

  4. Large Scale Survey Data in Career Development Research

    ERIC Educational Resources Information Center

    Diemer, Matthew A.

    2008-01-01

    Large scale survey datasets have been underutilized but offer numerous advantages for career development scholars, as they contain numerous career development constructs with large and diverse samples that are followed longitudinally. Constructs such as work salience, vocational expectations, educational expectations, work satisfaction, and…

  5. Polymers in 2D Turbulence: Suppression of Large Scale Fluctuations

    NASA Astrophysics Data System (ADS)

    Amarouchene, Y.; Kellay, H.

    2002-08-01

    Small quantities of a long chain molecule or polymer affect two-dimensional turbulence in unexpected ways. Their presence inhibits the transfers of energy to large scales causing their suppression in the energy density spectrum. This also leads to the change of the spectral properties of a passive scalar which turns out to be highly sensitive to the presence of energy transfers.

  6. Creating a Large-Scale, Third Generation, Distance Education Course.

    ERIC Educational Resources Information Center

    Weller, Martin James

    2000-01-01

    Outlines the course development of an introductory large-scale distance education course offered via the World Wide Web at the Open University in the United Kingdom. Topics include developing appropriate student skills; maintaining quality control; facilitating easy updating of material; ensuring student interaction; and making materials…

  7. Cosmic strings and the large-scale structure

    NASA Technical Reports Server (NTRS)

    Stebbins, Albert

    1988-01-01

    A possible problem for cosmic string models of galaxy formation is presented. If very large voids are common and if loop fragmentation is not much more efficient than presently believed, then it may be impossible for string scenarios to produce the observed large-scale structure with Omega sub 0 = 1 and without strong environmental biasing.

  8. International Large-Scale Assessments: What Uses, What Consequences?

    ERIC Educational Resources Information Center

    Johansson, Stefan

    2016-01-01

    Background: International large-scale assessments (ILSAs) are a much-debated phenomenon in education. Increasingly, their outcomes attract considerable media attention and influence educational policies in many jurisdictions worldwide. The relevance, uses and consequences of these assessments are often the focus of research scrutiny. Whilst some…

  9. Measurement, Sampling, and Equating Errors in Large-Scale Assessments

    ERIC Educational Resources Information Center

    Wu, Margaret

    2010-01-01

    In large-scale assessments, such as state-wide testing programs, national sample-based assessments, and international comparative studies, there are many steps involved in the measurement and reporting of student achievement. There are always sources of inaccuracies in each of the steps. It is of interest to identify the source and magnitude of…

  10. A bibliographical surveys of large-scale systems

    NASA Technical Reports Server (NTRS)

    Corliss, W. R.

    1970-01-01

    A limited, partly annotated bibliography was prepared on the subject of large-scale system control. Approximately 400 references are divided into thirteen application areas, such as large societal systems and large communication systems. A first-author index is provided.

  11. Large-Scale Networked Virtual Environments: Architecture and Applications

    ERIC Educational Resources Information Center

    Lamotte, Wim; Quax, Peter; Flerackers, Eddy

    2008-01-01

    Purpose: Scalability is an important research topic in the context of networked virtual environments (NVEs). This paper aims to describe the ALVIC (Architecture for Large-scale Virtual Interactive Communities) approach to NVE scalability. Design/methodology/approach: The setup and results from two case studies are shown: a 3-D learning environment…

  12. Response of Tradewind Cumuli to Large-Scale Processes.

    NASA Astrophysics Data System (ADS)

    Soong, S.-T.; Ogura, Y.

    1980-09-01

    The two-dimensional slab-symmetric numerical cloud model used by Soong and Ogura (1973) for studying the evolution of an isolated cumulus cloud is extended to investigate the statistical properties of cumulus clouds which would be generated under a given large-scale forcing composed of the horizontal advection of temperature and water vapor mixing ratio, vertical velocity, sea surface temperature and radiative cooling. Random disturbances of small amplitude are introduced into the model at low levels to provide random motion for cloud formation.The model is applied to a case of suppressed weather conditions during BOMEX for the period 22-23 June 1969 when a nearly steady state prevailed. The composited temperature and mixing ratio profiles of these two days are used as initial conditions and the time-independent large-scale forcing terms estimated from the observations are applied to the model. The result of numerical integration shows that a number of small clouds start developing after 1 h. Some of them decay quickly, but some of them develop and reach the tradewind inversion. After a few hours of simulation, the vertical profiles of the horizontally averaged temperature and moisture are found to deviate only slightly from the observed profiles, indicating that the large-scale effect and the feedback effects of clouds on temperature and mixing ratio reach an equilibrium state. The three major components of the cloud feedback effect, i.e., condensation, evaporation and vertical fluxes associated with the clouds, are determined from the model output. The vertical profiles of vertical heat and moisture fluxes in the subcloud layer in the model are found to be in general agreement with the observations.Sensitivity tests of the model are made for different magnitudes of the large-scale vertical velocity. The most striking result is that the temperature and humidity in the cloud layer below the inversion do not change significantly in spite of a relatively large

  13. Molecular Mechanisms of Chronic Kidney Transplant Rejection via Large-Scale Proteogenomic Analysis of Tissue Biopsies

    PubMed Central

    Nakorchevsky, Aleksey; Hewel, Johannes A.; Kurian, Sunil M.; Mondala, Tony S.; Campbell, Daniel; Head, Steve R.; Marsh, Christopher L.; Yates, John R.

    2010-01-01

    The most common cause of kidney transplant failure is the poorly characterized histopathologic entity interstitial fibrosis and tubular atrophy (IFTA). There are no known unifying mechanisms, no effective therapy, and no proven preventive strategies. Possible mechanisms include chronic immune rejection, inflammation, drug toxicity, and chronic kidney injury from secondary factors. To gain further mechanistic insight, we conducted a large-scale proteogenomic study of kidney transplant biopsies with IFTA of varying severity. We acquired proteomic data using tandem mass spectrometry with subsequent quantification, analysis of differential protein expression, validation, and functional annotations to known molecular networks. We performed genome-wide expression profiling in parallel. More than 1400 proteins with unique expression profiles traced the progression from normal transplant biopsies to biopsies with mild to moderate and severe disease. Multiple sets of proteins were mapped to different functional pathways, many increasing with histologic severity, including immune responses, inflammatory cell activation, and apoptosis consistent with the chronic rejection hypothesis. Two examples include the extensive population of the alternative rather than the classical complement pathway, previously not appreciated for IFTA, and a comprehensive control network for the actin cytoskeleton and cell signaling of the acute-phase response. In summary, this proteomic effort using kidney tissue contributes mechanistic insight into several biologic processes associated with IFTA. PMID:20093355

  14. Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering.

    PubMed

    Flikka, Kristian; Martens, Lennart; Vandekerckhove, Joël; Gevaert, Kris; Eidhammer, Ingvar

    2006-04-01

    In contemporary peptide-centric or non-gel proteome studies, vast amounts of peptide fragmentation data are generated of which only a small part leads to peptide or protein identification. This motivates the development and use of a filtering algorithm that removes spectra that contribute little to protein identification. Removal of unidentifiable spectra reduced both the amount of computational and human time spent on analyzing spectra as well as the chances of obtaining false identifications. Thorough testing on various proteome datasets from different instruments showed that the best suggested machine-learning classifier is, on average, able to recognize half of the unidentified spectra as bad spectra. Further analyses showed that several unidentified spectra classified as good were derived from peptides carrying unanticipated amino acid modifications or contained sequence tags that allowed peptide identification using homology searches. The implementation of the classifiers is available under the GNU General Public License at http://www.bioinfo.no/software/spectrumquality. PMID:16518876

  15. A Global View of Large-Scale Precipitation Variability.

    NASA Astrophysics Data System (ADS)

    Rasmusson, Eugene M.; Arkin, Phillip A.

    1993-08-01

    Observational studies and model experiments make abundantly clear the need for a global perspective in order to understand the nature and causes of persistent regional precipitation anomalies. Rainfall in the deep tropics is particularly important as a forcing mechanism for the atmosphere's large-scale circulation and climate. Analysis of systematic space-based observations and surface marine data over the past three decades has vastly improved our understanding of tropical convective regimes and their relationship to surface conditions. The characteristics of the annual cycle of tropical convection and its relationship to sea surface temperature field and the general circulation of the tropics are reviewed. The hierarchal nature of tropical precipitation variability on time/space scales ranging from synoptic cloud clusters through the intraseasonal Madden-Julian Oscillation to multiyear El Niño-Southern Oscillation cycle is discussed. Links between tropical convection and extratropical precipitation on time scales ranging from synoptic to multiyear are examined, with emphasis on conditions over the North Pacific-North American sector during winter.Precipitation variability over a number of regions bordering the Atlantic basin are related to Atlantic sector modes of SST and circulation variability. Systematic modes of Atlantic variability and their relationship to regional precipitation variability are described with emphasis on the tropics.Changes in landscape characteristics (vegetative cover, soil moisture, surface roughness), whether natural or human induced, result in changes in the surface radiation balance and the fluxes of heat and moisture. Our current understanding of the role of land surface processes in sustaining or intensifying anomalous precipitation regimes is briefly discussed. Identification of an anthropogenic trend in the presence of decadal-scale natural variations in precipitation is a formidable challenge. Three examples of large

  16. Exogenous melatonin improves corn (Zea mays L.) embryo proteome in seeds subjected to chilling stress.

    PubMed

    Kołodziejczyk, Izabela; Dzitko, Katarzyna; Szewczyk, Rafał; Posmyk, Małgorzata M

    2016-04-01

    Melatonin (MEL; N-acetyl-5-methoxytryptamine) plays an important role in plant stress defense. Various plant species rich in this indoleamine have shown a higher capacity for stress tolerance. Moreover, it has great potential for plant biostimulation, is biodegradable and non-toxic for the environment. All this indicates that our concept of seed enrichment with exogenous MEL is justified. This work concerns the effects of corn (Zea mays L.) seed pre-sowing treatments supplemented with MEL. Non-treated seeds (nt), and those hydroprimed with water (H) or with MEL solutions 50 and 500 μM (HMel50, HMel500) were compared. Positive effects of seed priming are particularly apparent during germination under suboptimal conditions. The impact of MEL applied by priming on seed protein profiles during imbibition/germination at low temperature has not been investigated to date. In order to identify changes in the corn seed proteome after applying hydropriming techniques, purified protein extracts of chilling stressed seed embryos (14 days, 5°C) were separated by two-dimensional electrophoresis. Then proteome maps were graphically and statistically compared and selected protein spots were qualitatively analyzed using mass spectrometry techniques and identified. This study aimed to analyze the priming-induced changes in maize embryo proteome and at identifying priming-associated and MEL-associated proteins in maize seeds subjected to chilling. We attempt to explain how MEL expands plant capacity for stress tolerance. PMID:26945210

  17. Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling.

    PubMed

    Nilse, Lars; Sigloch, Florian Christoph; Biniossek, Martin L; Schilling, Oliver

    2015-08-01

    Reliable detection of peptides in LC-MS data is a key algorithmic step in the analysis of quantitative proteomics experiments. While highly abundant peptides can be detected reliably by most modern software tools, there is much less agreement on medium and low-intensity peptides in a sample. The choice of software tools can have a big impact on the quantification of proteins, especially for proteins that appear in lower concentrations. However, in many experiments, it is precisely this region of less abundant but substantially regulated proteins that holds the biggest potential for discoveries. This is particularly true for discovery proteomics in the pharmacological sector with a specific interest in key regulatory proteins. In this viewpoint article, we discuss how the development of novel software algorithms allows us to study this region of the proteome with increased confidence. Reliable results are one of many aspects to be considered when deciding on a bioinformatics software platform. Deployment into existing IT infrastructures, compatibility with other software packages, scalability, automation, flexibility, and support need to be considered and are briefly addressed in this viewpoint article. PMID:25931027

  18. Leveraging Proteomics to Understand Plant–Microbe Interactions

    PubMed Central

    Jayaraman, Dhileepkumar; Forshey, Kari L.; Grimsrud, Paul A.; Ané, Jean-Michel

    2012-01-01

    Understanding the interactions of plants with beneficial and pathogenic microbes is a promising avenue to improve crop productivity and agriculture sustainability. Proteomic techniques provide a unique angle to describe these intricate interactions and test hypotheses. The various approaches for proteomic analysis generally include protein/peptide separation and identification, but can also provide quantification and the characterization of post-translational modifications. In this review, we discuss how these techniques have been applied to the study of plant–microbe interactions. We also present some areas where this field of study would benefit from the utilization of newly developed methods that overcome previous limitations. Finally, we reinforce the need for expanding, integrating, and curating protein databases, as well as the benefits of combining protein-level datasets with those from genetic analyses and other high-throughput large-scale approaches for a systems-level view of plant–microbe interactions. PMID:22645586

  19. Advanced proteomic liquid chromatography

    SciTech Connect

    Xie, Fang; Smith, Richard D.; Shen, Yufeng

    2012-10-26

    Liquid chromatography coupled with mass spectrometry is the predominant platform used to analyze proteomics samples consisting of large numbers of proteins and their proteolytic products (e.g., truncated polypeptides) and spanning a wide range of relative concentrations. This review provides an overview of advanced capillary liquid chromatography techniques and methodologies that greatly improve separation resolving power and proteomics analysis coverage, sensitivity, and throughput.

  20. Large-scale quantification of CVD graphene surface coverage

    NASA Astrophysics Data System (ADS)

    Ambrosi, Adriano; Bonanni, Alessandra; Sofer, Zdeněk; Pumera, Martin

    2013-02-01

    The extraordinary properties demonstrated for graphene and graphene-related materials can be fully exploited when a large-scale fabrication procedure is made available. Chemical vapor deposition (CVD) of graphene on Cu and Ni substrates is one of the most promising procedures to synthesize large-area and good quality graphene films. Parallel to the fabrication process, a large-scale quality monitoring technique is equally crucial. We demonstrate here a rapid and simple methodology that is able to probe the effectiveness of the growth process over a large substrate area for both Ni and Cu substrates. This method is based on inherent electrochemical signals generated by the underlying metal catalysts when fractures or discontinuities of the graphene film are present. The method can be applied immediately after the CVD growth process without the need for any graphene transfer step and represents a powerful quality monitoring technique for the assessment of large-scale fabrication of graphene by the CVD process.The extraordinary properties demonstrated for graphene and graphene-related materials can be fully exploited when a large-scale fabrication procedure is made available. Chemical vapor deposition (CVD) of graphene on Cu and Ni substrates is one of the most promising procedures to synthesize large-area and good quality graphene films. Parallel to the fabrication process, a large-scale quality monitoring technique is equally crucial. We demonstrate here a rapid and simple methodology that is able to probe the effectiveness of the growth process over a large substrate area for both Ni and Cu substrates. This method is based on inherent electrochemical signals generated by the underlying metal catalysts when fractures or discontinuities of the graphene film are present. The method can be applied immediately after the CVD growth process without the need for any graphene transfer step and represents a powerful quality monitoring technique for the assessment of large-scale

  1. Analysis of large scale spatial variability of soil moisture using a geostatistical method.

    PubMed

    Lakhankar, Tarendra; Jones, Andrew S; Combs, Cynthia L; Sengupta, Manajit; Vonder Haar, Thomas H; Khanbilvardi, Reza

    2010-01-01

    Spatial and temporal soil moisture dynamics are critically needed to improve the parameterization for hydrological and meteorological modeling processes. This study evaluates the statistical spatial structure of large-scale observed and simulated estimates of soil moisture under pre- and post-precipitation event conditions. This large scale variability is a crucial in calibration and validation of large-scale satellite based data assimilation systems. Spatial analysis using geostatistical approaches was used to validate modeled soil moisture by the Agriculture Meteorological (AGRMET) model using in situ measurements of soil moisture from a state-wide environmental monitoring network (Oklahoma Mesonet). The results show that AGRMET data produces larger spatial decorrelation compared to in situ based soil moisture data. The precipitation storms drive the soil moisture spatial structures at large scale, found smaller decorrelation length after precipitation. This study also evaluates the geostatistical approach for mitigation for quality control issues within in situ soil moisture network to estimates at soil moisture at unsampled stations. PMID:22315576

  2. Self-consistency tests of large-scale dynamics parameterizations for single-column modeling

    SciTech Connect

    Edman, Jacob P.; Romps, David M.

    2015-03-18

    Large-scale dynamics parameterizations are tested numerically in cloud-resolving simulations, including a new version of the weak-pressure-gradient approximation (WPG) introduced by Edman and Romps (2014), the weak-temperature-gradient approximation (WTG), and a prior implementation of WPG. We perform a series of self-consistency tests with each large-scale dynamics parameterization, in which we compare the result of a cloud-resolving simulation coupled to WTG or WPG with an otherwise identical simulation with prescribed large-scale convergence. In self-consistency tests based on radiative-convective equilibrium (RCE; i.e., no large-scale convergence), we find that simulations either weakly coupled or strongly coupled to either WPG or WTG are self-consistent, but WPG-coupled simulations exhibit a nonmonotonic behavior as the strength of the coupling to WPG is varied. We also perform self-consistency tests based on observed forcings from two observational campaigns: the Tropical Warm Pool International Cloud Experiment (TWP-ICE) and the ARM Southern Great Plains (SGP) Summer 1995 IOP. In these tests, we show that the new version of WPG improves upon prior versions of WPG by eliminating a potentially troublesome gravity-wave resonance.

  3. Self-consistency tests of large-scale dynamics parameterizations for single-column modeling

    DOE PAGESBeta

    Edman, Jacob P.; Romps, David M.

    2015-03-18

    Large-scale dynamics parameterizations are tested numerically in cloud-resolving simulations, including a new version of the weak-pressure-gradient approximation (WPG) introduced by Edman and Romps (2014), the weak-temperature-gradient approximation (WTG), and a prior implementation of WPG. We perform a series of self-consistency tests with each large-scale dynamics parameterization, in which we compare the result of a cloud-resolving simulation coupled to WTG or WPG with an otherwise identical simulation with prescribed large-scale convergence. In self-consistency tests based on radiative-convective equilibrium (RCE; i.e., no large-scale convergence), we find that simulations either weakly coupled or strongly coupled to either WPG or WTG are self-consistent, butmore » WPG-coupled simulations exhibit a nonmonotonic behavior as the strength of the coupling to WPG is varied. We also perform self-consistency tests based on observed forcings from two observational campaigns: the Tropical Warm Pool International Cloud Experiment (TWP-ICE) and the ARM Southern Great Plains (SGP) Summer 1995 IOP. In these tests, we show that the new version of WPG improves upon prior versions of WPG by eliminating a potentially troublesome gravity-wave resonance.« less

  4. A Calibration Routine for Efficient ETD in Large-Scale Proteomics

    NASA Astrophysics Data System (ADS)

    Rose, Christopher M.; Rush, Matthew J. P.; Riley, Nicholas M.; Merrill, Anna E.; Kwiecien, Nicholas W.; Holden, Dustin D.; Mullen, Christopher; Westphall, Michael S.; Coon, Joshua J.

    2015-11-01

    Electron transfer dissociation (ETD) has been broadly adopted and is now available on a variety of commercial mass spectrometers. Unlike collisional activation techniques, optimal performance of ETD requires considerable user knowledge and input. ETD reaction duration is one key parameter that can greatly influence spectral quality and overall experiment outcome. We describe a calibration routine that determines the correct number of reagent anions necessary to reach a defined ETD reaction rate. Implementation of this automated calibration routine on two hybrid Orbitrap platforms illustrate considerable advantages, namely, increased product ion yield with concomitant reduction in scan rates netting up to 75% more unique peptide identifications in a shotgun experiment.

  5. Science and engineering of large scale socio-technical simulations.

    SciTech Connect

    Barrett, C. L.; Eubank, S. G.; Marathe, M. V.; Mortveit, H. S.; Reidys, C. M.

    2001-01-01

    Computer simulation is a computational approach whereby global system properties are produced as dynamics by direct computation of interactions among representations of local system elements. A mathematical theory of simulation consists of an account of the formal properties of sequential evaluation and composition of interdependent local mappings. When certain local mappings and their interdependencies can be related to particular real world objects and interdependencies, it is common to compute the interactions to derive a symbolic model of the global system made up of the corresponding interdependent objects. The formal mathematical and computational account of the simulation provides a particular kind of theoretical explanation of the global system properties and, therefore, insight into how to engineer a complex system to exhibit those properties. This paper considers the methematical foundations and engineering princaples necessary for building large scale simulations of socio-technical systems. Examples of such systems are urban regional transportation systems, the national electrical power markets and grids, the world-wide Internet, vaccine design and deployment, theater war, etc. These systems are composed of large numbers of interacting human, physical and technological components. Some components adapt and learn, exhibit perception, interpretation, reasoning, deception, cooperation and noncooperation, and have economic motives as well as the usual physical properties of interaction. The systems themselves are large and the behavior of sociotechnical systems is tremendously complex. The state of affairs f o r these kinds of systems is characterized by very little satisfactory formal theory, a good decal of very specialized knowledge of subsystems, and a dependence on experience-based practitioners' art. However, these systems are vital and require policy, control, design, implementation and investment. Thus there is motivation to improve the ability to

  6. A Limited-Memory BFGS Algorithm Based on a Trust-Region Quadratic Model for Large-Scale Nonlinear Equations

    PubMed Central

    Li, Yong; Yuan, Gonglin; Wei, Zengxin

    2015-01-01

    In this paper, a trust-region algorithm is proposed for large-scale nonlinear equations, where the limited-memory BFGS (L-M-BFGS) update matrix is used in the trust-region subproblem to improve the effectiveness of the algorithm for large-scale problems. The global convergence of the presented method is established under suitable conditions. The numerical results of the test problems show that the method is competitive with the norm method. PMID:25950725

  7. LARGE-SCALE MOTIONS IN THE PERSEUS GALAXY CLUSTER

    SciTech Connect

    Simionescu, A.; Werner, N.; Urban, O.; Allen, S. W.; Fabian, A. C.; Sanders, J. S.; Mantz, A.; Nulsen, P. E. J.; Takei, Y.

    2012-10-01

    By combining large-scale mosaics of ROSAT PSPC, XMM-Newton, and Suzaku X-ray observations, we present evidence for large-scale motions in the intracluster medium of the nearby, X-ray bright Perseus Cluster. These motions are suggested by several alternating and interleaved X-ray bright, low-temperature, low-entropy arcs located along the east-west axis, at radii ranging from {approx}10 kpc to over a Mpc. Thermodynamic features qualitatively similar to these have previously been observed in the centers of cool-core clusters, and were successfully modeled as a consequence of the gas sloshing/swirling motions induced by minor mergers. Our observations indicate that such sloshing/swirling can extend out to larger radii than previously thought, on scales approaching the virial radius.

  8. Generating Large-Scale Longitudinal Data Resources for Aging Research

    PubMed Central

    Hofer, Scott M.

    2011-01-01

    Objectives. The need for large studies and the types of large-scale data resources (LSDRs) are discussed along with their general scientific utility, role in aging research, and affordability. The diversification of approaches to large-scale data resourcing is described in order to facilitate their use in aging research. Methods. The need for LSDRs is discussed in terms of (a) large sample size; (b) longitudinal design; (c) as platforms for additional investigator-initiated research projects; and (d) broad-based access to core genetic, biological, and phenotypic data. Discussion. It is concluded that a “lite-touch, lo-tech, lo-cost” approach to LSDRs is a viable strategy for the development of LSDRs and would enhance the likelihood of LSDRs being established which are dedicated to the wide range of important aging-related issues. PMID:21743049

  9. Lagrangian space consistency relation for large scale structure

    NASA Astrophysics Data System (ADS)

    Horn, Bart; Hui, Lam; Xiao, Xiao

    2015-09-01

    Consistency relations, which relate the squeezed limit of an (N+1)-point correlation function to an N-point function, are non-perturbative symmetry statements that hold even if the associated high momentum modes are deep in the nonlinear regime and astrophysically complex. Recently, Kehagias & Riotto and Peloso & Pietroni discovered a consistency relation applicable to large scale structure. We show that this can be recast into a simple physical statement in Lagrangian space: that the squeezed correlation function (suitably normalized) vanishes. This holds regardless of whether the correlation observables are at the same time or not, and regardless of whether multiple-streaming is present. The simplicity of this statement suggests that an analytic understanding of large scale structure in the nonlinear regime may be particularly promising in Lagrangian space.

  10. Instrumentation Development for Large Scale Hypersonic Inflatable Aerodynamic Decelerator Characterization

    NASA Technical Reports Server (NTRS)

    Swanson, Gregory T.; Cassell, Alan M.

    2011-01-01

    Hypersonic Inflatable Aerodynamic Decelerator (HIAD) technology is currently being considered for multiple atmospheric entry applications as the limitations of traditional entry vehicles have been reached. The Inflatable Re-entry Vehicle Experiment (IRVE) has successfully demonstrated this technology as a viable candidate with a 3.0 m diameter vehicle sub-orbital flight. To further this technology, large scale HIADs (6.0 8.5 m) must be developed and tested. To characterize the performance of large scale HIAD technology new instrumentation concepts must be developed to accommodate the flexible nature inflatable aeroshell. Many of the concepts that are under consideration for the HIAD FY12 subsonic wind tunnel test series are discussed below.

  11. The Large Scale Synthesis of Aligned Plate Nanostructures.

    PubMed

    Zhou, Yang; Nash, Philip; Liu, Tian; Zhao, Naiqin; Zhu, Shengli

    2016-01-01

    We propose a novel technique for the large-scale synthesis of aligned-plate nanostructures that are self-assembled and self-supporting. The synthesis technique involves developing nanoscale two-phase microstructures through discontinuous precipitation followed by selective etching to remove one of the phases. The method may be applied to any alloy system in which the discontinuous precipitation transformation goes to completion. The resulting structure may have many applications in catalysis, filtering and thermal management depending on the phase selection and added functionality through chemical reaction with the retained phase. The synthesis technique is demonstrated using the discontinuous precipitation of a γ' phase, (Ni, Co)3Al, followed by selective dissolution of the γ matrix phase. The production of the nanostructure requires heat treatments on the order of minutes and can be performed on a large scale making this synthesis technique of great economic potential. PMID:27439672

  12. Large-scale processes in the solar nebula

    NASA Technical Reports Server (NTRS)

    Boss, A. P.

    1994-01-01

    Theoretical models of the structure of a minimum mass solar nebula should be able to provide the physical context to help evaluate the efficacy of any mechanism proposed for the formation of chondrules or Ca, Al-rich inclusions (CAI's). These models generally attempt to use the equations of radiative hydrodynamics to calculate the large-scale structure of the solar nebula throughout the planet-forming region. In addition, it has been suggested that chondrules and CAI's (=Ch&CAI's) may have been formed as a direct result of large-scale nebula processing such as passage of material through high-temperature regions associated with the global structure of the nebula. In this report we assess the status of global models of solar nebula structure and of various related mechanisms that have been suggested for Ch and CAI formation.

  13. Planar Doppler Velocimetry for Large-Scale Wind Tunnel Applications

    NASA Technical Reports Server (NTRS)

    McKenzie, Robert L.

    1998-01-01

    Planar Doppler Velocimetry (PDV) concepts using a pulsed laser are described and the obtainable minimum resolved velocities in large-scale wind tunnels are evaluated. Velocity-field measurements are shown to be possible at ranges of tens of meters and with single pulse resolutions as low as 2 m/s. Velocity measurements in the flow of a low-speed, turbulent jet are reported that demonstrate the ability of PDV to acquire both average velocity fields and their fluctuation amplitudes, using procedures that are compatible with large-scale facility operations. The advantages of PDV over current Laser Doppler Anemometry and Particle Image Velocimetry techniques appear to be significant for applications to large facilities.

  14. Transparent and Flexible Large-scale Graphene-based Heater

    NASA Astrophysics Data System (ADS)

    Kang, Junmo; Lee, Changgu; Kim, Young-Jin; Choi, Jae-Boong; Hong, Byung Hee

    2011-03-01

    We report the application of transparent and flexible heater with high optical transmittance and low sheet resistance using graphene films, showing outstanding thermal and electrical properties. The large-scale graphene films were grown on Cu foil by chemical vapor deposition methods, and transferred to transparent substrates by multiple stacking. The wet chemical doping process enhanced the electrical properties, showing a sheet resistance as low as 35 ohm/sq with 88.5 % transmittance. The temperature response usually depends on the dimension and the sheet resistance of the graphene-based heater. We show that a 4x4 cm2 heater can reach 80& circ; C within 40 seconds and large-scale (9x9 cm2) heater shows uniformly heating performance, which was measured using thermocouple and infra-red camera. These heaters would be very useful for defogging systems and smart windows.

  15. Large Scale Diffuse X-ray Emission from Abell 3571

    NASA Technical Reports Server (NTRS)

    Molnar, Sandor M.; White, Nicholas E. (Technical Monitor)

    2001-01-01

    Observations of the Luman alpha forest suggest that there are many more baryons at high redshift than we can find in the Universe nearby. The largest known concentration of baryons in the nearby Universe is the Shapley supercluster. We scanned the Shapley supercluster to search for large scale diffuse emission with the Rossi X-ray Timing Explorer (RXTE), and found some evidence for such emission. Large scale diffuse emission may be associated to the supercluster, or the clusters of galaxies within the supercluster. In this paper we present results of scans near Abell 3571. We found that the sum of a cooling flow and an isothermal beta model adequately describes the X-ray emission from the cluster. Our results suggest that diffuse emission from A3571 extends out to about two virial radii. We briefly discuss the importance of the determination of the cut off radius of the beta model.

  16. Large Scale Deformation of the Western US Cordillera

    NASA Technical Reports Server (NTRS)

    Bennett, Richard A.

    2001-01-01

    Destructive earthquakes occur throughout the western US Cordillera (WUSC), not just within the San Andreas fault zone. But because we do not understand the present-day large-scale deformations of the crust throughout the WUSC, our ability to assess the potential for seismic hazards in this region remains severely limited. To address this problem, we are using a large collection of Global Positioning System (GPS) networks which spans the WUSC to precisely quantify present-day large-scale crustal deformations in a single uniform reference frame. Our work can roughly be divided into an analysis of the GPS observations to infer the deformation field across and within the entire plate boundary zone and an investigation of the implications of this deformation field regarding plate boundary dynamics.

  17. The Large Scale Synthesis of Aligned Plate Nanostructures

    PubMed Central

    Zhou, Yang; Nash, Philip; Liu, Tian; Zhao, Naiqin; Zhu, Shengli

    2016-01-01

    We propose a novel technique for the large-scale synthesis of aligned-plate nanostructures that are self-assembled and self-supporting. The synthesis technique involves developing nanoscale two-phase microstructures through discontinuous precipitation followed by selective etching to remove one of the phases. The method may be applied to any alloy system in which the discontinuous precipitation transformation goes to completion. The resulting structure may have many applications in catalysis, filtering and thermal management depending on the phase selection and added functionality through chemical reaction with the retained phase. The synthesis technique is demonstrated using the discontinuous precipitation of a γ′ phase, (Ni, Co)3Al, followed by selective dissolution of the γ matrix phase. The production of the nanostructure requires heat treatments on the order of minutes and can be performed on a large scale making this synthesis technique of great economic potential. PMID:27439672

  18. Large scale meteorological influence during the Geysers 1979 field experiment

    SciTech Connect

    Barr, S.

    1980-01-01

    A series of meteorological field measurements conducted during July 1979 near Cobb Mountain in Northern California reveals evidence of several scales of atmospheric circulation consistent with the climatic pattern of the area. The scales of influence are reflected in the structure of wind and temperature in vertically stratified layers at a given observation site. Large scale synoptic gradient flow dominates the wind field above about twice the height of the topographic ridge. Below that there is a mixture of effects with evidence of a diurnal sea breeze influence and a sublayer of katabatic winds. The July observations demonstrate that weak migratory circulations in the large scale synoptic meteorological pattern have a significant influence on the day-to-day gradient winds and must be accounted for in planning meteorological programs including tracer experiments.

  19. Large-scale quantum effects in biological systems

    NASA Astrophysics Data System (ADS)

    Mesquita, Marcus V.; Vasconcellos, Áurea R.; Luzzi, Roberto; Mascarenhas, Sergio

    Particular aspects of large-scale quantum effects in biological systems, such as biopolymers and also microtubules in the cytoskeleton of neurons which can have relevance in brain functioning, are discussed. The microscopic (quantum mechanical) and macroscopic (quantum statistical mechanical) aspects, and the emergence of complex behavior, are described. This phenomena consists of the large-scale coherent process of Fröhlich-Bose-Einstein condensation in open and sufficiently far-from-equilibrium biopolymers. Associated with this phenomenon is the presence of Schrödinger-Davydov solitons, which propagate, undistorted and undamped, when embedded in the Fröhlich-Bose-Einstein condensate, thus allowing for the transmission of signals at long distances, involving a question relevant to bioenergetics.

  20. GAIA: A WINDOW TO LARGE-SCALE MOTIONS

    SciTech Connect

    Nusser, Adi; Branchini, Enzo; Davis, Marc E-mail: branchin@fis.uniroma3.it

    2012-08-10

    Using redshifts as a proxy for galaxy distances, estimates of the two-dimensional (2D) transverse peculiar velocities of distant galaxies could be obtained from future measurements of proper motions. We provide the mathematical framework for analyzing 2D transverse motions and show that they offer several advantages over traditional probes of large-scale motions. They are completely independent of any intrinsic relations between galaxy properties; hence, they are essentially free of selection biases. They are free from homogeneous and inhomogeneous Malmquist biases that typically plague distance indicator catalogs. They provide additional information to traditional probes that yield line-of-sight peculiar velocities only. Further, because of their 2D nature, fundamental questions regarding vorticity of large-scale flows can be addressed. Gaia, for example, is expected to provide proper motions of at least bright galaxies with high central surface brightness, making proper motions a likely contender for traditional probes based on current and future distance indicator measurements.

  1. Large-scale objective phenotyping of 3D facial morphology

    PubMed Central

    Hammond, Peter; Suttie, Michael

    2012-01-01

    Abnormal phenotypes have played significant roles in the discovery of gene function, but organized collection of phenotype data has been overshadowed by developments in sequencing technology. In order to study phenotypes systematically, large-scale projects with standardized objective assessment across populations are considered necessary. The report of the 2006 Human Variome Project meeting recommended documentation of phenotypes through electronic means by collaborative groups of computational scientists and clinicians using standard, structured descriptions of disease-specific phenotypes. In this report, we describe progress over the past decade in 3D digital imaging and shape analysis of the face, and future prospects for large-scale facial phenotyping. Illustrative examples are given throughout using a collection of 1107 3D face images of healthy controls and individuals with a range of genetic conditions involving facial dysmorphism. PMID:22434506

  2. Electron drift in a large scale solid xenon

    SciTech Connect

    Yoo, J.; Jaskierny, W. F.

    2015-08-21

    A study of charge drift in a large scale optically transparent solid xenon is reported. A pulsed high power xenon light source is used to liberate electrons from a photocathode. The drift speeds of the electrons are measured using a 8.7 cm long electrode in both the liquid and solid phase of xenon. In the liquid phase (163 K), the drift speed is 0.193 ± 0.003 cm/μs while the drift speed in the solid phase (157 K) is 0.397 ± 0.006 cm/μs at 900 V/cm over 8.0 cm of uniform electric fields. Furthermore, it is demonstrated that a factor two faster electron drift speed in solid phase xenon compared to that in liquid in a large scale solid xenon.

  3. Electron drift in a large scale solid xenon

    DOE PAGESBeta

    Yoo, J.; Jaskierny, W. F.

    2015-08-21

    A study of charge drift in a large scale optically transparent solid xenon is reported. A pulsed high power xenon light source is used to liberate electrons from a photocathode. The drift speeds of the electrons are measured using a 8.7 cm long electrode in both the liquid and solid phase of xenon. In the liquid phase (163 K), the drift speed is 0.193 ± 0.003 cm/μs while the drift speed in the solid phase (157 K) is 0.397 ± 0.006 cm/μs at 900 V/cm over 8.0 cm of uniform electric fields. Furthermore, it is demonstrated that a factor twomore » faster electron drift speed in solid phase xenon compared to that in liquid in a large scale solid xenon.« less

  4. Large-scale micropropagation system of plant cells.

    PubMed

    Honda, Hiroyuki; Kobayashi, Takeshi

    2004-01-01

    Plant micropropagation is an efficient method of propagating disease-free, genetically uniform and massive amounts of plants in vitro. The scale-up of the whole process for plant micropropagation should be established by an economically feasible technology for large-scale production of them in appropriate bioreactors. It is necessary to design suitable bioreactor configuration which can provide adequate mixing and mass transfer while minimizing the intensity of shear stress and hydrodynamic pressure. Automatic selection of embryogenic calli and regenerated plantlets using image analysis system should be associated with the system. The aim of this chapter is to identify the problems related to large-scale plant micropropagation via somatic embryogenesis, and to summarize the micropropagation technology and computer-aided image analysis. Viscous additive supplemented culture, which is including the successful results obtained by us for callus regeneration, is also introduced. PMID:15453194

  5. Individual skill differences and large-scale environmental learning.

    PubMed

    Fields, Alexa W; Shelton, Amy L

    2006-05-01

    Spatial skills are known to vary widely among normal individuals. This project was designed to address whether these individual differences are differentially related to large-scale environmental learning from route (ground-level) and survey (aerial) perspectives. Participants learned two virtual environments (route and survey) with limited exposure and tested on judgments about relative locations of objects. They also performed a series of spatial and nonspatial component skill tests. With limited learning, performance after route encoding was worse than performance after survey encoding. Furthermore, performance after route and survey encoding appeared to be preferentially linked to perspective and object-based transformations, respectively. Together, the results provide clues to how different skills might be engaged by different individuals for the same goal of learning a large-scale environment. PMID:16719662

  6. Quantum Noise in Large-Scale Coherent Nonlinear Photonic Circuits

    NASA Astrophysics Data System (ADS)

    Santori, Charles; Pelc, Jason S.; Beausoleil, Raymond G.; Tezak, Nikolas; Hamerly, Ryan; Mabuchi, Hideo

    2014-06-01

    A semiclassical simulation approach is presented for studying quantum noise in large-scale photonic circuits incorporating an ideal Kerr nonlinearity. A circuit solver is used to generate matrices defining a set of stochastic differential equations, in which the resonator field variables represent random samplings of the Wigner quasiprobability distributions. Although the semiclassical approach involves making a large-photon-number approximation, tests on one- and two-resonator circuits indicate satisfactory agreement between the semiclassical and full-quantum simulation results in the parameter regime of interest. The semiclassical model is used to simulate random errors in a large-scale circuit that contains 88 resonators and hundreds of components in total and functions as a four-bit ripple counter. The error rate as a function of on-state photon number is examined, and it is observed that the quantum fluctuation amplitudes do not increase as signals propagate through the circuit, an important property for scalability.

  7. Large-scale flow generation in turbulent convection

    PubMed Central

    Krishnamurti, Ruby; Howard, Louis N.

    1981-01-01

    In a horizontal layer of fluid heated from below and cooled from above, cellular convection with horizontal length scale comparable to the layer depth occurs for small enough values of the Rayleigh number. As the Rayleigh number is increased, cellular flow disappears and is replaced by a random array of transient plumes. Upon further increase, these plumes drift in one direction near the bottom and in the opposite direction near the top of the layer with the axes of plumes tilted in such a way that horizontal momentum is transported upward via the Reynolds stress. With the onset of this large-scale flow, the largest scale of motion has increased from that comparable to the layer depth to a scale comparable to the layer width. The conditions for occurrence and determination of the direction of this large-scale circulation are described. Images PMID:16592996

  8. The Large Scale Synthesis of Aligned Plate Nanostructures

    NASA Astrophysics Data System (ADS)

    Zhou, Yang; Nash, Philip; Liu, Tian; Zhao, Naiqin; Zhu, Shengli

    2016-07-01

    We propose a novel technique for the large-scale synthesis of aligned-plate nanostructures that are self-assembled and self-supporting. The synthesis technique involves developing nanoscale two-phase microstructures through discontinuous precipitation followed by selective etching to remove one of the phases. The method may be applied to any alloy system in which the discontinuous precipitation transformation goes to completion. The resulting structure may have many applications in catalysis, filtering and thermal management depending on the phase selection and added functionality through chemical reaction with the retained phase. The synthesis technique is demonstrated using the discontinuous precipitation of a γ‧ phase, (Ni, Co)3Al, followed by selective dissolution of the γ matrix phase. The production of the nanostructure requires heat treatments on the order of minutes and can be performed on a large scale making this synthesis technique of great economic potential.

  9. Large-scale behavior and statistical equilibria in rotating flows

    NASA Astrophysics Data System (ADS)

    Mininni, P. D.; Dmitruk, P.; Matthaeus, W. H.; Pouquet, A.

    2011-01-01

    We examine long-time properties of the ideal dynamics of three-dimensional flows, in the presence or not of an imposed solid-body rotation and with or without helicity (velocity-vorticity correlation). In all cases, the results agree with the isotropic predictions stemming from statistical mechanics. No accumulation of excitation occurs in the large scales, although, in the dissipative rotating case, anisotropy and accumulation, in the form of an inverse cascade of energy, are known to occur. We attribute this latter discrepancy to the linearity of the term responsible for the emergence of inertial waves. At intermediate times, inertial energy spectra emerge that differ somewhat from classical wave-turbulence expectations and with a trace of large-scale excitation that goes away for long times. These results are discussed in the context of partial two dimensionalization of the flow undergoing strong rotation as advocated by several authors.

  10. The workshop on iterative methods for large scale nonlinear problems

    SciTech Connect

    Walker, H.F.; Pernice, M.

    1995-12-01

    The aim of the workshop was to bring together researchers working on large scale applications with numerical specialists of various kinds. Applications that were addressed included reactive flows (combustion and other chemically reacting flows, tokamak modeling), porous media flows, cardiac modeling, chemical vapor deposition, image restoration, macromolecular modeling, and population dynamics. Numerical areas included Newton iterative (truncated Newton) methods, Krylov subspace methods, domain decomposition and other preconditioning methods, large scale optimization and optimal control, and parallel implementations and software. This report offers a brief summary of workshop activities and information about the participants. Interested readers are encouraged to look into an online proceedings available at http://www.usi.utah.edu/logan.proceedings. In this, the material offered here is augmented with hypertext abstracts that include links to locations such as speakers` home pages, PostScript copies of talks and papers, cross-references to related talks, and other information about topics addresses at the workshop.

  11. Prototype Vector Machine for Large Scale Semi-Supervised Learning

    SciTech Connect

    Zhang, Kai; Kwok, James T.; Parvin, Bahram

    2009-04-29

    Practicaldataminingrarelyfalls exactlyinto the supervisedlearning scenario. Rather, the growing amount of unlabeled data poses a big challenge to large-scale semi-supervised learning (SSL). We note that the computationalintensivenessofgraph-based SSLarises largely from the manifold or graph regularization, which in turn lead to large models that are dificult to handle. To alleviate this, we proposed the prototype vector machine (PVM), a highlyscalable,graph-based algorithm for large-scale SSL. Our key innovation is the use of"prototypes vectors" for effcient approximation on both the graph-based regularizer and model representation. The choice of prototypes are grounded upon two important criteria: they not only perform effective low-rank approximation of the kernel matrix, but also span a model suffering the minimum information loss compared with the complete model. We demonstrate encouraging performance and appealing scaling properties of the PVM on a number of machine learning benchmark data sets.

  12. Large-Scale Optimization for Bayesian Inference in Complex Systems

    SciTech Connect

    Willcox, Karen; Marzouk, Youssef

    2013-11-12

    The SAGUARO (Scalable Algorithms for Groundwater Uncertainty Analysis and Robust Optimization) Project focused on the development of scalable numerical algorithms for large-scale Bayesian inversion in complex systems that capitalize on advances in large-scale simulation-based optimization and inversion methods. The project was a collaborative effort among MIT, the University of Texas at Austin, Georgia Institute of Technology, and Sandia National Laboratories. The research was directed in three complementary areas: efficient approximations of the Hessian operator, reductions in complexity of forward simulations via stochastic spectral approximations and model reduction, and employing large-scale optimization concepts to accelerate sampling. The MIT--Sandia component of the SAGUARO Project addressed the intractability of conventional sampling methods for large-scale statistical inverse problems by devising reduced-order models that are faithful to the full-order model over a wide range of parameter values; sampling then employs the reduced model rather than the full model, resulting in very large computational savings. Results indicate little effect on the computed posterior distribution. On the other hand, in the Texas--Georgia Tech component of the project, we retain the full-order model, but exploit inverse problem structure (adjoint-based gradients and partial Hessian information of the parameter-to-observation map) to implicitly extract lower dimensional information on the posterior distribution; this greatly speeds up sampling methods, so that fewer sampling points are needed. We can think of these two approaches as ``reduce then sample'' and ``sample then reduce.'' In fact, these two approaches are complementary, and can be used in conjunction with each other. Moreover, they both exploit deterministic inverse problem structure, in the form of adjoint-based gradient and Hessian information of the underlying parameter-to-observation map, to achieve their

  13. Analysis plan for 1985 large-scale tests. Technical report

    SciTech Connect

    McMullan, F.W.

    1983-01-01

    The purpose of this effort is to assist DNA in planning for large-scale (upwards of 5000 tons) detonations of conventional explosives in the 1985 and beyond time frame. Primary research objectives were to investigate potential means to increase blast duration and peak pressures. This report identifies and analyzes several candidate explosives. It examines several charge designs and identifies advantages and disadvantages of each. Other factors including terrain and multiburst techniques are addressed as are test site considerations.

  14. Large-scale Alfvén vortices

    NASA Astrophysics Data System (ADS)

    Onishchenko, O. G.; Pokhotelov, O. A.; Horton, W.; Scullion, E.; Fedun, V.

    2015-12-01

    The new type of large-scale vortex structures of dispersionless Alfvén waves in collisionless plasma is investigated. It is shown that Alfvén waves can propagate in the form of Alfvén vortices of finite characteristic radius and characterised by magnetic flux ropes carrying orbital angular momentum. The structure of the toroidal and radial velocity, fluid and magnetic field vorticity, the longitudinal electric current in the plane orthogonal to the external magnetic field are discussed.

  15. Large-Scale Weather Disturbances in Mars’ Southern Extratropics

    NASA Astrophysics Data System (ADS)

    Hollingsworth, Jeffery L.; Kahre, Melinda A.

    2015-11-01

    Between late autumn and early spring, Mars’ middle and high latitudes within its atmosphere support strong mean thermal gradients between the tropics and poles. Observations from both the Mars Global Surveyor (MGS) and Mars Reconnaissance Orbiter (MRO) indicate that this strong baroclinicity supports intense, large-scale eastward traveling weather systems (i.e., transient synoptic-period waves). These extratropical weather disturbances are key components of the global circulation. Such wave-like disturbances act as agents in the transport of heat and momentum, and generalized scalar/tracer quantities (e.g., atmospheric dust, water-vapor and ice clouds). The character of large-scale, traveling extratropical synoptic-period disturbances in Mars' southern hemisphere during late winter through early spring is investigated using a moderately high-resolution Mars global climate model (Mars GCM). This Mars GCM imposes interactively lifted and radiatively active dust based on a threshold value of the surface stress. The model exhibits a reasonable "dust cycle" (i.e., globally averaged, a dustier atmosphere during southern spring and summer occurs). Compared to their northern-hemisphere counterparts, southern synoptic-period weather disturbances and accompanying frontal waves have smaller meridional and zonal scales, and are far less intense. Influences of the zonally asymmetric (i.e., east-west varying) topography on southern large-scale weather are examined. Simulations that adapt Mars’ full topography compared to simulations that utilize synthetic topographies emulating key large-scale features of the southern middle latitudes indicate that Mars’ transient barotropic/baroclinic eddies are highly influenced by the great impact basins of this hemisphere (e.g., Argyre and Hellas). The occurrence of a southern storm zone in late winter and early spring appears to be anchored to the western hemisphere via orographic influences from the Tharsis highlands, and the Argyre

  16. Cosmic string and formation of large scale structure.

    NASA Astrophysics Data System (ADS)

    Fang, L.-Z.; Xiang, S.-P.

    Cosmic string formed due to phase transition in the early universe may be the cause of galaxy formation and clustering. The advantage of string model is that it can give a consistent explanation of all observed results related to large scale structure, such as correlation functions of galaxies, clusters and superclusters, the existence of voids and/or bubbles, anisotropy of cosmic background radiation. A systematic review on string model has been done.

  17. Large-scale Alfvén vortices

    SciTech Connect

    Onishchenko, O. G.; Horton, W.; Scullion, E.; Fedun, V.

    2015-12-15

    The new type of large-scale vortex structures of dispersionless Alfvén waves in collisionless plasma is investigated. It is shown that Alfvén waves can propagate in the form of Alfvén vortices of finite characteristic radius and characterised by magnetic flux ropes carrying orbital angular momentum. The structure of the toroidal and radial velocity, fluid and magnetic field vorticity, the longitudinal electric current in the plane orthogonal to the external magnetic field are discussed.

  18. Climate: large-scale warming is not urban.

    PubMed

    Parker, David E

    2004-11-18

    Controversy has persisted over the influence of urban warming on reported large-scale surface-air temperature trends. Urban heat islands occur mainly at night and are reduced in windy conditions. Here we show that, globally, temperatures over land have risen as much on windy nights as on calm nights, indicating that the observed overall warming is not a consequence of urban development. PMID:15549087

  19. Relic vector field and CMB large scale anomalies

    SciTech Connect

    Chen, Xingang; Wang, Yi E-mail: yw366@cam.ac.uk

    2014-10-01

    We study the most general effects of relic vector fields on the inflationary background and density perturbations. Such effects are observable if the number of inflationary e-folds is close to the minimum requirement to solve the horizon problem. We show that this can potentially explain two CMB large scale anomalies: the quadrupole-octopole alignment and the quadrupole power suppression. We discuss its effect on the parity anomaly. We also provide analytical template for more detailed data comparison.

  20. Turbulent large-scale structure effects on wake meandering

    NASA Astrophysics Data System (ADS)

    Muller, Y.-A.; Masson, C.; Aubrun, S.

    2015-06-01

    This work studies effects of large-scale turbulent structures on wake meandering using Large Eddy Simulations (LES) over an actuator disk. Other potential source of wake meandering such as the instablility mechanisms associated with tip vortices are not treated in this study. A crucial element of the efficient, pragmatic and successful simulations of large-scale turbulent structures in Atmospheric Boundary Layer (ABL) is the generation of the stochastic turbulent atmospheric flow. This is an essential capability since one source of wake meandering is these large - larger than the turbine diameter - turbulent structures. The unsteady wind turbine wake in ABL is simulated using a combination of LES and actuator disk approaches. In order to dedicate the large majority of the available computing power in the wake, the ABL ground region of the flow is not part of the computational domain. Instead, mixed Dirichlet/Neumann boundary conditions are applied at all the computational surfaces except at the outlet. Prescribed values for Dirichlet contribution of these boundary conditions are provided by a stochastic turbulent wind generator. This allows to simulate large-scale turbulent structures - larger than the computational domain - leading to an efficient simulation technique of wake meandering. Since the stochastic wind generator includes shear, the turbulence production is included in the analysis without the necessity of resolving the flow near the ground. The classical Smagorinsky sub-grid model is used. The resulting numerical methodology has been implemented in OpenFOAM. Comparisons with experimental measurements in porous-disk wakes have been undertaken, and the agreements are good. While temporal resolution in experimental measurements is high, the spatial resolution is often too low. LES numerical results provide a more complete spatial description of the flow. They tend to demonstrate that inflow low frequency content - or large- scale turbulent structures - is

  1. Space transportation booster engine thrust chamber technology, large scale injector

    NASA Technical Reports Server (NTRS)

    Schneider, J. A.

    1993-01-01

    The objective of the Large Scale Injector (LSI) program was to deliver a 21 inch diameter, 600,000 lbf thrust class injector to NASA/MSFC for hot fire testing. The hot fire test program would demonstrate the feasibility and integrity of the full scale injector, including combustion stability, chamber wall compatibility (thermal management), and injector performance. The 21 inch diameter injector was delivered in September of 1991.

  2. Supporting large scale applications on networks of workstations

    NASA Technical Reports Server (NTRS)

    Cooper, Robert; Birman, Kenneth P.

    1989-01-01

    Distributed applications on networks of workstations are an increasingly common way to satisfy computing needs. However, existing mechanisms for distributed programming exhibit poor performance and reliability as application size increases. Extension of the ISIS distributed programming system to support large scale distributed applications by providing hierarchical process groups is discussed. Incorporation of hierarchy in the program structure and exploitation of this to limit the communication and storage required in any one component of the distributed system is examined.

  3. Homogenization of Large-Scale Movement Models in Ecology

    USGS Publications Warehouse

    Garlick, M.J.; Powell, J.A.; Hooten, M.B.; McFarlane, L.R.

    2011-01-01

    A difficulty in using diffusion models to predict large scale animal population dispersal is that individuals move differently based on local information (as opposed to gradients) in differing habitat types. This can be accommodated by using ecological diffusion. However, real environments are often spatially complex, limiting application of a direct approach. Homogenization for partial differential equations has long been applied to Fickian diffusion (in which average individual movement is organized along gradients of habitat and population density). We derive a homogenization procedure for ecological diffusion and apply it to a simple model for chronic wasting disease in mule deer. Homogenization allows us to determine the impact of small scale (10-100 m) habitat variability on large scale (10-100 km) movement. The procedure generates asymptotic equations for solutions on the large scale with parameters defined by small-scale variation. The simplicity of this homogenization procedure is striking when compared to the multi-dimensional homogenization procedure for Fickian diffusion,and the method will be equally straightforward for more complex models. ?? 2010 Society for Mathematical Biology.

  4. Dispersal Mutualism Incorporated into Large-Scale, Infrequent Disturbances

    PubMed Central

    Parker, V. Thomas

    2015-01-01

    Because of their influence on succession and other community interactions, large-scale, infrequent natural disturbances also should play a major role in mutualistic interactions. Using field data and experiments, I test whether mutualisms have been incorporated into large-scale wildfire by whether the outcomes of a mutualism depend on disturbance. In this study a seed dispersal mutualism is shown to depend on infrequent, large-scale disturbances. A dominant shrubland plant (Arctostaphylos species) produces seeds that make up a persistent soil seed bank and requires fire to germinate. In post-fire stands, I show that seedlings emerging from rodent caches dominate sites experiencing higher fire intensity. Field experiments show that rodents (Perimyscus californicus, P. boylii) do cache Arctostaphylos fruit and bury most seed caches to a sufficient depth to survive a killing heat pulse that a fire might drive into the soil. While the rodent dispersal and caching behavior itself has not changed compared to other habitats, the environmental transformation caused by wildfire converts the caching burial of seed from a dispersal process to a plant fire adaptive trait, and provides the context for stimulating subsequent life history evolution in the plant host. PMID:26151560

  5. Large-scale flow experiments for managing river systems

    USGS Publications Warehouse

    Konrad, C.P.; Olden, J.D.; Lytle, D.A.; Melis, T.S.; Schmidt, J.C.; Bray, E.N.; Freeman, Mary C.; Gido, K.B.; Hemphill, N.P.; Kennard, M.J.; McMullen, L.E.; Mims, M.C.; Pyron, M.; Robinson, C.T.; Williams, J.G.

    2011-01-01

    Experimental manipulations of streamflow have been used globally in recent decades to mitigate the impacts of dam operations on river systems. Rivers are challenging subjects for experimentation, because they are open systems that cannot be isolated from their social context. We identify principles to address the challenges of conducting effective large-scale flow experiments. Flow experiments have both scientific and social value when they help to resolve specific questions about the ecological action of flow with a clear nexus to water policies and decisions. Water managers must integrate new information into operating policies for large-scale experiments to be effective. Modeling and monitoring can be integrated with experiments to analyze long-term ecological responses. Experimental design should include spatially extensive observations and well-defined, repeated treatments. Large-scale flow manipulations are only a part of dam operations that affect river systems. Scientists can ensure that experimental manipulations continue to be a valuable approach for the scientifically based management of river systems. ?? 2011 by American Institute of Biological Sciences. All rights reserved.

  6. Large-scale flow experiments for managing river systems

    USGS Publications Warehouse

    Konrad, Christopher P.; Olden, Julian D.; Lytle, David A.; Melis, Theodore S.; Schmidt, John C.; Bray, Erin N.; Freeman, Mary C.; Gido, Keith B.; Hemphill, Nina P.; Kennard, Mark J.; McMullen, Laura E.; Mims, Meryl C.; Pyron, Mark; Robinson, Christopher T.; Williams, John G.

    2011-01-01

    Experimental manipulations of streamflow have been used globally in recent decades to mitigate the impacts of dam operations on river systems. Rivers are challenging subjects for experimentation, because they are open systems that cannot be isolated from their social context. We identify principles to address the challenges of conducting effective large-scale flow experiments. Flow experiments have both scientific and social value when they help to resolve specific questions about the ecological action of flow with a clear nexus to water policies and decisions. Water managers must integrate new information into operating policies for large-scale experiments to be effective. Modeling and monitoring can be integrated with experiments to analyze long-term ecological responses. Experimental design should include spatially extensive observations and well-defined, repeated treatments. Large-scale flow manipulations are only a part of dam operations that affect river systems. Scientists can ensure that experimental manipulations continue to be a valuable approach for the scientifically based management of river systems.

  7. Large-scale flow generation by inhomogeneous helicity

    NASA Astrophysics Data System (ADS)

    Yokoi, N.; Brandenburg, A.

    2016-03-01

    The effect of kinetic helicity (velocity-vorticity correlation) on turbulent momentum transport is investigated. The turbulent kinetic helicity (pseudoscalar) enters the Reynolds stress (mirror-symmetric tensor) expression in the form of a helicity gradient as the coupling coefficient for the mean vorticity and/or the angular velocity (axial vector), which suggests the possibility of mean-flow generation in the presence of inhomogeneous helicity. This inhomogeneous helicity effect, which was previously confirmed at the level of a turbulence- or closure-model simulation, is examined with the aid of direct numerical simulations of rotating turbulence with nonuniform helicity sustained by an external forcing. The numerical simulations show that the spatial distribution of the Reynolds stress is in agreement with the helicity-related term coupled with the angular velocity, and that a large-scale flow is generated in the direction of angular velocity. Such a large-scale flow is not induced in the case of homogeneous turbulent helicity. This result confirms the validity of the inhomogeneous helicity effect in large-scale flow generation and suggests that a vortex dynamo is possible even in incompressible turbulence where there is no baroclinicity effect.

  8. Dispersal Mutualism Incorporated into Large-Scale, Infrequent Disturbances.

    PubMed

    Parker, V Thomas

    2015-01-01

    Because of their influence on succession and other community interactions, large-scale, infrequent natural disturbances also should play a major role in mutualistic interactions. Using field data and experiments, I test whether mutualisms have been incorporated into large-scale wildfire by whether the outcomes of a mutualism depend on disturbance. In this study a seed dispersal mutualism is shown to depend on infrequent, large-scale disturbances. A dominant shrubland plant (Arctostaphylos species) produces seeds that make up a persistent soil seed bank and requires fire to germinate. In post-fire stands, I show that seedlings emerging from rodent caches dominate sites experiencing higher fire intensity. Field experiments show that rodents (Perimyscus californicus, P. boylii) do cache Arctostaphylos fruit and bury most seed caches to a sufficient depth to survive a killing heat pulse that a fire might drive into the soil. While the rodent dispersal and caching behavior itself has not changed compared to other habitats, the environmental transformation caused by wildfire converts the caching burial of seed from a dispersal process to a plant fire adaptive trait, and provides the context for stimulating subsequent life history evolution in the plant host. PMID:26151560

  9. Large-scale quantification of CVD graphene surface coverage.

    PubMed

    Ambrosi, Adriano; Bonanni, Alessandra; Sofer, Zdeněk; Pumera, Martin

    2013-03-21

    The extraordinary properties demonstrated for graphene and graphene-related materials can be fully exploited when a large-scale fabrication procedure is made available. Chemical vapor deposition (CVD) of graphene on Cu and Ni substrates is one of the most promising procedures to synthesize large-area and good quality graphene films. Parallel to the fabrication process, a large-scale quality monitoring technique is equally crucial. We demonstrate here a rapid and simple methodology that is able to probe the effectiveness of the growth process over a large substrate area for both Ni and Cu substrates. This method is based on inherent electrochemical signals generated by the underlying metal catalysts when fractures or discontinuities of the graphene film are present. The method can be applied immediately after the CVD growth process without the need for any graphene transfer step and represents a powerful quality monitoring technique for the assessment of large-scale fabrication of graphene by the CVD process. PMID:23396554

  10. Photorealistic large-scale urban city model reconstruction.

    PubMed

    Poullis, Charalambos; You, Suya

    2009-01-01

    The rapid and efficient creation of virtual environments has become a crucial part of virtual reality applications. In particular, civil and defense applications often require and employ detailed models of operations areas for training, simulations of different scenarios, planning for natural or man-made events, monitoring, surveillance, games, and films. A realistic representation of the large-scale environments is therefore imperative for the success of such applications since it increases the immersive experience of its users and helps reduce the difference between physical and virtual reality. However, the task of creating such large-scale virtual environments still remains a time-consuming and manual work. In this work, we propose a novel method for the rapid reconstruction of photorealistic large-scale virtual environments. First, a novel, extendible, parameterized geometric primitive is presented for the automatic building identification and reconstruction of building structures. In addition, buildings with complex roofs containing complex linear and nonlinear surfaces are reconstructed interactively using a linear polygonal and a nonlinear primitive, respectively. Second, we present a rendering pipeline for the composition of photorealistic textures, which unlike existing techniques, can recover missing or occluded texture information by integrating multiple information captured from different optical sensors (ground, aerial, and satellite). PMID:19423889

  11. Large scale structure in universes dominated by cold dark matter

    NASA Technical Reports Server (NTRS)

    Bond, J. Richard

    1986-01-01

    The theory of Gaussian random density field peaks is applied to a numerical study of the large-scale structure developing from adiabatic fluctuations in models of biased galaxy formation in universes with Omega = 1, h = 0.5 dominated by cold dark matter (CDM). The angular anisotropy of the cross-correlation function demonstrates that the far-field regions of cluster-scale peaks are asymmetric, as recent observations indicate. These regions will generate pancakes or filaments upon collapse. One-dimensional singularities in the large-scale bulk flow should arise in these CDM models, appearing as pancakes in position space. They are too rare to explain the CfA bubble walls, but pancakes that are just turning around now are sufficiently abundant and would appear to be thin walls normal to the line of sight in redshift space. Large scale streaming velocities are significantly smaller than recent observations indicate. To explain the reported 700 km/s coherent motions, mass must be significantly more clustered than galaxies with a biasing factor of less than 0.4 and a nonlinear redshift at cluster scales greater than one for both massive neutrino and cold models.

  12. Line segment extraction for large scale unorganized point clouds

    NASA Astrophysics Data System (ADS)

    Lin, Yangbin; Wang, Cheng; Cheng, Jun; Chen, Bili; Jia, Fukai; Chen, Zhonggui; Li, Jonathan

    2015-04-01

    Line segment detection in images is already a well-investigated topic, although it has received considerably less attention in 3D point clouds. Benefiting from current LiDAR devices, large-scale point clouds are becoming increasingly common. Most human-made objects have flat surfaces. Line segments that occur where pairs of planes intersect give important information regarding the geometric content of point clouds, which is especially useful for automatic building reconstruction and segmentation. This paper proposes a novel method that is capable of accurately extracting plane intersection line segments from large-scale raw scan points. The 3D line-support region, namely, a point set near a straight linear structure, is extracted simultaneously. The 3D line-support region is fitted by our Line-Segment-Half-Planes (LSHP) structure, which provides a geometric constraint for a line segment, making the line segment more reliable and accurate. We demonstrate our method on the point clouds of large-scale, complex, real-world scenes acquired by LiDAR devices. We also demonstrate the application of 3D line-support regions and their LSHP structures on urban scene abstraction.

  13. Large-scale data mining pilot project in human genome

    SciTech Connect

    Musick, R.; Fidelis, R.; Slezak, T.

    1997-05-01

    This whitepaper briefly describes a new, aggressive effort in large- scale data Livermore National Labs. The implications of `large- scale` will be clarified Section. In the short term, this effort will focus on several @ssion-critical questions of Genome project. We will adapt current data mining techniques to the Genome domain, to quantify the accuracy of inference results, and lay the groundwork for a more extensive effort in large-scale data mining. A major aspect of the approach is that we will be fully-staffed data warehousing effort in the human Genome area. The long term goal is strong applications- oriented research program in large-@e data mining. The tools, skill set gained will be directly applicable to a wide spectrum of tasks involving a for large spatial and multidimensional data. This includes applications in ensuring non-proliferation, stockpile stewardship, enabling Global Ecology (Materials Database Industrial Ecology), advancing the Biosciences (Human Genome Project), and supporting data for others (Battlefield Management, Health Care).

  14. How Large Scales Flows May Influence Solar Activity

    NASA Technical Reports Server (NTRS)

    Hathaway, D. H.

    2004-01-01

    Large scale flows within the solar convection zone are the primary drivers of the Sun's magnetic activity cycle and play important roles in shaping the Sun's magnetic field. Differential rotation amplifies the magnetic field through its shearing action and converts poloidal field into toroidal field. Poleward meridional flow near the surface carries magnetic flux that reverses the magnetic poles at about the time of solar maximum. The deeper, equatorward meridional flow can carry magnetic flux back toward the lower latitudes where it erupts through the surface to form tilted active regions that convert toroidal fields into oppositely directed poloidal fields. These axisymmetric flows are themselves driven by large scale convective motions. The effects of the Sun's rotation on convection produce velocity correlations that can maintain both the differential rotation and the meridional circulation. These convective motions can also influence solar activity directly by shaping the magnetic field pattern. While considerable theoretical advances have been made toward understanding these large scale flows, outstanding problems in matching theory to observations still remain.

  15. New Large-scale Control Strategies for Turbulent Boundary Layers

    NASA Astrophysics Data System (ADS)

    Schoppa, Wade; Hussain, Fazle

    1997-11-01

    Using direct numerical simulations of turbulent channel flow, we present robust strategies for drag reduction by prevention of streamwise vortex formation near the wall. Instability of lifted, vortex-free low-speed streaks is shown to generate new streamwise vortices, which dominate near-wall turbulence phenomena. The newly-found instability mechanism initiates streak waviness in the (x,z) plane which leads to ωx sheets. Streak waviness induces positive partial u/partial x (i.e. positive VISA) which causes these sheets to then collapse via stretching (rather than roll up) into streamwise vortices. Significantly, the 3D features of the (instantaneous) instability-generated vortices agree well with the coherent structures educed (i.e. ensemble-averaged) from fully turbulent flow, suggesting the prevalence of this instability mechanism. The new control via large-scale streak manipulation exploits this crucial role of streak instability in vortex generation. An x-independent forcing with a z wavelength of 4 streak spacings, with an amplitude of only 5% of the centerline velocity, produces a significant sustained drag reduction: 20% for imposed counterrotating large-scale swirls and 50% for colliding spanwise wall jet-like forcing. These results suggest promising drag reduction strategies, involving large-scale (hence more durable) actuation and requiring no wall sensors or feedback logic.

  16. Large scale anisotropy of UHECRs for the Telescope Array

    SciTech Connect

    Kido, E.

    2011-09-22

    The origin of Ultra High Energy Cosmic Rays (UHECRs) is one of the most interesting questions in astroparticle physics. Despite of the efforts by other previous measurements, there is no consensus of both of the origin and the mechanism of UHECRs generation and propagation yet. In this context, Telescope Array (TA) experiment is expected to play an important role as the largest detector in the northern hemisphere which consists of an array of surface particle detectors (SDs) and fluorescence detectors (FDs) and other important calibration devices. We searched for large scale anisotropy using SD data of TA. UHECRs are expected to be restricted in GZK horizon when the composition of UHECRs is proton, so the observed arrival directions are expected to exhibit local large scale anisotropy if UHECR sources are some astrophysical objects. We used the SD data set from 11 May 2008 to 7 September 2010 to search for large-scale anisotropy. The discrimination power between LSS and isotropy is not enough yet, but the statistics in TA is expected to discriminate between those in about 95% confidence level on average in near future.

  17. Large-scale functional connectivity networks in the rodent brain.

    PubMed

    Gozzi, Alessandro; Schwarz, Adam J

    2016-02-15

    Resting-state functional Magnetic Resonance Imaging (rsfMRI) of the human brain has revealed multiple large-scale neural networks within a hierarchical and complex structure of coordinated functional activity. These distributed neuroanatomical systems provide a sensitive window on brain function and its disruption in a variety of neuropathological conditions. The study of macroscale intrinsic connectivity networks in preclinical species, where genetic and environmental conditions can be controlled and manipulated with high specificity, offers the opportunity to elucidate the biological determinants of these alterations. While rsfMRI methods are now widely used in human connectivity research, these approaches have only relatively recently been back-translated into laboratory animals. Here we review recent progress in the study of functional connectivity in rodent species, emphasising the ability of this approach to resolve large-scale brain networks that recapitulate neuroanatomical features of known functional systems in the human brain. These include, but are not limited to, a distributed set of regions identified in rats and mice that may represent a putative evolutionary precursor of the human default mode network (DMN). The impact and control of potential experimental and methodological confounds are also critically discussed. Finally, we highlight the enormous potential and some initial application of connectivity mapping in transgenic models as a tool to investigate the neuropathological underpinnings of the large-scale connectional alterations associated with human neuropsychiatric and neurological conditions. We conclude by discussing the translational potential of these methods in basic and applied neuroscience. PMID:26706448

  18. Upscaling of elastic properties for large scale geomechanical simulations

    NASA Astrophysics Data System (ADS)

    Chalon, F.; Mainguy, M.; Longuemare, P.; Lemonnier, P.

    2004-09-01

    Large scale geomechanical simulations are being increasingly used to model the compaction of stress dependent reservoirs, predict the long term integrity of under-ground radioactive waste disposals, and analyse the viability of hot-dry rock geothermal sites. These large scale simulations require the definition of homogenous mechanical properties for each geomechanical cell whereas the rock properties are expected to vary at a smaller scale. Therefore, this paper proposes a new methodology that makes possible to define the equivalent mechanical properties of the geomechanical cells using the fine scale information given in the geological model. This methodology is implemented on a synthetic reservoir case and two upscaling procedures providing the effective elastic properties of the Hooke's law are tested. The first upscaling procedure is an analytical method for perfectly stratified rock mass, whereas the second procedure computes lower and upper bounds of the equivalent properties with no assumption on the small scale heterogeneity distribution. Both procedures are applied to one geomechanical cell extracted from the reservoir structure. The results show that the analytical and numerical upscaling procedures provide accurate estimations of the effective parameters. Furthermore, a large scale simulation using the homogenized properties of each geomechanical cell calculated with the analytical method demonstrates that the overall behaviour of the reservoir structure is well reproduced for two different loading cases. Copyright

  19. Large-scale analysis of peptide sequence variants: the case for high-field asymmetric waveform ion mobility spectrometry.

    PubMed

    Creese, Andrew J; Smart, Jade; Cooper, Helen J

    2013-05-21

    Large scale analysis of proteins by mass spectrometry is becoming increasingly routine; however, the presence of peptide isomers remains a significant challenge for both identification and quantitation in proteomics. Classes of isomers include sequence inversions, structural isomers, and localization variants. In many cases, liquid chromatography is inadequate for separation of peptide isomers. The resulting tandem mass spectra are composite, containing fragments from multiple precursor ions. The benefits of high-field asymmetric waveform ion mobility spectrometry (FAIMS) for proteomics have been demonstrated by a number of groups, but previously work has focused on extending proteome coverage generally. Here, we present a systematic study of the benefits of FAIMS for a key challenge in proteomics, that of peptide isomers. We have applied FAIMS to the analysis of a phosphopeptide library comprising the sequences GPSGXVpSXAQLX(K/R) and SXPFKXpSPLXFG(K/R), where X = ADEFGLSTVY. The library has defined limits enabling us to make valid conclusions regarding FAIMS performance. The library contains numerous sequence inversions and structural isomers. In addition, there are large numbers of theoretical localization variants, allowing false localization rates to be determined. The FAIMS approach is compared with reversed-phase liquid chromatography and strong cation exchange chromatography. The FAIMS approach identified 35% of the peptide library, whereas LC-MS/MS alone identified 8% and LC-MS/MS with strong cation exchange chromatography prefractionation identified 17.3% of the library. PMID:23646896

  20. Large-Scale Covariability Between Aerosol and Precipitation Over the 7-SEAS Region: Observations and Simulations

    NASA Technical Reports Server (NTRS)

    Huang, Jingfeng; Hsu, N. Christina; Tsay, Si-Chee; Zhang, Chidong; Jeong, Myeong Jae; Gautam, Ritesh; Bettenhausen, Corey; Sayer, Andrew M.; Hansell, Richard A.; Liu, Xiaohong; Jiang, Jonathan H.

    2012-01-01

    One of the seven scientific areas of interests of the 7-SEAS field campaign is to evaluate the impact of aerosol on cloud and precipitation (http://7-seas.gsfc.nasa.gov). However, large-scale covariability between aerosol, cloud and precipitation is complicated not only by ambient environment and a variety of aerosol effects, but also by effects from rain washout and climate factors. This study characterizes large-scale aerosol-cloud-precipitation covariability through synergy of long-term multi ]sensor satellite observations with model simulations over the 7-SEAS region [10S-30N, 95E-130E]. Results show that climate factors such as ENSO significantly modulate aerosol and precipitation over the region simultaneously. After removal of climate factor effects, aerosol and precipitation are significantly anti-correlated over the southern part of the region, where high aerosols loading is associated with overall reduced total precipitation with intensified rain rates and decreased rain frequency, decreased tropospheric latent heating, suppressed cloud top height and increased outgoing longwave radiation, enhanced clear-sky shortwave TOA flux but reduced all-sky shortwave TOA flux in deep convective regimes; but such covariability becomes less notable over the northern counterpart of the region where low ]level stratus are found. Using CO as a proxy of biomass burning aerosols to minimize the washout effect, large-scale covariability between CO and precipitation was also investigated and similar large-scale covariability observed. Model simulations with NCAR CAM5 were found to show similar effects to observations in the spatio-temporal patterns. Results from both observations and simulations are valuable for improving our understanding of this region's meteorological system and the roles of aerosol within it. Key words: aerosol; precipitation; large-scale covariability; aerosol effects; washout; climate factors; 7- SEAS; CO; CAM5

  1. Ultra-large-scale Cosmology in Next-generation Experiments with Single Tracers

    NASA Astrophysics Data System (ADS)

    Alonso, David; Bull, Philip; Ferreira, Pedro G.; Maartens, Roy; Santos, Mário G.

    2015-12-01

    Future surveys of large-scale structure will be able to measure perturbations on the scale of the cosmological horizon, and so could potentially probe a number of novel relativistic effects that are negligibly small on sub-horizon scales. These effects leave distinctive signatures in the power spectra of clustering observables and, if measurable, would open a new window on relativistic cosmology. We quantify the size and detectability of the effects for the most relevant future large-scale structure experiments: spectroscopic and photometric galaxy redshift surveys, intensity mapping surveys of neutral hydrogen, and radio continuum surveys. Our forecasts show that next-generation experiments, reaching out to redshifts z≃ 4, will not be able to detect previously undetected general-relativistic effects by using individual tracers of the density field, although the contribution of weak lensing magnification on large scales should be clearly detectable. We also perform a rigorous joint forecast for the detection of primordial non-Gaussianity through the excess power it produces in the clustering of biased tracers on large scales, finding that uncertainties of σ ({f}{{NL}})∼ 1-2 should be achievable. We study the level of degeneracy of these large-scale effects with several tracer-dependent nuisance parameters, quantifying the minimal priors on the latter that are needed for an optimal measurement of the former. Finally, we discuss the systematic effects that must be mitigated to achieve this level of sensitivity, and some alternative approaches that should help to improve the constraints. The computational tools developed to carry out this study, which requires the full-sky computation of the theoretical angular power spectra for {O}(100) redshift bins, as well as realistic models of the luminosity function, are publicly available at http://intensitymapping.physics.ox.ac.uk/codes.html.

  2. A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; McCue, Lee Ann; Beagley, Nathaniel; McDermott, Jason E.; Wunschel, David S.; Varnum, Susan M.; Hu, Jian Z.; Isern, Nancy G.; Buchko, Garry W.; Mcateer, Kathleen; Pounds, Joel G.; Skerret, Shawn J.; Liggitt, Denny; Frevert, Charles W.

    2009-03-01

    High-throughput (HTP) technologies offer the capability to evaluate the genome, proteome, and metabolome of organisms at a global scale. This opens up new opportunities to define complex signatures of disease that involve signals from multiple types of biomolecules. Integrating these data types however is difficult due to the heterogeneity of the data. We present a Bayesian approach to integration that uses posterior probabilities to assign class memberships to samples using individual and multiple data sources; these probabilities are based on lower level likelihood functions derived from standard statistical learning algorithms. We demonstrate this approach on microbial infections of mice, where the bronchial alveolar lavage fluid was analyzed by two HTP proteomic and one HTP metabolomic technologies. We demonstrate that integration of the three datasets improves classification accuracy to ~89% from the best individual dataset at ~83%. In addition, we present a new visualization tool called Visual Integration for Bayesian Evaluation (VIBE) that allows the user to observe classification accuracies at the class level and evaluate classification accuracies on any subset of available data types based on the posterior probability models defined for the individual and integrated data.

  3. Robust large-scale parallel nonlinear solvers for simulations.

    SciTech Connect

    Bader, Brett William; Pawlowski, Roger Patrick; Kolda, Tamara Gibson

    2005-11-01

    This report documents research to develop robust and efficient solution techniques for solving large-scale systems of nonlinear equations. The most widely used method for solving systems of nonlinear equations is Newton's method. While much research has been devoted to augmenting Newton-based solvers (usually with globalization techniques), little has been devoted to exploring the application of different models. Our research has been directed at evaluating techniques using different models than Newton's method: a lower order model, Broyden's method, and a higher order model, the tensor method. We have developed large-scale versions of each of these models and have demonstrated their use in important applications at Sandia. Broyden's method replaces the Jacobian with an approximation, allowing codes that cannot evaluate a Jacobian or have an inaccurate Jacobian to converge to a solution. Limited-memory methods, which have been successful in optimization, allow us to extend this approach to large-scale problems. We compare the robustness and efficiency of Newton's method, modified Newton's method, Jacobian-free Newton-Krylov method, and our limited-memory Broyden method. Comparisons are carried out for large-scale applications of fluid flow simulations and electronic circuit simulations. Results show that, in cases where the Jacobian was inaccurate or could not be computed, Broyden's method converged in some cases where Newton's method failed to converge. We identify conditions where Broyden's method can be more efficient than Newton's method. We also present modifications to a large-scale tensor method, originally proposed by Bouaricha, for greater efficiency, better robustness, and wider applicability. Tensor methods are an alternative to Newton-based methods and are based on computing a step based on a local quadratic model rather than a linear model. The advantage of Bouaricha's method is that it can use any existing linear solver, which makes it simple to write

  4. Foundational perspectives on causality in large-scale brain networks.

    PubMed

    Mannino, Michael; Bressler, Steven L

    2015-12-01

    A profusion of recent work in cognitive neuroscience has been concerned with the endeavor to uncover causal influences in large-scale brain networks. However, despite the fact that many papers give a nod to the important theoretical challenges posed by the concept of causality, this explosion of research has generally not been accompanied by a rigorous conceptual analysis of the nature of causality in the brain. This review provides both a descriptive and prescriptive account of the nature of causality as found within and between large-scale brain networks. In short, it seeks to clarify the concept of causality in large-scale brain networks both philosophically and scientifically. This is accomplished by briefly reviewing the rich philosophical history of work on causality, especially focusing on contributions by David Hume, Immanuel Kant, Bertrand Russell, and Christopher Hitchcock. We go on to discuss the impact that various interpretations of modern physics have had on our understanding of causality. Throughout all this, a central focus is the distinction between theories of deterministic causality (DC), whereby causes uniquely determine their effects, and probabilistic causality (PC), whereby causes change the probability of occurrence of their effects. We argue that, given the topological complexity of its large-scale connectivity, the brain should be considered as a complex system and its causal influences treated as probabilistic in nature. We conclude that PC is well suited for explaining causality in the brain for three reasons: (1) brain causality is often mutual; (2) connectional convergence dictates that only rarely is the activity of one neuronal population uniquely determined by another one; and (3) the causal influences exerted between neuronal populations may not have observable effects. A number of different techniques are currently available to characterize causal influence in the brain. Typically, these techniques quantify the statistical

  5. Large-scale magnetic topologies of early M dwarfs

    NASA Astrophysics Data System (ADS)

    Donati, J.-F.; Morin, J.; Petit, P.; Delfosse, X.; Forveille, T.; Aurière, M.; Cabanac, R.; Dintrans, B.; Fares, R.; Gastine, T.; Jardine, M. M.; Lignières, F.; Paletou, F.; Ramirez Velez, J. C.; Théado, S.

    2008-10-01

    We present here additional results of a spectropolarimetric survey of a small sample of stars ranging from spectral type M0 to M8 aimed at investigating observationally how dynamo processes operate in stars on both sides of the full convection threshold (spectral type M4). The present paper focuses on early M stars (M0-M3), that is above the full convection threshold. Applying tomographic imaging techniques to time series of rotationally modulated circularly polarized profiles collected with the NARVAL spectropolarimeter, we determine the rotation period and reconstruct the large-scale magnetic topologies of six early M dwarfs. We find that early-M stars preferentially host large-scale fields with dominantly toroidal and non-axisymmetric poloidal configurations, along with significant differential rotation (and long-term variability); only the lowest-mass star of our subsample is found to host an almost fully poloidal, mainly axisymmetric large-scale field resembling those found in mid-M dwarfs. This abrupt change in the large-scale magnetic topologies of M dwarfs (occurring at spectral type M3) has no related signature on X-ray luminosities (measuring the total amount of magnetic flux); it thus suggests that underlying dynamo processes become more efficient at producing large-scale fields (despite producing the same flux) at spectral types later than M3. We suspect that this change relates to the rapid decrease in the radiative cores of low-mass stars and to the simultaneous sharp increase of the convective turnover times (with decreasing stellar mass) that models predict to occur at M3; it may also be (at least partly) responsible for the reduced magnetic braking reported for fully convective stars. Based on observations obtained at the Télescope Bernard Lyot (TBL), operated by the Institut National des Science de l'Univers of the Centre National de la Recherche Scientifique of France. E-mail: donati@ast.obs-mip.fr (J-FD); jmorin@ast.obs-mip.fr (JM); petit

  6. Foundational perspectives on causality in large-scale brain networks

    NASA Astrophysics Data System (ADS)

    Mannino, Michael; Bressler, Steven L.

    2015-12-01

    A profusion of recent work in cognitive neuroscience has been concerned with the endeavor to uncover causal influences in large-scale brain networks. However, despite the fact that many papers give a nod to the important theoretical challenges posed by the concept of causality, this explosion of research has generally not been accompanied by a rigorous conceptual analysis of the nature of causality in the brain. This review provides both a descriptive and prescriptive account of the nature of causality as found within and between large-scale brain networks. In short, it seeks to clarify the concept of causality in large-scale brain networks both philosophically and scientifically. This is accomplished by briefly reviewing the rich philosophical history of work on causality, especially focusing on contributions by David Hume, Immanuel Kant, Bertrand Russell, and Christopher Hitchcock. We go on to discuss the impact that various interpretations of modern physics have had on our understanding of causality. Throughout all this, a central focus is the distinction between theories of deterministic causality (DC), whereby causes uniquely determine their effects, and probabilistic causality (PC), whereby causes change the probability of occurrence of their effects. We argue that, given the topological complexity of its large-scale connectivity, the brain should be considered as a complex system and its causal influences treated as probabilistic in nature. We conclude that PC is well suited for explaining causality in the brain for three reasons: (1) brain causality is often mutual; (2) connectional convergence dictates that only rarely is the activity of one neuronal population uniquely determined by another one; and (3) the causal influences exerted between neuronal populations may not have observable effects. A number of different techniques are currently available to characterize causal influence in the brain. Typically, these techniques quantify the statistical

  7. Quantitative proteome-based guidelines for intrinsic disorder characterization.

    PubMed

    Vincent, Michael; Whidden, Mark; Schnell, Santiago

    2016-06-01

    Intrinsically disordered proteins fail to adopt a stable three-dimensional structure under physiological conditions. It is now understood that many disordered proteins are not dysfunctional, but instead engage in numerous cellular processes, including signaling and regulation. Disorder characterization from amino acid sequence relies on computational disorder prediction algorithms. While numerous large-scale investigations of disorder have been performed using these algorithms, and have offered valuable insight regarding the prevalence of protein disorder in many organisms, critical proteome-based descriptive statistical guidelines that would enable the objective assessment of intrinsic disorder in a protein of interest remain to be established. Here we present a quantitative characterization of numerous disorder features using a rigorous non-parametric statistical approach, providing expected values and percentile cutoffs for each feature in ten eukaryotic proteomes. Our estimates utilize multiple ab initio disorder prediction algorithms grounded on physicochemical principles. Furthermore, we present novel threshold values, specific to both the prediction algorithms and the proteomes, defining the longest primary sequence length in which the significance of a continuous disordered region can be evaluated on the basis of length alone. The guidelines presented here are intended to improve the interpretation of disorder content and continuous disorder predictions from the proteomic point of view. PMID:27085142

  8. Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

    PubMed

    Verheggen, Kenneth; Maddelein, Davy; Hulstaert, Niels; Martens, Lennart; Barsnes, Harald; Vaudel, Marc

    2016-03-01

    The use of proteomics bioinformatics substantially contributes to an improved understanding of proteomes, but this novel and in-depth knowledge comes at the cost of increased computational complexity. Parallelization across multiple computers, a strategy termed distributed computing, can be used to handle this increased complexity; however, setting up and maintaining a distributed computing infrastructure requires resources and skills that are not readily available to most research groups. Here we propose a free and open-source framework named Pladipus that greatly facilitates the establishment of distributed computing networks for proteomics bioinformatics tools. Pladipus is straightforward to install and operate thanks to its user-friendly graphical interface, allowing complex bioinformatics tasks to be run easily on a network instead of a single computer. As a result, any researcher can benefit from the increased computational efficiency provided by distributed computing, hence empowering them to tackle more complex bioinformatics challenges. Notably, it enables any research group to perform large-scale reprocessing of publicly available proteomics data, thus supporting the scientific community in mining these data for novel discoveries. PMID:26510693

  9. Large-Scale Sequencing: The Future of Genomic Sciences Colloquium

    SciTech Connect

    Margaret Riley; Merry Buckley

    2009-01-01

    Genetic sequencing and the various molecular techniques it has enabled have revolutionized the field of microbiology. Examining and comparing the genetic sequences borne by microbes - including bacteria, archaea, viruses, and microbial eukaryotes - provides researchers insights into the processes microbes carry out, their pathogenic traits, and new ways to use microorganisms in medicine and manufacturing. Until recently, sequencing entire microbial genomes has been laborious and expensive, and the decision to sequence the genome of an organism was made on a case-by-case basis by individual researchers and funding agencies. Now, thanks to new technologies, the cost and effort of sequencing is within reach for even the smallest facilities, and the ability to sequence the genomes of a significant fraction of microbial life may be possible. The availability of numerous microbial genomes will enable unprecedented insights into microbial evolution, function, and physiology. However, the current ad hoc approach to gathering sequence data has resulted in an unbalanced and highly biased sampling of microbial diversity. A well-coordinated, large-scale effort to target the breadth and depth of microbial diversity would result in the greatest impact. The American Academy of Microbiology convened a colloquium to discuss the scientific benefits of engaging in a large-scale, taxonomically-based sequencing project. A group of individuals with expertise in microbiology, genomics, informatics, ecology, and evolution deliberated on the issues inherent in such an effort and generated a set of specific recommendations for how best to proceed. The vast majority of microbes are presently uncultured and, thus, pose significant challenges to such a taxonomically-based approach to sampling genome diversity. However, we have yet to even scratch the surface of the genomic diversity among cultured microbes. A coordinated sequencing effort of cultured organisms is an appropriate place to begin

  10. Numerical Modeling of Large-Scale Rocky Coastline Evolution

    NASA Astrophysics Data System (ADS)

    Limber, P.; Murray, A. B.; Littlewood, R.; Valvo, L.

    2008-12-01

    Seventy-five percent of the world's ocean coastline is rocky. On large scales (i.e. greater than a kilometer), many intertwined processes drive rocky coastline evolution, including coastal erosion and sediment transport, tectonics, antecedent topography, and variations in sea cliff lithology. In areas such as California, an additional aspect of rocky coastline evolution involves submarine canyons that cut across the continental shelf and extend into the nearshore zone. These types of canyons intercept alongshore sediment transport and flush sand to abyssal depths during periodic turbidity currents, thereby delineating coastal sediment transport pathways and affecting shoreline evolution over large spatial and time scales. How tectonic, sediment transport, and canyon processes interact with inherited topographic and lithologic settings to shape rocky coastlines remains an unanswered, and largely unexplored, question. We will present numerical model results of rocky coastline evolution that starts with an immature fractal coastline. The initial shape is modified by headland erosion, wave-driven alongshore sediment transport, and submarine canyon placement. Our previous model results have shown that, as expected, an initial sediment-free irregularly shaped rocky coastline with homogeneous lithology will undergo smoothing in response to wave attack; headlands erode and mobile sediment is swept into bays, forming isolated pocket beaches. As this diffusive process continues, pocket beaches coalesce, and a continuous sediment transport pathway results. However, when a randomly placed submarine canyon is introduced to the system as a sediment sink, the end results are wholly different: sediment cover is reduced, which in turn increases weathering and erosion rates and causes the entire shoreline to move landward more rapidly. The canyon's alongshore position also affects coastline morphology. When placed offshore of a headland, the submarine canyon captures local sediment

  11. Large-scale smart passive system for civil engineering applications

    NASA Astrophysics Data System (ADS)

    Jung, Hyung-Jo; Jang, Dong-Doo; Lee, Heon-Jae; Cho, Sang-Won

    2008-03-01

    The smart passive system consisting of a magnetorheological (MR) damper and an electromagnetic induction (EMI) part has been recently proposed. An EMI part can generate the input current for an MR damper from vibration of a structure according to Faraday's law of electromagnetic induction. The control performance of the smart passive system has been demonstrated mainly by numerical simulations. It was verified from the numerical results that the system could be effective to reduce the structural responses in the cases of civil engineering structures such as buildings and bridges. On the other hand, the experimental validation of the system is not sufficiently conducted yet. In this paper, the feasibility of the smart passive system to real-scale structures is investigated. To do this, the large-scale smart passive system is designed, manufactured, and tested. The system consists of the large-capacity MR damper, which has a maximum force level of approximately +/-10,000N, a maximum stroke level of +/-35mm and the maximum current level of 3 A, and the large-scale EMI part, which is designed to generate sufficient induced current for the damper. The applicability of the smart passive system to large real-scale structures is examined through a series of shaking table tests. The magnitudes of the induced current of the EMI part with various sinusoidal excitation inputs are measured. According to the test results, the large-scale EMI part shows the possibility that it could generate the sufficient current or power for changing the damping characteristics of the large-capacity MR damper.

  12. Constraints on large-scale dark acoustic oscillations from cosmology

    NASA Astrophysics Data System (ADS)

    Cyr-Racine, Francis-Yan; de Putter, Roland; Raccanelli, Alvise; Sigurdson, Kris

    2014-03-01

    If all or a fraction of the dark matter (DM) were coupled to a bath of dark radiation (DR) in the early Universe, we expect the combined DM-DR system to give rise to acoustic oscillations of the dark matter until it decouples from the DR. Much like the standard baryon acoustic oscillations, these dark acoustic oscillations (DAO) imprint a characteristic scale, the sound horizon of dark matter, on the matter power spectrum. We compute in detail how the microphysics of the DM-DR interaction affects the clustering of matter in the Universe and show that the DAO physics also gives rise to unique signatures in the temperature and polarization spectra of the cosmic microwave background (CMB). We use cosmological data from the CMB, baryon acoustic oscillations, and large-scale structure to constrain the possible fraction of interacting DM as well as the strength of its interaction with DR. Like nearly all knowledge we have gleaned about DM since inferring its existence this constraint rests on the betrayal by gravity of the location of otherwise invisible DM. Although our results can be straightforwardly applied to a broad class of models that couple dark matter particles to various light relativistic species, in order to make quantitative predictions, we model the interacting component as dark atoms coupled to a bath of dark photons. We find that linear cosmological data and CMB lensing put strong constraints on the existence of DAO features in the CMB and the large-scale structure of the Universe. Interestingly, we find that at most ˜5% of all DM can be very strongly interacting with DR. We show that our results are surprisingly constraining for the recently proposed double-disk DM model, a novel example of how large-scale precision cosmological data can be used to constrain galactic physics and subgalactic structure.

  13. Solving large scale structure in ten easy steps with COLA

    NASA Astrophysics Data System (ADS)

    Tassev, Svetlin; Zaldarriaga, Matias; Eisenstein, Daniel J.

    2013-06-01

    We present the COmoving Lagrangian Acceleration (COLA) method: an N-body method for solving for Large Scale Structure (LSS) in a frame that is comoving with observers following trajectories calculated in Lagrangian Perturbation Theory (LPT). Unlike standard N-body methods, the COLA method can straightforwardly trade accuracy at small-scales in order to gain computational speed without sacrificing accuracy at large scales. This is especially useful for cheaply generating large ensembles of accurate mock halo catalogs required to study galaxy clustering and weak lensing, as those catalogs are essential for performing detailed error analysis for ongoing and future surveys of LSS. As an illustration, we ran a COLA-based N-body code on a box of size 100 Mpc/h with particles of mass ≈ 5 × 109Msolar/h. Running the code with only 10 timesteps was sufficient to obtain an accurate description of halo statistics down to halo masses of at least 1011Msolar/h. This is only at a modest speed penalty when compared to mocks obtained with LPT. A standard detailed N-body run is orders of magnitude slower than our COLA-based code. The speed-up we obtain with COLA is due to the fact that we calculate the large-scale dynamics exactly using LPT, while letting the N-body code solve for the small scales, without requiring it to capture exactly the internal dynamics of halos. Achieving a similar level of accuracy in halo statistics without the COLA method requires at least 3 times more timesteps than when COLA is employed.

  14. Large-Scale Hybrid Motor Testing. Chapter 10

    NASA Technical Reports Server (NTRS)

    Story, George

    2006-01-01

    Hybrid rocket motors can be successfully demonstrated at a small scale virtually anywhere. There have been many suitcase sized portable test stands assembled for demonstration of hybrids. They show the safety of hybrid rockets to the audiences. These small show motors and small laboratory scale motors can give comparative burn rate data for development of different fuel/oxidizer combinations, however questions that are always asked when hybrids are mentioned for large scale applications are - how do they scale and has it been shown in a large motor? To answer those questions, large scale motor testing is required to verify the hybrid motor at its true size. The necessity to conduct large-scale hybrid rocket motor tests to validate the burn rate from the small motors to application size has been documented in several place^'^^.^. Comparison of small scale hybrid data to that of larger scale data indicates that the fuel burn rate goes down with increasing port size, even with the same oxidizer flux. This trend holds for conventional hybrid motors with forward oxidizer injection and HTPB based fuels. While the reason this is occurring would make a great paper or study or thesis, it is not thoroughly understood at this time. Potential causes include the fact that since hybrid combustion is boundary layer driven, the larger port sizes reduce the interaction (radiation, mixing and heat transfer) from the core region of the port. This chapter focuses on some of the large, prototype sized testing of hybrid motors. The largest motors tested have been AMROC s 250K-lbf thrust motor at Edwards Air Force Base and the Hybrid Propulsion Demonstration Program s 250K-lbf thrust motor at Stennis Space Center. Numerous smaller tests were performed to support the burn rate, stability and scaling concepts that went into the development of those large motors.

  15. LARGE-SCALE CO2 TRANSPORTATION AND DEEP OCEAN SEQUESTRATION

    SciTech Connect

    Hamid Sarv

    1999-03-01

    Technical and economical feasibility of large-scale CO{sub 2} transportation and ocean sequestration at depths of 3000 meters or grater was investigated. Two options were examined for transporting and disposing the captured CO{sub 2}. In one case, CO{sub 2} was pumped from a land-based collection center through long pipelines laid on the ocean floor. Another case considered oceanic tanker transport of liquid carbon dioxide to an offshore floating structure for vertical injection to the ocean floor. In the latter case, a novel concept based on subsurface towing of a 3000-meter pipe, and attaching it to the offshore structure was considered. Budgetary cost estimates indicate that for distances greater than 400 km, tanker transportation and offshore injection through a 3000-meter vertical pipe provides the best method for delivering liquid CO{sub 2} to deep ocean floor depressions. For shorter distances, CO{sub 2} delivery by parallel-laid, subsea pipelines is more cost-effective. Estimated costs for 500-km transport and storage at a depth of 3000 meters by subsea pipelines and tankers were 1.5 and 1.4 dollars per ton of stored CO{sub 2}, respectively. At these prices, economics of ocean disposal are highly favorable. Future work should focus on addressing technical issues that are critical to the deployment of a large-scale CO{sub 2} transportation and disposal system. Pipe corrosion, structural design of the transport pipe, and dispersion characteristics of sinking CO{sub 2} effluent plumes have been identified as areas that require further attention. Our planned activities in the next Phase include laboratory-scale corrosion testing, structural analysis of the pipeline, analytical and experimental simulations of CO{sub 2} discharge and dispersion, and the conceptual economic and engineering evaluation of large-scale implementation.

  16. Solving large scale structure in ten easy steps with COLA

    SciTech Connect

    Tassev, Svetlin; Zaldarriaga, Matias; Eisenstein, Daniel J. E-mail: matiasz@ias.edu

    2013-06-01

    We present the COmoving Lagrangian Acceleration (COLA) method: an N-body method for solving for Large Scale Structure (LSS) in a frame that is comoving with observers following trajectories calculated in Lagrangian Perturbation Theory (LPT). Unlike standard N-body methods, the COLA method can straightforwardly trade accuracy at small-scales in order to gain computational speed without sacrificing accuracy at large scales. This is especially useful for cheaply generating large ensembles of accurate mock halo catalogs required to study galaxy clustering and weak lensing, as those catalogs are essential for performing detailed error analysis for ongoing and future surveys of LSS. As an illustration, we ran a COLA-based N-body code on a box of size 100 Mpc/h with particles of mass ≈ 5 × 10{sup 9}M{sub s}un/h. Running the code with only 10 timesteps was sufficient to obtain an accurate description of halo statistics down to halo masses of at least 10{sup 11}M{sub s}un/h. This is only at a modest speed penalty when compared to mocks obtained with LPT. A standard detailed N-body run is orders of magnitude slower than our COLA-based code. The speed-up we obtain with COLA is due to the fact that we calculate the large-scale dynamics exactly using LPT, while letting the N-body code solve for the small scales, without requiring it to capture exactly the internal dynamics of halos. Achieving a similar level of accuracy in halo statistics without the COLA method requires at least 3 times more timesteps than when COLA is employed.

  17. Infectious diseases in large-scale cat hoarding investigations.

    PubMed

    Polak, K C; Levy, J K; Crawford, P C; Leutenegger, C M; Moriello, K A

    2014-08-01

    Animal hoarders accumulate animals in over-crowded conditions without adequate nutrition, sanitation, and veterinary care. As a result, animals rescued from hoarding frequently have a variety of medical conditions including respiratory infections, gastrointestinal disease, parasitism, malnutrition, and other evidence of neglect. The purpose of this study was to characterize the infectious diseases carried by clinically affected cats and to determine the prevalence of retroviral infections among cats in large-scale cat hoarding investigations. Records were reviewed retrospectively from four large-scale seizures of cats from failed sanctuaries from November 2009 through March 2012. The number of cats seized in each case ranged from 387 to 697. Cats were screened for feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) in all four cases and for dermatophytosis in one case. A subset of cats exhibiting signs of upper respiratory disease or diarrhea had been tested for infections by PCR and fecal flotation for treatment planning. Mycoplasma felis (78%), calicivirus (78%), and Streptococcus equi subspecies zooepidemicus (55%) were the most common respiratory infections. Feline enteric coronavirus (88%), Giardia (56%), Clostridium perfringens (49%), and Tritrichomonas foetus (39%) were most common in cats with diarrhea. The seroprevalence of FeLV and FIV were 8% and 8%, respectively. In the one case in which cats with lesions suspicious for dermatophytosis were cultured for Microsporum canis, 69/76 lesional cats were culture-positive; of these, half were believed to be truly infected and half were believed to be fomite carriers. Cats from large-scale hoarding cases had high risk for enteric and respiratory infections, retroviruses, and dermatophytosis. Case responders should be prepared for mass treatment of infectious diseases and should implement protocols to prevent transmission of feline or zoonotic infections during the emergency response and when

  18. Statistical Modeling of Large-Scale Scientific Simulation Data

    SciTech Connect

    Eliassi-Rad, T; Baldwin, C; Abdulla, G; Critchlow, T

    2003-11-15

    With the advent of massively parallel computer systems, scientists are now able to simulate complex phenomena (e.g., explosions of a stars). Such scientific simulations typically generate large-scale data sets over the spatio-temporal space. Unfortunately, the sheer sizes of the generated data sets make efficient exploration of them impossible. Constructing queriable statistical models is an essential step in helping scientists glean new insight from their computer simulations. We define queriable statistical models to be descriptive statistics that (1) summarize and describe the data within a user-defined modeling error, and (2) are able to answer complex range-based queries over the spatiotemporal dimensions. In this chapter, we describe systems that build queriable statistical models for large-scale scientific simulation data sets. In particular, we present our Ad-hoc Queries for Simulation (AQSim) infrastructure, which reduces the data storage requirements and query access times by (1) creating and storing queriable statistical models of the data at multiple resolutions, and (2) evaluating queries on these models of the data instead of the entire data set. Within AQSim, we focus on three simple but effective statistical modeling techniques. AQSim's first modeling technique (called univariate mean modeler) computes the ''true'' (unbiased) mean of systematic partitions of the data. AQSim's second statistical modeling technique (called univariate goodness-of-fit modeler) uses the Andersen-Darling goodness-of-fit method on systematic partitions of the data. Finally, AQSim's third statistical modeling technique (called multivariate clusterer) utilizes the cosine similarity measure to cluster the data into similar groups. Our experimental evaluations on several scientific simulation data sets illustrate the value of using these statistical models on large-scale simulation data sets.

  19. Solving Large-scale Eigenvalue Problems in SciDACApplications

    SciTech Connect

    Yang, Chao

    2005-06-29

    Large-scale eigenvalue problems arise in a number of DOE applications. This paper provides an overview of the recent development of eigenvalue computation in the context of two SciDAC applications. We emphasize the importance of Krylov subspace methods, and point out its limitations. We discuss the value of alternative approaches that are more amenable to the use of preconditioners, and report the progression using the multi-level algebraic sub-structuring techniques to speed up eigenvalue calculation. In addition to methods for linear eigenvalue problems, we also examine new approaches to solving two types of non-linear eigenvalue problems arising from SciDAC applications.

  20. Towards large scale production and separation of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Alvarez, Noe T.

    Since their discovery, carbon nanotubes (CNTs) have boosted the research and applications of nanotechnology; however, many applications of CNTs are inaccessible because they depend upon large-scale CNT production and separations. Type, chirality and diameter control of CNTs determine many of their physical properties, and such control is still not accesible. This thesis studies the fundamentals for scalable selective reactions of HiPCo CNTs as well as the early phase of routes to an inexpensive approach for large-scale CNT production. In the growth part, this thesis covers a complete wet-chemistry process of catalyst and catalyst support deposition for growth of vertically aligned (VA) CNTs. A wet-chemistry preparation process has significant importance for CNT synthesis through chemical vapor deposition (CVD). CVD is by far, the most suitable and inexpensive process for large-scale CNT production when compared to other common processes such as laser ablation and arc discharge. However, its potential has been limited by low-yielding and difficult preparation processes of catalyst and its support, therefore its competitiveness has been reduced. The wet-chemistry process takes advantage of current nanoparticle technology to deposit the catalyst and the catalyst support as a thin film of nanoparticles, making the protocol simple compared to electron beam evaporation and sputtering processes. In the CNT selective reactions part, this thesis studies UV irradiation of individually dispersed HiPCo CNTs that generates auto-selective reactions in the liquid phase with good control over their diameter and chirality. This technique is ideal for large-scale and continuous-process of separations of CNTs by diameter and type. Additionally, an innovative simple catalyst deposition through abrasion is demonstrated. Simple friction between the catalyst and the substrates deposit a high enough density of metal catalyst particles for successful CNT growth. This simple approach has

  1. Quantum computation for large-scale image classification

    NASA Astrophysics Data System (ADS)

    Ruan, Yue; Chen, Hanwu; Tan, Jianing; Li, Xi

    2016-07-01

    Due to the lack of an effective quantum feature extraction method, there is currently no effective way to perform quantum image classification or recognition. In this paper, for the first time, a global quantum feature extraction method based on Schmidt decomposition is proposed. A revised quantum learning algorithm is also proposed that will classify images by computing the Hamming distance of these features. From the experimental results derived from the benchmark database Caltech 101, and an analysis of the algorithm, an effective approach to large-scale image classification is derived and proposed against the background of big data.

  2. UAV Data Processing for Large Scale Topographical Mapping

    NASA Astrophysics Data System (ADS)

    Tampubolon, W.; Reinhardt, W.

    2014-06-01

    Large scale topographical mapping in the third world countries is really a prominent challenge in geospatial industries nowadays. On one side the demand is significantly increasing while on the other hand it is constrained by limited budgets available for mapping projects. Since the advent of Act Nr.4/yr.2011 about Geospatial Information in Indonesia, large scale topographical mapping has been on high priority for supporting the nationwide development e.g. detail spatial planning. Usually large scale topographical mapping relies on conventional aerial survey campaigns in order to provide high resolution 3D geospatial data sources. Widely growing on a leisure hobby, aero models in form of the so-called Unmanned Aerial Vehicle (UAV) bring up alternative semi photogrammetric aerial data acquisition possibilities suitable for relatively small Area of Interest (AOI) i.e. <5,000 hectares. For detail spatial planning purposes in Indonesia this area size can be used as a mapping unit since it usually concentrates on the basis of sub district area (kecamatan) level. In this paper different camera and processing software systems will be further analyzed for identifying the best optimum UAV data acquisition campaign components in combination with the data processing scheme. The selected AOI is covering the cultural heritage of Borobudur Temple as one of the Seven Wonders of the World. A detailed accuracy assessment will be concentrated within the object feature of the temple at the first place. Feature compilation involving planimetric objects (2D) and digital terrain models (3D) will be integrated in order to provide Digital Elevation Models (DEM) as the main interest of the topographic mapping activity. By doing this research, incorporating the optimum amount of GCPs in the UAV photo data processing will increase the accuracy along with its high resolution in 5 cm Ground Sampling Distance (GSD). Finally this result will be used as the benchmark for alternative geospatial

  3. Inflation in de Sitter spacetime and CMB large scale anomaly

    NASA Astrophysics Data System (ADS)

    Zhao, Dong; Li, Ming-Hua; Wang, Ping; Chang, Zhe

    2015-09-01

    The influence of cosmological constant-type dark energy in the early universe is investigated. This is accommodated by a new dispersion relation in de Sitter spacetime. We perform a global fit to explore the cosmological parameter space by using the CosmoMC package with the recently released Planck TT and WMAP polarization datasets. Using the results from the global fit, we compute a new CMB temperature-temperature (TT) spectrum. The obtained TT spectrum has lower power compared with that based on the ACDM model at large scales. Supported by National Natural Science Foundation of China (11375203)

  4. Large scale obscuration and related climate effects open literature bibliography

    SciTech Connect

    Russell, N.A.; Geitgey, J.; Behl, Y.K.; Zak, B.D.

    1994-05-01

    Large scale obscuration and related climate effects of nuclear detonations first became a matter of concern in connection with the so-called ``Nuclear Winter Controversy`` in the early 1980`s. Since then, the world has changed. Nevertheless, concern remains about the atmospheric effects of nuclear detonations, but the source of concern has shifted. Now it focuses less on global, and more on regional effects and their resulting impacts on the performance of electro-optical and other defense-related systems. This bibliography reflects the modified interest.

  5. Large-scale genotoxicity assessments in the marine environment.

    PubMed

    Hose, J E

    1994-12-01

    There are a number of techniques for detecting genotoxicity in the marine environment, and many are applicable to large-scale field assessments. Certain tests can be used to evaluate responses in target organisms in situ while others utilize surrogate organisms exposed to field samples in short-term laboratory bioassays. Genotoxicity endpoints appear distinct from traditional toxicity endpoints, but some have chemical or ecotoxicologic correlates. One versatile end point, the frequency of anaphase aberrations, has been used in several large marine assessments to evaluate genotoxicity in the New York Bight, in sediment from San Francisco Bay, and following the Exxon Valdez oil spill. PMID:7713029

  6. Synthesis and sensing application of large scale bilayer graphene

    NASA Astrophysics Data System (ADS)

    Hong, Sung Ju; Yoo, Jung Hoon; Baek, Seung Jae; Park, Yung Woo

    2012-02-01

    We have synthesized large scale bilayer graphene by using Chemical Vapor Deposition (CVD) in atmospheric pressure. Bilayer graphene was grown by using CH4, H2 and Ar gases. The growth temperature was 1050^o. Conventional FET measurement shows ambipolar transfer characteristics. Results of Raman spectroscopy, Atomic Force microscope (AFM) and Transmission Electron Microscope (TEM) indicate the film is bilayer graphene. Especially, adlayer structure which interrupt uniformity was reduced in low methane flow condition. Furthermore, large size CVD bilayer graphene film can be investigated to apply sensor devices. By using conventional photolithography process, we have fabricated device array structure and studied sensing behavior.

  7. Large-scale sodium spray fire code validation (SOFICOV) test

    SciTech Connect

    Jeppson, D.W.; Muhlestein, L.D.

    1985-01-01

    A large-scale, sodium, spray fire code validation test was performed in the HEDL 850-m/sup 3/ Containment System Test Facility (CSTF) as part of the Sodium Spray Fire Code Validation (SOFICOV) program. Six hundred fifty eight kilograms of sodium spray was sprayed in an air atmosphere for a period of 2400 s. The sodium spray droplet sizes and spray pattern distribution were estimated. The containment atmosphere temperature and pressure response, containment wall temperature response and sodium reaction rate with oxygen were measured. These results are compared to post-test predictions using SPRAY and NACOM computer codes.

  8. Radiative shocks on large scale lasers. Preliminary results

    NASA Astrophysics Data System (ADS)

    Leygnac, S.; Bouquet, S.; Stehle, C.; Barroso, P.; Batani, D.; Benuzzi, A.; Cathala, B.; Chièze, J.-P.; Fleury, X.; Grandjouan, N.; Grenier, J.; Hall, T.; Henry, E.; Koenig, M.; Lafon, J. P. J.; Malka, V.; Marchet, B.; Merdji, H.; Michaut, C.; Poles, L.; Thais, F.

    2001-05-01

    Radiative shocks, those structure is strongly influenced by the radiation field, are present in various astrophysical objects (circumstellar envelopes of variable stars, supernovae ...). Their modeling is very difficult and thus will take benefit from experimental informations. This approach is now possible using large scale lasers. Preliminary experiments have been performed with the nanosecond LULI laser at Ecole Polytechnique (France) in 2000. A radiative shock has been obtained in a low pressure xenon cell. The preparation of such experiments and their interpretation is performed using analytical calculations and numerical simulations.

  9. On the analysis of large-scale genomic structures.

    PubMed

    Oiwa, Nestor Norio; Goldman, Carla

    2005-01-01

    We apply methods from statistical physics (histograms, correlation functions, fractal dimensions, and singularity spectra) to characterize large-scale structure of the distribution of nucleotides along genomic sequences. We discuss the role of the extension of noncoding segments ("junk DNA") for the genomic organization, and the connection between the coding segment distribution and the high-eukaryotic chromatin condensation. The following sequences taken from GenBank were analyzed: complete genome of Xanthomonas campestri, complete genome of yeast, chromosome V of Caenorhabditis elegans, and human chromosome XVII around gene BRCA1. The results are compared with the random and periodic sequences and those generated by simple and generalized fractal Cantor sets. PMID:15858230

  10. Large-scale genotoxicity assessments in the marine environment

    SciTech Connect

    Hose, J.E.

    1994-12-01

    There are a number of techniques for detecting genotoxicity in the marine environment, and many are applicable to large-scale field assessments. Certain tests can be used to evaluate responses in target organisms in situ while others utilize surrogate organisms exposed to field samples in short-term laboratory bioassays. Genotoxicity endpoints appear distinct from traditional toxicity endpoints, but some have chemical or ecotoxicologic correlates. One versatile end point, the frequency of anaphase aberrations, has been used in several large marine assessments to evaluate genotoxicity in the New York Bight, in sediment from San Francisco Bay, and following the Exxon Valdez oil spill. 31 refs., 2 tabs.

  11. Floodplain management in Africa: Large scale analysis of flood data

    NASA Astrophysics Data System (ADS)

    Padi, Philip Tetteh; Baldassarre, Giuliano Di; Castellarin, Attilio

    2011-01-01

    To mitigate a continuously increasing flood risk in Africa, sustainable actions are urgently needed. In this context, we describe a comprehensive statistical analysis of flood data in the African continent. The study refers to quality-controlled, large and consistent databases of flood data, i.e. maximum discharge value and times series of annual maximum flows. Probabilistic envelope curves are derived for the African continent by means of a large scale regional analysis. Moreover, some initial insights on the statistical characteristics of African floods are provided. The results of this study are relevant and can be used to get some indications to support flood management in Africa.

  12. Novel algorithm of large-scale simultaneous linear equations.

    PubMed

    Fujiwara, T; Hoshi, T; Yamamoto, S; Sogabe, T; Zhang, S-L

    2010-02-24

    We review our recently developed methods of solving large-scale simultaneous linear equations and applications to electronic structure calculations both in one-electron theory and many-electron theory. This is the shifted COCG (conjugate orthogonal conjugate gradient) method based on the Krylov subspace, and the most important issue for applications is the shift equation and the seed switching method, which greatly reduce the computational cost. The applications to nano-scale Si crystals and the double orbital extended Hubbard model are presented. PMID:21386384

  13. Large Scale Composite Manufacturing for Heavy Lift Launch Vehicles

    NASA Technical Reports Server (NTRS)

    Stavana, Jacob; Cohen, Leslie J.; Houseal, Keth; Pelham, Larry; Lort, Richard; Zimmerman, Thomas; Sutter, James; Western, Mike; Harper, Robert; Stuart, Michael

    2012-01-01

    Risk reduction for the large scale composite manufacturing is an important goal to produce light weight components for heavy lift launch vehicles. NASA and an industry team successfully employed a building block approach using low-cost Automated Tape Layup (ATL) of autoclave and Out-of-Autoclave (OoA) prepregs. Several large, curved sandwich panels were fabricated at HITCO Carbon Composites. The aluminum honeycomb core sandwich panels are segments of a 1/16th arc from a 10 meter cylindrical barrel. Lessons learned highlight the manufacturing challenges required to produce light weight composite structures such as fairings for heavy lift launch vehicles.

  14. Design of a large-scale CFB boiler

    SciTech Connect

    Darling, S.; Li, S.

    1997-12-31

    Many CFB boilers sized 100--150 MWe are in operation, and several others sized 150--250 MWe are in operation or under construction. The next step for CFB technology is the 300--400 MWe size range. This paper will describe Foster Wheeler`s large-scale CFB boiler experience and the design for a 300 MWe CFB boiler. The authors will show how the design incorporates Foster Wheeler`s unique combination of extensive utility experience and CFB boiler experience. All the benefits of CFB technology which include low emissions, fuel flexibility, low maintenance and competitive cost are now available in the 300--400 MWe size range.

  15. [National Strategic Promotion for Large-Scale Clinical Cancer Research].

    PubMed

    Toyama, Senya

    2016-04-01

    The number of clinical research by clinical cancer study groups has been decreasing this year in Japan. They say the reason is the abolition of donations to the groups from the pharmaceutical companies after the Diovan scandal. But I suppose fundamental problem is that government-supported large-scale clinical cancer study system for evidence based medicine (EBM) has not been fully established. An urgent establishment of the system based on the national strategy is needed for the cancer patients and the public health promotion. PMID:27220800

  16. Large-Scale periodic solar velocities: An observational study

    NASA Technical Reports Server (NTRS)

    Dittmer, P. H.

    1977-01-01

    Observations of large-scale solar velocities were made using the mean field telescope and Babcock magnetograph of the Stanford Solar Observatory. Observations were made in the magnetically insensitive ion line at 5124 A, with light from the center (limb) of the disk right (left) circularly polarized, so that the magnetograph measures the difference in wavelength between center and limb. Computer calculations are made of the wavelength difference produced by global pulsations for spherical harmonics up to second order and of the signal produced by displacing the solar image relative to polarizing optics or diffraction grating.

  17. Laser Welding of Large Scale Stainless Steel Aircraft Structures

    NASA Astrophysics Data System (ADS)

    Reitemeyer, D.; Schultz, V.; Syassen, F.; Seefeld, T.; Vollertsen, F.

    In this paper a welding process for large scale stainless steel structures is presented. The process was developed according to the requirements of an aircraft application. Therefore, stringers are welded on a skin sheet in a t-joint configuration. The 0.6 mm thickness parts are welded with a thin disc laser, seam length up to 1920 mm are demonstrated. The welding process causes angular distortions of the skin sheet which are compensated by a subsequent laser straightening process. Based on a model straightening process parameters matching the induced welding distortion are predicted. The process combination is successfully applied to stringer stiffened specimens.

  18. Enabling Large-Scale Biomedical Analysis in the Cloud

    PubMed Central

    Lin, Ying-Chih; Yu, Chin-Sheng; Lin, Yen-Jen

    2013-01-01

    Recent progress in high-throughput instrumentations has led to an astonishing growth in both volume and complexity of biomedical data collected from various sources. The planet-size data brings serious challenges to the storage and computing technologies. Cloud computing is an alternative to crack the nut because it gives concurrent consideration to enable storage and high-performance computing on large-scale data. This work briefly introduces the data intensive computing system and summarizes existing cloud-based resources in bioinformatics. These developments and applications would facilitate biomedical research to make the vast amount of diversification data meaningful and usable. PMID:24288665

  19. Generation of Large-Scale Winds in Horizontally Anisotropic Convection.

    PubMed

    von Hardenberg, J; Goluskin, D; Provenzale, A; Spiegel, E A

    2015-09-25

    We simulate three-dimensional, horizontally periodic Rayleigh-Bénard convection, confined between free-slip horizontal plates and rotating about a distant horizontal axis. When both the temperature difference between the plates and the rotation rate are sufficiently large, a strong horizontal wind is generated that is perpendicular to both the rotation vector and the gravity vector. The wind is turbulent, large-scale, and vertically sheared. Horizontal anisotropy, engendered here by rotation, appears necessary for such wind generation. Most of the kinetic energy of the flow resides in the wind, and the vertical turbulent heat flux is much lower on average than when there is no wind. PMID:26451558

  20. Large-Scale Purification of Peroxisomes for Preparative Applications.

    PubMed

    Cramer, Jana; Effelsberg, Daniel; Girzalsky, Wolfgang; Erdmann, Ralf

    2015-09-01

    This protocol is designed for large-scale isolation of highly purified peroxisomes from Saccharomyces cerevisiae using two consecutive density gradient centrifugations. Instructions are provided for harvesting up to 60 g of oleic acid-induced yeast cells for the preparation of spheroplasts and generation of organellar pellets (OPs) enriched in peroxisomes and mitochondria. The OPs are loaded onto eight continuous 36%-68% (w/v) sucrose gradients. After centrifugation, the peak peroxisomal fractions are determined by measurement of catalase activity. These fractions are subsequently pooled and subjected to a second density gradient centrifugation using 20%-40% (w/v) Nycodenz. PMID:26330621

  1. Enabling large-scale biomedical analysis in the cloud.

    PubMed

    Lin, Ying-Chih; Yu, Chin-Sheng; Lin, Yen-Jen

    2013-01-01

    Recent progress in high-throughput instrumentations has led to an astonishing growth in both volume and complexity of biomedical data collected from various sources. The planet-size data brings serious challenges to the storage and computing technologies. Cloud computing is an alternative to crack the nut because it gives concurrent consideration to enable storage and high-performance computing on large-scale data. This work briefly introduces the data intensive computing system and summarizes existing cloud-based resources in bioinformatics. These developments and applications would facilitate biomedical research to make the vast amount of diversification data meaningful and usable. PMID:24288665

  2. Monochromatic waves induced by large-scale parametric forcing.

    PubMed

    Nepomnyashchy, A; Abarzhi, S I

    2010-03-01

    We study the formation and stability of monochromatic waves induced by large-scale modulations in the framework of the complex Ginzburg-Landau equation with parametric nonresonant forcing dependent on the spatial coordinate. In the limiting case of forcing with very large characteristic length scale, analytical solutions for the equation are found and conditions of their existence are outlined. Stability analysis indicates that the interval of existence of a monochromatic wave can contain a subinterval where the wave is stable. We discuss potential applications of the model in rheology, fluid dynamics, and optics. PMID:20365907

  3. Support Vector Machine Classification of Probability Models and Peptide Features for Improved Peptide Identification from Shotgun Proteomics

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Oehmen, Chris S.; Cannon, William R.

    2007-12-01

    Proteomics is a rapidly advancing field offering a new perspective to biological systems. Mass spectrometry (MS) is a popular experimental approach because it allows global protein characterization of a sample in a high-throughput manner. The identification of a protein is based on the spectral signature of fragments of the constituent proteins, i.e., peptides. This peptide identification is typically performed with a computational database search algorithm; however, these database search algorithms return a large number of false positive identifications. We present a new scoring algorithm that uses a SVM to integrate database scoring metrics with peptide physiochemical properties, resulting in an improved ability to separate true from false peptide identification from MS. The Peptide Identification Classifier SVM (PICS) score using only five variables is significantly more accurate than the single best database metric, quantified as the area under a Receive Operating Characteristic curve of ~0.94 versus ~0.90.

  4. A Sydney proteome story.

    PubMed

    Williams, Keith L; Gooley, Andrew A; Wilkins, Marc R; Packer, Nicolle H

    2014-07-31

    This is the story of the experience of a multidisciplinary group at Macquarie University in Sydney as we participated in, and impacted upon, major currents that washed through protein science as the field of Proteomics emerged. The large scale analysis of proteins became possible. This is not a history of the field. Instead we have tried to encapsulate the stimulating personal ride we had transiting from conventional academe, to a Major National Research Facility, to the formation of Proteomics company Proteome Systems Ltd. There were lots of blind alleys, wrong directions, but we also got some things right and our efforts, along with those of many other groups around the world, did change the face of protein science. While the transformation is by no means yet complete, protein science is very different from the field in the 1990s. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez. PMID:24735915

  5. Large-scale solar magnetic fields and H-alpha patterns

    NASA Technical Reports Server (NTRS)

    Mcintosh, P. S.

    1972-01-01

    Coronal and interplanetary magnetic fields computed from measurements of large-scale photospheric magnetic fields suffer from interruptions in day-to-day observations and the limitation of using only measurements made near the solar central meridian. Procedures were devised for inferring the lines of polarity reversal from H-alpha solar patrol photographs that map the same large-scale features found on Mt. Wilson magnetograms. These features may be monitored without interruption by combining observations from the global network of observatories associated with NOAA's Space Environment Services Center. The patterns of inferred magnetic fields may be followed accurately as far as 60 deg from central meridian. Such patterns will be used to improve predictions of coronal features during the next solar eclipse.

  6. Ethical and practical challenges to studying patients who opt out of large-scale biorepository research

    PubMed Central

    Rosenbloom, S Trent; Madison, Jennifer L; Brothers, Kyle B; Bowton, Erica A; Clayton, Ellen Wright; Malin, Bradley A; Roden, Dan M; Pulley, Jill

    2013-01-01

    Large-scale biorepositories that couple biologic specimens with electronic health records containing documentation of phenotypic expression can accelerate scientific research and discovery. However, differences between those subjects who participate in biorepository-based research and the population from which they are drawn may influence research validity. While an opt-out approach to biorepository-based research enhances inclusiveness, empirical research evaluating voluntariness, risk, and the feasibility of an opt-out approach is sparse, and factors influencing patients’ decisions to opt out are understudied. Determining why patients choose to opt out may help to improve voluntariness, however there may be ethical and logistical challenges to studying those who opt out. In this perspective paper, the authors explore what is known about research based on the opt-out model, describe a large-scale biorepository that leverages the opt-out model, and review specific ethical and logistical challenges to bridging the research gaps that remain. PMID:23886923

  7. Oscillatory barrier-assisted Langmuir-Blodgett deposition of large-scale quantum dot monolayers

    NASA Astrophysics Data System (ADS)

    Xu, Shicheng; Dadlani, Anup L.; Acharya, Shinjita; Schindler, Peter; Prinz, Fritz B.

    2016-03-01

    Depositing continuous, large-scale quantum dot films with low pinhole density is an inevitable but nontrivial step for studying their properties for applications in catalysis, electronic devices, and optoelectronics. This rising interest in high-quality quantum dot films has provided research impetus to improve the deposition technique. We show that by incorporating oscillatory barriers in the commonly used Langmuir-Blodgett method, large-scale monolayers of quantum dots with full coverage up to several millimeters have been achieved. With assistance of perturbation provided by the oscillatory barriers, the film has been shown to relax towards thermal equilibrium, and this physical process has been supported by molecular dynamics simulation. In addition, time evolution of dilatational moduli has been shown to give a clear indication of the film morphology and its stability.

  8. Iterative methods for large scale nonlinear and linear systems. Final report, 1994--1996

    SciTech Connect

    Walker, H.F.

    1997-09-01

    The major goal of this research has been to develop improved numerical methods for the solution of large-scale systems of linear and nonlinear equations, such as occur almost ubiquitously in the computational modeling of physical phenomena. The numerical methods of central interest have been Krylov subspace methods for linear systems, which have enjoyed great success in many large-scale applications, and newton-Krylov methods for nonlinear problems, which use Krylov subspace methods to solve approximately the linear systems that characterize Newton steps. Krylov subspace methods have undergone a remarkable development over the last decade or so and are now very widely used for the iterative solution of large-scale linear systems, particularly those that arise in the discretization of partial differential equations (PDEs) that occur in computational modeling. Newton-Krylov methods have enjoyed parallel success and are currently used in many nonlinear applications of great scientific and industrial importance. In addition to their effectiveness on important problems, Newton-Krylov methods also offer a nonlinear framework within which to transfer to the nonlinear setting any advances in Krylov subspace methods or preconditioning techniques, or new algorithms that exploit advanced machine architectures. This research has resulted in a number of improved Krylov and Newton-Krylov algorithms together with applications of these to important linear and nonlinear problems.

  9. Dealing with missing values in large-scale studies: microarray data imputation and beyond.

    PubMed

    Aittokallio, Tero

    2010-03-01

    High-throughput biotechnologies, such as gene expression microarrays or mass-spectrometry-based proteomic assays, suffer from frequent missing values due to various experimental reasons. Since the missing data points can hinder downstream analyses, there exists a wide variety of ways in which to deal with missing values in large-scale data sets. Nowadays, it has become routine to estimate (or impute) the missing values prior to the actual data analysis. After nearly a decade since the publication of the first missing value imputation methods for gene expression microarray data, new imputation approaches are still being developed at an increasing rate. However, what is lagging behind is a systematic and objective evaluation of the strengths and weaknesses of the different approaches when faced with different types of data sets and experimental questions. In this review, the present strategies for missing value imputation and the measures for evaluating their performance are described. The imputation methods are first reviewed in the context of gene expression microarray data, since most of the methods have been developed for estimating gene expression levels; then, we turn to other large-scale data sets that also suffer from the problems posed by missing values, together with pointers to possible imputation approaches in these settings. Along with a description of the basic principles behind the different imputation approaches, the review tries to provide practical guidance for the users of high-throughput technologies on how to choose the imputation tool for their data and questions, and some additional research directions for the developers of imputation methodologies. PMID:19965979

  10. Topographically Engineered Large Scale Nanostructures for Plasmonic Biosensing

    NASA Astrophysics Data System (ADS)

    Xiao, Bo; Pradhan, Sangram K.; Santiago, Kevin C.; Rutherford, Gugu N.; Pradhan, Aswini K.

    2016-04-01

    We demonstrate that a nanostructured metal thin film can achieve enhanced transmission efficiency and sharp resonances and use a large-scale and high-throughput nanofabrication technique for the plasmonic structures. The fabrication technique combines the features of nanoimprint and soft lithography to topographically construct metal thin films with nanoscale patterns. Metal nanogratings developed using this method show significantly enhanced optical transmission (up to a one-order-of-magnitude enhancement) and sharp resonances with full width at half maximum (FWHM) of ~15nm in the zero-order transmission using an incoherent white light source. These nanostructures are sensitive to the surrounding environment, and the resonance can shift as the refractive index changes. We derive an analytical method using a spatial Fourier transformation to understand the enhancement phenomenon and the sensing mechanism. The use of real-time monitoring of protein-protein interactions in microfluidic cells integrated with these nanostructures is demonstrated to be effective for biosensing. The perpendicular transmission configuration and large-scale structures provide a feasible platform without sophisticated optical instrumentation to realize label-free surface plasmon resonance (SPR) sensing.

  11. THE LARGE-SCALE MAGNETIC FIELDS OF THIN ACCRETION DISKS

    SciTech Connect

    Cao Xinwu; Spruit, Hendrik C. E-mail: henk@mpa-garching.mpg.de

    2013-03-10

    Large-scale magnetic field threading an accretion disk is a key ingredient in the jet formation model. The most attractive scenario for the origin of such a large-scale field is the advection of the field by the gas in the accretion disk from the interstellar medium or a companion star. However, it is realized that outward diffusion of the accreted field is fast compared with the inward accretion velocity in a geometrically thin accretion disk if the value of the Prandtl number P{sub m} is around unity. In this work, we revisit this problem considering the angular momentum of the disk to be removed predominantly by the magnetically driven outflows. The radial velocity of the disk is significantly increased due to the presence of the outflows. Using a simplified model for the vertical disk structure, we find that even moderately weak fields can cause sufficient angular momentum loss via a magnetic wind to balance outward diffusion. There are two equilibrium points, one at low field strengths corresponding to a plasma-beta at the midplane of order several hundred, and one for strong accreted fields, {beta} {approx} 1. We surmise that the first is relevant for the accretion of weak, possibly external, fields through the outer parts of the disk, while the latter one could explain the tendency, observed in full three-dimensional numerical simulations, of strong flux bundles at the centers of disk to stay confined in spite of strong magnetororational instability turbulence surrounding them.

  12. Development of large-scale functional brain networks in children.

    PubMed

    Supekar, Kaustubh; Musen, Mark; Menon, Vinod

    2009-07-01

    The ontogeny of large-scale functional organization of the human brain is not well understood. Here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children (ages 7-9 y) and 22 young-adults (ages 19-22 y). Comparison of network properties, including path-length, clustering-coefficient, hierarchy, and regional connectivity, revealed that although children and young-adults' brains have similar "small-world" organization at the global level, they differ significantly in hierarchical organization and interregional connectivity. We found that subcortical areas were more strongly connected with primary sensory, association, and paralimbic areas in children, whereas young-adults showed stronger cortico-cortical connectivity between paralimbic, limbic, and association areas. Further, combined analysis of functional connectivity with wiring distance measures derived from white-matter fiber tracking revealed that the development of large-scale brain networks is characterized by weakening of short-range functional connectivity and strengthening of long-range functional connectivity. Importantly, our findings show that the dynamic process of over-connectivity followed by pruning, which rewires connectivity at the neuronal level, also operates at the systems level, helping to reconfigure and rebalance subcortical and paralimbic connectivity in the developing brain. Our study demonstrates the usefulness of network analysis of brain connectivity to elucidate key principles underlying functional brain maturation, paving the way for novel studies of disrupted brain connectivity in neurodevelopmental disorders such as autism. PMID:19621066

  13. Topographically Engineered Large Scale Nanostructures for Plasmonic Biosensing.

    PubMed

    Xiao, Bo; Pradhan, Sangram K; Santiago, Kevin C; Rutherford, Gugu N; Pradhan, Aswini K

    2016-01-01

    We demonstrate that a nanostructured metal thin film can achieve enhanced transmission efficiency and sharp resonances and use a large-scale and high-throughput nanofabrication technique for the plasmonic structures. The fabrication technique combines the features of nanoimprint and soft lithography to topographically construct metal thin films with nanoscale patterns. Metal nanogratings developed using this method show significantly enhanced optical transmission (up to a one-order-of-magnitude enhancement) and sharp resonances with full width at half maximum (FWHM) of ~15nm in the zero-order transmission using an incoherent white light source. These nanostructures are sensitive to the surrounding environment, and the resonance can shift as the refractive index changes. We derive an analytical method using a spatial Fourier transformation to understand the enhancement phenomenon and the sensing mechanism. The use of real-time monitoring of protein-protein interactions in microfluidic cells integrated with these nanostructures is demonstrated to be effective for biosensing. The perpendicular transmission configuration and large-scale structures provide a feasible platform without sophisticated optical instrumentation to realize label-free surface plasmon resonance (SPR) sensing. PMID:27072067

  14. NIC-based Reduction Algorithms for Large-scale Clusters

    SciTech Connect

    Petrini, F; Moody, A T; Fernandez, J; Frachtenberg, E; Panda, D K

    2004-07-30

    Efficient algorithms for reduction operations across a group of processes are crucial for good performance in many large-scale, parallel scientific applications. While previous algorithms limit processing to the host CPU, we utilize the programmable processors and local memory available on modern cluster network interface cards (NICs) to explore a new dimension in the design of reduction algorithms. In this paper, we present the benefits and challenges, design issues and solutions, analytical models, and experimental evaluations of a family of NIC-based reduction algorithms. Performance and scalability evaluations were conducted on the ASCI Linux Cluster (ALC), a 960-node, 1920-processor machine at Lawrence Livermore National Laboratory, which uses the Quadrics QsNet interconnect. We find NIC-based reductions on modern interconnects to be more efficient than host-based implementations in both scalability and consistency. In particular, at large-scale--1812 processes--NIC-based reductions of small integer and floating-point arrays provided respective speedups of 121% and 39% over the host-based, production-level MPI implementation.

  15. Alignment of quasar polarizations with large-scale structures

    NASA Astrophysics Data System (ADS)

    Hutsemékers, D.; Braibant, L.; Pelgrims, V.; Sluse, D.

    2014-12-01

    We have measured the optical linear polarization of quasars belonging to Gpc scale quasar groups at redshift z ~ 1.3. Out of 93 quasars observed, 19 are significantly polarized. We found that quasar polarization vectors are either parallel or perpendicular to the directions of the large-scale structures to which they belong. Statistical tests indicate that the probability that this effect can be attributed to randomly oriented polarization vectors is on the order of 1%. We also found that quasars with polarization perpendicular to the host structure preferentially have large emission line widths while objects with polarization parallel to the host structure preferentially have small emission line widths. Considering that quasar polarization is usually either parallel or perpendicular to the accretion disk axis depending on the inclination with respect to the line of sight, and that broader emission lines originate from quasars seen at higher inclinations, we conclude that quasar spin axes are likely parallel to their host large-scale structures. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under program ID 092.A-0221.Table 1 is available in electronic form at http://www.aanda.org

  16. Evaluating Unmanned Aerial Platforms for Cultural Heritage Large Scale Mapping

    NASA Astrophysics Data System (ADS)

    Georgopoulos, A.; Oikonomou, C.; Adamopoulos, E.; Stathopoulou, E. K.

    2016-06-01

    When it comes to large scale mapping of limited areas especially for cultural heritage sites, things become critical. Optical and non-optical sensors are developed to such sizes and weights that can be lifted by such platforms, like e.g. LiDAR units. At the same time there is an increase in emphasis on solutions that enable users to get access to 3D information faster and cheaper. Considering the multitude of platforms, cameras and the advancement of algorithms in conjunction with the increase of available computing power this challenge should and indeed is further investigated. In this paper a short review of the UAS technologies today is attempted. A discussion follows as to their applicability and advantages, depending on their specifications, which vary immensely. The on-board cameras available are also compared and evaluated for large scale mapping. Furthermore a thorough analysis, review and experimentation with different software implementations of Structure from Motion and Multiple View Stereo algorithms, able to process such dense and mostly unordered sequence of digital images is also conducted and presented. As test data set, we use a rich optical and thermal data set from both fixed wing and multi-rotor platforms over an archaeological excavation with adverse height variations and using different cameras. Dense 3D point clouds, digital terrain models and orthophotos have been produced and evaluated for their radiometric as well as metric qualities.

  17. Exploring Cloud Computing for Large-scale Scientific Applications

    SciTech Connect

    Lin, Guang; Han, Binh; Yin, Jian; Gorton, Ian

    2013-06-27

    This paper explores cloud computing for large-scale data-intensive scientific applications. Cloud computing is attractive because it provides hardware and software resources on-demand, which relieves the burden of acquiring and maintaining a huge amount of resources that may be used only once by a scientific application. However, unlike typical commercial applications that often just requires a moderate amount of ordinary resources, large-scale scientific applications often need to process enormous amount of data in the terabyte or even petabyte range and require special high performance hardware with low latency connections to complete computation in a reasonable amount of time. To address these challenges, we build an infrastructure that can dynamically select high performance computing hardware across institutions and dynamically adapt the computation to the selected resources to achieve high performance. We have also demonstrated the effectiveness of our infrastructure by building a system biology application and an uncertainty quantification application for carbon sequestration, which can efficiently utilize data and computation resources across several institutions.

  18. The combustion behavior of large scale lithium titanate battery

    PubMed Central

    Huang, Peifeng; Wang, Qingsong; Li, Ke; Ping, Ping; Sun, Jinhua

    2015-01-01

    Safety problem is always a big obstacle for lithium battery marching to large scale application. However, the knowledge on the battery combustion behavior is limited. To investigate the combustion behavior of large scale lithium battery, three 50 Ah Li(NixCoyMnz)O2/Li4Ti5O12 batteries under different state of charge (SOC) were heated to fire. The flame size variation is depicted to analyze the combustion behavior directly. The mass loss rate, temperature and heat release rate are used to analyze the combustion behavior in reaction way deeply. Based on the phenomenon, the combustion process is divided into three basic stages, even more complicated at higher SOC with sudden smoke flow ejected. The reason is that a phase change occurs in Li(NixCoyMnz)O2 material from layer structure to spinel structure. The critical temperatures of ignition are at 112–121°C on anode tab and 139 to 147°C on upper surface for all cells. But the heating time and combustion time become shorter with the ascending of SOC. The results indicate that the battery fire hazard increases with the SOC. It is analyzed that the internal short and the Li+ distribution are the main causes that lead to the difference. PMID:25586064

  19. Large scale reconstruction of the solar coronal magnetic field

    NASA Astrophysics Data System (ADS)

    Amari, T.; Aly, J.-J.; Chopin, P.; Canou, A.; Mikic, Z.

    2014-10-01

    It is now becoming necessary to access the global magnetic structure of the solar low corona at a large scale in order to understand its physics and more particularly the conditions of energization of the magnetic fields and the multiple connections between distant active regions (ARs) which may trigger eruptive events in an almost coordinated way. Various vector magnetographs, either on board spacecraft or ground-based, currently allow to obtain vector synoptic maps, composite magnetograms made of multiple interactive ARs, and full disk magnetograms. We present a method recently developed for reconstructing the global solar coronal magnetic field as a nonlinear force-free magnetic field in spherical geometry, generalizing our previous results in Cartesian geometry. This method is implemented in the new code XTRAPOLS, which thus appears as an extension of our active region scale code XTRAPOL. We apply our method by performing a reconstruction at a specific time for which we dispose of a set of composite data constituted of a vector magnetogram provided by SDO/HMI, embedded in a larger full disk vector magnetogram provided by the same instrument, finally embedded in a synoptic map provided by SOLIS. It turns out to be possible to access the large scale structure of the corona and its energetic contents, and also the AR scale, at which we recover the presence of a twisted flux rope in equilibrium.

  20. High Speed Networking and Large-scale Simulation in Geodynamics

    NASA Technical Reports Server (NTRS)

    Kuang, Weijia; Gary, Patrick; Seablom, Michael; Truszkowski, Walt; Odubiyi, Jide; Jiang, Weiyuan; Liu, Dong

    2004-01-01

    Large-scale numerical simulation has been one of the most important approaches for understanding global geodynamical processes. In this approach, peta-scale floating point operations (pflops) are often required to carry out a single physically-meaningful numerical experiment. For example, to model convective flow in the Earth's core and generation of the geomagnetic field (geodynamo), simulation for one magnetic free-decay time (approximately 15000 years) with a modest resolution of 150 in three spatial dimensions would require approximately 0.2 pflops. If such a numerical model is used to predict geomagnetic secular variation over decades and longer, with e.g. an ensemble Kalman filter assimilation approach, approximately 30 (and perhaps more) independent simulations of similar scales would be needed for one data assimilation analysis. Obviously, such a simulation would require an enormous computing resource that exceeds the capacity of a single facility currently available at our disposal. One solution is to utilize a very fast network (e.g. 10Gb optical networks) and available middleware (e.g. Globus Toolkit) to allocate available but often heterogeneous resources for such large-scale computing efforts. At NASA GSFC, we are experimenting with such an approach by networking several clusters for geomagnetic data assimilation research. We shall present our initial testing results in the meeting.