Sample records for accelerated similarity searching

  1. SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

    PubMed

    Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

    2015-01-01

    In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.

  2. The HMMER Web Server for Protein Sequence Similarity Search.

    PubMed

    Prakash, Ananth; Jeffryes, Matt; Bateman, Alex; Finn, Robert D

    2017-12-08

    Protein sequence similarity search is one of the most commonly used bioinformatics methods for identifying evolutionarily related proteins. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software, which in the latest version (v3.1) uses a combination of sophisticated acceleration heuristics and mathematical and computational optimizations to enable the use of profile hidden Markov models (HMMs) for sequence analysis. The HMMER Web server provides a common platform by linking the HMMER algorithms to databases, thereby enabling the search for homologs, as well as providing sequence and functional annotation by linking external databases. This unit describes three basic protocols and two alternate protocols that explain how to use the HMMER Web server using various input formats and user defined parameters. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  3. Cloud4Psi: cloud computing for 3D protein structure similarity searching.

    PubMed

    Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

    2014-10-01

    Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. © The Author 2014. Published by Oxford University Press.

  4. Cloud4Psi: cloud computing for 3D protein structure similarity searching

    PubMed Central

    Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

    2014-01-01

    Summary: Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Availability and implementation: Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. Contact: dariusz.mrozek@polsl.pl PMID:24930141

  5. GPU Accelerated Chemical Similarity Calculation for Compound Library Comparison

    PubMed Central

    Ma, Chao; Wang, Lirong; Xie, Xiang-Qun

    2012-01-01

    Chemical similarity calculation plays an important role in compound library design, virtual screening, and “lead” optimization. In this manuscript, we present a novel GPU-accelerated algorithm for all-vs-all Tanimoto matrix calculation and nearest neighbor search. By taking advantage of multi-core GPU architecture and CUDA parallel programming technology, the algorithm is up to 39 times superior to the existing commercial software that runs on CPUs. Because of the utilization of intrinsic GPU instructions, this approach is nearly 10 times faster than existing GPU-accelerated sparse vector algorithm, when Unity fingerprints are used for Tanimoto calculation. The GPU program that implements this new method takes about 20 minutes to complete the calculation of Tanimoto coefficients between 32M PubChem compounds and 10K Active Probes compounds, i.e., 324G Tanimoto coefficients, on a 128-CUDA-core GPU. PMID:21692447

  6. Accelerated Profile HMM Searches

    PubMed Central

    Eddy, Sean R.

    2011-01-01

    Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches. PMID:22039361

  7. Protein structural similarity search by Ramachandran codes

    PubMed Central

    Lo, Wei-Cheng; Huang, Po-Jung; Chang, Chih-Hung; Lyu, Ping-Chiang

    2007-01-01

    Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation). SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE) and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era. PMID:17716377

  8. SymDex: increasing the efficiency of chemical fingerprint similarity searches for comparing large chemical libraries by using query set indexing.

    PubMed

    Tai, David; Fang, Jianwen

    2012-08-27

    The large sizes of today's chemical databases require efficient algorithms to perform similarity searches. It can be very time consuming to compare two large chemical databases. This paper seeks to build upon existing research efforts by describing a novel strategy for accelerating existing search algorithms for comparing large chemical collections. The quest for efficiency has focused on developing better indexing algorithms by creating heuristics for searching individual chemical against a chemical library by detecting and eliminating needless similarity calculations. For comparing two chemical collections, these algorithms simply execute searches for each chemical in the query set sequentially. The strategy presented in this paper achieves a speedup upon these algorithms by indexing the set of all query chemicals so redundant calculations that arise in the case of sequential searches are eliminated. We implement this novel algorithm by developing a similarity search program called Symmetric inDexing or SymDex. SymDex shows over a 232% maximum speedup compared to the state-of-the-art single query search algorithm over real data for various fingerprint lengths. Considerable speedup is even seen for batch searches where query set sizes are relatively small compared to typical database sizes. To the best of our knowledge, SymDex is the first search algorithm designed specifically for comparing chemical libraries. It can be adapted to most, if not all, existing indexing algorithms and shows potential for accelerating future similarity search algorithms for comparing chemical databases.

  9. SpolSimilaritySearch - A web tool to compare and search similarities between spoligotypes of Mycobacterium tuberculosis complex.

    PubMed

    Couvin, David; Zozio, Thierry; Rastogi, Nalin

    2017-07-01

    Spoligotyping is one of the most commonly used polymerase chain reaction (PCR)-based methods for identification and study of genetic diversity of Mycobacterium tuberculosis complex (MTBC). Despite its known limitations if used alone, the methodology is particularly useful when used in combination with other methods such as mycobacterial interspersed repetitive units - variable number of tandem DNA repeats (MIRU-VNTRs). At a worldwide scale, spoligotyping has allowed identification of information on 103,856 MTBC isolates (corresponding to 98049 clustered strains plus 5807 unique isolates from 169 countries of patient origin) contained within the SITVIT2 proprietary database of the Institut Pasteur de la Guadeloupe. The SpolSimilaritySearch web-tool described herein (available at: http://www.pasteur-guadeloupe.fr:8081/SpolSimilaritySearch) incorporates a similarity search algorithm allowing users to get a complete overview of similar spoligotype patterns (with information on presence or absence of 43 spacers) in the aforementioned worldwide database. This tool allows one to analyze spread and evolutionary patterns of MTBC by comparing similar spoligotype patterns, to distinguish between widespread, specific and/or confined patterns, as well as to pinpoint patterns with large deleted blocks, which play an intriguing role in the genetic epidemiology of M. tuberculosis. Finally, the SpolSimilaritySearch tool also provides with the country distribution patterns for each queried spoligotype. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Biosequence Similarity Search on the Mercury System

    PubMed Central

    Krishnamurthy, Praveen; Buhler, Jeremy; Chamberlain, Roger; Franklin, Mark; Gyang, Kwame; Jacob, Arpith; Lancaster, Joseph

    2007-01-01

    Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described. PMID:18846267

  11. A MiniBooNE Accelerator-Produced (sub)-GeV Dark Matter Search

    NASA Astrophysics Data System (ADS)

    Thornton, Remington; MiniBooNE-DM Collaboration

    2016-09-01

    Cosmological observations indicate that our universe contains dark matter (DM), yet we have no measurements of its microscopic properties. Whereas the gravitational interaction of DM is well understood, its interaction with the Standard Model is not. Direct detection experiments search for a nuclear recoil interaction produced by a DM relic particle and have a low-mass sensitivity edge of order 1 GeV. To detect DM with mass below 1 GeV, either the sensitivity of the experiments needs to be improved or use of accelerators producing boosted low-mass DM are needed. Using neutrino detectors to search for low-mass DM is logical due to the similarity of the DM and ν signatures in the detector. The MiniBooNE experiment, located at Fermilab on the Booster Neutrino Beamline, ran for 10 years in ν and ν modes and is already well understood, making it desirable to search for accelerator-produced boosted low-mass DM. A search for DM produced by 8 GeV protons hitting a steel beam-dump has finished, collecting 1 . 86 ×1020 POT . Final analysis containing 90% confidence limits and a model independent fit will be presented.

  12. Distributed Efficient Similarity Search Mechanism in Wireless Sensor Networks

    PubMed Central

    Ahmed, Khandakar; Gregory, Mark A.

    2015-01-01

    The Wireless Sensor Network similarity search problem has received considerable research attention due to sensor hardware imprecision and environmental parameter variations. Most of the state-of-the-art distributed data centric storage (DCS) schemes lack optimization for similarity queries of events. In this paper, a DCS scheme with metric based similarity searching (DCSMSS) is proposed. DCSMSS takes motivation from vector distance index, called iDistance, in order to transform the issue of similarity searching into the problem of an interval search in one dimension. In addition, a sector based distance routing algorithm is used to efficiently route messages. Extensive simulation results reveal that DCSMSS is highly efficient and significantly outperforms previous approaches in processing similarity search queries. PMID:25751081

  13. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

    PubMed

    Wang, Chunlin; Lefkowitz, Elliot J

    2004-10-28

    Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together

  14. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

    PubMed Central

    Wang, Chunlin; Lefkowitz, Elliot J

    2004-01-01

    Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single

  15. Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision

    PubMed Central

    2011-01-01

    Background Data fusion methods are widely used in virtual screening, and make the implicit assumption that the more often a molecule is retrieved in multiple similarity searches, the more likely it is to be active. This paper tests the correctness of this assumption. Results Sets of 25 searches using either the same reference structure and 25 different similarity measures (similarity fusion) or 25 different reference structures and the same similarity measure (group fusion) show that large numbers of unique molecules are retrieved by just a single search, but that the numbers of unique molecules decrease very rapidly as more searches are considered. This rapid decrease is accompanied by a rapid increase in the fraction of those retrieved molecules that are active. There is an approximately log-log relationship between the numbers of different molecules retrieved and the number of searches carried out, and a rationale for this power-law behaviour is provided. Conclusions Using multiple searches provides a simple way of increasing the precision of a similarity search, and thus provides a justification for the use of data fusion methods in virtual screening. PMID:21824430

  16. Using SQL Databases for Sequence Similarity Searching and Analysis.

    PubMed

    Pearson, William R; Mackey, Aaron J

    2017-09-13

    Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  17. Predicting the performance of fingerprint similarity searching.

    PubMed

    Vogt, Martin; Bajorath, Jürgen

    2011-01-01

    Fingerprints are bit string representations of molecular structure that typically encode structural fragments, topological features, or pharmacophore patterns. Various fingerprint designs are utilized in virtual screening and their search performance essentially depends on three parameters: the nature of the fingerprint, the active compounds serving as reference molecules, and the composition of the screening database. It is of considerable interest and practical relevance to predict the performance of fingerprint similarity searching. A quantitative assessment of the potential that a fingerprint search might successfully retrieve active compounds, if available in the screening database, would substantially help to select the type of fingerprint most suitable for a given search problem. The method presented herein utilizes concepts from information theory to relate the fingerprint feature distributions of reference compounds to screening libraries. If these feature distributions do not sufficiently differ, active database compounds that are similar to reference molecules cannot be retrieved because they disappear in the "background." By quantifying the difference in feature distribution using the Kullback-Leibler divergence and relating the divergence to compound recovery rates obtained for different benchmark classes, fingerprint search performance can be quantitatively predicted.

  18. BLAST and FASTA similarity searching for multiple sequence alignment.

    PubMed

    Pearson, William R

    2014-01-01

    BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

  19. Improving GPU-accelerated adaptive IDW interpolation algorithm using fast kNN search.

    PubMed

    Mei, Gang; Xu, Nengxiong; Xu, Liangliang

    2016-01-01

    This paper presents an efficient parallel Adaptive Inverse Distance Weighting (AIDW) interpolation algorithm on modern Graphics Processing Unit (GPU). The presented algorithm is an improvement of our previous GPU-accelerated AIDW algorithm by adopting fast k-nearest neighbors (kNN) search. In AIDW, it needs to find several nearest neighboring data points for each interpolated point to adaptively determine the power parameter; and then the desired prediction value of the interpolated point is obtained by weighted interpolating using the power parameter. In this work, we develop a fast kNN search approach based on the space-partitioning data structure, even grid, to improve the previous GPU-accelerated AIDW algorithm. The improved algorithm is composed of the stages of kNN search and weighted interpolating. To evaluate the performance of the improved algorithm, we perform five groups of experimental tests. The experimental results indicate: (1) the improved algorithm can achieve a speedup of up to 1017 over the corresponding serial algorithm; (2) the improved algorithm is at least two times faster than our previous GPU-accelerated AIDW algorithm; and (3) the utilization of fast kNN search can significantly improve the computational efficiency of the entire GPU-accelerated AIDW algorithm.

  20. Application of kernel functions for accurate similarity search in large chemical databases.

    PubMed

    Wang, Xiaohong; Huan, Jun; Smalter, Aaron; Lushington, Gerald H

    2010-04-29

    Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases. To bridge graph kernel function and similarity search in chemical databases, we applied a novel kernel-based similarity measurement, developed in our team, to measure similarity of graph represented chemicals. In our method, we utilize a hash table to support new graph kernel function definition, efficient storage and fast search. We have applied our method, named G-hash, to large chemical databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Moreover, the similarity measurement and the index structure is scalable to large chemical databases with smaller indexing size, and faster query processing time as compared to state-of-the-art indexing methods such as Daylight fingerprints, C-tree and GraphGrep. Efficient similarity query processing method for large chemical databases is challenging since we need to balance running time efficiency and similarity search accuracy. Our previous similarity search method, G-hash, provides a new way to perform similarity search in chemical databases. Experimental study validates the utility of G-hash in chemical databases.

  1. Relational Agreement Measures for Similarity Searching of Cheminformatic Data Sets.

    PubMed

    Rivera-Borroto, Oscar Miguel; García-de la Vega, José Manuel; Marrero-Ponce, Yovani; Grau, Ricardo

    2016-01-01

    Research on similarity searching of cheminformatic data sets has been focused on similarity measures using fingerprints. However, nominal scales are the least informative of all metric scales, increasing the tied similarity scores, and decreasing the effectivity of the retrieval engines. Tanimoto's coefficient has been claimed to be the most prominent measure for this task. Nevertheless, this field is far from being exhausted since the computer science no free lunch theorem predicts that "no similarity measure has overall superiority over the population of data sets". We introduce 12 relational agreement (RA) coefficients for seven metric scales, which are integrated within a group fusion-based similarity searching algorithm. These similarity measures are compared to a reference panel of 21 proximity quantifiers over 17 benchmark data sets (MUV), by using informative descriptors, a feature selection stage, a suitable performance metric, and powerful comparison tests. In this stage, RA coefficients perform favourably with repect to the state-of-the-art proximity measures. Afterward, the RA-based method outperform another four nearest neighbor searching algorithms over the same data domains. In a third validation stage, RA measures are successfully applied to the virtual screening of the NCI data set. Finally, we discuss a possible molecular interpretation for these similarity variants.

  2. Effects of Part-based Similarity on Visual Search: The Frankenbear Experiment

    PubMed Central

    Alexander, Robert G.; Zelinsky, Gregory J.

    2012-01-01

    Do the target-distractor and distractor-distractor similarity relationships known to exist for simple stimuli extend to real-world objects, and are these effects expressed in search guidance or target verification? Parts of photorealistic distractors were replaced with target parts to create four levels of target-distractor similarity under heterogenous and homogenous conditions. We found that increasing target-distractor similarity and decreasing distractor-distractor similarity impaired search guidance and target verification, but that target-distractor similarity and heterogeneity/homogeneity interacted only in measures of guidance; distractor homogeneity lessens effects of target-distractor similarity by causing gaze to fixate the target sooner, not by speeding target detection following its fixation. PMID:22227607

  3. A new method to improve network topological similarity search: applied to fold recognition

    PubMed Central

    Lhota, John; Hauptman, Ruth; Hart, Thomas; Ng, Clara; Xie, Lei

    2015-01-01

    Motivation: Similarity search is the foundation of bioinformatics. It plays a key role in establishing structural, functional and evolutionary relationships between biological sequences. Although the power of the similarity search has increased steadily in recent years, a high percentage of sequences remain uncharacterized in the protein universe. Thus, new similarity search strategies are needed to efficiently and reliably infer the structure and function of new sequences. The existing paradigm for studying protein sequence, structure, function and evolution has been established based on the assumption that the protein universe is discrete and hierarchical. Cumulative evidence suggests that the protein universe is continuous. As a result, conventional sequence homology search methods may be not able to detect novel structural, functional and evolutionary relationships between proteins from weak and noisy sequence signals. To overcome the limitations in existing similarity search methods, we propose a new algorithmic framework—Enrichment of Network Topological Similarity (ENTS)—to improve the performance of large scale similarity searches in bioinformatics. Results: We apply ENTS to a challenging unsolved problem: protein fold recognition. Our rigorous benchmark studies demonstrate that ENTS considerably outperforms state-of-the-art methods. As the concept of ENTS can be applied to any similarity metric, it may provide a general framework for similarity search on any set of biological entities, given their representation as a network. Availability and implementation: Source code freely available upon request Contact: lxie@iscb.org PMID:25717198

  4. G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases.

    PubMed

    Wang, Xiaohong; Smalter, Aaron; Huan, Jun; Lushington, Gerald H

    2009-01-01

    Structured data including sets, sequences, trees and graphs, pose significant challenges to fundamental aspects of data management such as efficient storage, indexing, and similarity search. With the fast accumulation of graph databases, similarity search in graph databases has emerged as an important research topic. Graph similarity search has applications in a wide range of domains including cheminformatics, bioinformatics, sensor network management, social network management, and XML documents, among others.Most of the current graph indexing methods focus on subgraph query processing, i.e. determining the set of database graphs that contains the query graph and hence do not directly support similarity search. In data mining and machine learning, various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models for supervised learning, graph kernel functions have (i) high computational complexity and (ii) non-trivial difficulty to be indexed in a graph database.Our objective is to bridge graph kernel function and similarity search in graph databases by proposing (i) a novel kernel-based similarity measurement and (ii) an efficient indexing structure for graph data management. Our method of similarity measurement builds upon local features extracted from each node and their neighboring nodes in graphs. A hash table is utilized to support efficient storage and fast search of the extracted local features. Using the hash table, a graph kernel function is defined to capture the intrinsic similarity of graphs and for fast similarity query processing. We have implemented our method, which we have named G-hash, and have demonstrated its utility on large chemical graph databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Most importantly, the new similarity measurement and the index

  5. RAPSearch: a fast protein similarity search tool for short reads

    PubMed Central

    2011-01-01

    Background Next Generation Sequencing (NGS) is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets. Results We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames) we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2%) of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1%) that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST. Conclusions RAPSearch is implemented as open-source software and is accessible at http://omics.informatics.indiana.edu/mg/RAPSearch. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated. PMID:21575167

  6. Robust hashing with local models for approximate similarity search.

    PubMed

    Song, Jingkuan; Yang, Yi; Li, Xuelong; Huang, Zi; Yang, Yang

    2014-07-01

    Similarity search plays an important role in many applications involving high-dimensional data. Due to the known dimensionality curse, the performance of most existing indexing structures degrades quickly as the feature dimensionality increases. Hashing methods, such as locality sensitive hashing (LSH) and its variants, have been widely used to achieve fast approximate similarity search by trading search quality for efficiency. However, most existing hashing methods make use of randomized algorithms to generate hash codes without considering the specific structural information in the data. In this paper, we propose a novel hashing method, namely, robust hashing with local models (RHLM), which learns a set of robust hash functions to map the high-dimensional data points into binary hash codes by effectively utilizing local structural information. In RHLM, for each individual data point in the training dataset, a local hashing model is learned and used to predict the hash codes of its neighboring data points. The local models from all the data points are globally aligned so that an optimal hash code can be assigned to each data point. After obtaining the hash codes of all the training data points, we design a robust method by employing l2,1 -norm minimization on the loss function to learn effective hash functions, which are then used to map each database point into its hash code. Given a query data point, the search process first maps it into the query hash code by the hash functions and then explores the buckets, which have similar hash codes to the query hash code. Extensive experimental results conducted on real-life datasets show that the proposed RHLM outperforms the state-of-the-art methods in terms of search quality and efficiency.

  7. Web Image Search Re-ranking with Click-based Similarity and Typicality.

    PubMed

    Yang, Xiaopeng; Mei, Tao; Zhang, Yong Dong; Liu, Jie; Satoh, Shin'ichi

    2016-07-20

    In image search re-ranking, besides the well known semantic gap, intent gap, which is the gap between the representation of users' query/demand and the real intent of the users, is becoming a major problem restricting the development of image retrieval. To reduce human effects, in this paper, we use image click-through data, which can be viewed as the "implicit feedback" from users, to help overcome the intention gap, and further improve the image search performance. Generally, the hypothesis visually similar images should be close in a ranking list and the strategy images with higher relevance should be ranked higher than others are widely accepted. To obtain satisfying search results, thus, image similarity and the level of relevance typicality are determinate factors correspondingly. However, when measuring image similarity and typicality, conventional re-ranking approaches only consider visual information and initial ranks of images, while overlooking the influence of click-through data. This paper presents a novel re-ranking approach, named spectral clustering re-ranking with click-based similarity and typicality (SCCST). First, to learn an appropriate similarity measurement, we propose click-based multi-feature similarity learning algorithm (CMSL), which conducts metric learning based on clickbased triplets selection, and integrates multiple features into a unified similarity space via multiple kernel learning. Then based on the learnt click-based image similarity measure, we conduct spectral clustering to group visually and semantically similar images into same clusters, and get the final re-rank list by calculating click-based clusters typicality and withinclusters click-based image typicality in descending order. Our experiments conducted on two real-world query-image datasets with diverse representative queries show that our proposed reranking approach can significantly improve initial search results, and outperform several existing re-ranking approaches.

  8. Combined semantic and similarity search in medical image databases

    NASA Astrophysics Data System (ADS)

    Seifert, Sascha; Thoma, Marisa; Stegmaier, Florian; Hammon, Matthias; Kramer, Martin; Huber, Martin; Kriegel, Hans-Peter; Cavallaro, Alexander; Comaniciu, Dorin

    2011-03-01

    The current diagnostic process at hospitals is mainly based on reviewing and comparing images coming from multiple time points and modalities in order to monitor disease progression over a period of time. However, for ambiguous cases the radiologist deeply relies on reference literature or second opinion. Although there is a vast amount of acquired images stored in PACS systems which could be reused for decision support, these data sets suffer from weak search capabilities. Thus, we present a search methodology which enables the physician to fulfill intelligent search scenarios on medical image databases combining ontology-based semantic and appearance-based similarity search. It enabled the elimination of 12% of the top ten hits which would arise without taking the semantic context into account.

  9. Towards novel organic high-Tc superconductors: Data mining using density of states similarity search

    NASA Astrophysics Data System (ADS)

    Geilhufe, R. Matthias; Borysov, Stanislav S.; Kalpakchi, Dmytro; Balatsky, Alexander V.

    2018-02-01

    Identifying novel functional materials with desired key properties is an important part of bridging the gap between fundamental research and technological advancement. In this context, high-throughput calculations combined with data-mining techniques highly accelerated this process in different areas of research during the past years. The strength of a data-driven approach for materials prediction lies in narrowing down the search space of thousands of materials to a subset of prospective candidates. Recently, the open-access organic materials database OMDB was released providing electronic structure data for thousands of previously synthesized three-dimensional organic crystals. Based on the OMDB, we report about the implementation of a novel density of states similarity search tool which is capable of retrieving materials with similar density of states to a reference material. The tool is based on the approximate nearest neighbor algorithm as implemented in the ANNOY library and can be applied via the OMDB web interface. The approach presented here is wide ranging and can be applied to various problems where the density of states is responsible for certain key properties of a material. As the first application, we report about materials exhibiting electronic structure similarities to the aromatic hydrocarbon p-terphenyl which was recently discussed as a potential organic high-temperature superconductor exhibiting a transition temperature in the order of 120 K under strong potassium doping. Although the mechanism driving the remarkable transition temperature remains under debate, we argue that the density of states, reflecting the electronic structure of a material, might serve as a crucial ingredient for the observed high Tc. To provide candidates which might exhibit comparable properties, we present 15 purely organic materials with similar features to p-terphenyl within the electronic structure, which also tend to have structural similarities with p

  10. Inference-Based Similarity Search in Randomized Montgomery Domains for Privacy-Preserving Biometric Identification.

    PubMed

    Wang, Yi; Wan, Jianwu; Guo, Jun; Cheung, Yiu-Ming; Yuen, Pong C; Yi Wang; Jianwu Wan; Jun Guo; Yiu-Ming Cheung; Yuen, Pong C; Cheung, Yiu-Ming; Guo, Jun; Yuen, Pong C; Wan, Jianwu; Wang, Yi

    2018-07-01

    Similarity search is essential to many important applications and often involves searching at scale on high-dimensional data based on their similarity to a query. In biometric applications, recent vulnerability studies have shown that adversarial machine learning can compromise biometric recognition systems by exploiting the biometric similarity information. Existing methods for biometric privacy protection are in general based on pairwise matching of secured biometric templates and have inherent limitations in search efficiency and scalability. In this paper, we propose an inference-based framework for privacy-preserving similarity search in Hamming space. Our approach builds on an obfuscated distance measure that can conceal Hamming distance in a dynamic interval. Such a mechanism enables us to systematically design statistically reliable methods for retrieving most likely candidates without knowing the exact distance values. We further propose to apply Montgomery multiplication for generating search indexes that can withstand adversarial similarity analysis, and show that information leakage in randomized Montgomery domains can be made negligibly small. Our experiments on public biometric datasets demonstrate that the inference-based approach can achieve a search accuracy close to the best performance possible with secure computation methods, but the associated cost is reduced by orders of magnitude compared to cryptographic primitives.

  11. δ-Similar Elimination to Enhance Search Performance of Multiobjective Evolutionary Algorithms

    NASA Astrophysics Data System (ADS)

    Aguirre, Hernán; Sato, Masahiko; Tanaka, Kiyoshi

    In this paper, we propose δ-similar elimination to improve the search performance of multiobjective evolutionary algorithms in combinatorial optimization problems. This method eliminates similar individuals in objective space to fairly distribute selection among the different regions of the instantaneous Pareto front. We investigate four eliminating methods analyzing their effects using NSGA-II. In addition, we compare the search performance of NSGA-II enhanced by our method and NSGA-II enhanced by controlled elitism.

  12. Similarity relations in visual search predict rapid visual categorization

    PubMed Central

    Mohan, Krithika; Arun, S. P.

    2012-01-01

    How do we perform rapid visual categorization?It is widely thought that categorization involves evaluating the similarity of an object to other category items, but the underlying features and similarity relations remain unknown. Here, we hypothesized that categorization performance is based on perceived similarity relations between items within and outside the category. To this end, we measured the categorization performance of human subjects on three diverse visual categories (animals, vehicles, and tools) and across three hierarchical levels (superordinate, basic, and subordinate levels among animals). For the same subjects, we measured their perceived pair-wise similarities between objects using a visual search task. Regardless of category and hierarchical level, we found that the time taken to categorize an object could be predicted using its similarity to members within and outside its category. We were able to account for several classic categorization phenomena, such as (a) the longer times required to reject category membership; (b) the longer times to categorize atypical objects; and (c) differences in performance across tasks and across hierarchical levels. These categorization times were also accounted for by a model that extracts coarse structure from an image. The striking agreement observed between categorization and visual search suggests that these two disparate tasks depend on a shared coarse object representation. PMID:23092947

  13. Using multidimensional scaling to quantify similarity in visual search and beyond

    PubMed Central

    Godwin, Hayward J.; Fitzsimmons, Gemma; Robbins, Arryn; Menneer, Tamaryn; Goldinger, Stephen D.

    2017-01-01

    Visual search is one of the most widely studied topics in vision science, both as an independent topic of interest, and as a tool for studying attention and visual cognition. A wide literature exists that seeks to understand how people find things under varying conditions of difficulty and complexity, and in situations ranging from the mundane (e.g., looking for one’s keys) to those with significant societal importance (e.g., baggage or medical screening). A primary determinant of the ease and probability of success during search are the similarity relationships that exist in the search environment, such as the similarity between the background and the target, or the likeness of the non-targets to one another. A sense of similarity is often intuitive, but it is seldom quantified directly. This presents a problem in that similarity relationships are imprecisely specified, limiting the capacity of the researcher to examine adequately their influence. In this article, we present a novel approach to overcoming this problem that combines multidimensional scaling (MDS) analyses with behavioral and eye-tracking measurements. We propose a method whereby MDS can be repurposed to successfully quantify the similarity of experimental stimuli, thereby opening up theoretical questions in visual search and attention that cannot currently be addressed. These quantifications, in conjunction with behavioral and oculomotor measures, allow for critical observations about how similarity affects performance, information selection, and information processing. We provide a demonstration and tutorial of the approach, identify documented examples of its use, discuss how complementary computer vision methods could also be adopted, and close with a discussion of potential avenues for future application of this technique. PMID:26494381

  14. Bioturbo similarity searching: combining chemical and biological similarity to discover structurally diverse bioactive molecules.

    PubMed

    Wassermann, Anne Mai; Lounkine, Eugen; Glick, Meir

    2013-03-25

    Virtual screening using bioactivity profiles has become an integral part of currently applied hit finding methods in pharmaceutical industry. However, a significant drawback of this approach is that it is only applicable to compounds that have been biologically tested in the past and have sufficient activity annotations for meaningful profile comparisons. Although bioactivity data generated in pharmaceutical institutions are growing on an unprecedented scale, the number of biologically annotated compounds still covers only a minuscule fraction of chemical space. For a newly synthesized compound or an isolated natural product to be biologically characterized across multiple assays, it may take a considerable amount of time. Consequently, this chemical matter will not be included in virtual screening campaigns based on bioactivity profiles. To overcome this problem, we herein introduce bioturbo similarity searching that uses chemical similarity to map molecules without biological annotations into bioactivity space and then searches for biologically similar compounds in this reference system. In benchmark calculations on primary screening data, we demonstrate that our approach generally achieves higher hit rates and identifies structurally more diverse compounds than approaches using chemical information only. Furthermore, our method is able to discover hits with novel modes of inhibition that traditional 2D and 3D similarity approaches are unlikely to discover. Test calculations on a set of natural products reveal the practical utility of the approach for identifying novel and synthetically more accessible chemical matter.

  15. Finding similar nucleotide sequences using network BLAST searches.

    PubMed

    Ladunga, Istvan

    2009-06-01

    The Basic Local Alignment Search Tool (BLAST) is a keystone of bioinformatics due to its performance and user-friendliness. Beginner and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNA, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn. Understanding results is assisted by taxonomy reports, genomic views, and multiple alignments. We interpret expected frequency thresholds, biological significance, and statistical significance. Weak hits provide no evidence, but hints for further analyses. We find genes that may code for homologous proteins by translated BLAST. We reduce false positives by filtering out low-complexity regions. Parsed BLAST results can be integrated into analysis pipelines. Links in the output connect to Entrez, PUBMED, structural, sequence, interaction, and expression databases. This facilitates integration with a wide spectrum of biological knowledge.

  16. Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

    PubMed

    Mackey, Aaron J; Pearson, William R

    2004-10-01

    Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

  17. Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.

    PubMed

    Suzuki, Hirofumi; Kawabata, Takeshi; Nakamura, Haruki

    2016-02-15

    Omokage search is a service to search the global shape similarity of biological macromolecules and their assemblies, in both the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB). The server compares global shapes of assemblies independent of sequence order and number of subunits. As a search query, the user inputs a structure ID (PDB ID or EMDB ID) or uploads an atomic model or 3D density map to the server. The search is performed usually within 1 min, using one-dimensional profiles (incremental distance rank profiles) to characterize the shapes. Using the gmfit (Gaussian mixture model fitting) program, the found structures are fitted onto the query structure and their superimposed structures are displayed on the Web browser. Our service provides new structural perspectives to life science researchers. Omokage search is freely accessible at http://pdbj.org/omokage/. © The Author 2015. Published by Oxford University Press.

  18. Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data.

    PubMed

    Su, Xiaoquan; Xu, Jian; Ning, Kang

    2012-10-01

    It has long been intriguing scientists to effectively compare different microbial communities (also referred as 'metagenomic samples' here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database. In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods. Meta-Storms method would serve as a suitable

  19. Perceptual Grouping in Haptic Search: The Influence of Proximity, Similarity, and Good Continuation

    ERIC Educational Resources Information Center

    Overvliet, Krista E.; Krampe, Ralf Th.; Wagemans, Johan

    2012-01-01

    We conducted a haptic search experiment to investigate the influence of the Gestalt principles of proximity, similarity, and good continuation. We expected faster search when the distractors could be grouped. We chose edges at different orientations as stimuli because they are processed similarly in the haptic and visual modality. We therefore…

  20. Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia.

    PubMed

    Ertl, Peter; Patiny, Luc; Sander, Thomas; Rufener, Christian; Zasso, Michaël

    2015-01-01

    Wikipedia, the world's largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, agrochemicals and industrial chemicals. To provide an easy access to this wealth of information we decided to develop a substructure and similarity search tool for chemical structures referenced in Wikipedia. We extracted chemical structures from entries in Wikipedia and implemented a web system allowing structure and similarity searching on these data. The whole search as well as visualization system is written in JavaScript and therefore can run locally within a web page and does not require a central server. The Wikipedia Chemical Structure Explorer is accessible on-line at www.cheminfo.org/wikipedia and is available also as an open source project from GitHub for local installation. The web-based Wikipedia Chemical Structure Explorer provides a useful resource for research as well as for chemical education enabling both researchers and students easy and user friendly chemistry searching and identification of relevant information in Wikipedia. The tool can also help to improve quality of chemical entries in Wikipedia by providing potential contributors regularly updated list of entries with problematic structures. And last but not least this search system is a nice example of how the modern web technology can be applied in the field of cheminformatics. Graphical abstractWikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

  1. Semantically enabled image similarity search

    NASA Astrophysics Data System (ADS)

    Casterline, May V.; Emerick, Timothy; Sadeghi, Kolia; Gosse, C. A.; Bartlett, Brent; Casey, Jason

    2015-05-01

    Georeferenced data of various modalities are increasingly available for intelligence and commercial use, however effectively exploiting these sources demands a unified data space capable of capturing the unique contribution of each input. This work presents a suite of software tools for representing geospatial vector data and overhead imagery in a shared high-dimension vector or embedding" space that supports fused learning and similarity search across dissimilar modalities. While the approach is suitable for fusing arbitrary input types, including free text, the present work exploits the obvious but computationally difficult relationship between GIS and overhead imagery. GIS is comprised of temporally-smoothed but information-limited content of a GIS, while overhead imagery provides an information-rich but temporally-limited perspective. This processing framework includes some important extensions of concepts in literature but, more critically, presents a means to accomplish them as a unified framework at scale on commodity cloud architectures.

  2. SlideSort: all pairs similarity search for short reads

    PubMed Central

    Shimizu, Kana; Tsuda, Koji

    2011-01-01

    Motivation: Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses. Results: In this study, we designed and implemented an exact algorithm SlideSort that finds all similar pairs from a string pool in terms of edit distance. Using an efficient pattern growth algorithm, SlideSort discovers chains of common k-mers to narrow down the search. Compared to existing methods based on single k-mers, our method is more effective in reducing the number of edit distance calculations. In comparison to backtracking methods such as BWA, our method is much faster in finding remote matches, scaling easily to tens of millions of sequences. Our software has an additional function of single link clustering, which is useful in summarizing short reads for further processing. Availability: Executable binary files and C++ libraries are available at http://www.cbrc.jp/~shimizu/slidesort/ for Linux and Windows. Contact: slidesort@m.aist.go.jp; shimizu-kana@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21148542

  3. OS2: Oblivious similarity based searching for encrypted data outsourced to an untrusted domain

    PubMed Central

    Pervez, Zeeshan; Ahmad, Mahmood; Khattak, Asad Masood; Ramzan, Naeem

    2017-01-01

    Public cloud storage services are becoming prevalent and myriad data sharing, archiving and collaborative services have emerged which harness the pay-as-you-go business model of public cloud. To ensure privacy and confidentiality often encrypted data is outsourced to such services, which further complicates the process of accessing relevant data by using search queries. Search over encrypted data schemes solve this problem by exploiting cryptographic primitives and secure indexing to identify outsourced data that satisfy the search criteria. Almost all of these schemes rely on exact matching between the encrypted data and search criteria. A few schemes which extend the notion of exact matching to similarity based search, lack realism as those schemes rely on trusted third parties or due to increase storage and computational complexity. In this paper we propose Oblivious Similarity based Search (OS2) for encrypted data. It enables authorized users to model their own encrypted search queries which are resilient to typographical errors. Unlike conventional methodologies, OS2 ranks the search results by using similarity measure offering a better search experience than exact matching. It utilizes encrypted bloom filter and probabilistic homomorphic encryption to enable authorized users to access relevant data without revealing results of search query evaluation process to the untrusted cloud service provider. Encrypted bloom filter based search enables OS2 to reduce search space to potentially relevant encrypted data avoiding unnecessary computation on public cloud. The efficacy of OS2 is evaluated on Google App Engine for various bloom filter lengths on different cloud configurations. PMID:28692697

  4. Querying Event Sequences by Exact Match or Similarity Search: Design and Empirical Evaluation

    PubMed Central

    Wongsuphasawat, Krist; Plaisant, Catherine; Taieb-Maimon, Meirav; Shneiderman, Ben

    2012-01-01

    Specifying event sequence queries is challenging even for skilled computer professionals familiar with SQL. Most graphical user interfaces for database search use an exact match approach, which is often effective, but near misses may also be of interest. We describe a new similarity search interface, in which users specify a query by simply placing events on a blank timeline and retrieve a similarity-ranked list of results. Behind this user interface is a new similarity measure for event sequences which the users can customize by four decision criteria, enabling them to adjust the impact of missing, extra, or swapped events or the impact of time shifts. We describe a use case with Electronic Health Records based on our ongoing collaboration with hospital physicians. A controlled experiment with 18 participants compared exact match and similarity search interfaces. We report on the advantages and disadvantages of each interface and suggest a hybrid interface combining the best of both. PMID:22379286

  5. Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces.

    PubMed

    Boehm, Markus; Wu, Tong-Ying; Claussen, Holger; Lemmen, Christian

    2008-04-24

    Large collections of combinatorial libraries are an integral element in today's pharmaceutical industry. It is of great interest to perform similarity searches against all virtual compounds that are synthetically accessible by any such library. Here we describe the successful application of a new software tool CoLibri on 358 combinatorial libraries based on validated reaction protocols to create a single chemistry space containing over 10 (12) possible products. Similarity searching with FTrees-FS allows the systematic exploration of this space without the need to enumerate all product structures. The search result is a set of virtual hits which are synthetically accessible by one or more of the existing reaction protocols. Grouping these virtual hits by their synthetic protocols allows the rapid design and synthesis of multiple follow-up libraries. Such library ideas support hit-to-lead design efforts for tasks like follow-up from high-throughput screening hits or scaffold hopping from one hit to another attractive series.

  6. Acceleration of saddle-point searches with machine learning.

    PubMed

    Peterson, Andrew A

    2016-08-21

    In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the number of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.

  7. Earthquake detection through computationally efficient similarity search

    PubMed Central

    Yoon, Clara E.; O’Reilly, Ossian; Bergen, Karianne J.; Beroza, Gregory C.

    2015-01-01

    Seismology is experiencing rapid growth in the quantity of data, which has outpaced the development of processing algorithms. Earthquake detection—identification of seismic events in continuous data—is a fundamental operation for observational seismology. We developed an efficient method to detect earthquakes using waveform similarity that overcomes the disadvantages of existing detection methods. Our method, called Fingerprint And Similarity Thresholding (FAST), can analyze a week of continuous seismic waveform data in less than 2 hours, or 140 times faster than autocorrelation. FAST adapts a data mining algorithm, originally designed to identify similar audio clips within large databases; it first creates compact “fingerprints” of waveforms by extracting key discriminative features, then groups similar fingerprints together within a database to facilitate fast, scalable search for similar fingerprint pairs, and finally generates a list of earthquake detections. FAST detected most (21 of 24) cataloged earthquakes and 68 uncataloged earthquakes in 1 week of continuous data from a station located near the Calaveras Fault in central California, achieving detection performance comparable to that of autocorrelation, with some additional false detections. FAST is expected to realize its full potential when applied to extremely long duration data sets over a distributed network of seismic stations. The widespread application of FAST has the potential to aid in the discovery of unexpected seismic signals, improve seismic monitoring, and promote a greater understanding of a variety of earthquake processes. PMID:26665176

  8. A search for structurally similar cellular internal ribosome entry sites

    PubMed Central

    Baird, Stephen D.; Lewis, Stephen M.; Turcotte, Marcel; Holcik, Martin

    2007-01-01

    Internal ribosome entry sites (IRES) allow ribosomes to be recruited to mRNA in a cap-independent manner. Some viruses that impair cap-dependent translation initiation utilize IRES to ensure that the viral RNA will efficiently compete for the translation machinery. IRES are also employed for the translation of a subset of cellular messages during conditions that inhibit cap-dependent translation initiation. IRES from viruses like Hepatitis C and Classical Swine Fever virus share a similar structure/function without sharing primary sequence similarity. Of the cellular IRES structures derived so far, none were shown to share an overall structural similarity. Therefore, we undertook a genome-wide search of human 5′UTRs (untranslated regions) with an empirically derived structure of the IRES from the key inhibitor of apoptosis, X-linked inhibitor of apoptosis protein (XIAP), to identify novel IRES that share structure/function similarity. Three of the top matches identified by this search that exhibit IRES activity are the 5′UTRs of Aquaporin 4, ELG1 and NF-kappaB repressing factor (NRF). The structures of AQP4 and ELG1 IRES have limited similarity to the XIAP IRES; however, they share trans-acting factors that bind the XIAP IRES. We therefore propose that cellular IRES are not defined by overall structure, as viral IRES, but are instead dependent upon short motifs and trans-acting factors for their function. PMID:17591613

  9. Optimal neighborhood indexing for protein similarity search.

    PubMed

    Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Nguyen, Van Hoa; Kucherov, Gregory; Giraud, Mathieu

    2008-12-16

    Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum. We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

  10. Optimal neighborhood indexing for protein similarity search

    PubMed Central

    Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Nguyen, Van Hoa; Kucherov, Gregory; Giraud, Mathieu

    2008-01-01

    Background Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. Results The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website . Conclusion We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction. PMID:19087280

  11. Acceleration of saddle-point searches with machine learning

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Peterson, Andrew A., E-mail: andrew-peterson@brown.edu

    In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the numbermore » of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.« less

  12. [Formula: see text]: Oblivious similarity based searching for encrypted data outsourced to an untrusted domain.

    PubMed

    Pervez, Zeeshan; Ahmad, Mahmood; Khattak, Asad Masood; Ramzan, Naeem; Khan, Wajahat Ali

    2017-01-01

    Public cloud storage services are becoming prevalent and myriad data sharing, archiving and collaborative services have emerged which harness the pay-as-you-go business model of public cloud. To ensure privacy and confidentiality often encrypted data is outsourced to such services, which further complicates the process of accessing relevant data by using search queries. Search over encrypted data schemes solve this problem by exploiting cryptographic primitives and secure indexing to identify outsourced data that satisfy the search criteria. Almost all of these schemes rely on exact matching between the encrypted data and search criteria. A few schemes which extend the notion of exact matching to similarity based search, lack realism as those schemes rely on trusted third parties or due to increase storage and computational complexity. In this paper we propose Oblivious Similarity based Search ([Formula: see text]) for encrypted data. It enables authorized users to model their own encrypted search queries which are resilient to typographical errors. Unlike conventional methodologies, [Formula: see text] ranks the search results by using similarity measure offering a better search experience than exact matching. It utilizes encrypted bloom filter and probabilistic homomorphic encryption to enable authorized users to access relevant data without revealing results of search query evaluation process to the untrusted cloud service provider. Encrypted bloom filter based search enables [Formula: see text] to reduce search space to potentially relevant encrypted data avoiding unnecessary computation on public cloud. The efficacy of [Formula: see text] is evaluated on Google App Engine for various bloom filter lengths on different cloud configurations.

  13. Semantic similarity measure in biomedical domain leverage web search engine.

    PubMed

    Chen, Chi-Huang; Hsieh, Sheau-Ling; Weng, Yung-Ching; Chang, Wen-Yung; Lai, Feipei

    2010-01-01

    Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

  14. Fast structure similarity searches among protein models: efficient clustering of protein fragments

    PubMed Central

    2012-01-01

    Background For many predictive applications a large number of models is generated and later clustered in subsets based on structure similarity. In most clustering algorithms an all-vs-all root mean square deviation (RMSD) comparison is performed. Most of the time is typically spent on comparison of non-similar structures. For sets with more than, say, 10,000 models this procedure is very time-consuming and alternative faster algorithms, restricting comparisons only to most similar structures would be useful. Results We exploit the inverse triangle inequality on the RMSD between two structures given the RMSDs with a third structure. The lower bound on RMSD may be used, when restricting the search of similarity to a reasonably low RMSD threshold value, to speed up similarity searches significantly. Tests are performed on large sets of decoys which are widely used as test cases for predictive methods, with a speed-up of up to 100 times with respect to all-vs-all comparison depending on the set and parameters used. Sample applications are shown. Conclusions The algorithm presented here allows fast comparison of large data sets of structures with limited memory requirements. As an example of application we present clustering of more than 100000 fragments of length 5 from the top500H dataset into few hundred representative fragments. A more realistic scenario is provided by the search of similarity within the very large decoy sets used for the tests. Other applications regard filtering nearly-indentical conformation in selected CASP9 datasets and clustering molecular dynamics snapshots. Availability A linux executable and a Perl script with examples are given in the supplementary material (Additional file 1). The source code is available upon request from the authors. PMID:22642815

  15. Generating "fragment-based virtual library" using pocket similarity search of ligand-receptor complexes.

    PubMed

    Khashan, Raed S

    2015-01-01

    As the number of available ligand-receptor complexes is increasing, researchers are becoming more dedicated to mine these complexes to aid in the drug design and development process. We present free software which is developed as a tool for performing similarity search across ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. For each match identified, the ligand's fragment(s) corresponding to that binding pocket are extracted, thus forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design. The program provides a very useful tool to explore available databases.

  16. Efficient blind search for similar-waveform earthquakes in years of continuous seismic data

    NASA Astrophysics Data System (ADS)

    Yoon, C. E.; Bergen, K.; Rong, K.; Elezabi, H.; Bailis, P.; Levis, P.; Beroza, G. C.

    2017-12-01

    Cross-correlating an earthquake waveform template with continuous seismic data has proven to be a sensitive, discriminating detector of small events missing from earthquake catalogs, but a key limitation of this approach is that it requires advance knowledge of the earthquake signals we wish to detect. To overcome this limitation, we can perform a blind search for events with similar waveforms, comparing waveforms from all possible times within the continuous data (Brown et al., 2008). However, the runtime for naive blind search scales quadratically with the duration of continuous data, making it impractical to process years of continuous data. The Fingerprint And Similarity Thresholding (FAST) detection method (Yoon et al., 2015) enables a comprehensive blind search for similar-waveform earthquakes in a fast, scalable manner by adapting data-mining techniques originally developed for audio and image search within massive databases. FAST converts seismic waveforms into compact "fingerprints", which are efficiently organized and searched within a database. In this way, FAST avoids the unnecessary comparison of dissimilar waveforms. To date, the longest duration of continuous data used for event detection with FAST was 3 months at a single station near Guy-Greenbrier, Arkansas, which revealed microearthquakes closely correlated with stages of hydraulic fracturing (Yoon et al., 2017). In this presentation we introduce an optimized, parallel version of the FAST software with improvements to the fingerprinting algorithm and the ability to detect events using continuous data from a network of stations (Bergen et al., 2016). We demonstrate its ability to detect low-magnitude earthquakes within several years of continuous data at locations of interest in California.

  17. Fast parallel tandem mass spectral library searching using GPU hardware acceleration

    PubMed Central

    Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K.; Martin, Daniel B.

    2011-01-01

    Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching) is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment. PMID:21545112

  18. Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

    PubMed

    Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K; Martin, Daniel B

    2011-06-03

    Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.

  19. Target-distractor similarity has a larger impact on visual search in school-age children than spacing.

    PubMed

    Huurneman, Bianca; Boonstra, F Nienke

    2015-01-22

    In typically developing children, crowding decreases with increasing age. The influence of target-distractor similarity with respect to orientation and element spacing on visual search performance was investigated in 29 school-age children with normal vision (4- to 6-year-olds [N = 16], 7- to 8-year-olds [N = 13]). Children were instructed to search for a target E among distractor Es (feature search: all flanking Es pointing right; conjunction search: flankers in three orientations). Orientation of the target was manipulated in four directions: right (target absent), left (inversed), up, and down (vertical). Spacing was varied in four steps: 0.04°, 0.5°, 1°, and 2°. During feature search, high target-distractor similarity had a stronger impact on performance than spacing: Orientation affected accuracy until spacing was 1°, and spacing only influenced accuracy for identifying inversed targets. Spatial analyses showed that orientation affected oculomotor strategy: Children made more fixations in the "inversed" target area (4.6) than the vertical target areas (1.8 and 1.9). Furthermore, age groups differed in fixation duration: 4- to 6-year-old children showed longer fixation durations than 7- to 8-year-olds at the two largest element spacings (p = 0.039 and p = 0.027). Conjunction search performance was unaffected by spacing. Four conclusions can be drawn from this study: (a) Target-distractor similarity governs visual search performance in school-age children, (b) children make more fixations in target areas when target-distractor similarity is high, (c) 4- to 6-year-olds show longer fixation durations than 7- to 8-year-olds at 1° and 2° element spacing, and (d) spacing affects feature but not conjunction search-a finding that might indicate top-down control ameliorates crowding in children. © 2015 ARVO.

  20. GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering.

    PubMed

    Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

    2016-01-01

    Sequence homology searches are used in various fields and require large amounts of computation time, especially for metagenomic analysis, owing to the large number of queries and the database size. To accelerate computing analyses, graphics processing units (GPUs) are widely used as a low-cost, high-performance computing platform. Therefore, we mapped the time-consuming steps involved in GHOSTZ, which is a state-of-the-art homology search algorithm for protein sequences, onto a GPU and implemented it as GHOSTZ-GPU. In addition, we optimized memory access for GPU calculations and for communication between the CPU and GPU. As per results of the evaluation test involving metagenomic data, GHOSTZ-GPU with 12 CPU threads and 1 GPU was approximately 3.0- to 4.1-fold faster than GHOSTZ with 12 CPU threads. Moreover, GHOSTZ-GPU with 12 CPU threads and 3 GPUs was approximately 5.8- to 7.7-fold faster than GHOSTZ with 12 CPU threads.

  1. GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering

    PubMed Central

    Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

    2016-01-01

    Sequence homology searches are used in various fields and require large amounts of computation time, especially for metagenomic analysis, owing to the large number of queries and the database size. To accelerate computing analyses, graphics processing units (GPUs) are widely used as a low-cost, high-performance computing platform. Therefore, we mapped the time-consuming steps involved in GHOSTZ, which is a state-of-the-art homology search algorithm for protein sequences, onto a GPU and implemented it as GHOSTZ-GPU. In addition, we optimized memory access for GPU calculations and for communication between the CPU and GPU. As per results of the evaluation test involving metagenomic data, GHOSTZ-GPU with 12 CPU threads and 1 GPU was approximately 3.0- to 4.1-fold faster than GHOSTZ with 12 CPU threads. Moreover, GHOSTZ-GPU with 12 CPU threads and 3 GPUs was approximately 5.8- to 7.7-fold faster than GHOSTZ with 12 CPU threads. PMID:27482905

  2. Accelerated search for materials with targeted properties by adaptive design

    PubMed Central

    Xue, Dezhen; Balachandran, Prasanna V.; Hogden, John; Theiler, James; Xue, Deqing; Lookman, Turab

    2016-01-01

    Finding new materials with targeted properties has traditionally been guided by intuition, and trial and error. With increasing chemical complexity, the combinatorial possibilities are too large for an Edisonian approach to be practical. Here we show how an adaptive design strategy, tightly coupled with experiments, can accelerate the discovery process by sequentially identifying the next experiments or calculations, to effectively navigate the complex search space. Our strategy uses inference and global optimization to balance the trade-off between exploitation and exploration of the search space. We demonstrate this by finding very low thermal hysteresis (ΔT) NiTi-based shape memory alloys, with Ti50.0Ni46.7Cu0.8Fe2.3Pd0.2 possessing the smallest ΔT (1.84 K). We synthesize and characterize 36 predicted compositions (9 feedback loops) from a potential space of ∼800,000 compositions. Of these, 14 had smaller ΔT than any of the 22 in the original data set. PMID:27079901

  3. Localized saddle-point search and application to temperature-accelerated dynamics

    NASA Astrophysics Data System (ADS)

    Shim, Yunsic; Callahan, Nathan B.; Amar, Jacques G.

    2013-03-01

    We present a method for speeding up temperature-accelerated dynamics (TAD) simulations by carrying out a localized saddle-point (LSAD) search. In this method, instead of using the entire system to determine the energy barriers of activated processes, the calculation is localized by only including a small chunk of atoms around the atoms directly involved in the transition. Using this method, we have obtained N-independent scaling for the computational cost of the saddle-point search as a function of system size N. The error arising from localization is analyzed using a variety of model systems, including a variety of activated processes on Ag(100) and Cu(100) surfaces, as well as multiatom moves in Cu radiation damage and metal heteroepitaxial growth. Our results show significantly improved performance of TAD with the LSAD method, for the case of Ag/Ag(100) annealing and Cu/Cu(100) growth, while maintaining a negligibly small error in energy barriers.

  4. Efficient searching and annotation of metabolic networks using chemical similarity

    PubMed Central

    Pertusi, Dante A.; Stine, Andrew E.; Broadbelt, Linda J.; Tyo, Keith E.J.

    2015-01-01

    Motivation: The urgent need for efficient and sustainable biological production of fuels and high-value chemicals has elicited a wave of in silico techniques for identifying promising novel pathways to these compounds in large putative metabolic networks. To date, these approaches have primarily used general graph search algorithms, which are prohibitively slow as putative metabolic networks may exceed 1 million compounds. To alleviate this limitation, we report two methods—SimIndex (SI) and SimZyme—which use chemical similarity of 2D chemical fingerprints to efficiently navigate large metabolic networks and propose enzymatic connections between the constituent nodes. We also report a Byers–Waterman type pathway search algorithm for further paring down pertinent networks. Results: Benchmarking tests run with SI show it can reduce the number of nodes visited in searching a putative network by 100-fold with a computational time improvement of up to 105-fold. Subsequent Byers–Waterman search application further reduces the number of nodes searched by up to 100-fold, while SimZyme demonstrates ∼90% accuracy in matching query substrates with enzymes. Using these modules, we have designed and annotated an alternative to the methylerythritol phosphate pathway to produce isopentenyl pyrophosphate with more favorable thermodynamics than the native pathway. These algorithms will have a significant impact on our ability to use large metabolic networks that lack annotation of promiscuous reactions. Availability and implementation: Python files will be available for download at http://tyolab.northwestern.edu/tools/. Contact: k-tyo@northwestern.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25417203

  5. The Research and Test of Fast Radio Burst Real-time Search Algorithm Based on GPU Acceleration

    NASA Astrophysics Data System (ADS)

    Wang, J.; Chen, M. Z.; Pei, X.; Wang, Z. Q.

    2017-03-01

    In order to satisfy the research needs of Nanshan 25 m radio telescope of Xinjiang Astronomical Observatory (XAO) and study the key technology of the planned QiTai radio Telescope (QTT), the receiver group of XAO studied the GPU (Graphics Processing Unit) based real-time FRB searching algorithm which developed from the original FRB searching algorithm based on CPU (Central Processing Unit), and built the FRB real-time searching system. The comparison of the GPU system and the CPU system shows that: on the basis of ensuring the accuracy of the search, the speed of the GPU accelerated algorithm is improved by 35-45 times compared with the CPU algorithm.

  6. Accelerating Smith-Waterman Algorithm for Biological Database Search on CUDA-Compatible GPUs

    NASA Astrophysics Data System (ADS)

    Munekawa, Yuma; Ino, Fumihiko; Hagihara, Kenichi

    This paper presents a fast method capable of accelerating the Smith-Waterman algorithm for biological database search on a cluster of graphics processing units (GPUs). Our method is implemented using compute unified device architecture (CUDA), which is available on the nVIDIA GPU. As compared with previous methods, our method has four major contributions. (1) The method efficiently uses on-chip shared memory to reduce the data amount being transferred between off-chip video memory and processing elements in the GPU. (2) It also reduces the number of data fetches by applying a data reuse technique to query and database sequences. (3) A pipelined method is also implemented to overlap GPU execution with database access. (4) Finally, a master/worker paradigm is employed to accelerate hundreds of database searches on a cluster system. In experiments, the peak performance on a GeForce GTX 280 card reaches 8.32 giga cell updates per second (GCUPS). We also find that our method reduces the amount of data fetches to 1/140, achieving approximately three times higher performance than a previous CUDA-based method. Our 32-node cluster version is approximately 28 times faster than a single GPU version. Furthermore, the effective performance reaches 75.6 giga instructions per second (GIPS) using 32 GeForce 8800 GTX cards.

  7. Efficient searching and annotation of metabolic networks using chemical similarity.

    PubMed

    Pertusi, Dante A; Stine, Andrew E; Broadbelt, Linda J; Tyo, Keith E J

    2015-04-01

    The urgent need for efficient and sustainable biological production of fuels and high-value chemicals has elicited a wave of in silico techniques for identifying promising novel pathways to these compounds in large putative metabolic networks. To date, these approaches have primarily used general graph search algorithms, which are prohibitively slow as putative metabolic networks may exceed 1 million compounds. To alleviate this limitation, we report two methods--SimIndex (SI) and SimZyme--which use chemical similarity of 2D chemical fingerprints to efficiently navigate large metabolic networks and propose enzymatic connections between the constituent nodes. We also report a Byers-Waterman type pathway search algorithm for further paring down pertinent networks. Benchmarking tests run with SI show it can reduce the number of nodes visited in searching a putative network by 100-fold with a computational time improvement of up to 10(5)-fold. Subsequent Byers-Waterman search application further reduces the number of nodes searched by up to 100-fold, while SimZyme demonstrates ∼ 90% accuracy in matching query substrates with enzymes. Using these modules, we have designed and annotated an alternative to the methylerythritol phosphate pathway to produce isopentenyl pyrophosphate with more favorable thermodynamics than the native pathway. These algorithms will have a significant impact on our ability to use large metabolic networks that lack annotation of promiscuous reactions. Python files will be available for download at http://tyolab.northwestern.edu/tools/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. Query-seeded iterative sequence similarity searching improves selectivity 5–20-fold

    PubMed Central

    Li, Weizhong; Lopez, Rodrigo

    2017-01-01

    Abstract Iterative similarity search programs, like psiblast, jackhmmer, and psisearch, are much more sensitive than pairwise similarity search methods like blast and ssearch because they build a position specific scoring model (a PSSM or HMM) that captures the pattern of sequence conservation characteristic to a protein family. But models are subject to contamination; once an unrelated sequence has been added to the model, homologs of the unrelated sequence will also produce high scores, and the model can diverge from the original protein family. Examination of alignment errors during psiblast PSSM contamination suggested a simple strategy for dramatically reducing PSSM contamination. psiblast PSSMs are built from the query-based multiple sequence alignment (MSA) implied by the pairwise alignments between the query model (PSSM, HMM) and the subject sequences in the library. When the original query sequence residues are inserted into gapped positions in the aligned subject sequence, the resulting PSSM rarely produces alignment over-extensions or alignments to unrelated sequences. This simple step, which tends to anchor the PSSM to the original query sequence and slightly increase target percent identity, can reduce the frequency of false-positive alignments more than 20-fold compared with psiblast and jackhmmer, with little loss in search sensitivity. PMID:27923999

  9. Applying Statistical Models and Parametric Distance Measures for Music Similarity Search

    NASA Astrophysics Data System (ADS)

    Lukashevich, Hanna; Dittmar, Christian; Bastuck, Christoph

    Automatic deriving of similarity relations between music pieces is an inherent field of music information retrieval research. Due to the nearly unrestricted amount of musical data, the real-world similarity search algorithms have to be highly efficient and scalable. The possible solution is to represent each music excerpt with a statistical model (ex. Gaussian mixture model) and thus to reduce the computational costs by applying the parametric distance measures between the models. In this paper we discuss the combinations of applying different parametric modelling techniques and distance measures and weigh the benefits of each one against the others.

  10. Evolution and Optimality of Similar Neural Mechanisms for Perception and Action during Search

    PubMed Central

    Zhang, Sheng; Eckstein, Miguel P.

    2010-01-01

    A prevailing theory proposes that the brain's two visual pathways, the ventral and dorsal, lead to differing visual processing and world representations for conscious perception than those for action. Others have claimed that perception and action share much of their visual processing. But which of these two neural architectures is favored by evolution? Successful visual search is life-critical and here we investigate the evolution and optimality of neural mechanisms mediating perception and eye movement actions for visual search in natural images. We implement an approximation to the ideal Bayesian searcher with two separate processing streams, one controlling the eye movements and the other stream determining the perceptual search decisions. We virtually evolved the neural mechanisms of the searchers' two separate pathways built from linear combinations of primary visual cortex receptive fields (V1) by making the simulated individuals' probability of survival depend on the perceptual accuracy finding targets in cluttered backgrounds. We find that for a variety of targets, backgrounds, and dependence of target detectability on retinal eccentricity, the mechanisms of the searchers' two processing streams converge to similar representations showing that mismatches in the mechanisms for perception and eye movements lead to suboptimal search. Three exceptions which resulted in partial or no convergence were a case of an organism for which the targets are equally detectable across the retina, an organism with sufficient time to foveate all possible target locations, and a strict two-pathway model with no interconnections and differential pre-filtering based on parvocellular and magnocellular lateral geniculate cell properties. Thus, similar neural mechanisms for perception and eye movement actions during search are optimal and should be expected from the effects of natural selection on an organism with limited time to search for food that is not equi-detectable across

  11. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

    PubMed

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

    2011-09-01

    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

  12. BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

    PubMed

    Worley, K C; Wiese, B A; Smith, R F

    1995-09-01

    BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html > ).

  13. Visual search accelerates during adolescence.

    PubMed

    Burggraaf, Rudolf; van der Geest, Jos N; Frens, Maarten A; Hooge, Ignace T C

    2018-05-01

    We studied changes in visual-search performance and behavior during adolescence. Search performance was analyzed in terms of reaction time and response accuracy. Search behavior was analyzed in terms of the objects fixated and the duration of these fixations. A large group of adolescents (N = 140; age: 12-19 years; 47% female, 53% male) participated in a visual-search experiment in which their eye movements were recorded with an eye tracker. The experiment consisted of 144 trials (50% with a target present), and participants had to decide whether a target was present. Each trial showed a search display with 36 Gabor patches placed on a hexagonal grid. The target was a vertically oriented element with a high spatial frequency. Nontargets differed from the target in spatial frequency, orientation, or both. Search performance and behavior changed during adolescence; with increasing age, fixation duration and reaction time decreased. Response accuracy, number of fixations, and selection of elements to fixate upon did not change with age. Thus, the speed of foveal discrimination increases with age, while the efficiency of peripheral selection does not change. We conclude that the way visual information is gathered does not change during adolescence, but the processing of visual information becomes faster.

  14. Search by mariner 10 for electrons and protons accelerated in association with venus.

    PubMed

    Simpson, J A; Eraker, J H; Lamport, J E; Walpole, P H

    1974-03-29

    The University of Chicago instrumnents on board the Mariner 10 spacecraft bound for Mercury have measured energy spectra and fluxes of electrons from 0.18 to 30 million electron volts and protons from 0.5 to 68 million electron volts along the plasma wake and in the bow shock regions associated with Venus. Unusually quiet solar conditions and improved instrumentation made it possible to search for much lower fluxes of protons and electrons in similar energy regions as compared to earlier Mariner missions to Venus-that is, lower by a factor of 10(2) for protons and 10(3) for electrons. We found no evidence for electrons or protons either in the form of increases of intensity or energy spectral changes in the vicinity of the planet, nor any evidence of bursts of radiation in or near the observed bow shock where bursts of electrons might have been expected in analogy with the bow shock at the earth. The importance of these null results for determining the necessary and sufficient conditions for particle acceleration is discussed with respect to magnetometer evidence that Venus does not have a magnetosphere.

  15. GPU-accelerated low-latency real-time searches for gravitational waves from compact binary coalescence

    NASA Astrophysics Data System (ADS)

    Liu, Yuan; Du, Zhihui; Chung, Shin Kee; Hooper, Shaun; Blair, David; Wen, Linqing

    2012-12-01

    We present a graphics processing unit (GPU)-accelerated time-domain low-latency algorithm to search for gravitational waves (GWs) from coalescing binaries of compact objects based on the summed parallel infinite impulse response (SPIIR) filtering technique. The aim is to facilitate fast detection of GWs with a minimum delay to allow prompt electromagnetic follow-up observations. To maximize the GPU acceleration, we apply an efficient batched parallel computing model that significantly reduces the number of synchronizations in SPIIR and optimizes the usage of the memory and hardware resource. Our code is tested on the CUDA ‘Fermi’ architecture in a GTX 480 graphics card and its performance is compared with a single core of Intel Core i7 920 (2.67 GHz). A 58-fold speedup is achieved while giving results in close agreement with the CPU implementation. Our result indicates that it is possible to conduct a full search for GWs from compact binary coalescence in real time with only one desktop computer equipped with a Fermi GPU card for the initial LIGO detectors which in the past required more than 100 CPUs.

  16. SHOP: scaffold HOPping by GRID-based similarity searches.

    PubMed

    Bergmann, Rikke; Linusson, Anna; Zamora, Ismael

    2007-05-31

    A new GRID-based method for scaffold hopping (SHOP) is presented. In a fully automatic manner, scaffolds were identified in a database based on three types of 3D-descriptors. SHOP's ability to recover scaffolds was assessed and validated by searching a database spiked with fragments of known ligands of three different protein targets relevant for drug discovery using a rational approach based on statistical experimental design. Five out of eight and seven out of eight thrombin scaffolds and all seven HIV protease scaffolds were recovered within the top 10 and 31 out of 31 neuraminidase scaffolds were in the 31 top-ranked scaffolds. SHOP also identified new scaffolds with substantially different chemotypes from the queries. Docking analysis indicated that the new scaffolds would have similar binding modes to those of the respective query scaffolds observed in X-ray structures. The databases contained scaffolds from published combinatorial libraries to ensure that identified scaffolds could be feasibly synthesized.

  17. Semantic similarity measures in the biomedical domain by leveraging a web search engine.

    PubMed

    Hsieh, Sheau-Ling; Chang, Wen-Yung; Chen, Chi-Huang; Weng, Yung-Ching

    2013-07-01

    Various researches in web related semantic similarity measures have been deployed. However, measuring semantic similarity between two terms remains a challenging task. The traditional ontology-based methodologies have a limitation that both concepts must be resided in the same ontology tree(s). Unfortunately, in practice, the assumption is not always applicable. On the other hand, if the corpus is sufficiently adequate, the corpus-based methodologies can overcome the limitation. Now, the web is a continuous and enormous growth corpus. Therefore, a method of estimating semantic similarity is proposed via exploiting the page counts of two biomedical concepts returned by Google AJAX web search engine. The features are extracted as the co-occurrence patterns of two given terms P and Q, by querying P, Q, as well as P AND Q, and the web search hit counts of the defined lexico-syntactic patterns. These similarity scores of different patterns are evaluated, by adapting support vector machines for classification, to leverage the robustness of semantic similarity measures. Experimental results validating against two datasets: dataset 1 provided by A. Hliaoutakis; dataset 2 provided by T. Pedersen, are presented and discussed. In dataset 1, the proposed approach achieves the best correlation coefficient (0.802) under SNOMED-CT. In dataset 2, the proposed method obtains the best correlation coefficient (SNOMED-CT: 0.705; MeSH: 0.723) with physician scores comparing with measures of other methods. However, the correlation coefficients (SNOMED-CT: 0.496; MeSH: 0.539) with coder scores received opposite outcomes. In conclusion, the semantic similarity findings of the proposed method are close to those of physicians' ratings. Furthermore, the study provides a cornerstone investigation for extracting fully relevant information from digitizing, free-text medical records in the National Taiwan University Hospital database.

  18. Twin Similarities in Holland Types as Shown by Scores on the Self-Directed Search

    ERIC Educational Resources Information Center

    Chauvin, Ida; McDaniel, Janelle R.; Miller, Mark J.; King, James M.; Eddlemon, Ondie L. M.

    2012-01-01

    This study examined the degree of similarity between scores on the Self-Directed Search from one set of identical twins. Predictably, a high congruence score was found. Results from a biographical sheet are discussed as well as implications of the results for career counselors.

  19. Efficient protein structure search using indexing methods

    PubMed Central

    2013-01-01

    Understanding functions of proteins is one of the most important challenges in many studies of biological processes. The function of a protein can be predicted by analyzing the functions of structurally similar proteins, thus finding structurally similar proteins accurately and efficiently from a large set of proteins is crucial. A protein structure can be represented as a vector by 3D-Zernike Descriptor (3DZD) which compactly represents the surface shape of the protein tertiary structure. This simplified representation accelerates the searching process. However, computing the similarity of two protein structures is still computationally expensive, thus it is hard to efficiently process many simultaneous requests of structurally similar protein search. This paper proposes indexing techniques which substantially reduce the search time to find structurally similar proteins. In particular, we first exploit two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. After that, we extend the techniques to further improve the search speed for protein structures. The extended indexing techniques build and utilize an reduced index constructed from the first few attributes of 3DZDs of protein structures. To retrieve top-k similar structures, top-10 × k similar structures are first found using the reduced index, and top-k structures are selected among them. We also modify the indexing techniques to support θ-based nearest neighbor search, which returns data points less than θ to the query point. The results show that both iDistance and iKernel significantly enhance the searching speed. In top-k nearest neighbor search, the searching time is reduced 69.6%, 77%, 77.4% and 87.9%, respectively using iDistance, iKernel, the extended iDistance, and the extended iKernel. In θ-based nearest neighbor serach, the searching time is reduced 80%, 81%, 95.6% and 95.6% using iDistance, iKernel, the extended iDistance, and the extended iKernel, respectively. PMID:23691543

  20. Efficient protein structure search using indexing methods.

    PubMed

    Kim, Sungchul; Sael, Lee; Yu, Hwanjo

    2013-01-01

    Understanding functions of proteins is one of the most important challenges in many studies of biological processes. The function of a protein can be predicted by analyzing the functions of structurally similar proteins, thus finding structurally similar proteins accurately and efficiently from a large set of proteins is crucial. A protein structure can be represented as a vector by 3D-Zernike Descriptor (3DZD) which compactly represents the surface shape of the protein tertiary structure. This simplified representation accelerates the searching process. However, computing the similarity of two protein structures is still computationally expensive, thus it is hard to efficiently process many simultaneous requests of structurally similar protein search. This paper proposes indexing techniques which substantially reduce the search time to find structurally similar proteins. In particular, we first exploit two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. After that, we extend the techniques to further improve the search speed for protein structures. The extended indexing techniques build and utilize an reduced index constructed from the first few attributes of 3DZDs of protein structures. To retrieve top-k similar structures, top-10 × k similar structures are first found using the reduced index, and top-k structures are selected among them. We also modify the indexing techniques to support θ-based nearest neighbor search, which returns data points less than θ to the query point. The results show that both iDistance and iKernel significantly enhance the searching speed. In top-k nearest neighbor search, the searching time is reduced 69.6%, 77%, 77.4% and 87.9%, respectively using iDistance, iKernel, the extended iDistance, and the extended iKernel. In θ-based nearest neighbor serach, the searching time is reduced 80%, 81%, 95.6% and 95.6% using iDistance, iKernel, the extended iDistance, and the extended iKernel, respectively.

  1. Detecting atypical examples of known domain types by sequence similarity searching: the SBASE domain library approach.

    PubMed

    Dhir, Somdutta; Pacurar, Mircea; Franklin, Dino; Gáspári, Zoltán; Kertész-Farkas, Attila; Kocsor, András; Eisenhaber, Frank; Pongor, Sándor

    2010-11-01

    SBASE is a project initiated to detect known domain types and predicting domain architectures using sequence similarity searching (Simon et al., Protein Seq Data Anal, 5: 39-42, 1992, Pongor et al, Nucl. Acids. Res. 21:3111-3115, 1992). The current approach uses a curated collection of domain sequences - the SBASE domain library - and standard similarity search algorithms, followed by postprocessing which is based on a simple statistics of the domain similarity network (http://hydra.icgeb.trieste.it/sbase/). It is especially useful in detecting rare, atypical examples of known domain types which are sometimes missed even by more sophisticated methodologies. This approach does not require multiple alignment or machine learning techniques, and can be a useful complement to other domain detection methodologies. This article gives an overview of the project history as well as of the concepts and principles developed within this the project.

  2. Accelerated damage visualization using binary search with fixed pitch-catch distance laser ultrasonic scanning

    NASA Astrophysics Data System (ADS)

    Park, Byeongjin; Sohn, Hoon

    2017-07-01

    Laser ultrasonic scanning, especially full-field wave propagation imaging, is attractive for damage visualization thanks to its noncontact nature, sensitivity to local damage, and high spatial resolution. However, its practicality is limited because scanning at a high spatial resolution demands a prohibitively long scanning time. Inspired by binary search, an accelerated damage visualization technique is developed to visualize damage with a reduced scanning time. The pitch-catch distance between the excitation point and the sensing point is also fixed during scanning to maintain a high signal-to-noise ratio (SNR) of measured ultrasonic responses. The approximate damage boundary is identified by examining the interactions between ultrasonic waves and damage observed at the scanning points that are sparsely selected by a binary search algorithm. Here, a time-domain laser ultrasonic response is transformed into a spatial ultrasonic domain response using a basis pursuit approach so that the interactions between ultrasonic waves and damage, such as reflections and transmissions, can be better identified in the spatial ultrasonic domain. Then, the area inside the identified damage boundary is visualized as damage. The performance of the proposed damage visualization technique is validated excusing a numerical simulation performed on an aluminum plate with a notch and experiments performed on an aluminum plate with a crack and a wind turbine blade with delamination. The proposed damage visualization technique accelerates the damage visualization process in three aspects: (1) the number of measurements that is necessary for damage visualization is dramatically reduced by a binary search algorithm; (2) the number of averaging that is necessary to achieve a high SNR is reduced by maintaining the wave propagation distance short; and (3) with the proposed technique, the same damage can be identified with a lower spatial resolution than the spatial resolution required by full

  3. Accelerated Cure Project for Multiple Sclerosis

    MedlinePlus

    ... main content Accelerating research toward a cure for multiple sclerosis Toggle navigation Search form Search Connect Volunteer Donate ... is to accelerate efforts toward a cure for multiple sclerosis by rapidly advancing research that determines its causes ...

  4. Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies

    PubMed Central

    Köhler, Sebastian; Schulz, Marcel H.; Krawitz, Peter; Bauer, Sebastian; Dölken, Sandra; Ott, Claus E.; Mundlos, Christine; Horn, Denise; Mundlos, Stefan; Robinson, Peter N.

    2009-01-01

    The differential diagnostic process attempts to identify candidate diseases that best explain a set of clinical features. This process can be complicated by the fact that the features can have varying degrees of specificity, as well as by the presence of features unrelated to the disease itself. Depending on the experience of the physician and the availability of laboratory tests, clinical abnormalities may be described in greater or lesser detail. We have adapted semantic similarity metrics to measure phenotypic similarity between queries and hereditary diseases annotated with the use of the Human Phenotype Ontology (HPO) and have developed a statistical model to assign p values to the resulting similarity scores, which can be used to rank the candidate diseases. We show that our approach outperforms simpler term-matching approaches that do not take the semantic interrelationships between terms into account. The advantage of our approach was greater for queries containing phenotypic noise or imprecise clinical descriptions. The semantic network defined by the HPO can be used to refine the differential diagnosis by suggesting clinical features that, if present, best differentiate among the candidate diagnoses. Thus, semantic similarity searches in ontologies represent a useful way of harnessing the semantic structure of human phenotypic abnormalities to help with the differential diagnosis. We have implemented our methods in a freely available web application for the field of human Mendelian disorders. PMID:19800049

  5. Attrition and success rates of accelerated students in nursing courses: a systematic review.

    PubMed

    Doggrell, Sheila Anne; Schaffer, Sally

    2016-01-01

    There is a comprehensive literature on the academic outcomes (attrition and success) of students in traditional/baccalaureate nursing programs, but much less is known about the academic outcomes of students in accelerated nursing programs. The aim of this systematic review is to report on the attrition and success rates (either internal examination or NCLEX-RN) of accelerated students, compared to traditional students. For the systematic review, the databases (Pubmed, Cinahl and PsychINFO) and Google Scholar were searched using the search terms 'accelerated' or 'accreditation for prior learning', 'fast-track' or 'top up' and 'nursing' with 'attrition' or 'retention' or 'withdrawal' or 'success' from 1994 to January 2016. All relevant articles were included, regardless of quality. The findings of 19 studies of attrition rates and/or success rates for accelerated students are reported. For international accelerated students, there were only three studies, which are heterogeneous, and have major limitations. One of three studies has lower attrition rates, and one has shown higher success rates, than traditional students. In contrast, another study has shown high attrition and low success for international accelerated students. For graduate accelerated students, most of the studies are high quality, and showed that they have rates similar or better than traditional students. Thus, five of six studies have shown similar or lower attrition rates. Four of these studies with graduate accelerated students and an additional seven studies of success rates only, have shown similar or better success rates, than traditional students. There are only three studies of non-university graduate accelerated students, and these had weaknesses, but were consistent in reporting higher attrition rates than traditional students. The paucity and weakness of information available makes it unclear as to the attrition and/or success of international accelerated students in nursing programs. The

  6. Accelerating atomic structure search with cluster regularization

    NASA Astrophysics Data System (ADS)

    Sørensen, K. H.; Jørgensen, M. S.; Bruix, A.; Hammer, B.

    2018-06-01

    We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

  7. Accelerated Bayesian model-selection and parameter-estimation in continuous gravitational-wave searches with pulsar-timing arrays

    NASA Astrophysics Data System (ADS)

    Taylor, Stephen; Ellis, Justin; Gair, Jonathan

    2014-11-01

    We describe several new techniques which accelerate Bayesian searches for continuous gravitational-wave emission from supermassive black-hole binaries using pulsar-timing arrays. These techniques mitigate the problematic increase of search dimensionality with the size of the pulsar array which arises from having to include an extra parameter per pulsar as the array is expanded. This extra parameter corresponds to searching over the phase of the gravitational wave as it propagates past each pulsar so that we can coherently include the pulsar term in our search strategies. Our techniques make the analysis tractable with powerful evidence-evaluation packages like MultiNest. We find good agreement of our techniques with the parameter-estimation and Bayes factor evaluation performed with full signal templates and conclude that these techniques make excellent first-cut tools for detection and characterization of continuous gravitational-wave signals with pulsar-timing arrays. Crucially, at low to moderate signal-to-noise ratios the factor by which the analysis is sped up can be ≳100 , permitting rigorous programs of systematic injection and recovery of signals to establish robust detection criteria within a Bayesian formalism.

  8. On Solar Wind Origin and Acceleration: Measurements from ACE

    NASA Astrophysics Data System (ADS)

    Stakhiv, Mark; Lepri, Susan T.; Landi, Enrico; Tracy, Patrick; Zurbuchen, Thomas H.

    2016-10-01

    The origin and acceleration of the solar wind are still debated. In this paper, we search for signatures of the source region and acceleration mechanism of the solar wind in the plasma properties measured in situ by the Advanced Composition Explorer spacecraft. Using the elemental abundances as a proxy for the source region and the differential velocity and ion temperature ratios as a proxy for the acceleration mechanism, we are able to identify signatures pointing toward possible source regions and acceleration mechanisms. We find that the fast solar wind in the ecliptic plane is the same as that observed from the polar regions and is consistent with wave acceleration and coronal-hole origin. We also find that the slow wind is composed of two components: one similar to the fast solar wind (with slower velocity) and the other likely originating from closed magnetic loops. Both components of the slow solar wind show signatures of wave acceleration. From these findings, we draw a scenario that envisions two types of wind, with different source regions and release mechanisms, but the same wave acceleration mechanism.

  9. Accelerated defect visualization of microelectronic systems using binary search with fixed pitch-catch distance laser ultrasonic scanning

    NASA Astrophysics Data System (ADS)

    Park, Byeongjin; Sohn, Hoon

    2018-04-01

    The practicality of laser ultrasonic scanning is limited because scanning at a high spatial resolution demands a prohibitively long scanning time. Inspired by binary search, an accelerated defect visualization technique is developed to visualize defect with a reduced scanning time. The pitch-catch distance between the excitation point and the sensing point is also fixed during scanning to maintain a high signal-to-noise ratio of measured ultrasonic responses. The approximate defect boundary is identified by examining the interactions between ultrasonic waves and defect observed at the scanning points that are sparsely selected by a binary search algorithm. Here, a time-domain laser ultrasonic response is transformed into a spatial ultrasonic domain response using a basis pursuit approach so that the interactions between ultrasonic waves and defect can be better identified in the spatial ultrasonic domain. Then, the area inside the identified defect boundary is visualized as defect. The performance of the proposed defect visualization technique is validated through an experiment on a semiconductor chip. The proposed defect visualization technique accelerates the defect visualization process in three aspects: (1) The number of measurements that is necessary for defect visualization is dramatically reduced by a binary search algorithm; (2) The number of averaging that is necessary to achieve a high signal-to-noise ratio is reduced by maintaining the wave propagation distance short; and (3) With the proposed technique, defect can be identified with a lower spatial resolution than the spatial resolution required by full-field wave propagation imaging.

  10. How task demands influence scanpath similarity in a sequential number-search task.

    PubMed

    Dewhurst, Richard; Foulsham, Tom; Jarodzka, Halszka; Johansson, Roger; Holmqvist, Kenneth; Nyström, Marcus

    2018-06-07

    More and more researchers are considering the omnibus eye movement sequence-the scanpath-in their studies of visual and cognitive processing (e.g. Hayes, Petrov, & Sederberg, 2011; Madsen, Larson, Loschky, & Rebello, 2012; Ni et al., 2011; von der Malsburg & Vasishth, 2011). However, it remains unclear how recent methods for comparing scanpaths perform in experiments producing variable scanpaths, and whether these methods supplement more traditional analyses of individual oculomotor statistics. We address this problem for MultiMatch (Jarodzka et al., 2010; Dewhurst et al., 2012), evaluating its performance with a visual search-like task in which participants must fixate a series of target numbers in a prescribed order. This task should produce predictable sequences of fixations and thus provide a testing ground for scanpath measures. Task difficulty was manipulated by making the targets more or less visible through changes in font and the presence of distractors or visual noise. These changes in task demands led to slower search and more fixations. Importantly, they also resulted in a reduction in the between-subjects scanpath similarity, demonstrating that participants' gaze patterns became more heterogenous in terms of saccade length and angle, and fixation position. This implies a divergent strategy or random component to eye-movement behaviour which increases as the task becomes more difficult. Interestingly, the duration of fixations along aligned vectors showed the opposite pattern, becoming more similar between observers in 2 of the 3 difficulty manipulations. This provides important information for vision scientists who may wish to use scanpath metrics to quantify variations in gaze across a spectrum of perceptual and cognitive tasks. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. On-the-fly transition search and applications to temperature-accelerated dynamics

    NASA Astrophysics Data System (ADS)

    Shim, Yunsic; Amar, Jacques

    2015-03-01

    Temperature-accelerated dynamics (TAD) is a powerful method to study non-equilibrium processes and has been providing surprising insights for a variety of systems. While serial TAD simulations have been limited by the roughly N3 increase in the computational cost as a function of the number of atoms N in the system, recently we have shown that by carrying out parallel TAD simulations which combine spatial decomposition with our semi-rigorous synchronous sublattice algorithm, significantly improved scaling is possible. However, in this approach the size of activated events is limited by the processor size while the dynamics is not exact. Here we discuss progress in improving the scaling of serial TAD by combining the use of on-the-fly transition searching with our previously developed localized saddle-point method. We demonstrate improved performance for the cases of Ag/Ag(100) annealing and Cu/Cu(100) growth. Supported by NSF DMR-1410840.

  12. ON SOLAR WIND ORIGIN AND ACCELERATION: MEASUREMENTS FROM ACE

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Stakhiv, Mark; Lepri, Susan T.; Landi, Enrico

    The origin and acceleration of the solar wind are still debated. In this paper, we search for signatures of the source region and acceleration mechanism of the solar wind in the plasma properties measured in situ by the Advanced Composition Explorer spacecraft. Using the elemental abundances as a proxy for the source region and the differential velocity and ion temperature ratios as a proxy for the acceleration mechanism, we are able to identify signatures pointing toward possible source regions and acceleration mechanisms. We find that the fast solar wind in the ecliptic plane is the same as that observed frommore » the polar regions and is consistent with wave acceleration and coronal-hole origin. We also find that the slow wind is composed of two components: one similar to the fast solar wind (with slower velocity) and the other likely originating from closed magnetic loops. Both components of the slow solar wind show signatures of wave acceleration. From these findings, we draw a scenario that envisions two types of wind, with different source regions and release mechanisms, but the same wave acceleration mechanism.« less

  13. Accelerating Information Retrieval from Profile Hidden Markov Model Databases.

    PubMed

    Tamimi, Ahmad; Ashhab, Yaqoub; Tamimi, Hashem

    2016-01-01

    Profile Hidden Markov Model (Profile-HMM) is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases. This work presents a heuristic method to accelerate the current profile-HMM homology searching approaches. The method works by cluster-based remodeling of the database to reduce the search space, rather than focusing on the alignment algorithms. Using different clustering techniques, 4284 TIGRFAMs profiles were clustered based on their similarities. A representative for each cluster was assigned. To enhance sensitivity, we proposed an extended step that allows overlapping among clusters. A validation benchmark of 6000 randomly selected protein sequences was used to query the clustered profiles. To evaluate the efficiency of our approach, speed and recall values were measured and compared with the sequential search approach. Using hierarchical, k-means, and connected component clustering techniques followed by the extended overlapping step, we obtained an average reduction in time of 41%, and an average recall of 96%. Our results demonstrate that representation of profile-HMMs using a clustering-based approach can significantly accelerate data retrieval from profile-HMM databases.

  14. Similar head impact acceleration measured using instrumented ear patches in a junior rugby union team during matches in comparison with other sports.

    PubMed

    King, Doug A; Hume, Patria A; Gissane, Conor; Clark, Trevor N

    2016-07-01

    OBJECTIVE Direct impact with the head and the inertial loading of the head have been postulated as major mechanisms of head-related injuries, such as concussion. METHODS This descriptive observational study was conducted to quantify the head impact acceleration characteristics in under-9-year-old junior rugby union players in New Zealand. The impact magnitude, frequency, and location were collected with a wireless head impact sensor that was worn by 14 junior rugby players who participated in 4 matches. RESULTS A total of 721 impacts > 10g were recorded. The median (interquartile range [IQR]) number of impacts per player was 46 (IQR 37-58), resulting in 10 (IQR 4-18) impacts to the head per player per match. The median impact magnitudes recorded were 15g (IQR 12g-21g) for linear acceleration and 2296 rad/sec(2) (IQR 1352-4152 rad/sec(2)) for rotational acceleration. CONCLUSIONS There were 121 impacts (16.8%) above the rotational injury risk limit and 1 (0.1%) impact above the linear injury risk limit. The acceleration magnitude and number of head impacts in junior rugby union players were higher than those previously reported in similar age-group sports participants. The median linear acceleration for the under-9-year-old rugby players were similar to 7- to 8-year-old American football players, but lower than 9- to 12-year-old youth American football players. The median rotational accelerations measured were higher than the median and 95th percentiles in youth, high school, and collegiate American football players.

  15. Simrank: Rapid and sensitive general-purpose k-mer search tool

    PubMed Central

    2011-01-01

    Background Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project http://nihroadmap.nih.gov/hmp. Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Results Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Conclusions Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity. PMID:21524302

  16. Target-similarity search using Plasmodium falciparum proteome identifies approved drugs with anti-malarial activity and their possible targets

    PubMed Central

    Akala, Hoseah M.; Macharia, Rosaline W.; Juma, Dennis W.; Cheruiyot, Agnes C.; Andagalu, Ben; Brown, Mathew L.; El-Shemy, Hany A.; Nyanjom, Steven G.

    2017-01-01

    Malaria causes about half a million deaths annually, with Plasmodium falciparum being responsible for 90% of all the cases. Recent reports on artemisinin resistance in Southeast Asia warrant urgent discovery of novel drugs for the treatment of malaria. However, most bioactive compounds fail to progress to treatments due to safety concerns. Drug repositioning offers an alternative strategy where drugs that have already been approved as safe for other diseases could be used to treat malaria. This study screened approved drugs for antimalarial activity using an in silico chemogenomics approach prior to in vitro verification. All the P. falciparum proteins sequences available in NCBI RefSeq were mined and used to perform a similarity search against DrugBank, TTD and STITCH databases to identify similar putative drug targets. Druggability indices of the potential P. falciparum drug targets were obtained from TDR targets database. Functional amino acid residues of the drug targets were determined using ConSurf server which was used to fine tune the similarity search. This study predicted 133 approved drugs that could target 34 P. falciparum proteins. A literature search done at PubMed and Google Scholar showed 105 out of the 133 drugs to have been previously tested against malaria, with most showing activity. For further validation, drug susceptibility assays using SYBR Green I method were done on a representative group of 10 predicted drugs, eight of which did show activity against P. falciparum 3D7 clone. Seven had IC50 values ranging from 1 μM to 50 μM. This study also suggests drug-target association and hence possible mechanisms of action of drugs that did show antiplasmodial activity. The study results validate the use of proteome-wide target similarity approach in identifying approved drugs with activity against P. falciparum and could be adapted for other pathogens. PMID:29088219

  17. Massive problem reports mining and analysis based parallelism for similar search

    NASA Astrophysics Data System (ADS)

    Zhou, Ya; Hu, Cailin; Xiong, Han; Wei, Xiafei; Li, Ling

    2017-05-01

    Massive problem reports and solutions accumulated over time and continuously collected in XML Spreadsheet (XMLSS) format from enterprises and organizations, which record a series of comprehensive description about problems that can help technicians to trace problems and their solutions. It's a significant and challenging issue to effectively manage and analyze these massive semi-structured data to provide similar problem solutions, decisions of immediate problem and assisting product optimization for users during hardware and software maintenance. For this purpose, we build a data management system to manage, mine and analyze these data search results that can be categorized and organized into several categories for users to quickly find out where their interesting results locate. Experiment results demonstrate that this system is better than traditional centralized management system on the performance and the adaptive capability of heterogeneous data greatly. Besides, because of re-extracting topics, it enables each cluster to be described more precise and reasonable.

  18. One Shot Detection with Laplacian Object and Fast Matrix Cosine Similarity.

    PubMed

    Biswas, Sujoy Kumar; Milanfar, Peyman

    2016-03-01

    One shot, generic object detection involves searching for a single query object in a larger target image. Relevant approaches have benefited from features that typically model the local similarity patterns. In this paper, we combine local similarity (encoded by local descriptors) with a global context (i.e., a graph structure) of pairwise affinities among the local descriptors, embedding the query descriptors into a low dimensional but discriminatory subspace. Unlike principal components that preserve global structure of feature space, we actually seek a linear approximation to the Laplacian eigenmap that permits us a locality preserving embedding of high dimensional region descriptors. Our second contribution is an accelerated but exact computation of matrix cosine similarity as the decision rule for detection, obviating the computationally expensive sliding window search. We leverage the power of Fourier transform combined with integral image to achieve superior runtime efficiency that allows us to test multiple hypotheses (for pose estimation) within a reasonably short time. Our approach to one shot detection is training-free, and experiments on the standard data sets confirm the efficacy of our model. Besides, low computation cost of the proposed (codebook-free) object detector facilitates rather straightforward query detection in large data sets including movie videos.

  19. Similar compounds searching system by using the gene expression microarray database.

    PubMed

    Toyoshiba, Hiroyoshi; Sawada, Hiroshi; Naeshiro, Ichiro; Horinouchi, Akira

    2009-04-10

    Numbers of microarrays have been examined and several public and commercial databases have been developed. However, it is not easy to compare in-house microarray data with those in a database because of insufficient reproducibility due to differences in the experimental conditions. As one of the approach to use these databases, we developed the similar compounds searching system (SCSS) on a toxicogenomics database. The datasets of 55 compounds administered to rats in the Toxicogenomics Project (TGP) database in Japan were used in this study. Using the fold-change ranking method developed by Lamb et al. [Lamb, J., Crawford, E.D., Peck, D., Modell, J.W., Blat, I.C., Wrobel, M.J., Lerner, J., Brunet, J.P., Subramanian, A., Ross, K.N., Reich, M., Hieronymus, H., Wei, G., Armstrong, S.A., Haggarty, S.J., Clemons, P.A., Wei, R., Carr, S.A., Lander, E.S., Golub, T.R., 2006. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313, 1929-1935] and criteria called hit ratio, the system let us compare in-house microarray data and those in the database. In-house generated data for clofibrate, phenobarbital, and a proprietary compound were tested to evaluate the performance of the SCSS method. Phenobarbital and clofibrate, which were included in the TGP database, scored highest by the SCSS method. Other high scoring compounds had effects similar to either phenobarbital (a cytochrome P450s inducer) or clofibrate (a peroxisome proliferator). Some of high scoring compounds identified using the proprietary compound-administered rats have been known to cause similar toxicological changes in different species. Our results suggest that the SCSS method could be used in drug discovery and development. Moreover, this method may be a powerful tool to understand the mechanisms by which biological systems respond to various chemical compounds and may also predict adverse effects of new compounds.

  20. VisSearch: A Collaborative Web Searching Environment

    ERIC Educational Resources Information Center

    Lee, Young-Jin

    2005-01-01

    VisSearch is a collaborative Web searching environment intended for sharing Web search results among people with similar interests, such as college students taking the same course. It facilitates students' Web searches by visualizing various Web searching processes. It also collects the visualized Web search results and applies an association rule…

  1. eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

    PubMed

    Kinoshita, Kengo; Murakami, Yoichi; Nakamura, Haruki

    2007-07-01

    We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).

  2. Accelerating execution of the integrated TIGER series Monte Carlo radiation transport codes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Smith, L.M.; Hochstedler, R.D.

    1997-02-01

    Execution of the integrated TIGER series (ITS) of coupled electron/photon Monte Carlo radiation transport codes has been accelerated by modifying the FORTRAN source code for more efficient computation. Each member code of ITS was benchmarked and profiled with a specific test case that directed the acceleration effort toward the most computationally intensive subroutines. Techniques for accelerating these subroutines included replacing linear search algorithms with binary versions, replacing the pseudo-random number generator, reducing program memory allocation, and proofing the input files for geometrical redundancies. All techniques produced identical or statistically similar results to the original code. Final benchmark timing of themore » accelerated code resulted in speed-up factors of 2.00 for TIGER (the one-dimensional slab geometry code), 1.74 for CYLTRAN (the two-dimensional cylindrical geometry code), and 1.90 for ACCEPT (the arbitrary three-dimensional geometry code).« less

  3. In silico search for functionally similar proteins involved in meiosis and recombination in evolutionarily distant organisms.

    PubMed

    Bogdanov, Yuri F; Dadashev, Sergei Y; Grishaeva, Tatiana M

    2003-01-01

    Evolutionarily distant organisms have not only orthologs, but also nonhomologous proteins that build functionally similar subcellular structures. For instance, this is true with protein components of the synaptonemal complex (SC), a universal ultrastructure that ensures the successful pairing and recombination of homologous chromosomes during meiosis. We aimed at developing a method to search databases for genes that code for such nonhomologous but functionally analogous proteins. Advantage was taken of the ultrastructural parameters of SC and the conformation of SC proteins responsible for these. Proteins involved in SC central space are known to be similar in secondary structure. Using published data, we found a highly significant correlation between the width of the SC central space and the length of rod-shaped central domain of mammalian and yeast intermediate proteins forming transversal filaments in the SC central space. Basing on this, we suggested a method for searching genome databases of distant organisms for genes whose virtual proteins meet the above correlation requirement. Our recent finding of the Drosophila melanogaster CG17604 gene coding for synaptonemal complex transversal filament protein received experimental support from another lab. With the same strategy, we showed that the Arabidopsis thaliana and Caenorhabditis elegans genomes contain unique genes coding for such proteins.

  4. Managing biomedical image metadata for search and retrieval of similar images.

    PubMed

    Korenblum, Daniel; Rubin, Daniel; Napel, Sandy; Rodriguez, Cesar; Beaulieu, Chris

    2011-08-01

    Radiology images are generally disconnected from the metadata describing their contents, such as imaging observations ("semantic" metadata), which are usually described in text reports that are not directly linked to the images. We developed a system, the Biomedical Image Metadata Manager (BIMM) to (1) address the problem of managing biomedical image metadata and (2) facilitate the retrieval of similar images using semantic feature metadata. Our approach allows radiologists, researchers, and students to take advantage of the vast and growing repositories of medical image data by explicitly linking images to their associated metadata in a relational database that is globally accessible through a Web application. BIMM receives input in the form of standard-based metadata files using Web service and parses and stores the metadata in a relational database allowing efficient data query and maintenance capabilities. Upon querying BIMM for images, 2D regions of interest (ROIs) stored as metadata are automatically rendered onto preview images included in search results. The system's "match observations" function retrieves images with similar ROIs based on specific semantic features describing imaging observation characteristics (IOCs). We demonstrate that the system, using IOCs alone, can accurately retrieve images with diagnoses matching the query images, and we evaluate its performance on a set of annotated liver lesion images. BIMM has several potential applications, e.g., computer-aided detection and diagnosis, content-based image retrieval, automating medical analysis protocols, and gathering population statistics like disease prevalences. The system provides a framework for decision support systems, potentially improving their diagnostic accuracy and selection of appropriate therapies.

  5. Semantic search during divergent thinking.

    PubMed

    Hass, Richard W

    2017-09-01

    Divergent thinking, as a method of examining creative cognition, has not been adequately analyzed in the context of modern cognitive theories. This article casts divergent thinking responding in the context of theories of memory search. First, it was argued that divergent thinking tasks are similar to semantic fluency tasks, but are more constrained, and less well structured. Next, response time distributions from 54 participants were analyzed for temporal and semantic clustering. Participants responded to two prompts from the alternative uses test: uses for a brick and uses for a bottle, for two minutes each. Participants' cumulative response curves were negatively accelerating, in line with theories of search of associative memory. However, results of analyses of semantic and temporal clustering suggested that clustering is less evident in alternative uses responding compared to semantic fluency tasks. This suggests either that divergent thinking responding does not involve an exhaustive search through a clustered memory trace, but rather that the process is more exploratory, yielding fewer overall responses that tend to drift away from close associates of the divergent thinking prompt. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Beyond the search surface: visual search and attentional engagement.

    PubMed

    Duncan, J; Humphreys, G

    1992-05-01

    Treisman (1991) described a series of visual search studies testing feature integration theory against an alternative (Duncan & Humphreys, 1989) in which feature and conjunction search are basically similar. Here the latter account is noted to have 2 distinct levels: (a) a summary of search findings in terms of stimulus similarities, and (b) a theory of how visual attention is brought to bear on relevant objects. Working at the 1st level, Treisman found that even when similarities were calibrated and controlled, conjunction search was much harder than feature search. The theory, however, can only really be tested at the 2nd level, because the 1st is an approximation. An account of the findings is developed at the 2nd level, based on the 2 processes of input-template matching and spreading suppression. New data show that, when both of these factors are controlled, feature and conjunction search are equally difficult. Possibilities for unification of the alternative views are considered.

  7. The baryonic self similarity of dark matter

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Alard, C., E-mail: alard@iap.fr

    2014-06-20

    The cosmological simulations indicates that dark matter halos have specific self-similar properties. However, the halo similarity is affected by the baryonic feedback. By using momentum-driven winds as a model to represent the baryon feedback, an equilibrium condition is derived which directly implies the emergence of a new type of similarity. The new self-similar solution has constant acceleration at a reference radius for both dark matter and baryons. This model receives strong support from the observations of galaxies. The new self-similar properties imply that the total acceleration at larger distances is scale-free, the transition between the dark matter and baryons dominatedmore » regime occurs at a constant acceleration, and the maximum amplitude of the velocity curve at larger distances is proportional to M {sup 1/4}. These results demonstrate that this self-similar model is consistent with the basics of modified Newtonian dynamics (MOND) phenomenology. In agreement with the observations, the coincidence between the self-similar model and MOND breaks at the scale of clusters of galaxies. Some numerical experiments show that the behavior of the density near the origin is closely approximated by a Einasto profile.« less

  8. Combination of Pharmacophore Matching, 2D Similarity Search, and In Vitro Biological Assays in the Selection of Potential 5-HT6 Antagonists from Large Commercial Repositories.

    PubMed

    Dobi, Krisztina; Flachner, Beáta; Pukáncsik, Mária; Máthé, Enikő; Bognár, Melinda; Szaszkó, Mária; Magyar, Csaba; Hajdú, István; Lőrincz, Zsolt; Simon, István; Fülöp, Ferenc; Cseh, Sándor; Dormán, György

    2015-10-01

    Rapid in silico selection of target-focused libraries from commercial repositories is an attractive and cost-effective approach. If structures of active compounds are available, rapid 2D similarity search can be performed on multimillion compound databases, but the generated library requires further focusing. We report here a combination of the 2D approach with pharmacophore matching which was used for selecting 5-HT6 antagonists. In the first screening round, 12 compounds showed >85% antagonist efficacy of the 91 screened. For the second-round (hit validation) screening phase, pharmacophore models were built, applied, and compared with the routine 2D similarity search. Three pharmacophore models were created based on the structure of the reference compounds and the first-round hit compounds. The pharmacophore search resulted in a high hit rate (40%) and led to novel chemotypes, while 2D similarity search had slightly better hit rate (51%), but lacking the novelty. To demonstrate the power of the virtual screening cascade, ligand efficiency indices were also calculated and their steady improvement was confirmed. © 2015 John Wiley & Sons A/S.

  9. Linear Accelerator (LINAC)

    MedlinePlus

    ... equipment? How is safety ensured? What is this equipment used for? A linear accelerator (LINAC) is the ... Therapy (SBRT) . top of page How does the equipment work? The linear accelerator uses microwave technology (similar ...

  10. Homology search with binary and trinary scoring matrices.

    PubMed

    Smith, Scott F

    2006-01-01

    Protein homology search can be accelerated with the use of bit-parallel algorithms in conjunction with constraints on the values contained in the scoring matrices. Trinary scoring matrices (containing only the values -1, 0, and 1) allow for significant acceleration without significant reduction in the receiver operating characteristic (ROC) score of a Smith-Waterman search. Binary scoring matrices (containing the values 0 and 1) result in some reduction in ROC score, but result in even more acceleration. Binary scoring matrices and five-bit saturating scores can be used for fast prefilters to the Smith-Waterman algorithm.

  11. Accelerating object detection via a visual-feature-directed search cascade: algorithm and field programmable gate array implementation

    NASA Astrophysics Data System (ADS)

    Kyrkou, Christos; Theocharides, Theocharis

    2016-07-01

    Object detection is a major step in several computer vision applications and a requirement for most smart camera systems. Recent advances in hardware acceleration for real-time object detection feature extensive use of reconfigurable hardware [field programmable gate arrays (FPGAs)], and relevant research has produced quite fascinating results, in both the accuracy of the detection algorithms as well as the performance in terms of frames per second (fps) for use in embedded smart camera systems. Detecting objects in images, however, is a daunting task and often involves hardware-inefficient steps, both in terms of the datapath design and in terms of input/output and memory access patterns. We present how a visual-feature-directed search cascade composed of motion detection, depth computation, and edge detection, can have a significant impact in reducing the data that needs to be examined by the classification engine for the presence of an object of interest. Experimental results on a Spartan 6 FPGA platform for face detection indicate data search reduction of up to 95%, which results in the system being able to process up to 50 1024×768 pixels images per second with a significantly reduced number of false positives.

  12. The High Time Resolution Universe Pulsar Survey - XII. Galactic plane acceleration search and the discovery of 60 pulsars

    NASA Astrophysics Data System (ADS)

    Ng, C.; Champion, D. J.; Bailes, M.; Barr, E. D.; Bates, S. D.; Bhat, N. D. R.; Burgay, M.; Burke-Spolaor, S.; Flynn, C. M. L.; Jameson, A.; Johnston, S.; Keith, M. J.; Kramer, M.; Levin, L.; Petroff, E.; Possenti, A.; Stappers, B. W.; van Straten, W.; Tiburzi, C.; Eatough, R. P.; Lyne, A. G.

    2015-07-01

    We present initial results from the low-latitude Galactic plane region of the High Time Resolution Universe pulsar survey conducted at the Parkes 64-m radio telescope. We discuss the computational challenges arising from the processing of the terabyte-sized survey data. Two new radio interference mitigation techniques are introduced, as well as a partially coherent segmented acceleration search algorithm which aims to increase our chances of discovering highly relativistic short-orbit binary systems, covering a parameter space including potential pulsar-black hole binaries. We show that under a constant acceleration approximation, a ratio of data length over orbital period of ≈0.1 results in the highest effectiveness for this search algorithm. From the 50 per cent of data processed thus far, we have redetected 435 previously known pulsars and discovered a further 60 pulsars, two of which are fast-spinning pulsars with periods less than 30 ms. PSR J1101-6424 is a millisecond pulsar whose heavy white dwarf (WD) companion and short spin period of 5.1 ms indicate a rare example of full-recycling via Case A Roche lobe overflow. PSR J1757-27 appears to be an isolated recycled pulsar with a relatively long spin period of 17 ms. In addition, PSR J1244-6359 is a mildly recycled binary system with a heavy WD companion, PSR J1755-25 has a significant orbital eccentricity of 0.09 and PSR J1759-24 is likely to be a long-orbit eclipsing binary with orbital period of the order of tens of years. Comparison of our newly discovered pulsar sample to the known population suggests that they belong to an older population. Furthermore, we demonstrate that our current pulsar detection yield is as expected from population synthesis.

  13. Finding Protein and Nucleotide Similarities with FASTA

    PubMed Central

    Pearson, William R.

    2016-01-01

    The FASTA programs provide a comprehensive set of rapid similarity searching tools ( fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local and global similarity searches ( ssearch36, ggsearch36) and for searching with short peptides and oligonucleotides ( fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity (Unit 3.5). The FASTA programs can produce “BLAST-like” alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases (Unit 9.4). The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons. PMID:27010337

  14. Finding Protein and Nucleotide Similarities with FASTA.

    PubMed

    Pearson, William R

    2016-03-24

    The FASTA programs provide a comprehensive set of rapid similarity searching tools (fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local, and global similarity searches (ssearch36, ggsearch36), and for searching with short peptides and oligonucleotides (fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity. The FASTA programs can produce "BLAST-like" alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases. The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons. Copyright © 2016 John Wiley & Sons, Inc.

  15. Intermittent search strategies

    NASA Astrophysics Data System (ADS)

    Bénichou, O.; Loverdo, C.; Moreau, M.; Voituriez, R.

    2011-01-01

    This review examines intermittent target search strategies, which combine phases of slow motion, allowing the searcher to detect the target, and phases of fast motion during which targets cannot be detected. It is first shown that intermittent search strategies are actually widely observed at various scales. At the macroscopic scale, this is, for example, the case of animals looking for food; at the microscopic scale, intermittent transport patterns are involved in a reaction pathway of DNA-binding proteins as well as in intracellular transport. Second, generic stochastic models are introduced, which show that intermittent strategies are efficient strategies that enable the minimization of search time. This suggests that the intrinsic efficiency of intermittent search strategies could justify their frequent observation in nature. Last, beyond these modeling aspects, it is proposed that intermittent strategies could also be used in a broader context to design and accelerate search processes.

  16. Earthquake Fingerprints: Representing Earthquake Waveforms for Similarity-Based Detection

    NASA Astrophysics Data System (ADS)

    Bergen, K.; Beroza, G. C.

    2016-12-01

    New earthquake detection methods, such as Fingerprint and Similarity Thresholding (FAST), use fast approximate similarity search to identify similar waveforms in long-duration data without templates (Yoon et al. 2015). These methods have two key components: fingerprint extraction and an efficient search algorithm. Fingerprint extraction converts waveforms into fingerprints, compact signatures that represent short-duration waveforms for identification and search. Earthquakes are detected using an efficient indexing and search scheme, such as locality-sensitive hashing, that identifies similar waveforms in a fingerprint database. The quality of the search results, and thus the earthquake detection results, is strongly dependent on the fingerprinting scheme. Fingerprint extraction should map similar earthquake waveforms to similar waveform fingerprints to ensure a high detection rate, even under additive noise and small distortions. Additionally, fingerprints corresponding to noise intervals should have mutually dissimilar fingerprints to minimize false detections. In this work, we compare the performance of multiple fingerprint extraction approaches for the earthquake waveform similarity search problem. We apply existing audio fingerprinting (used in content-based audio identification systems) and time series indexing techniques and present modified versions that are specifically adapted for seismic data. We also explore data-driven fingerprinting approaches that can take advantage of labeled or unlabeled waveform data. For each fingerprinting approach we measure its ability to identify similar waveforms in a low signal-to-noise setting, and quantify the trade-off between true and false detection rates in the presence of persistent noise sources. We compare the performance using known event waveforms from eight independent stations in the Northern California Seismic Network.

  17. Search for Light Dark Matter Produced in a Proton Beam Dump

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Thornton, Remington Tyler

    Cosmological observations indicate that our universe contains dark matter (DM), yet we have no measurements of its microscopic properties. Whereas the gravitational interaction of DM is well understood, its interaction with the Standard Model is not. Direct detection experiments, the current standard, search for a nuclear recoil interaction and have a low-mass sensitivity edge of order 1 GeV. A path to detect DM with mass below 1 GeV is the use of accelerators producing boosted low-mass DM. Using neutrino detectors to search for low-mass DM is logical due to the similarity of the DM and neutrino signatures in the detector.more » The MiniBooNE experiment, located at Fermilab on the Booster Neutrino Beamline, has produced the first proton beam-dump light DM search results. Using dark matter scattering from nucleons 90% confidence limits were set over a large parameter space and, to allow tests of other theories, a model independent DM rate was extracted.« less

  18. Search for light dark matter produced in a proton beam dump

    NASA Astrophysics Data System (ADS)

    Thornton, Remington Tyler

    Cosmological observations indicate that our universe contains dark matter (DM), yet we have no measurements of its microscopic properties. Whereas the gravitational interaction of DM is well understood, its interaction with the Standard Model is not. Direct detection experiments, the current standard, search for a nuclear recoil interaction and have a low-mass sensitivity edge of order 1 GeV. A path to detect DM with mass below 1 GeV is the use of accelerators producing boosted low-mass DM. Using neutrino detectors to search for low-mass DM is logical due to the similarity of the DM and neutrino signatures in the detector. The MiniBooNE experiment, located at Fermilab on the Booster Neutrino Beamline, has produced the first proton beam-dump light DM search results. Using dark matter scattering from nucleons 90% confidence limits were set over a large parameter space and, to allow tests of other theories, a model independent DM rate was extracted.

  19. AIR-MRF: Accelerated iterative reconstruction for magnetic resonance fingerprinting.

    PubMed

    Cline, Christopher C; Chen, Xiao; Mailhe, Boris; Wang, Qiu; Pfeuffer, Josef; Nittka, Mathias; Griswold, Mark A; Speier, Peter; Nadar, Mariappan S

    2017-09-01

    Existing approaches for reconstruction of multiparametric maps with magnetic resonance fingerprinting (MRF) are currently limited by their estimation accuracy and reconstruction time. We aimed to address these issues with a novel combination of iterative reconstruction, fingerprint compression, additional regularization, and accelerated dictionary search methods. The pipeline described here, accelerated iterative reconstruction for magnetic resonance fingerprinting (AIR-MRF), was evaluated with simulations as well as phantom and in vivo scans. We found that the AIR-MRF pipeline provided reduced parameter estimation errors compared to non-iterative and other iterative methods, particularly at shorter sequence lengths. Accelerated dictionary search methods incorporated into the iterative pipeline reduced the reconstruction time at little cost of quality. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Pharmacological Interventions for Acceleration of the Onset Time of Rocuronium: A Meta-Analysis

    PubMed Central

    Dong, Jing; Gao, Lingqi; Lu, Wenqing; Xu, Zifeng; Zheng, Jijian

    2014-01-01

    Background Rocuronium is an acceptable alternative when succinylcholine is contraindicated for facilitating the endotracheal intubation. However, the onset time of rocuronium for good intubation condition is still slower than that condition of succinylcholine. This study systematically investigated the most efficacious pharmacological interventions for accelerating the onset time of rocuronium. Methods Medline, Embase, Cochrane Library databases, www.clinicaltrials.gov, and hand searching from the reference lists of identified papers were searched for randomized controlled trials comparing drug interventions with placebo or another drug to shorten the onset time of rocuronium. Statistical analyses were performed using RevMan5.2 and ADDIS 1.16.5 softwares. Mean differences (MDs) with their 95% confidence intervals (95% CIs) were used to analyze the effects of drug interventions on the onset time of rocuronium. Results 43 randomized controlled trials with 2,465 patients were analyzed. The average onset time of rocuronium was 102.4±24.9 s. Priming with rocuronium [Mean difference (MD) −21.0 s, 95% confidence interval (95% CI) (−27.6 to −14.3 s)], pretreatment with ephedrine [−22.3 s (−29.1 to −15.5 s)], pretreatment with magnesium sulphate [−28.2 s (−50.9 to −5.6 s)] were all effective in reducing the onset time of rocuronium. Statistical testing of indirect comparisons showed that rocuronium priming, pretreatment with ephedrine, and pretreatment with magnesium sulphate had the similar efficacy. Conclusion Rocuronium priming, pretreatment with ephedrine, and pretreatment with magnesium sulphate were all effective in accelerating the onset time of rocuronium, and furthermore their efficacies were similar. Considering the convenience and efficacy, priming with rocuronium is recommended for accelerating the onset time of rocuronium. However, more strict clinical trials are still needed to reach a more solid conclusion due to the large heterogeneities

  1. Pharmacological interventions for acceleration of the onset time of rocuronium: a meta-analysis.

    PubMed

    Dong, Jing; Gao, Lingqi; Lu, Wenqing; Xu, Zifeng; Zheng, Jijian

    2014-01-01

    Rocuronium is an acceptable alternative when succinylcholine is contraindicated for facilitating the endotracheal intubation. However, the onset time of rocuronium for good intubation condition is still slower than that condition of succinylcholine. This study systematically investigated the most efficacious pharmacological interventions for accelerating the onset time of rocuronium. Medline, Embase, Cochrane Library databases, www.clinicaltrials.gov, and hand searching from the reference lists of identified papers were searched for randomized controlled trials comparing drug interventions with placebo or another drug to shorten the onset time of rocuronium. Statistical analyses were performed using RevMan5.2 and ADDIS 1.16.5 softwares. Mean differences (MDs) with their 95% confidence intervals (95% CIs) were used to analyze the effects of drug interventions on the onset time of rocuronium. 43 randomized controlled trials with 2,465 patients were analyzed. The average onset time of rocuronium was 102.4±24.9 s. Priming with rocuronium [Mean difference (MD) -21.0 s, 95% confidence interval (95% CI) (-27.6 to -14.3 s)], pretreatment with ephedrine [-22.3 s (-29.1 to -15.5 s)], pretreatment with magnesium sulphate [-28.2 s (-50.9 to -5.6 s)] were all effective in reducing the onset time of rocuronium. Statistical testing of indirect comparisons showed that rocuronium priming, pretreatment with ephedrine, and pretreatment with magnesium sulphate had the similar efficacy. Rocuronium priming, pretreatment with ephedrine, and pretreatment with magnesium sulphate were all effective in accelerating the onset time of rocuronium, and furthermore their efficacies were similar. Considering the convenience and efficacy, priming with rocuronium is recommended for accelerating the onset time of rocuronium. However, more strict clinical trials are still needed to reach a more solid conclusion due to the large heterogeneities exist among different studies.

  2. World Wide Web-based system for the calculation of substituent parameters and substituent similarity searches.

    PubMed

    Ertl, P

    1998-02-01

    Easy to use, interactive, and platform-independent WWW-based tools are ideal for development of chemical applications. By using the newly emerging Web technologies such as Java applets and sophisticated scripting, it is possible to deliver powerful molecular processing capabilities directly to the desk of synthetic organic chemists. In Novartis Crop Protection in Basel, a Web-based molecular modelling system has been in use since 1995. In this article two new modules of this system are presented: a program for interactive calculation of important hydrophobic, electronic, and steric properties of organic substituents, and a module for substituent similarity searches enabling the identification of bioisosteric functional groups. Various possible applications of calculated substituent parameters are also discussed, including automatic design of molecules with the desired properties and creation of targeted virtual combinatorial libraries.

  3. Rayleigh-Taylor mixing with time-dependent acceleration

    NASA Astrophysics Data System (ADS)

    Abarzhi, Snezhana

    2016-10-01

    We extend the momentum model to describe Rayleigh-Taylor (RT) mixing driven by a time-dependent acceleration. The acceleration is a power-law function of time, similarly to astrophysical and plasma fusion applications. In RT flow the dynamics of a fluid parcel is driven by a balance per unit mass of the rates of momentum gain and loss. We find analytical solutions in the cases of balanced and imbalanced gains and losses, and identify their dependence on the acceleration exponent. The existence is shown of two typical regimes of self-similar RT mixing-acceleration-driven Rayleigh-Taylor-type and dissipation-driven Richtymer-Meshkov-type with the latter being in general non-universal. Possible scenarios are proposed for transitions from the balanced dynamics to the imbalanced self-similar dynamics. Scaling and correlations properties of RT mixing are studied on the basis of dimensional analysis. Departures are outlined of RT dynamics with time-dependent acceleration from canonical cases of homogeneous turbulence as well as blast waves with first and second kind self-similarity. The work is supported by the US National Science Foundation.

  4. Searching for Single Pulses Using Heimdall

    NASA Astrophysics Data System (ADS)

    Walsh, Gregory; Lynch, Ryan

    2018-01-01

    In radio pulsar surveys, the interstellar medium causes a frequency dependent dispersive delay of a pulsed signal across the observing band. If not corrected, this delay substantially lowers S/N and makes most pulses undetectable. The delay is proportional to an unknown dispersion measure (DM), which must be searched over with many trial values. A number of new, GPU-accelerated codes are now available to optimize this dedispersion task, and to search for transient pulsed radio emission. We report on the use of Heimdall, one such GPU-accelerated tree dedispersion utility, to search for transient radio sources in a Green Bank Telescope survey of the Cygnus Region and North Galactic Plane. The survey is carried out at central frequency of 820 MHz with a goal of finding Fast Radio Bursts, Rotating Radio Transients, young pulsars, and millisecond pulsars. We describe the the survey, data processing pipeline, and follow-up of candidate sources.

  5. Domain similarity based orthology detection.

    PubMed

    Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

    2015-05-13

    Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

  6. Overview of Accelerator Applications for Security and Defense

    DOE PAGES

    Antolak, Arlyn J.

    2015-01-01

    Particle accelerators play a key role in a broad set of defense and security applications including war-fighter and asset protection, cargo inspection, nonproliferation, materials characterization and stockpile stewardship. Accelerators can replace the high activity radioactive sources that pose a security threat for developing a radiological dispersal device and be used to produce isotopes for medical, industrial, and re-search purposes. Lastly, we present an overview of current and emerging accelerator technologies relevant to addressing the needs of defense and security.

  7. FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules

    NASA Astrophysics Data System (ADS)

    Pitman, Michael C.; Huber, Wolfgang K.; Horn, Hans; Krämer, Andreas; Rice, Julia E.; Swope, William C.

    2001-07-01

    A three-dimensional field-based similarity search and alignment method for flexible molecules is introduced. The conformational space of a flexible molecule is represented in terms of fragments and torsional angles of allowed conformations. A user-definable property field is used to compute features of fragment pairs. Features are generalizations of CoMMA descriptors (Silverman, B.D. and Platt, D.E., J. Med. Chem., 39 (1996) 2129.) that characterize local regions of the property field by its local moments. The features are invariant under coordinate system transformations. Features taken from a query molecule are used to form alignments with fragment pairs in the database. An assembly algorithm is then used to merge the fragment pairs into full structures, aligned to the query. Key to the method is the use of a context adaptive descriptor scaling procedure as the basis for similarity. This allows the user to tune the weights of the various feature components based on examples relevant to the particular context under investigation. The property fields may range from simple, phenomenological fields, to fields derived from quantum mechanical calculations. We apply the method to the dihydrofolate/methotrexate benchmark system, and show that when one injects relevant contextual information into the descriptor scaling procedure, better results are obtained more efficiently. We also show how the method works and include computer times for a query from a database that represents approximately 23 million conformers of seventeen flexible molecules.

  8. Search predicts and changes patience in intertemporal choice

    PubMed Central

    Johnson, Eric J.

    2017-01-01

    Intertemporal choice impacts many important outcomes, such as decisions about health, education, wealth, and the environment. However, the psychological processes underlying decisions involving outcomes at different points in time remain unclear, limiting opportunities to intervene and improve people’s patience. This research examines information-search strategies used during intertemporal choice and their impact on decisions. In experiment 1, we demonstrate that search strategies vary substantially across individuals. We subsequently identify two distinct search strategies across individuals. Comparative searchers, who compare features across options, discount future options less and are more susceptible to acceleration versus delay framing than integrative searchers, who integrate the features of an option. Experiment 2 manipulates search using an unobtrusive method to establish a causal relationship between strategy and choice, randomly assigning participants to conditions promoting either comparative or integrative search. Again, comparative search promotes greater patience than integrative search. Additionally, when participants adopt a comparative search strategy, they also exhibit greater effects of acceleration versus delay framing. Although most participants reported that the manipulation did not change their behavior, promoting comparative search decreased discounting of future rewards substantially and speeded patient choices. These findings highlight the central role that heterogeneity in psychological processes plays in shaping intertemporal choice. Importantly, these results indicate that theories that ignore variability in search strategies may be inadvertently aggregating over different subpopulations that use very different processes. The findings also inform interventions in choice architecture to increase patience and improve consumer welfare. PMID:29078303

  9. The application of similar image retrieval in electronic commerce.

    PubMed

    Hu, YuPing; Yin, Hua; Han, Dezhi; Yu, Fei

    2014-01-01

    Traditional online shopping platform (OSP), which searches product information by keywords, faces three problems: indirect search mode, large search space, and inaccuracy in search results. For solving these problems, we discuss and research the application of similar image retrieval in electronic commerce. Aiming at improving the network customers' experience and providing merchants with the accuracy of advertising, we design a reasonable and extensive electronic commerce application system, which includes three subsystems: image search display subsystem, image search subsystem, and product information collecting subsystem. This system can provide seamless connection between information platform and OSP, on which consumers can automatically and directly search similar images according to the pictures from information platform. At the same time, it can be used to provide accuracy of internet marketing for enterprises. The experiment shows the efficiency of constructing the system.

  10. The Application of Similar Image Retrieval in Electronic Commerce

    PubMed Central

    Hu, YuPing; Yin, Hua; Han, Dezhi; Yu, Fei

    2014-01-01

    Traditional online shopping platform (OSP), which searches product information by keywords, faces three problems: indirect search mode, large search space, and inaccuracy in search results. For solving these problems, we discuss and research the application of similar image retrieval in electronic commerce. Aiming at improving the network customers' experience and providing merchants with the accuracy of advertising, we design a reasonable and extensive electronic commerce application system, which includes three subsystems: image search display subsystem, image search subsystem, and product information collecting subsystem. This system can provide seamless connection between information platform and OSP, on which consumers can automatically and directly search similar images according to the pictures from information platform. At the same time, it can be used to provide accuracy of internet marketing for enterprises. The experiment shows the efficiency of constructing the system. PMID:24883411

  11. Application of 3D Zernike descriptors to shape-based ligand similarity searching.

    PubMed

    Venkatraman, Vishwesh; Chakravarthy, Padmasini Ramji; Kihara, Daisuke

    2009-12-17

    The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability. The 3DZD has unique ability for fast comparison of three-dimensional shape of compounds. Examples analyzed illustrate the advantages and the room for improvements for the 3DZD.

  12. Rayleigh-Taylor mixing with space-dependent acceleration

    NASA Astrophysics Data System (ADS)

    Abarzhi, Snezhana

    2016-11-01

    We extend the momentum model to describe Rayleigh-Taylor (RT) mixing driven by a space-dependent acceleration. The acceleration is a power-law function of space coordinate, similarly to astrophysical and plasma fusion applications. In RT flow the dynamics of a fluid parcel is driven by a balance per unit mass of the rates of momentum gain and loss. We find analytical solutions in the cases of balanced and imbalanced gains and losses, and identify their dependence on the acceleration exponent. The existence is shown of two typical sub-regimes of self-similar RT mixing - the acceleration-driven Rayleigh-Taylor-type mixing and dissipation-driven Richtymer-Meshkov-type mixing with the latter being in general non-universal. Possible scenarios are proposed for transitions from the balanced dynamics to the imbalanced self-similar dynamics. Scaling and correlations properties of RT mixing are studied on the basis of dimensional analysis. Departures are outlined of RT dynamics with space-dependent acceleration from canonical cases of homogeneous turbulence as well as blast waves with first and second kind self-similarity. The work is supported by the US National Science Foundation.

  13. Document similarity measures and document browsing

    NASA Astrophysics Data System (ADS)

    Ahmadullin, Ildus; Fan, Jian; Damera-Venkata, Niranjan; Lim, Suk Hwan; Lin, Qian; Liu, Jerry; Liu, Sam; O'Brien-Strain, Eamonn; Allebach, Jan

    2011-03-01

    Managing large document databases is an important task today. Being able to automatically com- pare document layouts and classify and search documents with respect to their visual appearance proves to be desirable in many applications. We measure single page documents' similarity with respect to distance functions between three document components: background, text, and saliency. Each document component is represented as a Gaussian mixture distribution; and distances between dierent documents' components are calculated as probabilistic similarities between corresponding distributions. The similarity measure between documents is represented as a weighted sum of the components' distances. Using this document similarity measure, we propose a browsing mechanism operating on a document dataset. For these purposes, we use a hierarchical browsing environment which we call the document similarity pyramid. It allows the user to browse a large document dataset and to search for documents in the dataset that are similar to the query. The user can browse the dataset on dierent levels of the pyramid, and zoom into the documents that are of interest.

  14. Perception of linear acceleration in weightlessness

    NASA Technical Reports Server (NTRS)

    Arrott, A. P.; Young, L. R.

    1987-01-01

    Eye movements and subjective detection of acceleration were measured on human experimental subjects during vestibular sled acceleration during the D1 Spacelab Mission. Methods and results are reported on the time to detection of small acceleration steps, the threshold for detection of linear acceleration, perceived motion path, and CLOAT. A consistently shorter time to detection of small acceleration steps is found. Subjective reports of perceived motion during sinusoidal oscillation in weightlessness were qualitatively similar to reports on earth.

  15. Motivation and short-term memory in visual search: Attention's accelerator revisited.

    PubMed

    Schneider, Daniel; Bonmassar, Claudia; Hickey, Clayton

    2018-05-01

    A cue indicating the possibility of cash reward will cause participants to perform memory-based visual search more efficiently. A recent study has suggested that this performance benefit might reflect the use of multiple memory systems: when needed, participants may maintain the to-be-remembered object in both long-term and short-term visual memory, with this redundancy benefitting target identification during search (Reinhart, McClenahan & Woodman, 2016). Here we test this compelling hypothesis. We had participants complete a memory-based visual search task involving a reward cue that either preceded presentation of the to-be-remembered target (pre-cue) or followed it (retro-cue). Following earlier work, we tracked memory representation using two components of the event-related potential (ERP): the contralateral delay activity (CDA), reflecting short-term visual memory, and the anterior P170, reflecting long-term storage. We additionally tracked attentional preparation and deployment in the contingent negative variation (CNV) and N2pc, respectively. Results show that only the reward pre-cue impacted our ERP indices of memory. However, both types of cue elicited a robust CNV, reflecting an influence on task preparation, both had equivalent impact on deployment of attention to the target, as indexed in the N2pc, and both had equivalent impact on visual search behavior. Reward prospect thus has an influence on memory-guided visual search, but this does not appear to be necessarily mediated by a change in the visual memory representations indexed by CDA. Our results demonstrate that the impact of motivation on search is not a simple product of improved memory for target templates. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Does linear separability really matter? Complex visual search is explained by simple search

    PubMed Central

    Vighneshvel, T.; Arun, S. P.

    2013-01-01

    Visual search in real life involves complex displays with a target among multiple types of distracters, but in the laboratory, it is often tested using simple displays with identical distracters. Can complex search be understood in terms of simple searches? This link may not be straightforward if complex search has emergent properties. One such property is linear separability, whereby search is hard when a target cannot be separated from its distracters using a single linear boundary. However, evidence in favor of linear separability is based on testing stimulus configurations in an external parametric space that need not be related to their true perceptual representation. We therefore set out to assess whether linear separability influences complex search at all. Our null hypothesis was that complex search performance depends only on classical factors such as target-distracter similarity and distracter homogeneity, which we measured using simple searches. Across three experiments involving a variety of artificial and natural objects, differences between linearly separable and nonseparable searches were explained using target-distracter similarity and distracter heterogeneity. Further, simple searches accurately predicted complex search regardless of linear separability (r = 0.91). Our results show that complex search is explained by simple search, refuting the widely held belief that linear separability influences visual search. PMID:24029822

  17. Search predicts and changes patience in intertemporal choice.

    PubMed

    Reeck, Crystal; Wall, Daniel; Johnson, Eric J

    2017-11-07

    Intertemporal choice impacts many important outcomes, such as decisions about health, education, wealth, and the environment. However, the psychological processes underlying decisions involving outcomes at different points in time remain unclear, limiting opportunities to intervene and improve people's patience. This research examines information-search strategies used during intertemporal choice and their impact on decisions. In experiment 1, we demonstrate that search strategies vary substantially across individuals. We subsequently identify two distinct search strategies across individuals. Comparative searchers, who compare features across options, discount future options less and are more susceptible to acceleration versus delay framing than integrative searchers, who integrate the features of an option. Experiment 2 manipulates search using an unobtrusive method to establish a causal relationship between strategy and choice, randomly assigning participants to conditions promoting either comparative or integrative search. Again, comparative search promotes greater patience than integrative search. Additionally, when participants adopt a comparative search strategy, they also exhibit greater effects of acceleration versus delay framing. Although most participants reported that the manipulation did not change their behavior, promoting comparative search decreased discounting of future rewards substantially and speeded patient choices. These findings highlight the central role that heterogeneity in psychological processes plays in shaping intertemporal choice. Importantly, these results indicate that theories that ignore variability in search strategies may be inadvertently aggregating over different subpopulations that use very different processes. The findings also inform interventions in choice architecture to increase patience and improve consumer welfare. Copyright © 2017 the Author(s). Published by PNAS.

  18. Privacy-preserving search for chemical compound databases.

    PubMed

    Shimizu, Kana; Nuida, Koji; Arai, Hiromi; Mitsunari, Shigeo; Attrapadung, Nuttapong; Hamada, Michiaki; Tsuda, Koji; Hirokawa, Takatsugu; Sakuma, Jun; Hanaoka, Goichiro; Asai, Kiyoshi

    2015-01-01

    Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the database and uses them in a closed network. However, a serious dilemma arises when the database holder also wants to output no information except for the search results, and such a dilemma prevents the use of many important data resources. In order to overcome this dilemma, we developed a novel cryptographic protocol that enables database searching while keeping both the query holder's privacy and database holder's privacy. Generally, the application of cryptographic techniques to practical problems is difficult because versatile techniques are computationally expensive while computationally inexpensive techniques can perform only trivial computation tasks. In this study, our protocol is successfully built only from an additive-homomorphic cryptosystem, which allows only addition performed on encrypted values but is computationally efficient compared with versatile techniques such as general purpose multi-party computation. In an experiment searching ChEMBL, which consists of more than 1,200,000 compounds, the proposed method was 36,900 times faster in CPU time and 12,000 times as efficient in communication size compared with general purpose multi-party computation. We proposed a novel privacy-preserving protocol for searching chemical compound databases. The proposed method, easily scaling for large-scale databases, may help to accelerate drug discovery research by making full use of unused but valuable data that includes sensitive information.

  19. Privacy-preserving search for chemical compound databases

    PubMed Central

    2015-01-01

    Background Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the database and uses them in a closed network. However, a serious dilemma arises when the database holder also wants to output no information except for the search results, and such a dilemma prevents the use of many important data resources. Results In order to overcome this dilemma, we developed a novel cryptographic protocol that enables database searching while keeping both the query holder's privacy and database holder's privacy. Generally, the application of cryptographic techniques to practical problems is difficult because versatile techniques are computationally expensive while computationally inexpensive techniques can perform only trivial computation tasks. In this study, our protocol is successfully built only from an additive-homomorphic cryptosystem, which allows only addition performed on encrypted values but is computationally efficient compared with versatile techniques such as general purpose multi-party computation. In an experiment searching ChEMBL, which consists of more than 1,200,000 compounds, the proposed method was 36,900 times faster in CPU time and 12,000 times as efficient in communication size compared with general purpose multi-party computation. Conclusion We proposed a novel privacy-preserving protocol for searching chemical compound databases. The proposed method, easily scaling for large-scale databases, may help to accelerate drug discovery research by making full use of unused but valuable data that includes sensitive information. PMID:26678650

  20. Application of 3D Zernike descriptors to shape-based ligand similarity searching

    PubMed Central

    2009-01-01

    Background The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. Results In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability. Conclusion The 3DZD has unique ability for fast comparison of three-dimensional shape of compounds. Examples analyzed illustrate the advantages and the room for improvements for the 3DZD. PMID:20150998

  1. Speeding Up Chemical Searches Using the Inverted Index: the Convergence of Chemoinformatics and Text Search Methods

    PubMed Central

    Nasr, Ramzi; Vernica, Rares; Li, Chen; Baldi, Pierre

    2012-01-01

    In ligand-based screening, retrosynthesis, and other chemoinformatics applications, one of-ten seeks to search large databases of molecules in order to retrieve molecules that are similar to a given query. With the expanding size of molecular databases, the efficiency and scalability of data structures and algorithms for chemical searches are becoming increasingly important. Remarkably, both the chemoinformatics and information retrieval communities have converged on similar solutions whereby molecules or documents are represented by binary vectors, or fingerprints, indexing their substructures such as labeled paths for molecules and n-grams for text, with the same Jaccard-Tanimoto similarity measure. As a result, similarity search methods from one field can be adapted to the other. Here we adapt recent, state-of-the-art, inverted index methods from information retrieval to speed up similarity searches in chemoinformatics. Our results show a several-fold speed-up improvement over previous methods for both thresh-old searches and top-K searches. We also provide a mathematical analysis that allows one to predict the level of pruning achieved by the inverted index approach, and validate the quality of these predictions through simulation experiments. All results can be replicated using data freely downloadable from http://cdb.ics.uci.edu/. PMID:22462644

  2. Similar muscles contribute to horizontal and vertical acceleration of center of mass in forward and backward walking: implications for neural control

    PubMed Central

    Jansen, Karen; De Groote, Friedl; Massaad, Firas; Meyns, Pieter; Jonkers, Ilse

    2012-01-01

    Leg kinematics during backward walking (BW) are very similar to the time-reversed kinematics during forward walking (FW). This suggests that the underlying muscle activation pattern could originate from a simple time reversal, as well. Experimental electromyography studies have confirmed that this is the case for some muscles. Furthermore, it has been hypothesized that muscles showing a time reversal should also exhibit a reversal in function [from accelerating the body center of mass (COM) to decelerating]. However, this has not yet been verified in simulation studies. In the present study, forward simulations were used to study the effects of muscles on the acceleration of COM in FW and BW. We found that a reversal in function was indeed present in the muscle control of the horizontal movement of COM (e.g., tibialis anterior and gastrocnemius). In contrast, muscles' antigravity contributions maintained their function for both directions of movement. An important outcome of the present study is therefore that similar muscles can be used to achieve opposite functional demands at the level of control of the COM when walking direction is reversed. However, some muscles showed direction-specific contributions (i.e., dorsiflexors). We concluded that the changes in muscle contributions imply that a simple time reversal would be insufficient to produce BW from FW. We therefore propose that BW utilizes extra elements, presumably supraspinal, in addition to a common spinal drive. These additions are needed for propulsion and require a partial reconfiguration of lower level common networks. PMID:22423005

  3. Improvement of Space Shuttle Main Engine Low Frequency Acceleration Measurements

    NASA Technical Reports Server (NTRS)

    Stec, Robert C.

    1999-01-01

    The noise floor of low frequency acceleration data acquired on the Space Shuttle Main Engines is higher than desirable. Difficulties of acquiring high quality acceleration data on this engine are discussed. The approach presented in this paper for reducing the acceleration noise floor focuses on a search for an accelerometer more capable of measuring low frequency accelerations. An overview is given of the current measurement system used to acquire engine vibratory data. The severity of vibration, temperature, and moisture environments are considered. Vibratory measurements from both laboratory and rocket engine tests are presented.

  4. FunSimMat: a comprehensive functional similarity database

    PubMed Central

    Schlicker, Andreas; Albrecht, Mario

    2008-01-01

    Functional similarity based on Gene Ontology (GO) annotation is used in diverse applications like gene clustering, gene expression data analysis, protein interaction prediction and evaluation. However, there exists no comprehensive resource of functional similarity values although such a database would facilitate the use of functional similarity measures in different applications. Here, we describe FunSimMat (Functional Similarity Matrix, http://funsimmat.bioinf.mpi-inf.mpg.de/), a large new database that provides several different semantic similarity measures for GO terms. It offers various precomputed functional similarity values for proteins contained in UniProtKB and for protein families in Pfam and SMART. The web interface allows users to efficiently perform both semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. All results can be downloaded in tab-delimited files for use with other tools. An additional XML–RPC interface gives automatic online access to FunSimMat for programs and remote services. PMID:17932054

  5. Transfer Learning to Accelerate Interface Structure Searches

    NASA Astrophysics Data System (ADS)

    Oda, Hiromi; Kiyohara, Shin; Tsuda, Koji; Mizoguchi, Teruyasu

    2017-12-01

    Interfaces have atomic structures that are significantly different from those in the bulk, and play crucial roles in material properties. The central structures at the interfaces that provide properties have been extensively investigated. However, determination of even one interface structure requires searching for the stable configuration among many thousands of candidates. Here, a powerful combination of machine learning techniques based on kriging and transfer learning (TL) is proposed as a method for unveiling the interface structures. Using the kriging+TL method, thirty-three grain boundaries were systematically determined from 1,650,660 candidates in only 462 calculations, representing an increase in efficiency over conventional all-candidate calculation methods, by a factor of approximately 3,600.

  6. [Eye movement study in multiple object search process].

    PubMed

    Xu, Zhaofang; Liu, Zhongqi; Wang, Xingwei; Zhang, Xin

    2017-04-01

    The aim of this study is to investigate the search time regulation of objectives and eye movement behavior characteristics in the multi-objective visual search. The experimental task was accomplished with computer programming and presented characters on a 24 inch computer display. The subjects were asked to search three targets among the characters. Three target characters in the same group were of high similarity degree while those in different groups of target characters and distraction characters were in different similarity degrees. We recorded the search time and eye movement data through the whole experiment. It could be seen from the eye movement data that the quantity of fixation points was large when the target characters and distraction characters were similar. There were three kinds of visual search patterns for the subjects including parallel search, serial search, and parallel-serial search. In addition, the last pattern had the best search performance among the three search patterns, that is, the subjects who used parallel-serial search pattern spent shorter time finding the target. The order that the targets presented were able to affect the search performance significantly; and the similarity degree between target characters and distraction characters could also affect the search performance.

  7. CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions.

    PubMed

    Liu, Yongchao; Wirawan, Adrianto; Schmidt, Bertil

    2013-04-04

    The maximal sensitivity for local alignments makes the Smith-Waterman algorithm a popular choice for protein sequence database search based on pairwise alignment. However, the algorithm is compute-intensive due to a quadratic time complexity. Corresponding runtimes are further compounded by the rapid growth of sequence databases. We present CUDASW++ 3.0, a fast Smith-Waterman protein database search algorithm, which couples CPU and GPU SIMD instructions and carries out concurrent CPU and GPU computations. For the CPU computation, this algorithm employs SSE-based vector execution units as accelerators. For the GPU computation, we have investigated for the first time a GPU SIMD parallelization, which employs CUDA PTX SIMD video instructions to gain more data parallelism beyond the SIMT execution model. Moreover, sequence alignment workloads are automatically distributed over CPUs and GPUs based on their respective compute capabilities. Evaluation on the Swiss-Prot database shows that CUDASW++ 3.0 gains a performance improvement over CUDASW++ 2.0 up to 2.9 and 3.2, with a maximum performance of 119.0 and 185.6 GCUPS, on a single-GPU GeForce GTX 680 and a dual-GPU GeForce GTX 690 graphics card, respectively. In addition, our algorithm has demonstrated significant speedups over other top-performing tools: SWIPE and BLAST+. CUDASW++ 3.0 is written in CUDA C++ and PTX assembly languages, targeting GPUs based on the Kepler architecture. This algorithm obtains significant speedups over its predecessor: CUDASW++ 2.0, by benefiting from the use of CPU and GPU SIMD instructions as well as the concurrent execution on CPUs and GPUs. The source code and the simulated data are available at http://cudasw.sourceforge.net.

  8. Searching through synaesthetic colors.

    PubMed

    Laeng, Bruno

    2009-10-01

    Synaesthesia can be characterized by illusory colors being elicited automatically when one reads an alphanumeric symbol. These colors can affect attention; synaesthetes can show advantages in visual search of achromatic symbols that normally cause slow searches. However, some studies have failed to find these advantages, challenging the conclusion that synaesthetic colors influence attention in a manner similar to the influence of perceptual colors. In the present study, we investigated 2 synaesthetes who reported colors localized in space over alphanumeric symbols' shapes. The Euclidian distance in CIE xyY color space between two synaesthetic colors was computed for each specific visual search, so that the relationship between color distance (CD) and efficiency of search could be explored with simple regression analyses. Target-to-distractors color salience systematically predicted the speed of search, but the CD between a target or distractors and the physically presented achromatic color did not. When the synaesthetic colors of a target and distractors were nearly complementary, searches resembled popout performance with real colors. Control participants who performed searches for the same symbols (which were colored according to the synaesthetic colors) showed search functions very similar to those shown by the synaesthetes for the physically achromatic symbols.

  9. SETI The Search for Extraterrestrial Intelligence.

    ERIC Educational Resources Information Center

    Jones, Barrie W.

    1991-01-01

    Discussed is the search for life on other planets similar to Earth based on the Drake equation. Described are search strategies and microwave searches. The reasons why people are searching are also discussed. (KR)

  10. Custom Search Engines: Tools & Tips

    ERIC Educational Resources Information Center

    Notess, Greg R.

    2008-01-01

    Few have the resources to build a Google or Yahoo! from scratch. Yet anyone can build a search engine based on a subset of the large search engines' databases. Use Google Custom Search Engine or Yahoo! Search Builder or any of the other similar programs to create a vertical search engine targeting sites of interest to users. The basic steps to…

  11. Index Relativity and Patron Search Strategy.

    ERIC Educational Resources Information Center

    Allison, DeeAnn; Childers Scott

    2002-01-01

    Describes a study at the University of Nebraska-Lincoln that compared searches in two different keyword indexes with similar content where search results were dependent on search strategy quality, search engine execution, and content. Results showed search engine execution had an impact on the number of matches and that users ignored search help…

  12. Evolutionary optimization methods for accelerator design

    NASA Astrophysics Data System (ADS)

    Poklonskiy, Alexey A.

    Many problems from the fields of accelerator physics and beam theory can be formulated as optimization problems and, as such, solved using optimization methods. Despite growing efficiency of the optimization methods, the adoption of modern optimization techniques in these fields is rather limited. Evolutionary Algorithms (EAs) form a relatively new and actively developed optimization methods family. They possess many attractive features such as: ease of the implementation, modest requirements on the objective function, a good tolerance to noise, robustness, and the ability to perform a global search efficiently. In this work we study the application of EAs to problems from accelerator physics and beam theory. We review the most commonly used methods of unconstrained optimization and describe the GATool, evolutionary algorithm and the software package, used in this work, in detail. Then we use a set of test problems to assess its performance in terms of computational resources, quality of the obtained result, and the tradeoff between them. We justify the choice of GATool as a heuristic method to generate cutoff values for the COSY-GO rigorous global optimization package for the COSY Infinity scientific computing package. We design the model of their mutual interaction and demonstrate that the quality of the result obtained by GATool increases as the information about the search domain is refined, which supports the usefulness of this model. We Giscuss GATool's performance on the problems suffering from static and dynamic noise and study useful strategies of GATool parameter tuning for these and other difficult problems. We review the challenges of constrained optimization with EAs and methods commonly used to overcome them. We describe REPA, a new constrained optimization method based on repairing, in exquisite detail, including the properties of its two repairing techniques: REFIND and REPROPT. We assess REPROPT's performance on the standard constrained

  13. Automatic search for maximum similarity between molecular electrostatic potential distributions

    NASA Astrophysics Data System (ADS)

    Manaut, Francesc; Sanz, Ferran; José, Jaume; Milesi, Massimo

    1991-08-01

    A new computer program has been developed to automatically obtain the relative position of two molecules in which the similarity between molecular electrostatic-potential distributions is greatest. These distributions are considered in a volume around the molecules, and the similarity is measured by the Spearman rank coefficient. The program has been tested using several pairs of molecules: water vs. water; phenylethylamine and phenylpropylamine vs. benzylamine; and methotrexate vs. dihydrofolic acid.

  14. Design of transonic airfoil sections using a similarity theory

    NASA Technical Reports Server (NTRS)

    Nixon, D.

    1978-01-01

    A study of the available methods for transonic airfoil and wing design indicates that the most powerful technique is the numerical optimization procedure. However, the computer time for this method is relatively large because of the amount of computation required in the searches during optimization. The optimization method requires that base and calibration solutions be computed to determine a minimum drag direction. The design space is then computationally searched in this direction; it is these searches that dominate the computation time. A recent similarity theory allows certain transonic flows to be calculated rapidly from the base and calibration solutions. In this paper the application of the similarity theory to design problems is examined with the object of at least partially eliminating the costly searches of the design optimization method. An example of an airfoil design is presented.

  15. Parallel, exhaustive processing underlies logarithmic search functions: Visual search with cortical magnification.

    PubMed

    Wang, Zhiyuan; Lleras, Alejandro; Buetti, Simona

    2018-04-17

    Our lab recently found evidence that efficient visual search (with a fixed target) is characterized by logarithmic Reaction Time (RT) × Set Size functions whose steepness is modulated by the similarity between target and distractors. To determine whether this pattern of results was based on low-level visual factors uncontrolled by previous experiments, we minimized the possibility of crowding effects in the display, compensated for the cortical magnification factor by magnifying search items based on their eccentricity, and compared search performance on such displays to performance on displays without magnification compensation. In both cases, the RT × Set Size functions were found to be logarithmic, and the modulation of the log slopes by target-distractor similarity was replicated. Consistent with previous results in the literature, cortical magnification compensation eliminated most target eccentricity effects. We conclude that the log functions and their modulation by target-distractor similarity relations reflect a parallel exhaustive processing architecture for early vision.

  16. Search for optimal 3D wave launching configurations for the acceleration of charged particles in a magnetized plasma: Resonant Moments Method

    NASA Astrophysics Data System (ADS)

    Ponomarjov, Maxim; Carati, Daniele

    2004-11-01

    Three-dimensional electromagnetic wave configurations are proposed for accelerating charged particles in an external magnetic field. A primary wave responsible for the acceleration is coupled to a secondary wave generating the chaotic motion of the particles. The wave vectors and the magnetic field are not supposed to be co-planar and create a fully three dimensional system. This configuration produces faster acceleration with low amplitude. The idea considered here is similar to Refs. [1-2] although no constraint is imposed on the refraction indices. The theoretical analysis of the acceleration mechanism is based on the Resonance Moments Method (RMM) in which the velocity distribution and its moments are approximated by using an average over the resonant layers (RL)i only instead of a complete phase-space averages. The quantities obtained using this approach, referred to as Resonant Moments (RM), suggest the existence of optimal angles of propagation for the primary and secondary waves as long as the maximization of the parallel flux of charged particles is considered The secondary wave tends to maintain a pseudo-equilibrium velocity distribution by continuously re-filling the RL. Our suggestions are confirmed by direct numerical simulations of particle trajectories. The parameters for these simulations are relevant to magnetic plasma fusion experiments in electron cyclotron resonance heating and electron acceleration in planetary magnetospheres. Although measures of the distributions clearly show a departure from thermal equilibrium, the stochastization effect of the secondary wave yields a clear increase (up to one order of magnitude) of the average parallel velocity of the particles. It is a quite promising result since the amplitude of the secondary wave is ten times lower the one of the first wave. 1 H. Karimabadi and V. Angelopoulos, Phys. Rev. Lett., 62, 2342 (1989). 2 B. I. Cohen, R. H Cohen, W. M. Nevins, and T. D. Rognlien, Rev. Mod. Phys., 63, 949 (1991).

  17. Selective scanpath repetition during memory-guided visual search.

    PubMed

    Wynn, Jordana S; Bone, Michael B; Dragan, Michelle C; Hoffman, Kari L; Buchsbaum, Bradley R; Ryan, Jennifer D

    2016-01-02

    Visual search efficiency improves with repetition of a search display, yet the mechanisms behind these processing gains remain unclear. According to Scanpath Theory, memory retrieval is mediated by repetition of the pattern of eye movements or "scanpath" elicited during stimulus encoding. Using this framework, we tested the prediction that scanpath recapitulation reflects relational memory guidance during repeated search events. Younger and older subjects were instructed to find changing targets within flickering naturalistic scenes. Search efficiency (search time, number of fixations, fixation duration) and scanpath similarity (repetition) were compared across age groups for novel (V1) and repeated (V2) search events. Younger adults outperformed older adults on all efficiency measures at both V1 and V2, while the search time benefit for repeated viewing (V1-V2) did not differ by age. Fixation-binned scanpath similarity analyses revealed repetition of initial and final (but not middle) V1 fixations at V2, with older adults repeating more initial V1 fixations than young adults. In young adults only, early scanpath similarity correlated negatively with search time at test, indicating increased efficiency, whereas the similarity of V2 fixations to middle V1 fixations predicted poor search performance. We conclude that scanpath compression mediates increased search efficiency by selectively recapitulating encoding fixations that provide goal-relevant input. Extending Scanpath Theory, results suggest that scanpath repetition varies as a function of time and memory integrity.

  18. Selective scanpath repetition during memory-guided visual search

    PubMed Central

    Wynn, Jordana S.; Bone, Michael B.; Dragan, Michelle C.; Hoffman, Kari L.; Buchsbaum, Bradley R.; Ryan, Jennifer D.

    2016-01-01

    ABSTRACT Visual search efficiency improves with repetition of a search display, yet the mechanisms behind these processing gains remain unclear. According to Scanpath Theory, memory retrieval is mediated by repetition of the pattern of eye movements or “scanpath” elicited during stimulus encoding. Using this framework, we tested the prediction that scanpath recapitulation reflects relational memory guidance during repeated search events. Younger and older subjects were instructed to find changing targets within flickering naturalistic scenes. Search efficiency (search time, number of fixations, fixation duration) and scanpath similarity (repetition) were compared across age groups for novel (V1) and repeated (V2) search events. Younger adults outperformed older adults on all efficiency measures at both V1 and V2, while the search time benefit for repeated viewing (V1–V2) did not differ by age. Fixation-binned scanpath similarity analyses revealed repetition of initial and final (but not middle) V1 fixations at V2, with older adults repeating more initial V1 fixations than young adults. In young adults only, early scanpath similarity correlated negatively with search time at test, indicating increased efficiency, whereas the similarity of V2 fixations to middle V1 fixations predicted poor search performance. We conclude that scanpath compression mediates increased search efficiency by selectively recapitulating encoding fixations that provide goal-relevant input. Extending Scanpath Theory, results suggest that scanpath repetition varies as a function of time and memory integrity. PMID:27570471

  19. rfpipe: Radio interferometric transient search pipeline

    NASA Astrophysics Data System (ADS)

    Law, Casey J.

    2017-10-01

    rfpipe supports Python-based analysis of radio interferometric data (especially from the Very Large Array) and searches for fast radio transients. This extends on the rtpipe library (ascl:1706.002) with new approaches to parallelization, acceleration, and more portable data products. rfpipe can run in standalone mode or be in a cluster environment.

  20. Social-emotional characteristics of gifted accelerated and non-accelerated students in the Netherlands.

    PubMed

    Hoogeveen, Lianne; van Hell, Janet G; Verhoeven, Ludo

    2012-12-01

    In the studies of acceleration conducted so far a multidimensional perspective has largely been neglected. No attempt has been made to relate social-emotional characteristics of accelerated versus non-accelerated students in perspective of environmental factors. In this study, social-emotional characteristics of accelerated gifted students in the Netherlands were examined in relation to personal and environmental factors. Self-concept and social contacts of accelerated (n = 148) and non-accelerated (n = 55) gifted students, aged 4 to 27 (M = 11.22, SD = 4.27) were measured. Self-concept and social contacts of accelerated and non-accelerated gifted students were measured using a questionnaire and a diary, and parents of these students evaluated their behavioural characteristics. Gender and birth order were studied as personal factors and grade, classroom, teachers' gender, teaching experience, and the quality of parent-school contact as environmental factors. The results showed minimal differences in the social-emotional characteristics of accelerated and non-accelerated gifted students. The few differences we found favoured the accelerated students. We also found that multiple grade skipping does not have negative effects on social-emotional characteristics, and that long-term effects of acceleration tend to be positive. As regards the possible modulation of personal and environmental factors, we merely found an impact of such factors in the non-accelerated group. The results of this study strongly suggest that social-emotional characteristics of accelerated gifted students and non-accelerated gifted students are largely similar. These results thus do not support worries expressed by teachers about the acceleration of gifted students. Our findings parallel the outcomes of earlier studies in the United States and Germany in that we observed that acceleration does not harm gifted students, not even in the case of multiple grade skipping. On the contrary, there is a

  1. gWEGA: GPU-accelerated WEGA for molecular superposition and shape comparison.

    PubMed

    Yan, Xin; Li, Jiabo; Gu, Qiong; Xu, Jun

    2014-06-05

    Virtual screening of a large chemical library for drug lead identification requires searching/superimposing a large number of three-dimensional (3D) chemical structures. This article reports a graphic processing unit (GPU)-accelerated weighted Gaussian algorithm (gWEGA) that expedites shape or shape-feature similarity score-based virtual screening. With 86 GPU nodes (each node has one GPU card), gWEGA can screen 110 million conformations derived from an entire ZINC drug-like database with diverse antidiabetic agents as query structures within 2 s (i.e., screening more than 55 million conformations per second). The rapid screening speed was accomplished through the massive parallelization on multiple GPU nodes and rapid prescreening of 3D structures (based on their shape descriptors and pharmacophore feature compositions). Copyright © 2014 Wiley Periodicals, Inc.

  2. Does race matter in the search for housing? An exploratory study of search strategies, experiences, and locations.

    PubMed

    Krysan, Maria

    2008-06-01

    In a departure from most studies of the causes of racial residential segregation that focus on the three main factors of economics, preferences, and discrimination, this paper examines one of the mechanisms through which segregation may be perpetuated: the housing search process itself. Data come from a 2004 face-to-face survey of an area probability sample of African American and white householders living in the three counties of the Detroit metropolitan area (n = 734). These data are used to address three research questions: (1) What are the strategies people use to find housing, and are there racial differences in those strategies? (2) Do whites and African Americans report similar or different experiences in the search for housing? (3) Do the locations in which people search for housing vary by race? Results show that once controlling for the type of search and background characteristics, the search strategies are generally similar for whites and blacks, though more so for buyers than renters: for example, black renters use more informal strategies and networks than do white renters. Analyses that look at the features of these strategies, however, reveal some significant racial differences. Search experiences are similar in terms of length and number of homes inspected, but other objective and subjective questions about the search show blacks at a disadvantage compared to whites: African Americans submit more offers/applications for homes, report more difficulties, and are much more likely to feel they were taken advantage of during the search. The racial characteristics of the communities in which blacks and whites search are quite different: whites mainly search in white communities, while African Americans search in communities with a variety of racial compositions. The paper concludes with a call for further research on housing search strategies, with particular attention to the role of social networks.

  3. Does Race Matter in the Search for Housing? An Exploratory Study of Search Strategies, Experiences, and Locations*

    PubMed Central

    Krysan, Maria

    2008-01-01

    In a departure from most studies of the causes of racial residential segregation that focus on the three main factors of economics, preferences, and discrimination, this paper examines one of the mechanisms through which segregation may be perpetuated: the housing search process itself. Data come from a 2004 face-to-face survey of an area probability sample of African American and white householders living in the three counties of the Detroit metropolitan area (n=734). These data are used to address three research questions: (1) What are the strategies people use to find housing, and are there racial differences in those strategies? (2) Do whites and African Americans report similar or different experiences in the search for housing? (3) Do the locations in which people search for housing vary by race? Results show that once controlling for the type of search and background characteristics, the search strategies are generally similar for whites and blacks, though more so for buyers than renters: for example, black renters use more informal strategies and networks than do white renters. Analyses that look at the features of these strategies, however, reveal some significant racial differences. Search experiences are similar in terms of length and number of homes inspected, but other objective and subjective questions about the search show blacks at a disadvantage compared to whites: African Americans submit more offers/applications for homes, report more difficulties, and are much more likely to feel they were taken advantage of during the search. The racial characteristics of the communities in which blacks and whites search are quite different: whites mainly search in white communities, while African Americans search in communities with a variety of racial compositions. The paper concludes with a call for further research on housing search strategies, with particular attention to the role of social networks. PMID:19069060

  4. Category and Word Search: Generalizing Search Principles to Complex Processing.

    DTIC Science & Technology

    1982-03-01

    complex processing (e.g., LaBerge & Samels, 1974; Shiffrin & Schneider, 1977). In the present paper we examine how well the major phenomena in simple visual...subjects are searching for novel characters ( LaBerge , 1973). The relatively large and rapid CH practice effects for word and category search are analogous...1974) demonstrated interference effects of irrelevant flanking letters. Shaffer and Laberge (1979) showed a similar effect with words and semantic

  5. COBRA: a Bayesian approach to pulsar searching

    NASA Astrophysics Data System (ADS)

    Lentati, L.; Champion, D. J.; Kramer, M.; Barr, E.; Torne, P.

    2018-02-01

    We introduce COBRA, a GPU-accelerated Bayesian analysis package for performing pulsar searching, that uses candidates from traditional search techniques to set the prior used for the periodicity of the source, and performs a blind search in all remaining parameters. COBRA incorporates models for both isolated and accelerated systems, as well as both Keplerian and relativistic binaries, and exploits pulse phase information to combine search epochs coherently, over time, frequency or across multiple telescopes. We demonstrate the efficacy of our approach in a series of simulations that challenge typical search techniques, including highly aliased signals, and relativistic binary systems. In the most extreme case, we simulate an 8 h observation containing 24 orbits of a pulsar in a binary with a 30 M⊙ companion. Even in this scenario we show that we can build up from an initial low-significance candidate, to fully recovering the signal. We also apply the method to survey data of three pulsars from the globular cluster 47Tuc: PSRs J0024-7204D, J0023-7203J and J0024-7204R. This final pulsar is in a 1.6 h binary, the shortest of any pulsar in 47Tuc, and additionally shows significant scintillation. By allowing the amplitude of the source to vary as a function of time, however, we show that we are able to obtain optimal combinations of such noisy data. We also demonstrate the ability of COBRA to perform high-precision pulsar timing directly on the single pulse survey data, and obtain a 95 per cent upper limit on the eccentricity of PSR J0024-7204R of εb < 0.0007.

  6. Stochastic modeling of Lagrangian accelerations

    NASA Astrophysics Data System (ADS)

    Reynolds, Andy

    2002-11-01

    It is shown how Sawford's second-order Lagrangian stochastic model (Phys. Fluids A 3, 1577-1586, 1991) for fluid-particle accelerations can be combined with a model for the evolution of the dissipation rate (Pope and Chen, Phys. Fluids A 2, 1437-1449, 1990) to produce a Lagrangian stochastic model that is consistent with both the measured distribution of Lagrangian accelerations (La Porta et al., Nature 409, 1017-1019, 2001) and Kolmogorov's similarity theory. The later condition is found not to be satisfied when a constant dissipation rate is employed and consistency with prescribed acceleration statistics is enforced through fulfilment of a well-mixed condition.

  7. Cube search, revisited.

    PubMed

    Zhang, Xuetao; Huang, Jie; Yigit-Elliott, Serap; Rosenholtz, Ruth

    2015-03-16

    Observers can quickly search among shaded cubes for one lit from a unique direction. However, replace the cubes with similar 2-D patterns that do not appear to have a 3-D shape, and search difficulty increases. These results have challenged models of visual search and attention. We demonstrate that cube search displays differ from those with "equivalent" 2-D search items in terms of the informativeness of fairly low-level image statistics. This informativeness predicts peripheral discriminability of target-present from target-absent patches, which in turn predicts visual search performance, across a wide range of conditions. Comparing model performance on a number of classic search tasks, cube search does not appear unexpectedly easy. Easy cube search, per se, does not provide evidence for preattentive computation of 3-D scene properties. However, search asymmetries derived from rotating and/or flipping the cube search displays cannot be explained by the information in our current set of image statistics. This may merely suggest a need to modify the model's set of 2-D image statistics. Alternatively, it may be difficult cube search that provides evidence for preattentive computation of 3-D scene properties. By attributing 2-D luminance variations to a shaded 3-D shape, 3-D scene understanding may slow search for 2-D features of the target. © 2015 ARVO.

  8. Cube search, revisited

    PubMed Central

    Zhang, Xuetao; Huang, Jie; Yigit-Elliott, Serap; Rosenholtz, Ruth

    2015-01-01

    Observers can quickly search among shaded cubes for one lit from a unique direction. However, replace the cubes with similar 2-D patterns that do not appear to have a 3-D shape, and search difficulty increases. These results have challenged models of visual search and attention. We demonstrate that cube search displays differ from those with “equivalent” 2-D search items in terms of the informativeness of fairly low-level image statistics. This informativeness predicts peripheral discriminability of target-present from target-absent patches, which in turn predicts visual search performance, across a wide range of conditions. Comparing model performance on a number of classic search tasks, cube search does not appear unexpectedly easy. Easy cube search, per se, does not provide evidence for preattentive computation of 3-D scene properties. However, search asymmetries derived from rotating and/or flipping the cube search displays cannot be explained by the information in our current set of image statistics. This may merely suggest a need to modify the model's set of 2-D image statistics. Alternatively, it may be difficult cube search that provides evidence for preattentive computation of 3-D scene properties. By attributing 2-D luminance variations to a shaded 3-D shape, 3-D scene understanding may slow search for 2-D features of the target. PMID:25780063

  9. Combination of 2D/3D ligand-based similarity search in rapid virtual screening from multimillion compound repositories. Selection and biological evaluation of potential PDE4 and PDE5 inhibitors.

    PubMed

    Dobi, Krisztina; Hajdú, István; Flachner, Beáta; Fabó, Gabriella; Szaszkó, Mária; Bognár, Melinda; Magyar, Csaba; Simon, István; Szisz, Dániel; Lőrincz, Zsolt; Cseh, Sándor; Dormán, György

    2014-05-28

    Rapid in silico selection of target focused libraries from commercial repositories is an attractive and cost effective approach. If structures of active compounds are available rapid 2D similarity search can be performed on multimillion compound databases but the generated library requires further focusing by various 2D/3D chemoinformatics tools. We report here a combination of the 2D approach with a ligand-based 3D method (Screen3D) which applies flexible matching to align reference and target compounds in a dynamic manner and thus to assess their structural and conformational similarity. In the first case study we compared the 2D and 3D similarity scores on an existing dataset derived from the biological evaluation of a PDE5 focused library. Based on the obtained similarity metrices a fusion score was proposed. The fusion score was applied to refine the 2D similarity search in a second case study where we aimed at selecting and evaluating a PDE4B focused library. The application of this fused 2D/3D similarity measure led to an increase of the hit rate from 8.5% (1st round, 47% inhibition at 10 µM) to 28.5% (2nd round at 50% inhibition at 10 µM) and the best two hits had 53 nM inhibitory activities.

  10. Accelerated Peer-Review Journal Usage Technique for Undergraduates

    ERIC Educational Resources Information Center

    Wallace, J. D.

    2008-01-01

    The internet has given undergraduate students ever-increasing access to academic journals via search engines and online databases. However, students typically do not have the ability to use these journals effectively. This often poses a dilemma for instructors. The accelerated peer-review journal usage (APJU) technique provides a way for…

  11. Tempest: Accelerated MS/MS database search software for heterogeneous computing platforms

    PubMed Central

    Adamo, Mark E.; Gerber, Scott A.

    2017-01-01

    MS/MS database search algorithms derive a set of candidate peptide sequences from in-silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU generates peptide candidates that are asynchronously sent to a discrete GPU to be scored against experimental spectra in parallel (Milloy et al., 2012). The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. PMID:27603022

  12. BIOCONAID System (Bionic Control of Acceleration Induced Dimming). Final Report.

    ERIC Educational Resources Information Center

    Rogers, Dana B.; And Others

    The system described represents a new technique for enhancing the fidelity of flight simulators during high acceleration maneuvers. This technique forces the simulator pilot into active participation and energy expenditure similar to the aircraft pilot undergoing actual accelerations. The Bionic Control of Acceleration Induced Dimming (BIOCONAID)…

  13. Tempest: Accelerated MS/MS Database Search Software for Heterogeneous Computing Platforms.

    PubMed

    Adamo, Mark E; Gerber, Scott A

    2016-09-07

    MS/MS database search algorithms derive a set of candidate peptide sequences from in silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU (central processing unit) generates peptide candidates that are asynchronously sent to a discrete GPU (graphics processing unit) to be scored against experimental spectra in parallel. The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

  14. Accelerating Families of Fuzzy K-Means Algorithms for Vector Quantization Codebook Design

    PubMed Central

    Mata, Edson; Bandeira, Silvio; de Mattos Neto, Paulo; Lopes, Waslon; Madeiro, Francisco

    2016-01-01

    The performance of signal processing systems based on vector quantization depends on codebook design. In the image compression scenario, the quality of the reconstructed images depends on the codebooks used. In this paper, alternatives are proposed for accelerating families of fuzzy K-means algorithms for codebook design. The acceleration is obtained by reducing the number of iterations of the algorithms and applying efficient nearest neighbor search techniques. Simulation results concerning image vector quantization have shown that the acceleration obtained so far does not decrease the quality of the reconstructed images. Codebook design time savings up to about 40% are obtained by the accelerated versions with respect to the original versions of the algorithms. PMID:27886061

  15. Accelerating Families of Fuzzy K-Means Algorithms for Vector Quantization Codebook Design.

    PubMed

    Mata, Edson; Bandeira, Silvio; de Mattos Neto, Paulo; Lopes, Waslon; Madeiro, Francisco

    2016-11-23

    The performance of signal processing systems based on vector quantization depends on codebook design. In the image compression scenario, the quality of the reconstructed images depends on the codebooks used. In this paper, alternatives are proposed for accelerating families of fuzzy K-means algorithms for codebook design. The acceleration is obtained by reducing the number of iterations of the algorithms and applying efficient nearest neighbor search techniques. Simulation results concerning image vector quantization have shown that the acceleration obtained so far does not decrease the quality of the reconstructed images. Codebook design time savings up to about 40% are obtained by the accelerated versions with respect to the original versions of the algorithms.

  16. Global Acceleration of Coronal Mass Ejections

    NASA Technical Reports Server (NTRS)

    Gopalswamy, Nat; Lara, Alejandro; Lepping, Ronald; Kaiser, Michael; Berdichevsky, Daniel; St. Cyr, O. Chris; Lazarus, Al

    1999-01-01

    Using the observed relation between speeds of coronal mass ejections (CMEs) near the Sun and in the solar wind, we estimate a global acceleration acting on the CMEs. Our study quantifies the qualitative results of Gosling [1997] and numerical simulations that CMEs at 1 AU with speeds closer to the solar wind. We found a linear relation between the global acceleration and the initial speed of the CMEs and the absolute value of the acceleration is similar to the slow solar wind acceleration. Our study naturally divides CMEs into fast and slow ones, the dividing line being the solar wind speed. Our results have important implications to space weather prediction models which need to incorporate this effect in estimating the CME arrival time at 1 AU. We show that the arrival times of CMEs at 1 AU are drastically different from the zero acceleration case.

  17. The Talent Search Model: Implications for Secondary School Reform.

    ERIC Educational Resources Information Center

    VanTassel-Baska, Joyce

    1985-01-01

    The Midwest Talent Search Project is an effort to identify and provide an appropriate accelerated curriculum for gifted secondary school students in the midwest. Many aspects of the project are discussed here, including testing, programming, benefits, and implications for curriculum reform. (Author/MCG)

  18. Genetic algorithms as global random search methods

    NASA Technical Reports Server (NTRS)

    Peck, Charles C.; Dhawan, Atam P.

    1995-01-01

    Genetic algorithm behavior is described in terms of the construction and evolution of the sampling distributions over the space of candidate solutions. This novel perspective is motivated by analysis indicating that the schema theory is inadequate for completely and properly explaining genetic algorithm behavior. Based on the proposed theory, it is argued that the similarities of candidate solutions should be exploited directly, rather than encoding candidate solutions and then exploiting their similarities. Proportional selection is characterized as a global search operator, and recombination is characterized as the search process that exploits similarities. Sequential algorithms and many deletion methods are also analyzed. It is shown that by properly constraining the search breadth of recombination operators, convergence of genetic algorithms to a global optimum can be ensured.

  19. Genetic algorithms as global random search methods

    NASA Technical Reports Server (NTRS)

    Peck, Charles C.; Dhawan, Atam P.

    1995-01-01

    Genetic algorithm behavior is described in terms of the construction and evolution of the sampling distributions over the space of candidate solutions. This novel perspective is motivated by analysis indicating that that schema theory is inadequate for completely and properly explaining genetic algorithm behavior. Based on the proposed theory, it is argued that the similarities of candidate solutions should be exploited directly, rather than encoding candidate solution and then exploiting their similarities. Proportional selection is characterized as a global search operator, and recombination is characterized as the search process that exploits similarities. Sequential algorithms and many deletion methods are also analyzed. It is shown that by properly constraining the search breadth of recombination operators, convergence of genetic algorithms to a global optimum can be ensured.

  20. Timescales for detecting a significant acceleration in sea level rise

    PubMed Central

    Haigh, Ivan D.; Wahl, Thomas; Rohling, Eelco J.; Price, René M.; Pattiaratchi, Charitha B.; Calafat, Francisco M.; Dangendorf, Sönke

    2014-01-01

    There is observational evidence that global sea level is rising and there is concern that the rate of rise will increase, significantly threatening coastal communities. However, considerable debate remains as to whether the rate of sea level rise is currently increasing and, if so, by how much. Here we provide new insights into sea level accelerations by applying the main methods that have been used previously to search for accelerations in historical data, to identify the timings (with uncertainties) at which accelerations might first be recognized in a statistically significant manner (if not apparent already) in sea level records that we have artificially extended to 2100. We find that the most important approach to earliest possible detection of a significant sea level acceleration lies in improved understanding (and subsequent removal) of interannual to multidecadal variability in sea level records. PMID:24728012

  1. SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

    PubMed Central

    Arnold, Roland; Goldenberg, Florian; Mewes, Hans-Werner; Rattei, Thomas

    2014-01-01

    The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories. As of September 2013, SIMAP contains >163 million proteins corresponding to ∼70 million non-redundant sequences. SIMAP uses the sensitive FASTA search heuristics, the Smith–Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm. SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe. Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource. All-against-all protein sequence similarity matrices of project-specific protein collections are generated on request. Recent improvements allow SIMAP to cover the rapidly growing sequenced protein sequence universe. New Web-Service interfaces enhance the connectivity of SIMAP. Novel tools for interactive extraction of protein similarity networks have been added. Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads. PMID:24165881

  2. Comparing image search behaviour in the ARRS GoldMiner search engine and a clinical PACS/RIS.

    PubMed

    De-Arteaga, Maria; Eggel, Ivan; Do, Bao; Rubin, Daniel; Kahn, Charles E; Müller, Henning

    2015-08-01

    Information search has changed the way we manage knowledge and the ubiquity of information access has made search a frequent activity, whether via Internet search engines or increasingly via mobile devices. Medical information search is in this respect no different and much research has been devoted to analyzing the way in which physicians aim to access information. Medical image search is a much smaller domain but has gained much attention as it has different characteristics than search for text documents. While web search log files have been analysed many times to better understand user behaviour, the log files of hospital internal systems for search in a PACS/RIS (Picture Archival and Communication System, Radiology Information System) have rarely been analysed. Such a comparison between a hospital PACS/RIS search and a web system for searching images of the biomedical literature is the goal of this paper. Objectives are to identify similarities and differences in search behaviour of the two systems, which could then be used to optimize existing systems and build new search engines. Log files of the ARRS GoldMiner medical image search engine (freely accessible on the Internet) containing 222,005 queries, and log files of Stanford's internal PACS/RIS search called radTF containing 18,068 queries were analysed. Each query was preprocessed and all query terms were mapped to the RadLex (Radiology Lexicon) terminology, a comprehensive lexicon of radiology terms created and maintained by the Radiological Society of North America, so the semantic content in the queries and the links between terms could be analysed, and synonyms for the same concept could be detected. RadLex was mainly created for the use in radiology reports, to aid structured reporting and the preparation of educational material (Lanlotz, 2006) [1]. In standard medical vocabularies such as MeSH (Medical Subject Headings) and UMLS (Unified Medical Language System) specific terms of radiology are often

  3. Interdisciplinary glossary — particle accelerators and medicine

    NASA Astrophysics Data System (ADS)

    Dmitrieva, V. V.; Dyubkov, V. S.; Nikitaev, V. G.; Ulin, S. E.

    2016-02-01

    A general concept of a new interdisciplinary glossary, which includes particle accelerator terminology used in medicine, as well as relevant medical concepts, is presented. Its structure and usage rules are described. An example, illustrating the quickly searching technique of relevant information in this Glossary, is considered. A website address, where one can get an access to the Glossary, is specified. Glossary can be refined and supplemented.

  4. Heavy Ion Acceleration at J-PARC

    NASA Astrophysics Data System (ADS)

    SATO, Susumu

    2018-02-01

    J-PARC, the Japan Proton Accelerator Research Complex, is an accelerator, which provides a high-intensity proton beam. Recently as a very attractive project, the acceleration of heavy ions produced by supplementary ion sources, called J-PARC-HI, is seriously contemplated by domestic as well as international communities. The planned facility would accelerate heavy ions up to U92+ with a beam energy 20 AGeV ( of 6.2 AGeV). The highlight of the J-PARC-HI project is its very high beam rate up to 1011 Hz, which will enable the study of very rare events. Taking advantage of this high intensity, J-PARC-HI will carry out frontier studies of new and rare observables in this energy region: (i) nuclear medium modification of chiral property of vector mesons through low-mass di-lepton signal, (ii) QCD critical pointcharacterization through event-by-event fluctuation signals of particle production, (iii) systematic measurements related to the equation of state through collective flow signal or two-particle momentum correlation signal, or (iv) the search of hyper nuclei with multi strangeness including or exceeding S = 3. The current plan of J-PARC-HI aims to carrying out the first experimental measurements in 2025.

  5. Visual search in divided areas: dividers initially interfere with and later facilitate visual search.

    PubMed

    Nakashima, Ryoichi; Yokosawa, Kazuhiko

    2013-02-01

    A common search paradigm requires observers to search for a target among undivided spatial arrays of many items. Yet our visual environment is populated with items that are typically arranged within smaller (subdivided) spatial areas outlined by dividers (e.g., frames). It remains unclear how dividers impact visual search performance. In this study, we manipulated the presence and absence of frames and the number of frames subdividing search displays. Observers searched for a target O among Cs, a typically inefficient search task, and for a target C among Os, a typically efficient search. The results indicated that the presence of divider frames in a search display initially interferes with visual search tasks when targets are quickly detected (i.e., efficient search), leading to early interference; conversely, frames later facilitate visual search in tasks in which targets take longer to detect (i.e., inefficient search), leading to late facilitation. Such interference and facilitation appear only for conditions with a specific number of frames. Relative to previous studies of grouping (due to item proximity or similarity), these findings suggest that frame enclosures of multiple items may induce a grouping effect that influences search performance.

  6. Are supernova remnants quasi-parallel or quasi-perpendicular accelerators

    NASA Technical Reports Server (NTRS)

    Spangler, S. R.; Leckband, J. A.; Cairns, I. H.

    1989-01-01

    Observations of shock waves in the solar system which show a pronounced difference in the plasma wave and particle environment depending on whether the shock is propagating along or perpendicular to the interplanetary magnetic field are discussed. Theories for particle acceleration developed for quasi-parallel and quasi-perpendicular shocks, when extended to the interstellar medium suggest that the relativistic electrons in radio supernova remnants are accelerated by either the Q parallel or Q perpendicular mechanisms. A model for the galactic magnetic field and published maps of supernova remnants were used to search for a dependence of structure on the angle Phi. Results show no tendency for the remnants as a whole to favor the relationship expected for either mechanism, although individual sources resemble model remnants of one or the other acceleration process.

  7. Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins

    PubMed Central

    Kemme, Catherine A.; Marquez, Rolando; Luu, Ross H.

    2017-01-01

    Abstract Eukaryotic genomes contain numerous non-functional high-affinity sequences for transcription factors. These sequences potentially serve as natural decoys that sequester transcription factors. We have previously shown that the presence of sequences similar to the target sequence could substantially impede association of the transcription factor Egr-1 with its targets. In this study, using a stopped-flow fluorescence method, we examined the kinetic impact of DNA methylation of decoys on the search process of the Egr-1 zinc-finger protein. We analyzed its association with an unmethylated target site on fluorescence-labeled DNA in the presence of competitor DNA duplexes, including Egr-1 decoys. DNA methylation of decoys alone did not affect target search kinetics. In the presence of the MeCP2 methyl-CpG-binding domain (MBD), however, DNA methylation of decoys substantially (∼10-30-fold) accelerated the target search process of the Egr-1 zinc-finger protein. This acceleration did not occur when the target was also methylated. These results suggest that when decoys are methylated, MBD proteins can block them and thereby allow Egr-1 to avoid sequestration in non-functional locations. This effect may occur in vivo for DNA methylation outside CpG islands (CGIs) and could facilitate localization of some transcription factors within regulatory CGIs, where DNA methylation is rare. PMID:28486614

  8. In search of late time evolution self-similar scaling laws of Rayleigh-Taylor and Richtmyer-Meshkov hydrodynamic instabilities - recent theorical advance and NIF Discovery-Science experiments

    NASA Astrophysics Data System (ADS)

    Shvarts, Dov

    2017-10-01

    Hydrodynamic instabilities, and the mixing that they cause, are of crucial importance in describing many phenomena, from very large scales such as stellar explosions (supernovae) to very small scales, such as inertial confinement fusion (ICF) implosions. Such mixing causes the ejection of stellar core material in supernovae, and impedes attempts at ICF ignition. The Rayleigh-Taylor instability (RTI) occurs at an accelerated interface between two fluids with the lower density accelerating the higher density fluid. The Richtmyer-Meshkov (RM) instability occurs when a shock wave passes an interface between the two fluids of different density. In the RTI, buoyancy causes ``bubbles'' of the light fluid to rise through (penetrate) the denser fluid, while ``spikes'' of the heavy fluid sink through (penetrate) the lighter fluid. With realistic multi-mode initial conditions, in the deep nonlinear regime, the mixing zone width, H, and its internal structure, progress through an inverse cascade of spatial scales, reaching an asymptotic self-similar evolution: hRT =αRT Agt2 for RT and hRM =αRM tθ for RM. While this characteristic behavior has been known for years, the self-similar parameters αRT and θRM and their dependence on dimensionality and density ratio have continued to be intensively studied and a relatively wide distribution of those values have emerged. This talk will describe recent theoretical advances in the description of this turbulent mixing evolution that sheds light on the spread in αRT and θRM. Results of new and specially designed experiments, done by scientists from several laboratories, were performed recently using NIF, the only facility that is powerful enough to reach the self-similar regime, for quantitative testing of this theoretical advance, will be presented.

  9. Implicit Object Naming in Visual Search: Evidence from Phonological Competition

    PubMed Central

    Walenchok, Stephen C.; Hout, Michael C.; Goldinger, Stephen D.

    2016-01-01

    During visual search, people are distracted by objects that visually resemble search targets; search is impaired when targets and distractors share overlapping features. In this study, we examined whether a nonvisual form of similarity, overlapping object names, can also affect search performance. In three experiments, people searched for images of real-world objects (e.g., a beetle) among items whose names either all shared the same phonological onset (/bi/), or were phonologically varied. Participants either searched for one or three potential targets per trial, with search targets designated either visually or verbally. We examined standard visual search (Experiments 1 and 3) and a self-paced serial search task wherein participants manually rejected each distractor (Experiment 2). We hypothesized that people would maintain visual templates when searching for single targets, but would rely more on object names when searching for multiple items and when targets were verbally cued. This reliance on target names would make performance susceptible to interference from similar-sounding distractors. Experiments 1 and 2 showed the predicted interference effect in conditions with high memory load and verbal cues. In Experiment 3, eye-movement results showed that phonological interference resulted from small increases in dwell time to all distractors. The results suggest that distractor names are implicitly activated during search, slowing attention disengagement when targets and distractors share similar names. PMID:27531018

  10. Online Information Search Performance and Search Strategies in a Health Problem-Solving Scenario.

    PubMed

    Sharit, Joseph; Taha, Jessica; Berkowsky, Ronald W; Profita, Halley; Czaja, Sara J

    2015-01-01

    Although access to Internet health information can be beneficial, solving complex health-related problems online is challenging for many individuals. In this study, we investigated the performance of a sample of 60 adults ages 18 to 85 years in using the Internet to resolve a relatively complex health information problem. The impact of age, Internet experience, and cognitive abilities on measures of search time, amount of search, and search accuracy was examined, and a model of Internet information seeking was developed to guide the characterization of participants' search strategies. Internet experience was found to have no impact on performance measures. Older participants exhibited longer search times and lower amounts of search but similar search accuracy performance as their younger counterparts. Overall, greater search accuracy was related to an increased amount of search but not to increased search duration and was primarily attributable to higher cognitive abilities, such as processing speed, reasoning ability, and executive function. There was a tendency for those who were younger, had greater Internet experience, and had higher cognitive abilities to use a bottom-up (i.e., analytic) search strategy, although use of a top-down (i.e., browsing) strategy was not necessarily unsuccessful. Implications of the findings for future studies and design interventions are discussed.

  11. Online Information Search Performance and Search Strategies in a Health Problem-Solving Scenario

    PubMed Central

    Sharit, Joseph; Taha, Jessica; Berkowsky, Ronald W.; Profita, Halley; Czaja, Sara J.

    2017-01-01

    Although access to Internet health information can be beneficial, solving complex health-related problems online is challenging for many individuals. In this study, we investigated the performance of a sample of 60 adults ages 18 to 85 years in using the Internet to resolve a relatively complex health information problem. The impact of age, Internet experience, and cognitive abilities on measures of search time, amount of search, and search accuracy was examined, and a model of Internet information seeking was developed to guide the characterization of participants’ search strategies. Internet experience was found to have no impact on performance measures. Older participants exhibited longer search times and lower amounts of search but similar search accuracy performance as their younger counterparts. Overall, greater search accuracy was related to an increased amount of search but not to increased search duration and was primarily attributable to higher cognitive abilities, such as processing speed, reasoning ability, and executive function. There was a tendency for those who were younger, had greater Internet experience, and had higher cognitive abilities to use a bottom-up (i.e., analytic) search strategy, although use of a top-down (i.e., browsing) strategy was not necessarily unsuccessful. Implications of the findings for future studies and design interventions are discussed. PMID:29056885

  12. 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)

    PubMed Central

    Li, Isaac TS; Shum, Warren; Truong, Kevin

    2007-01-01

    Background To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching sequence databases that may contain hundreds of millions of sequences, this algorithm becomes computationally expensive. Results In this paper, we focused on accelerating the Smith-Waterman algorithm by using FPGA-based hardware that implemented a module for computing the score of a single cell of the SW matrix. Then using a grid of this module, the entire SW matrix was computed at the speed of field propagation through the FPGA circuit. These modifications dramatically accelerated the algorithm's computation time by up to 160 folds compared to a pure software implementation running on the same FPGA with an Altera Nios II softprocessor. Conclusion This design of FPGA accelerated hardware offers a new promising direction to seeking computation improvement of genomic database searching. PMID:17555593

  13. 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA).

    PubMed

    Li, Isaac T S; Shum, Warren; Truong, Kevin

    2007-06-07

    To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching sequence databases that may contain hundreds of millions of sequences, this algorithm becomes computationally expensive. In this paper, we focused on accelerating the Smith-Waterman algorithm by using FPGA-based hardware that implemented a module for computing the score of a single cell of the SW matrix. Then using a grid of this module, the entire SW matrix was computed at the speed of field propagation through the FPGA circuit. These modifications dramatically accelerated the algorithm's computation time by up to 160 folds compared to a pure software implementation running on the same FPGA with an Altera Nios II softprocessor. This design of FPGA accelerated hardware offers a new promising direction to seeking computation improvement of genomic database searching.

  14. Turning Search into Knowledge Management.

    ERIC Educational Resources Information Center

    Kaufman, David

    2002-01-01

    Discussion of knowledge management for electronic data focuses on creating a high quality similarity ranking algorithm. Topics include similarity ranking and unstructured data management; searching, categorization, and summarization of documents; query evaluation; considering sentences in addition to keywords; and vector models. (LRW)

  15. Tachyon search speeds up retrieval of similar sequences by several orders of magnitude.

    PubMed

    Tan, Joshua; Kuchibhatla, Durga; Sirota, Fernanda L; Sherman, Westley A; Gattermayer, Tobias; Kwoh, Chia Yee; Eisenhaber, Frank; Schneider, Georg; Maurer-Stroh, Sebastian

    2012-06-15

    The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP.

  16. Nonthermally dominated electron acceleration during magnetic reconnection in a low- β plasma

    DOE PAGES

    Li, Xiaocan; Guo, Fan; Li, Hui; ...

    2015-09-24

    By means of fully kinetic simulations, we investigate electron acceleration during magnetic reconnection in a nonrelativistic proton–electron plasma with conditions similar to solar corona and flares. We demonstrate that reconnection leads to a nonthermally dominated electron acceleration with a power-law energy distribution in the nonrelativistic low-β regime but not in the high-β regime, where β is the ratio of the plasma thermal pressure and the magnetic pressure. The accelerated electrons contain most of the dissipated magnetic energy in the low-β regime. A guiding-center current description is used to reveal the role of electron drift motions during the bulk nonthermal energization.more » We find that the main acceleration mechanism is a Fermi-type acceleration accomplished by the particle curvature drift motion along the electric field induced by the reconnection outflows. Although the acceleration mechanism is similar for different plasma β, low-β reconnection drives fast acceleration on Alfvénic timescales and develops power laws out of thermal distribution. Thus, the nonthermally dominated acceleration resulting from magnetic reconnection in low-β plasma may have strong implications for the highly efficient electron acceleration in solar flares and other astrophysical systems.« less

  17. Linear accelerator stereotactic radiosurgery for trigeminal neuralgia.

    PubMed

    Varela-Lema, Leonor; Lopez-Garcia, Marisa; Maceira-Rozas, Maria; Munoz-Garzon, Victor

    2015-01-01

    Stereotactic radiosurgery is accepted as an alternative for patients with refractory trigeminal neuralgia, but existing evidence is fundamentally based on the Gamma Knife, which is a specific device for intracranial neurosurgery, available in few facilities. Over the last decade it has been shown that the use of linear accelerators can achieve similar diagnostic accuracy and equivalent dose distribution. To assess the effectiveness and safety of linear-accelerator stereotactic radiosurgery for the treatment of patients with refractory trigeminal neuralgia. We carried out a systematic search of the literature in the main electronic databases (PubMed, Embase, ISI Web of Knowledge, Cochrane, Biomed Central, IBECS, IME, CRD) and reviewed grey literature. All original studies on the subject published in Spanish, French, English, and Portuguese were eligible for inclusion. The selection and critical assessment was carried out by 2 independent reviewers based on pre-defined criteria. In view of the impossibility of carrying out a pooled analysis, data were analyzed in a qualitative way. Eleven case series were included. In these, satisfactory pain relief (BIN I-IIIb or reduction in pain = 50) was achieved in 75% to 95.7% of the patients treated. The mean time to relief from pain ranged from 8.5 days to 3.8 months. The percentage of patients who presented with recurrences after one year of follow-up ranged from 5% to 28.8%. Facial swelling or hypoesthesia, mostly of a mild-moderate grade appeared in 7.5% - 51.9% of the patients. Complete anaesthesia dolorosa was registered in only study (5.3%). Cases of hearing loss (2.5%), brainstem edema (5.8%), and neurotrophic keratoplasty (3.5%) were also isolated. The results suggest that stereotactic radiosurgery with linear accelerators could constitute an effective and safe therapeutic alternative for drug-resistant trigeminal neuralgia. However, existing studies leave important doubts as to optimal treatment doses or the

  18. Interest in Anesthesia as Reflected by Keyword Searches using Common Search Engines.

    PubMed

    Liu, Renyu; García, Paul S; Fleisher, Lee A

    2012-01-23

    Since current general interest in anesthesia is unknown, we analyzed internet keyword searches to gauge general interest in anesthesia in comparison with surgery and pain. The trend of keyword searches from 2004 to 2010 related to anesthesia and anaesthesia was investigated using Google Insights for Search. The trend of number of peer reviewed articles on anesthesia cited on PubMed and Medline from 2004 to 2010 was investigated. The average cost on advertising on anesthesia, surgery and pain was estimated using Google AdWords. Searching results in other common search engines were also analyzed. Correlation between year and relative number of searches was determined with p< 0.05 considered statistically significant. Searches for the keyword "anesthesia" or "anaesthesia" diminished since 2004 reflected by Google Insights for Search (p< 0.05). The search for "anesthesia side effects" is trending up over the same time period while the search for "anesthesia and safety" is trending down. The search phrase "before anesthesia" is searched more frequently than "preanesthesia" and the search for "before anesthesia" is trending up. Using "pain" as a keyword is steadily increasing over the years indicated. While different search engines may provide different total number of searching results (available posts), the ratios of searching results between some common keywords related to perioperative care are comparable, indicating similar trend. The peer reviewed manuscripts on "anesthesia" and the proportion of papers on "anesthesia and outcome" are trending up. Estimates for spending of advertising dollars are less for anesthesia-related terms when compared to that for pain or surgery due to relative smaller number of searching traffic. General interest in anesthesia (anaesthesia) as measured by internet searches appears to be decreasing. Pain, preanesthesia evaluation, anesthesia and outcome and side effects of anesthesia are the critical areas that anesthesiologists should

  19. Taboo search by successive confinement: Surveying a potential energy surface

    NASA Astrophysics Data System (ADS)

    Chekmarev, Sergei F.

    2001-09-01

    A taboo search for minima on a potential energy surface (PES) is performed by means of confinement molecular dynamics: the molecular dynamics trajectory of the system is successively confined to various basins on the PES that have not been sampled yet. The approach is illustrated for a 13-atom Lennard-Jones cluster. It is shown that the taboo search radically accelerates the process of surveying the PES, with the probability of finding a new minimum defined by a propagating Fermi-like distribution.

  20. Acceleration to failure in geophysical signals prior to laboratory rock failure and volcanic eruptions (Invited)

    NASA Astrophysics Data System (ADS)

    Main, I. G.; Bell, A. F.; Greenhough, J.; Heap, M. J.; Meredith, P. G.

    2010-12-01

    The nucleation processes that ultimately lead to earthquakes, volcanic eruptions, rock bursts in mines, and landslides from cliff slopes are likely to be controlled at some scale by brittle failure of the Earth’s crust. In laboratory brittle deformation experiments geophysical signals commonly exhibit an accelerating trend prior to dynamic failure. Similar signals have been observed prior to volcanic eruptions, including volcano-tectonic earthquake event and moment release rates. Despite a large amount of effort in the search, no such statistically robust systematic trend is found prior to natural earthquakes. Here we describe the results of a suite of laboratory tests on Mount Etna Basalt and other rocks to examine the nature of the non-linear scaling from laboratory to field conditions, notably using laboratory ‘creep’ tests to reduce the boundary strain rate to conditions more similar to those in the field. Seismic event rate, seismic moment release rate and rate of porosity change show a classic ‘bathtub’ graph that can be derived from a simple damage model based on separate transient and accelerating sub-critical crack growth mechanisms, resulting from separate processes of negative and positive feedback in the population dynamics. The signals exhibit clear precursors based on formal statistical model tests using maximum likelihood techniques with Poisson errors. After correcting for the finite loading time of the signal, the results show a transient creep rate that decays as a classic Omori law for earthquake aftershocks, and remarkably with an exponent near unity, as commonly observed for natural earthquake sequences. The accelerating trend follows an inverse power law when fitted in retrospect, i.e. with prior knowledge of the failure time. In contrast the strain measured on the sample boundary shows a less obvious but still accelerating signal that is often absent altogether in natural strain data prior to volcanic eruptions. To test the

  1. Face Search at Scale.

    PubMed

    Wang, Dayong; Otto, Charles; Jain, Anil K

    2017-06-01

    Given the prevalence of social media websites, one challenge facing computer vision researchers is to devise methods to search for persons of interest among the billions of shared photos on these websites. Despite significant progress in face recognition, searching a large collection of unconstrained face images remains a difficult problem. To address this challenge, we propose a face search system which combines a fast search procedure, coupled with a state-of-the-art commercial off the shelf (COTS) matcher, in a cascaded framework. Given a probe face, we first filter the large gallery of photos to find the top- k most similar faces using features learned by a convolutional neural network. The k retrieved candidates are re-ranked by combining similarities based on deep features and those output by the COTS matcher. We evaluate the proposed face search system on a gallery containing 80 million web-downloaded face images. Experimental results demonstrate that while the deep features perform worse than the COTS matcher on a mugshot dataset (93.7 percent versus 98.6 percent TAR@FAR of 0.01 percent), fusing the deep features with the COTS matcher improves the overall performance ( 99.5 percent TAR@FAR of 0.01 percent). This shows that the learned deep features provide complementary information over representations used in state-of-the-art face matchers. On the unconstrained face image benchmarks, the performance of the learned deep features is competitive with reported accuracies. LFW database: 98.20 percent accuracy under the standard protocol and 88.03 percent TAR@FAR of 0.1 percent under the BLUFR protocol; IJB-A benchmark: 51.0 percent TAR@FAR of 0.1 percent (verification), rank 1 retrieval of 82.2 percent (closed-set search), 61.5 percent FNIR@FAR of 1 percent (open-set search). The proposed face search system offers an excellent trade-off between accuracy and scalability on galleries with millions of images. Additionally, in a face search experiment involving

  2. Simultaneous Multislice Echo Planar Imaging With Blipped Controlled Aliasing in Parallel Imaging Results in Higher Acceleration: A Promising Technique for Accelerated Diffusion Tensor Imaging of Skeletal Muscle.

    PubMed

    Filli, Lukas; Piccirelli, Marco; Kenkel, David; Guggenberger, Roman; Andreisek, Gustav; Beck, Thomas; Runge, Val M; Boss, Andreas

    2015-07-01

    The aim of this study was to investigate the feasibility of accelerated diffusion tensor imaging (DTI) of skeletal muscle using echo planar imaging (EPI) applying simultaneous multislice excitation with a blipped controlled aliasing in parallel imaging results in higher acceleration unaliasing technique. After federal ethics board approval, the lower leg muscles of 8 healthy volunteers (mean [SD] age, 29.4 [2.9] years) were examined in a clinical 3-T magnetic resonance scanner using a 15-channel knee coil. The EPI was performed at a b value of 500 s/mm2 without slice acceleration (conventional DTI) as well as with 2-fold and 3-fold acceleration. Fractional anisotropy (FA) and mean diffusivity (MD) were measured in all 3 acquisitions. Fiber tracking performance was compared between the acquisitions regarding the number of tracks, average track length, and anatomical precision using multivariate analysis of variance and Mann-Whitney U tests. Acquisition time was 7:24 minutes for conventional DTI, 3:53 minutes for 2-fold acceleration, and 2:38 minutes for 3-fold acceleration. Overall FA and MD values ranged from 0.220 to 0.378 and 1.595 to 1.829 mm2/s, respectively. Two-fold acceleration yielded similar FA and MD values (P ≥ 0.901) and similar fiber tracking performance compared with conventional DTI. Three-fold acceleration resulted in comparable MD (P = 0.199) but higher FA values (P = 0.006) and significantly impaired fiber tracking in the soleus and tibialis anterior muscles (number of tracks, P < 0.001; anatomical precision, P ≤ 0.005). Simultaneous multislice EPI with blipped controlled aliasing in parallel imaging results in higher acceleration can remarkably reduce acquisition time in DTI of skeletal muscle with similar image quality and quantification accuracy of diffusion parameters. This may increase the clinical applicability of muscle anisotropy measurements.

  3. Parametric Quantum Search Algorithm as Quantum Walk: A Quantum Simulation

    NASA Astrophysics Data System (ADS)

    Ellinas, Demosthenes; Konstandakis, Christos

    2016-02-01

    Parametric quantum search algorithm (PQSA) is a form of quantum search that results by relaxing the unitarity of the original algorithm. PQSA can naturally be cast in the form of quantum walk, by means of the formalism of oracle algebra. This is due to the fact that the completely positive trace preserving search map used by PQSA, admits a unitarization (unitary dilation) a la quantum walk, at the expense of introducing auxiliary quantum coin-qubit space. The ensuing QW describes a process of spiral motion, chosen to be driven by two unitary Kraus generators, generating planar rotations of Bloch vector around an axis. The quadratic acceleration of quantum search translates into an equivalent quadratic saving of the number of coin qubits in the QW analogue. The associated to QW model Hamiltonian operator is obtained and is shown to represent a multi-particle long-range interacting quantum system that simulates parametric search. Finally, the relation of PQSA-QW simulator to the QW search algorithm is elucidated.

  4. Dual Target Search is Neither Purely Simultaneous nor Purely Successive.

    PubMed

    Cave, Kyle R; Menneer, Tamaryn; Nomani, Mohammad S; Stroud, Michael J; Donnelly, Nick

    2017-08-31

    Previous research shows that visual search for two different targets is less efficient than search for a single target. Stroud, Menneer, Cave and Donnelly (2012) concluded that two target colours are represented separately based on modeling the fixation patterns. Although those analyses provide evidence for two separate target representations, they do not show whether participants search simultaneously for both targets, or first search for one target and then the other. Some studies suggest that multiple target representations are simultaneously active, while others indicate that search can be voluntarily simultaneous, or switching, or a mixture of both. Stroud et al.'s participants were not explicitly instructed to use any particular strategy. These data were revisited to determine which strategy was employed. Each fixated item was categorised according to whether its colour was more similar to one target or the other. Once an item similar to one target is fixated, the next fixated item is more likely to be similar to that target than the other, showing that at a given moment during search, one target is generally favoured. However, the search for one target is not completed before search for the other begins. Instead, there are often short runs of one or two fixations to distractors similar to one target, with each run followed by a switch to the other target. Thus, the results suggest that one target is more highly weighted than the other at any given time, but not to the extent that search is purely successive.

  5. Power Supplies for High Energy Particle Accelerators

    NASA Astrophysics Data System (ADS)

    Dey, Pranab Kumar

    2016-06-01

    The on-going research and the development projects with Large Hadron Collider at CERN, Geneva, Switzerland has generated enormous enthusiasm and interest amongst all to know about the ultimate findings on `God's Particle'. This paper has made an attempt to unfold the power supply requirements and the methodology adopted to provide the stringent demand of such high energy particle accelerators during the initial stages of the search for the ultimate particles. An attempt has also been made to highlight the present status on the requirement of power supplies in some high energy accelerators with a view that, precautionary measures can be drawn during design and development from earlier experience which will be of help for the proposed third generation synchrotron to be installed in India at a huge cost.

  6. Accelerator mass spectrometry for measurement of long-lived radioisotopes.

    PubMed

    Elmore, D; Phillips, F M

    1987-05-01

    Particle accelerators, such as those built for research in nuclear physics, can also be used together with magnetic and electrostatic mass analyzers to measure rare isotopes at very low abundance ratios. All molecular ions can be eliminated when accelerated to energies of millions of electron volts. Some atomic isobars can be eliminated with the use of negative ions; others can be separated at high energies by measuring their rate of energy loss in a detector. The long-lived radioisotopes (10)Be, (14)C,(26)A1, 36Cl, and (129)1 can now be measured in small natural samples having isotopic abundances in the range 10(-12) to 10(- 5) and as few as 10(5) atoms. In the past few years, research applications of accelerator mass spectrometry have been concentrated in the earth sciences (climatology, cosmochemistry, environmental chemistry, geochronology, glaciology, hydrology, igneous petrogenesis, minerals exploration, sedimentology, and volcanology), in anthropology and archeology (radiocarbon dating), and in physics (searches for exotic particles and measurement of halflives). In addition, accelerator mass spectrometry may become an important tool for the materials and biological sciences.

  7. Accelerator Mass Spectrometry for Measurement of Long-Lived Radioisotopes

    NASA Astrophysics Data System (ADS)

    Elmore, David; Phillips, Fred M.

    1987-05-01

    Particle accelerators, such as those built for research in nuclear physics, can also be used together with magnetic and electrostatic mass analyzers to measure rare isotopes at very low abundance ratios. All molecular ions can be eliminated when accelerated to energies of millions of electron volts. Some atomic isobars can be eliminated with the use of negative ions; others can be separated at high energies by measuring their rate of energy loss in a detector. The long-lived radioisotopes 10Be, 14C, 26Al, 36Cl, and 129I can now be measured in small natural samples having isotopic abundances in the range 10-12 to 10-15 and as few as 105 atoms. In the past few years, research applications of accelerator mass spectrometry have been concentrated in the earth sciences (climatology, cosmochemistry, environmental chemistry, geochronology, glaciology, hydrology, igneous petrogenesis, minerals exploration, sedimentology, and volcanology), in anthropology and archeology (radiocarbon dating), and in physics (searches for exotic particles and measurement of half-lives). In addition, accelerator mass spectrometry may become an important tool for the materials and biological sciences.

  8. Fully vectorial accelerating diffraction-free Helmholtz beams.

    PubMed

    Aleahmad, Parinaz; Miri, Mohammad-Ali; Mills, Matthew S; Kaminer, Ido; Segev, Mordechai; Christodoulides, Demetrios N

    2012-11-16

    We show that new families of diffraction-free nonparaxial accelerating optical beams can be generated by considering the symmetries of the underlying vectorial Helmholtz equation. Both two-dimensional transverse electric and magnetic accelerating wave fronts are possible, capable of moving along elliptic trajectories. Experimental results corroborate these predictions when these waves are launched from either the major or minor axis of the ellipse. In addition, three-dimensional spherical nondiffracting field configurations are presented along with their evolution dynamics. Finally, fully vectorial self-similar accelerating optical wave solutions are obtained via oblate-prolate spheroidal wave functions. In all occasions, these effects are illustrated via pertinent examples.

  9. Mass spectrometry with accelerators.

    PubMed

    Litherland, A E; Zhao, X-L; Kieser, W E

    2011-01-01

    As one in a series of articles on Canadian contributions to mass spectrometry, this review begins with an outline of the history of accelerator mass spectrometry (AMS), noting roles played by researchers at three Canadian AMS laboratories. After a description of the unique features of AMS, three examples, (14)C, (10)Be, and (129)I are given to illustrate the methods. The capabilities of mass spectrometry have been extended by the addition of atomic isobar selection, molecular isobar attenuation, further ion acceleration, followed by ion detection and ion identification at essentially zero dark current or ion flux. This has been accomplished by exploiting the techniques and accelerators of atomic and nuclear physics. In 1939, the first principles of AMS were established using a cyclotron. In 1977 the selection of isobars in the ion source was established when it was shown that the (14)N(-) ion was very unstable, or extremely difficult to create, making a tandem electrostatic accelerator highly suitable for assisting the mass spectrometric measurement of the rare long-lived radioactive isotope (14)C in the environment. This observation, together with the large attenuation of the molecular isobars (13)CH(-) and (12)CH 2(-) during tandem acceleration and the observed very low background contamination from the ion source, was found to facilitate the mass spectrometry of (14)C to at least a level of (14)C/C ~ 6 × 10(-16), the equivalent of a radiocarbon age of 60,000 years. Tandem Accelerator Mass Spectrometry, or AMS, has now made possible the accurate radiocarbon dating of milligram-sized carbon samples by ion counting as well as dating and tracing with many other long-lived radioactive isotopes such as (10)Be, (26)Al, (36)Cl, and (129)I. The difficulty of obtaining large anion currents with low electron affinities and the difficulties of isobar separation, especially for the heavier mass ions, has prompted the use of molecular anions and the search for alternative

  10. Acceleration modules in linear induction accelerators

    NASA Astrophysics Data System (ADS)

    Wang, Shao-Heng; Deng, Jian-Jun

    2014-05-01

    The Linear Induction Accelerator (LIA) is a unique type of accelerator that is capable of accelerating kilo-Ampere charged particle current to tens of MeV energy. The present development of LIA in MHz bursting mode and the successful application into a synchrotron have broadened LIA's usage scope. Although the transformer model is widely used to explain the acceleration mechanism of LIAs, it is not appropriate to consider the induction electric field as the field which accelerates charged particles for many modern LIAs. We have examined the transition of the magnetic cores' functions during the LIA acceleration modules' evolution, distinguished transformer type and transmission line type LIA acceleration modules, and re-considered several related issues based on transmission line type LIA acceleration module. This clarified understanding should help in the further development and design of LIA acceleration modules.

  11. Analysis of a librarian-mediated literature search service.

    PubMed

    Friesen, Carol; Lê, Mê-Linh; Cooke, Carol; Raynard, Melissa

    2015-01-01

    Librarian-mediated literature searching is a key service provided at medical libraries. This analysis outlines ten years of data on 19,248 literature searches and describes information on the volume and frequency of search requests, time spent per search, databases used, and professional designations of the patron requestors. Combined with information on best practices for expert searching and evaluations of similar services, these findings were used to form recommendations on the improvement and standardization of a literature search service at a large health library system.

  12. Improving visual search in instruction manuals using pictograms.

    PubMed

    Kovačević, Dorotea; Brozović, Maja; Možina, Klementina

    2016-11-01

    Instruction manuals provide important messages about the proper use of a product. They should communicate in such a way that they facilitate users' searches for specific information. Despite the increasing research interest in visual search, there is a lack of empirical knowledge concerning the role of pictograms in search performance during the browsing of a manual's pages. This study investigates how the inclusion of pictograms improves the search for the target information. Furthermore, it examines whether this search process is influenced by the visual similarity between the pictograms and the searched for information. On the basis of eye-tracking measurements, as objective indicators of the participants' visual attention, it was found that pictograms can be a useful element of search strategy. Another interesting finding was that boldface highlighting is a more effective method for improving user experience in information seeking, rather than the similarity between the pictorial and adjacent textual information. Implications for designing effective user manuals are discussed. Practitioner Summary: Users often view instruction manuals with the aim of finding specific information. We used eye-tracking technology to examine different manual pages in order to improve the user's visual search for target information. The results indicate that the use of pictograms and bold highlighting of relevant information facilitate the search process.

  13. Photon spectral characteristics of dissimilar 6 MV linear accelerators.

    PubMed

    Hinson, William H; Kearns, William T; deGuzman, Allan F; Bourland, J Daniel

    2008-05-01

    This work measures and compares the energy spectra of four dosimetrically matched 6 MV beams, generated from four physically different linear accelerators. The goal of this work is twofold. First, this study determines whether the spectra of dosimetrically matched beams are measurably different. This study also demonstrates that the spectra of clinical photon beams can be measured as a part of the beam data collection process for input to a three-dimensional (3D) treatment planning system. The spectra of 6 MV beams that are dosimetrically matched for clinical use were studied to determine if the beam spectra are similarly matched. Each of the four accelerators examined had a standing waveguide, but with different physical designs. The four accelerators were two Varian 2100C/Ds (one 6 MV/18 MV waveguide and one 6 MV/10 MV waveguide), one Varian 600 C with a vertically mounted waveguide and no bending magnet, and one Siemens MD 6740 with a 6 MV/10 MV waveguide. All four accelerators had percent depth dose curves for the 6 MV beam that were matched within 1.3%. Beam spectra were determined from narrow beam transmission measurements through successive thicknesses of pure aluminum along the central axis of the accelerator, made with a graphite Farmer ion chamber with a Lucite buildup cap. An iterative nonlinear fit using a Marquardt algorithm was used to find each spectrum. Reconstructed spectra show that all four beams have similar energy distributions with only subtle differences, despite the differences in accelerator design. The measured spectra of different 6 MV beams are similar regardless of accelerator design. The measured spectra show excellent agreement with those found by the auto-modeling algorithm in a commercial 3D treatment planning system that uses a convolution dose calculation algorithm. Thus, beam spectra can be acquired in a clinical setting at the time of commissioning as a part of the routine beam data collection.

  14. Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins.

    PubMed

    Kemme, Catherine A; Marquez, Rolando; Luu, Ross H; Iwahara, Junji

    2017-07-27

    Eukaryotic genomes contain numerous non-functional high-affinity sequences for transcription factors. These sequences potentially serve as natural decoys that sequester transcription factors. We have previously shown that the presence of sequences similar to the target sequence could substantially impede association of the transcription factor Egr-1 with its targets. In this study, using a stopped-flow fluorescence method, we examined the kinetic impact of DNA methylation of decoys on the search process of the Egr-1 zinc-finger protein. We analyzed its association with an unmethylated target site on fluorescence-labeled DNA in the presence of competitor DNA duplexes, including Egr-1 decoys. DNA methylation of decoys alone did not affect target search kinetics. In the presence of the MeCP2 methyl-CpG-binding domain (MBD), however, DNA methylation of decoys substantially (∼10-30-fold) accelerated the target search process of the Egr-1 zinc-finger protein. This acceleration did not occur when the target was also methylated. These results suggest that when decoys are methylated, MBD proteins can block them and thereby allow Egr-1 to avoid sequestration in non-functional locations. This effect may occur in vivo for DNA methylation outside CpG islands (CGIs) and could facilitate localization of some transcription factors within regulatory CGIs, where DNA methylation is rare. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Interest in Anesthesia as Reflected by Keyword Searches using Common Search Engines

    PubMed Central

    Liu, Renyu; García, Paul S.; Fleisher, Lee A.

    2012-01-01

    Background Since current general interest in anesthesia is unknown, we analyzed internet keyword searches to gauge general interest in anesthesia in comparison with surgery and pain. Methods The trend of keyword searches from 2004 to 2010 related to anesthesia and anaesthesia was investigated using Google Insights for Search. The trend of number of peer reviewed articles on anesthesia cited on PubMed and Medline from 2004 to 2010 was investigated. The average cost on advertising on anesthesia, surgery and pain was estimated using Google AdWords. Searching results in other common search engines were also analyzed. Correlation between year and relative number of searches was determined with p< 0.05 considered statistically significant. Results Searches for the keyword “anesthesia” or “anaesthesia” diminished since 2004 reflected by Google Insights for Search (p< 0.05). The search for “anesthesia side effects” is trending up over the same time period while the search for “anesthesia and safety” is trending down. The search phrase “before anesthesia” is searched more frequently than “preanesthesia” and the search for “before anesthesia” is trending up. Using “pain” as a keyword is steadily increasing over the years indicated. While different search engines may provide different total number of searching results (available posts), the ratios of searching results between some common keywords related to perioperative care are comparable, indicating similar trend. The peer reviewed manuscripts on “anesthesia” and the proportion of papers on “anesthesia and outcome” are trending up. Estimates for spending of advertising dollars are less for anesthesia-related terms when compared to that for pain or surgery due to relative smaller number of searching traffic. Conclusions General interest in anesthesia (anaesthesia) as measured by internet searches appears to be decreasing. Pain, preanesthesia evaluation, anesthesia and outcome and side

  16. Perceptual load corresponds with factors known to influence visual search.

    PubMed

    Roper, Zachary J J; Cosman, Joshua D; Vecera, Shaun P

    2013-10-01

    One account of the early versus late selection debate in attention proposes that perceptual load determines the locus of selection. Attention selects stimuli at a late processing level under low-load conditions but selects stimuli at an early level under high-load conditions. Despite the successes of perceptual load theory, a noncircular definition of perceptual load remains elusive. We investigated the factors that influence perceptual load by using manipulations that have been studied extensively in visual search, namely target-distractor similarity and distractor-distractor similarity. Consistent with previous work, search was most efficient when targets and distractors were dissimilar and the displays contained homogeneous distractors; search became less efficient when target-distractor similarity increased irrespective of display heterogeneity. Importantly, we used these same stimuli in a typical perceptual load task that measured attentional spillover to a task-irrelevant flanker. We found a strong correspondence between search efficiency and perceptual load; stimuli that generated efficient searches produced flanker interference effects, suggesting that such displays involved low perceptual load. Flanker interference effects were reduced in displays that produced less efficient searches. Furthermore, our results demonstrate that search difficulty, as measured by search intercept, has little bearing on perceptual load. We conclude that rather than be arbitrarily defined, perceptual load might be defined by well-characterized, continuous factors that influence visual search. PsycINFO Database Record (c) 2013 APA, all rights reserved.

  17. Perceptual load corresponds with factors known to influence visual search

    PubMed Central

    Roper, Zachary J. J.; Cosman, Joshua D.; Vecera, Shaun P.

    2014-01-01

    One account of the early versus late selection debate in attention proposes that perceptual load determines the locus of selection. Attention selects stimuli at a late processing level under low-load conditions but selects stimuli at an early level under high-load conditions. Despite the successes of perceptual load theory, a non-circular definition of perceptual load remains elusive. We investigated the factors that influence perceptual load by using manipulations that have been studied extensively in visual search, namely target-distractor similarity and distractor-distractor similarity. Consistent with previous work, search was most efficient when targets and distractors were dissimilar and the displays contained homogeneous distractors; search became less efficient when target-distractor similarity increased irrespective of display heterogeneity. Importantly, we used these same stimuli in a typical perceptual load task that measured attentional spill-over to a task-irrelevant flanker. We found a strong correspondence between search efficiency and perceptual load; stimuli that generated efficient searches produced flanker interference effects, suggesting that such displays involved low perceptual load. Flanker interference effects were reduced in displays that produced less efficient searches. Furthermore, our results demonstrate that search difficulty, as measured by search intercept, has little bearing on perceptual load. These results suggest that perceptual load might be defined in part by well-characterized, continuous factors that influence visual search. PMID:23398258

  18. Dynamic Search and Working Memory in Social Recall

    ERIC Educational Resources Information Center

    Hills, Thomas T.; Pachur, Thorsten

    2012-01-01

    What are the mechanisms underlying search in social memory (e.g., remembering the people one knows)? Do the search mechanisms involve dynamic local-to-global transitions similar to semantic search, and are these transitions governed by the general control of attention, associated with working memory span? To find out, we asked participants to…

  19. GWFASTA: server for FASTA search in eukaryotic and microbial genomes.

    PubMed

    Issac, Biju; Raghava, G P S

    2002-09-01

    Similarity searches are a powerful method for solving important biological problems such as database scanning, evolutionary studies, gene prediction, and protein structure prediction. FASTA is a widely used sequence comparison tool for rapid database scanning. Here we describe the GWFASTA server that was developed to assist the FASTA user in similarity searches against partially and/or completely sequenced genomes. GWFASTA consists of more than 60 microbial genomes, eight eukaryote genomes, and proteomes of annotatedgenomes. Infact, it provides the maximum number of databases for similarity searching from a single platform. GWFASTA allows the submission of more than one sequence as a single query for a FASTA search. It also provides integrated post-processing of FASTA output, including compositional analysis of proteins, multiple sequences alignment, and phylogenetic analysis. Furthermore, it summarizes the search results organism-wise for prokaryotes and chromosome-wise for eukaryotes. Thus, the integration of different tools for sequence analyses makes GWFASTA a powerful toolfor biologists.

  20. Minimizing Head Acceleration in Soccer: A Review of the Literature.

    PubMed

    Caccese, Jaclyn B; Kaminski, Thomas W

    2016-11-01

    Physicians and healthcare professionals are often asked for recommendations on how to keep athletes safe during contact sports such as soccer. With an increase in concussion awareness and concern about repetitive subconcussion, many parents and athletes are interested in mitigating head acceleration in soccer, so we conducted a literature review on factors that affect head acceleration in soccer. We searched electronic databases and reference lists to find studies using the keywords 'soccer' OR 'football' AND 'head acceleration'. Because of a lack of current research in soccer heading biomechanics, this review was limited to 18 original research studies. Low head-neck segment mass predisposes athletes to high head acceleration, but head-neck-torso alignment during heading and follow-through after contact can be used to decrease head acceleration. Additionally, improvements in symmetric neck flexor and extensor strength and neuromuscular neck stiffness can decrease head acceleration. Head-to-head impacts and unanticipated ball contacts result in the highest head acceleration. Ball contacts at high velocity may also be dangerous. The risk of concussive impacts may be lessened through the use of headgear, but headgear may also cause athletes to play more recklessly because they feel a sense of increased security. Young, but physically capable, athletes should be taught proper heading technique in a controlled setting, using a carefully planned progression of the skill.

  1. Convectively driven decadal zonal accelerations in Earth's fluid core

    NASA Astrophysics Data System (ADS)

    More, Colin; Dumberry, Mathieu

    2018-04-01

    Azimuthal accelerations of cylindrical surfaces co-axial with the rotation axis have been inferred to exist in Earth's fluid core on the basis of magnetic field observations and changes in the length-of-day. These accelerations have a typical timescale of decades. However, the physical mechanism causing the accelerations is not well understood. Scaling arguments suggest that the leading order torque averaged over cylindrical surfaces should arise from the Lorentz force. Decadal fluctuations in the magnetic field inside the core, driven by convective flows, could then force decadal changes in the Lorentz torque and generate zonal accelerations. We test this hypothesis by constructing a quasi-geostrophic model of magnetoconvection, with thermally driven flows perturbing a steady, imposed background magnetic field. We show that when the Alfvén number in our model is similar to that in Earth's fluid core, temporal fluctuations in the torque balance are dominated by the Lorentz torque, with the latter generating mean zonal accelerations. Our model reproduces both fast, free Alfvén waves and slow, forced accelerations, with ratios of relative strength and relative timescale similar to those inferred for the Earth's core. The temporal changes in the magnetic field which drive the time-varying Lorentz torque are produced by the underlying convective flows, shearing and advecting the magnetic field on a timescale associated with convective eddies. Our results support the hypothesis that temporal changes in the magnetic field deep inside Earth's fluid core drive the observed decadal zonal accelerations of cylindrical surfaces through the Lorentz torque.

  2. Microgravity acceleration measurement and environment characterization science (17-IML-1)

    NASA Technical Reports Server (NTRS)

    1992-01-01

    The Space Acceleration Measurement System (SAMS) is a general purpose instrumentation system designed to measure the accelerations onboard the Shuttle Orbiter and Shuttle/Spacelab vehicles. These measurements are used to support microgravity experiments and investigation into the microgravity environment of the vehicle. Acceleration measurements can be made at locations remote from the SAMS main instrumentation unit by the use of up to three remote triaxial sensor heads. The prime objective for SAMS on the International Microgravity Lab (IML-1) mission will be to measure the accelerations experienced by the Fluid Experiment System (FES). The SAMS acceleration measurements for FES will be complemented by low level, low frequency acceleration measurements made by the Orbital Acceleration Research Experiment (OARE) installed on the shuttle. Secondary objectives for SAMS will be to measure accelerations at several specific locations to enable the acceleration transfer function of the Spacelab module to be analyzed. This analysis effort will be in conjunction with similar measurements analyses on other Spacelab missions.

  3. Visual search and autism symptoms: What young children search for and co-occurring ADHD matter.

    PubMed

    Doherty, Brianna R; Charman, Tony; Johnson, Mark H; Scerif, Gaia; Gliga, Teodora

    2018-05-03

    Superior visual search is one of the most common findings in the autism spectrum disorder (ASD) literature. Here, we ascertain how generalizable these findings are across task and participant characteristics, in light of recent replication failures. We tested 106 3-year-old children at familial risk for ASD, a sample that presents high ASD and ADHD symptoms, and 25 control participants, in three multi-target search conditions: easy exemplar search (look for cats amongst artefacts), difficult exemplar search (look for dogs amongst chairs/tables perceptually similar to dogs), and categorical search (look for animals amongst artefacts). Performance was related to dimensional measures of ASD and ADHD, in agreement with current research domain criteria (RDoC). We found that ASD symptom severity did not associate with enhanced performance in search, but did associate with poorer categorical search in particular, consistent with literature describing impairments in categorical knowledge in ASD. Furthermore, ASD and ADHD symptoms were both associated with more disorganized search paths across all conditions. Thus, ASD traits do not always convey an advantage in visual search; on the contrary, ASD traits may be associated with difficulties in search depending upon the nature of the stimuli (e.g., exemplar vs. categorical search) and the presence of co-occurring symptoms. © 2018 John Wiley & Sons Ltd.

  4. Acceleration mechanisms for energetic particles in the earth's magnetosphere

    NASA Technical Reports Server (NTRS)

    Schiferl, S.; Fan, C. Y.; Hsieh, K. C.; Erickson, K. N.; Gloeckler, G.

    1982-01-01

    By analyzing data on energetic particle fluxes measured simultaneously with detector systems on several earth satellites, signatures of different acceleration mechanisms for these particles were searched for. One of the samples is an event observed on ATS-6 and IMP-7. IMP-7 was in the dusk quarter at 38 earth radii while ATS-6 was located at local midnight at a distance of 6.6 earth radii. Although the flux variations as observed on the two spacecraft both showed 1.5 min periodicity, there was a 40-second time lag with IMP-7 behind. The results indicate that the particles are accelerated by magnetic field line annihilation, with the x-point located at about 10 earth radii.

  5. Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

    PubMed Central

    Tan, Joshua; Kuchibhatla, Durga; Sirota, Fernanda L.; Sherman, Westley A.; Gattermayer, Tobias; Kwoh, Chia Yee; Eisenhaber, Frank; Schneider, Georg; Maurer-Stroh, Sebastian

    2012-01-01

    Summary: The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. Availability and implementation: The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP. Contact: sebastianms@bii.a-star.edu.sg Supplementary information: Supplementary data are available at the Bioinformatics online. PMID:22531216

  6. Absolute acceleration measurements on STS-50 from the Orbital Acceleration Research Experiment (OARE)

    NASA Technical Reports Server (NTRS)

    Blanchard, Robert C.; Nicholson, John Y.; Ritter, James R.

    1994-01-01

    Orbital Acceleration Research Experiment (OARE) data on Space Transportation System (STS)-50 have been examined in detail during a 2-day time period. Absolute acceleration levels have been derived at the OARE location, the orbiter center-of-gravity, and at the STS-50 spacelab Crystal Growth Facility. During the interval, the tri-axial OARE raw telemetered acceleration measurements have been filtered using a sliding trimmed mean filter in order to remove large acceleration spikes (e.g., thrusters) and reduce the noise. Twelve OARE measured biases in each acceleration channel during the 2-day interval have been analyzed and applied to the filtered data. Similarly, the in situ measured x-axis scale factors in the sensor's most sensitive range were also analyzed and applied to the data. Due to equipment problem(s) on this flight, both y- and z-axis sensitive range scale factors were determined in a separate process using orbiter maneuvers and subsequently applied to the data. All known significant low-frequency corrections at the OARE location (i.e., both vertical and horizontal gravity-gradient, and rotational effects) were removed from the filtered data in order to produce the acceleration components at the orbiter center-of-gravity, which are the aerodynamic signals along each body axis. Results indicate that there is a force being applied to the Orbiter in addition to the aerodynamic forces. The OARE instrument and all known gravitational and electromagnetic forces have been reexamined, but none produces the observed effect. Thus, it is tentatively concluded that the orbiter is creating the environment observed. At least part of this force is thought to be due to the Flash Evaporator System.

  7. Distribution uniformity of laser-accelerated proton beams

    NASA Astrophysics Data System (ADS)

    Zhu, Jun-Gao; Zhu, Kun; Tao, Li; Xu, Xiao-Han; Lin, Chen; Ma, Wen-Jun; Lu, Hai-Yang; Zhao, Yan-Ying; Lu, Yuan-Rong; Chen, Jia-Er; Yan, Xue-Qing

    2017-09-01

    Compared with conventional accelerators, laser plasma accelerators can generate high energy ions at a greatly reduced scale, due to their TV/m acceleration gradient. A compact laser plasma accelerator (CLAPA) has been built at the Institute of Heavy Ion Physics at Peking University. It will be used for applied research like biological irradiation, astrophysics simulations, etc. A beamline system with multiple quadrupoles and an analyzing magnet for laser-accelerated ions is proposed here. Since laser-accelerated ion beams have broad energy spectra and large angular divergence, the parameters (beam waist position in the Y direction, beam line layout, drift distance, magnet angles etc.) of the beamline system are carefully designed and optimised to obtain a radially symmetric proton distribution at the irradiation platform. Requirements of energy selection and differences in focusing or defocusing in application systems greatly influence the evolution of proton distributions. With optimal parameters, radially symmetric proton distributions can be achieved and protons with different energy spread within ±5% have similar transverse areas at the experiment target. Supported by National Natural Science Foundation of China (11575011, 61631001) and National Grand Instrument Project (2012YQ030142)

  8. Extracting similar terms from multiple EMR-based semantic embeddings to support chart reviews.

    PubMed

    Cheng Ye, M S; Fabbri, Daniel

    2018-05-21

    Word embeddings project semantically similar terms into nearby points in a vector space. When trained on clinical text, these embeddings can be leveraged to improve keyword search and text highlighting. In this paper, we present methods to refine the selection process of similar terms from multiple EMR-based word embeddings, and evaluate their performance quantitatively and qualitatively across multiple chart review tasks. Word embeddings were trained on each clinical note type in an EMR. These embeddings were then combined, weighted, and truncated to select a refined set of similar terms to be used in keyword search and text highlighting. To evaluate their quality, we measured the similar terms' information retrieval (IR) performance using precision-at-K (P@5, P@10). Additionally a user study evaluated users' search term preferences, while a timing study measured the time to answer a question from a clinical chart. The refined terms outperformed the baseline method's information retrieval performance (e.g., increasing the average P@5 from 0.48 to 0.60). Additionally, the refined terms were preferred by most users, and reduced the average time to answer a question. Clinical information can be more quickly retrieved and synthesized when using semantically similar term from multiple embeddings. Copyright © 2018. Published by Elsevier Inc.

  9. Dusty-Plasma Particle Accelerator

    NASA Technical Reports Server (NTRS)

    Foster, John E.

    2005-01-01

    A dusty-plasma apparatus is being investigated as means of accelerating nanometer- and micrometer-sized particles. Applications for the dusty-plasma particle accelerators fall into two classes: Simulation of a variety of rapidly moving dust particles and micrometeoroids in outer-space environments that include micrometeoroid streams, comet tails, planetary rings, and nebulae and Deposition or implantation of nanoparticles on substrates for diverse industrial purposes that could include hardening, increasing thermal insulation, altering optical properties, and/or increasing permittivities of substrate materials. Relative to prior apparatuses used for similar applications, dusty-plasma particle accelerators offer such potential advantages as smaller size, lower cost, less complexity, and increased particle flux densities. A dusty-plasma particle accelerator exploits the fact that an isolated particle immersed in plasma acquires a net electric charge that depends on the relative mobilities of electrons and ions. Typically, a particle that is immersed in a low-temperature, partially ionized gas, wherein the average kinetic energy of electrons exceeds that of ions, causes the particle to become negatively charged. The particle can then be accelerated by applying an appropriate electric field. A dusty-plasma particle accelerator (see figure) includes a plasma source such as a radio-frequency induction discharge apparatus containing (1) a shallow cup with a biasable electrode to hold the particles to be accelerated and (2) a holder for the substrate on which the particles are to impinge. Depending on the specific design, a pair of electrostatic-acceleration grids between the substrate and discharge plasma can be used to both collimate and further accelerate particles exiting the particle holder. Once exposed to the discharge plasma, the particles in the cup quickly acquire a negative charge. Application of a negative voltage pulse to the biasable electrode results in the

  10. Collisionless Shocks and Particle Acceleration.

    NASA Astrophysics Data System (ADS)

    Malkov, M.

    2016-12-01

    Collisionless shocks emerged in the 50s and 60s of the last century as an important branch of plasma physics and have remained ever since. New applications pose new challenges to our understanding of collisionless shock mechanisms. Particle acceleration in astrophysical settings, primarily studied concerning the putative origin of cosmic rays (CR) in supernova remnant (SNR) shocks, stands out with the collisionless shock mechanism being the key. Among recent laboratory applications, a laser-based tabletop proton accelerator is an affordable compact alternative to big synchrotron accelerators. The much-anticipated proof of cosmic ray (CR) acceleration in supernova remnants is hindered by our limited understanding of collisionless shock mechanisms. Over the last decade, dramatically improved observations were puzzling the theorists with unexpected discoveries. The difference between the helium/carbon and proton CR rigidity (momentum to charge ratio) spectra, seemingly inconsistent with the acceleration and propagation theories, and the perplexing positron excess in the 10-300 GeV range are just two recent examples. The latter is now also actively discussed in the particle physics and CR communities as a possible signature of decay or annihilation of hypothetical dark matter particles. By considering an initial (injection) phase of a diffusive shock acceleration mechanism, including particle reflection off the shock front - where an elemental similarity of particle dynamics does not apply - I will discuss recent suggestions of how to address the new data from the collisionless shock perspective. The backreaction of accelerated particles on the shock structure, its environment, and visibility across the electromagnetic spectrum from radio to gamma rays is another key aspect of collisionless shock that will be discussed.

  11. Design of a bioactive small molecule that targets the myotonic dystrophy type 1 RNA via an RNA motif-ligand database and chemical similarity searching.

    PubMed

    Parkesh, Raman; Childs-Disney, Jessica L; Nakamori, Masayuki; Kumar, Amit; Wang, Eric; Wang, Thomas; Hoskins, Jason; Tran, Tuan; Housman, David; Thornton, Charles A; Disney, Matthew D

    2012-03-14

    Myotonic dystrophy type 1 (DM1) is a triplet repeating disorder caused by expanded CTG repeats in the 3'-untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. The transcribed repeats fold into an RNA hairpin with multiple copies of a 5'CUG/3'GUC motif that binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1). Sequestration of MBNL1 by expanded r(CUG) repeats causes splicing defects in a subset of pre-mRNAs including the insulin receptor, the muscle-specific chloride ion channel, sarco(endo)plasmic reticulum Ca(2+) ATPase 1, and cardiac troponin T. Based on these observations, the development of small-molecule ligands that target specifically expanded DM1 repeats could be of use as therapeutics. In the present study, chemical similarity searching was employed to improve the efficacy of pentamidine and Hoechst 33258 ligands that have been shown previously to target the DM1 triplet repeat. A series of in vitro inhibitors of the RNA-protein complex were identified with low micromolar IC(50)'s, which are >20-fold more potent than the query compounds. Importantly, a bis-benzimidazole identified from the Hoechst query improves DM1-associated pre-mRNA splicing defects in cell and mouse models of DM1 (when dosed with 1 mM and 100 mg/kg, respectively). Since Hoechst 33258 was identified as a DM1 binder through analysis of an RNA motif-ligand database, these studies suggest that lead ligands targeting RNA with improved biological activity can be identified by using a synergistic approach that combines analysis of known RNA-ligand interactions with chemical similarity searching.

  12. Accelerator-based Neutrino Physics at Fermilab

    NASA Astrophysics Data System (ADS)

    Dukes, Edmond

    2008-10-01

    The discovery of neutrino mass has excited great interest in elucidating the properties of neutrinos and their role in nature. Experiments around the world take advantage of solar, atmospheric, reactor, and accelerator sources of neutrinos. Accelerator-based sources are particularly convenient since their parameters can be tuned to optimize the measurement in question. At Fermilab an extensive neutrino program includes the MiniBooNE, SciBooNE, and MINOS experiments. Two major new experiments, MINERvA and NOvA, are being constructed, plans for a high-intensity neutrino source to DUSEL are underway, and an R&D effort towards a large liquid argon detector is being pursued. The NOvA experiment intends to search for electron neutrino appearance using a massive surface detector 811 km from Fermilab. In addition to measuring the last unknown mixing angle, theta(13), NOvA has the possibility of seeing matter-antimatter asymmetries in neutrinos and resolving the ordering of the neutrino mass states.

  13. Accelerator system and method of accelerating particles

    NASA Technical Reports Server (NTRS)

    Wirz, Richard E. (Inventor)

    2010-01-01

    An accelerator system and method that utilize dust as the primary mass flux for generating thrust are provided. The accelerator system can include an accelerator capable of operating in a self-neutralizing mode and having a discharge chamber and at least one ionizer capable of charging dust particles. The system can also include a dust particle feeder that is capable of introducing the dust particles into the accelerator. By applying a pulsed positive and negative charge voltage to the accelerator, the charged dust particles can be accelerated thereby generating thrust and neutralizing the accelerator system.

  14. On the predictability of protein database search complexity and its relevance to optimization of distributed searches.

    PubMed

    Deciu, Cosmin; Sun, Jun; Wall, Mark A

    2007-09-01

    We discuss several aspects related to load balancing of database search jobs in a distributed computing environment, such as Linux cluster. Load balancing is a technique for making the most of multiple computational resources, which is particularly relevant in environments in which the usage of such resources is very high. The particular case of the Sequest program is considered here, but the general methodology should apply to any similar database search program. We show how the runtimes for Sequest searches of tandem mass spectral data can be predicted from profiles of previous representative searches, and how this information can be used for better load balancing of novel data. A well-known heuristic load balancing method is shown to be applicable to this problem, and its performance is analyzed for a variety of search parameters.

  15. Adaptive and accelerated tracking-learning-detection

    NASA Astrophysics Data System (ADS)

    Guo, Pengyu; Li, Xin; Ding, Shaowen; Tian, Zunhua; Zhang, Xiaohu

    2013-08-01

    An improved online long-term visual tracking algorithm, named adaptive and accelerated TLD (AA-TLD) based on Tracking-Learning-Detection (TLD) which is a novel tracking framework has been introduced in this paper. The improvement focuses on two aspects, one is adaption, which makes the algorithm not dependent on the pre-defined scanning grids by online generating scale space, and the other is efficiency, which uses not only algorithm-level acceleration like scale prediction that employs auto-regression and moving average (ARMA) model to learn the object motion to lessen the detector's searching range and the fixed number of positive and negative samples that ensures a constant retrieving time, but also CPU and GPU parallel technology to achieve hardware acceleration. In addition, in order to obtain a better effect, some TLD's details are redesigned, which uses a weight including both normalized correlation coefficient and scale size to integrate results, and adjusts distance metric thresholds online. A contrastive experiment on success rate, center location error and execution time, is carried out to show a performance and efficiency upgrade over state-of-the-art TLD with partial TLD datasets and Shenzhou IX return capsule image sequences. The algorithm can be used in the field of video surveillance to meet the need of real-time video tracking.

  16. Using internet searches for influenza surveillance.

    PubMed

    Polgreen, Philip M; Chen, Yiling; Pennock, David M; Nelson, Forrest D

    2008-12-01

    The Internet is an important source of health information. Thus, the frequency of Internet searches may provide information regarding infectious disease activity. As an example, we examined the relationship between searches for influenza and actual influenza occurrence. Using search queries from the Yahoo! search engine ( http://search.yahoo.com ) from March 2004 through May 2008, we counted daily unique queries originating in the United States that contained influenza-related search terms. Counts were divided by the total number of searches, and the resulting daily fraction of searches was averaged over the week. We estimated linear models, using searches with 1-10-week lead times as explanatory variables to predict the percentage of cultures positive for influenza and deaths attributable to pneumonia and influenza in the United States. With use of the frequency of searches, our models predicted an increase in cultures positive for influenza 1-3 weeks in advance of when they occurred (P < .001), and similar models predicted an increase in mortality attributable to pneumonia and influenza up to 5 weeks in advance (P < .001). Search-term surveillance may provide an additional tool for disease surveillance.

  17. A comparison of constant acceleration swimming speeds when acceleration rates are different with critical swimming speeds in Chinese bream under two oxygen tensions.

    PubMed

    Wang, Jian-Wei; Cao, Zhen-Dong; Fu, Shi-Jian

    2016-10-01

    To investigate the effect of acceleration rates on the constant acceleration test speed (U cat) and to compare U cat with the critical swimming speed (U crit) in Chinese bream (Parabramis pekinensis), the U cat test at acceleration rates of 0.05, 0.1, 0.2, 0.4 and 0.8 cm s(-2) and the U crit test in juvenile fish at 20 °C in either normoxia (>90 % saturation oxygen tension) or hypoxia (30 % saturation) were compared. The lactate concentration ([lactate]) of white muscle, liver and plasma and the glycogen concentration ([glycogen]) of white muscle and liver were also measured to identify whether tissue substrate depletion or tissue lactate accumulation correlated with exhaustion. The U cat decreased with the acceleration rate, and there was no significant difference between U crit and U cat at lower acceleration rates. Hypoxia resulted in lower U cat and U crit, and the difference increased with decreased acceleration rates of the U cat test, possibly due to the increased contribution of aerobic components in U crit or U cat at low acceleration rates. Hypoxia elicited a significant decrease in muscle [glycogen] and an increase in muscle and liver [lactate] in resting fish. All post-exercise fish had similar muscle [lactate], suggesting that tissue lactate accumulation may correlate with exercise exhaustion. Unlike hypoxia, exercise induced an increase in muscle [lactate] and a significant increase in plasma [lactate], which were worthy of further investigation. The similar swimming speed and biochemical indicators after exercise in the U crit and U cat groups at low acceleration rates suggested that U cat can be an alternative for the more frequently adopted protocols in U crit in Chinese bream and possibly in other cyprinid fish species.

  18. Using the Dual-Target Cost to Explore the Nature of Search Target Representations

    ERIC Educational Resources Information Center

    Stroud, Michael J.; Menneer, Tamaryn; Cave, Kyle R.; Donnelly, Nick

    2012-01-01

    Eye movements were monitored to examine search efficiency and infer how color is mentally represented to guide search for multiple targets. Observers located a single color target very efficiently by fixating colors similar to the target. However, simultaneous search for 2 colors produced a dual-target cost. In addition, as the similarity between…

  19. Slowed Search in the Context of Unimpaired Grouping in Autism: Evidence from Multiple Conjunction Search.

    PubMed

    Keehn, Brandon; Joseph, Robert M

    2016-03-01

    In multiple conjunction search, the target is not known in advance but is defined only with respect to the distractors in a given search array, thus reducing the contributions of bottom-up and top-down attentional and perceptual processes during search. This study investigated whether the superior visual search skills typically demonstrated by individuals with autism spectrum disorder (ASD) would be evident in multiple conjunction search. Thirty-two children with ASD and 32 age- and nonverbal IQ-matched typically developing (TD) children were administered a multiple conjunction search task. Contrary to findings from the large majority of studies on visual search in ASD, response times of individuals with ASD were significantly slower than those of their TD peers. Evidence of slowed performance in ASD suggests that the mechanisms responsible for superior ASD performance in other visual search paradigms are not available in multiple conjunction search. Although the ASD group failed to exhibit superior performance, they showed efficient search and intertrial priming levels similar to the TD group. Efficient search indicates that ASD participants were able to group distractors into distinct subsets. In summary, while demonstrating grouping and priming effects comparable to those exhibited by their TD peers, children with ASD were slowed in their performance on a multiple conjunction search task, suggesting that their usual superior performance in visual search tasks is specifically dependent on top-down and/or bottom-up attentional and perceptual processes. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.

  20. Search for Hidden Particles: a new experiment proposal

    NASA Astrophysics Data System (ADS)

    De Lellis, G.

    2015-08-01

    Searches for new physics with accelerators are being performed at the LHC, looking for high massive particles coupled to matter with ordinary strength. We propose a new experiment meant to search for very weakly coupled particles in the few GeV mass domain. The existence of such particles, foreseen in different models beyond the Standard Model, is largely unexplored from the experimental point of view. A beam dump facility, built at CERN in the north area, using 400 GeV protons is a copious factory of charmed hadrons and it could be used to probe the existence of such particles. The beam dump is also an ideal source of tau neutrinos, the less known particle in the Standard Model. In particular, tau anti-neutrinos have not been observed so far. We therefore propose an experiment to search for hidden particles and study tau neutrino physics at the same time.

  1. Searches for Periodic Neutrino Emission from Binary Systems with 22 and 40 Strings of IceCube

    NASA Technical Reports Server (NTRS)

    Abassi, R.; Abdou, Y.; Abu-Zayyad, T.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Allen, M. M.; Altmann, D.; Andeen, K.; hide

    2011-01-01

    Recent observations of GeV /TeV photon emission from several X-ray binaries have sparked a renewed interest in these objects as galactic particle accelerators. In spite of the available multi-wavelength data, their acceleration mechanisms are not determined, and the nature of the accelerated particles (hadrons or leptons) is unknown. While much evidence favors leptonic emission, it is very likely that a hadronic component is also accelerated in the jets of these binary systems. The observation of neutrino emission would be clear evidence for the presence of a hadronic component in the outflow of these sources. In this paper we look for periodic neutrino emission from binary systems. Such modulation, observed in the photon flux, would be caused by the geometry of these systems. The results of two searches are presented that differ in the treatment of the spectral shape and phase of the emission. The 'generic' search allows parameters to vary freely and best fit values, in a 'model-dependent' search, predictions are used to constrain these parameters. We use the IceCube data taken from May 31, 2007 to April 5, 2008 with its 22-string configuration, and from April 5, 2008 and May 20, 2009 with its 40-string configuration. For the generic search and the 40 string sample, we find that the most significant source in the catalog of 7 binary stars is Cygnus X-3 with a 1.8% probability after trials (2.10" sigma one-sided) of being produced by statistical fluctuations of the background. The model-dependent method tested a range of system geometries - the inclination and the massive star's disk size - for LS I+61 deg 303, no significant excess was found.

  2. A Fast, Minimalist Search Tool for Remote Sensing Data

    NASA Astrophysics Data System (ADS)

    Lynnes, C. S.; Macharrie, P. G.; Elkins, M.; Joshi, T.; Fenichel, L. H.

    2005-12-01

    We present a tool that emphasizes speed and simplicity in searching remotely sensed Earth Science data. The tool, nicknamed "Mirador" (Spanish for a scenic overlook), provides only four freetext search form fields, for Keywords, Location, Data Start and Data Stop. This contrasts with many current Earth Science search tools that offer highly structured interfaces in order to ensure precise, non-zero results. The disadvantages of the structured approach lie in its complexity and resultant learning curve, as well as the time it takes to formulate and execute the search, thus discouraging iterative discovery. On the other hand, the success of the basic Google search interface shows that many users are willing to forgo high search precision if the search process is fast enough to enable rapid iteration. Therefore, we employ several methods to increase the speed of search formulation and execution. Search formulation is expedited by the minimalist search form, with only one required field. Also, a gazetteer enables the use of geographic terms as shorthand for latitude/longitude coordinates. The search execution is accelerated by initially presenting dataset results (returned from a Google Mini appliance) with an estimated number of "hits" for each dataset based on the user's space-time constraints. The more costly file-level search is executed against a PostGres database only when the user "drills down", and then covering only the fraction of the time period needed to return the next page of results. The simplicity of the search form makes the tool easy to learn and use, and the speed of the searches enables an iterative form of data discovery.

  3. Privacy-Preserving Patient Similarity Learning in a Federated Environment: Development and Analysis

    PubMed Central

    Sun, Jimeng; Wang, Fei; Wang, Shuang; Jun, Chi-Hyuck; Jiang, Xiaoqian

    2018-01-01

    Background There is an urgent need for the development of global analytic frameworks that can perform analyses in a privacy-preserving federated environment across multiple institutions without privacy leakage. A few studies on the topic of federated medical analysis have been conducted recently with the focus on several algorithms. However, none of them have solved similar patient matching, which is useful for applications such as cohort construction for cross-institution observational studies, disease surveillance, and clinical trials recruitment. Objective The aim of this study was to present a privacy-preserving platform in a federated setting for patient similarity learning across institutions. Without sharing patient-level information, our model can find similar patients from one hospital to another. Methods We proposed a federated patient hashing framework and developed a novel algorithm to learn context-specific hash codes to represent patients across institutions. The similarities between patients can be efficiently computed using the resulting hash codes of corresponding patients. To avoid security attack from reverse engineering on the model, we applied homomorphic encryption to patient similarity search in a federated setting. Results We used sequential medical events extracted from the Multiparameter Intelligent Monitoring in Intensive Care-III database to evaluate the proposed algorithm in predicting the incidence of five diseases independently. Our algorithm achieved averaged area under the curves of 0.9154 and 0.8012 with balanced and imbalanced data, respectively, in κ-nearest neighbor with κ=3. We also confirmed privacy preservation in similarity search by using homomorphic encryption. Conclusions The proposed algorithm can help search similar patients across institutions effectively to support federated data analysis in a privacy-preserving manner. PMID:29653917

  4. Diffusive Shock Acceleration and Turbulent Reconnection

    NASA Astrophysics Data System (ADS)

    Garrel, Christian; Vlahos, Loukas; Isliker, Heinz; Pisokas, Theophilos

    2018-05-01

    Diffusive Shock Acceleration (DSA) cannot efficiently accelerate particles without the presence of self-consistently generated or pre-existing strong turbulence (δB/B ˜ 1) in the vicinity of the shock. The problem we address in this article is: if large amplitude magnetic disturbances are present upstream and downstream of a shock then Turbulent Reconnection (TR) will set in and will participate not only in the elastic scattering of particles but also in their heating and acceleration. We demonstrate that large amplitude magnetic disturbances and Unstable Current Sheets (UCS), spontaneously formed in the strong turbulence in the vicinity of a shock, can accelerate particles as efficiently as DSA in large scale systems and on long time scales. We start our analysis with "elastic" scatterers upstream and downstream and estimate the energy distribution of particles escaping from the shock, recovering the well known results from the DSA theory. Next we analyze the additional interaction of the particles with active scatterers (magnetic disturbances and UCS) upstream and downstream of the shock. We show that the asymptotic energy distribution of the particles accelerated by DSA/TR has very similar characteristics with the one due to DSA alone, but the synergy of DSA with TR is much more efficient: The acceleration time is an order of magnitude shorter and the maximum energy reached two orders of magnitude higher. We claim that DSA is the dominant acceleration mechanism in a short period before TR is established, and then strong turbulence will dominate the heating and acceleration of the particles. In other words, the shock serves as the mechanism to set up a strongly turbulent environment, in which the acceleration mechanism will ultimately be the synergy of DSA and TR.

  5. Idiosyncratic Patterns of Representational Similarity in Prefrontal Cortex Predict Attentional Performance.

    PubMed

    Lee, Jeongmi; Geng, Joy J

    2017-02-01

    The efficiency of finding an object in a crowded environment depends largely on the similarity of nontargets to the search target. Models of attention theorize that the similarity is determined by representations stored within an "attentional template" held in working memory. However, the degree to which the contents of the attentional template are individually unique and where those idiosyncratic representations are encoded in the brain are unknown. We investigated this problem using representational similarity analysis of human fMRI data to measure the common and idiosyncratic representations of famous face morphs during an identity categorization task; data from the categorization task were then used to predict performance on a separate identity search task. We hypothesized that the idiosyncratic categorical representations of the continuous face morphs would predict their distractability when searching for each target identity. The results identified that patterns of activation in the lateral prefrontal cortex (LPFC) as well as in face-selective areas in the ventral temporal cortex were highly correlated with the patterns of behavioral categorization of face morphs and search performance that were common across subjects. However, the individually unique components of the categorization behavior were reliably decoded only in right LPFC. Moreover, the neural pattern in right LPFC successfully predicted idiosyncratic variability in search performance, such that reaction times were longer when distractors had a higher probability of being categorized as the target identity. These results suggest that the prefrontal cortex encodes individually unique components of categorical representations that are also present in attentional templates for target search. Everyone's perception of the world is uniquely shaped by personal experiences and preferences. Using functional MRI, we show that individual differences in the categorization of face morphs between two identities

  6. Resampling to accelerate cross-correlation searches for continuous gravitational waves from binary systems

    NASA Astrophysics Data System (ADS)

    Meadors, Grant David; Krishnan, Badri; Papa, Maria Alessandra; Whelan, John T.; Zhang, Yuanhao

    2018-02-01

    Continuous-wave (CW) gravitational waves (GWs) call for computationally-intensive methods. Low signal-to-noise ratio signals need templated searches with long coherent integration times and thus fine parameter-space resolution. Longer integration increases sensitivity. Low-mass x-ray binaries (LMXBs) such as Scorpius X-1 (Sco X-1) may emit accretion-driven CWs at strains reachable by current ground-based observatories. Binary orbital parameters induce phase modulation. This paper describes how resampling corrects binary and detector motion, yielding source-frame time series used for cross-correlation. Compared to the previous, detector-frame, templated cross-correlation method, used for Sco X-1 on data from the first Advanced LIGO observing run (O1), resampling is about 20 × faster in the costliest, most-sensitive frequency bands. Speed-up factors depend on integration time and search setup. The speed could be reinvested into longer integration with a forecast sensitivity gain, 20 to 125 Hz median, of approximately 51%, or from 20 to 250 Hz, 11%, given the same per-band cost and setup. This paper's timing model enables future setup optimization. Resampling scales well with longer integration, and at 10 × unoptimized cost could reach respectively 2.83 × and 2.75 × median sensitivities, limited by spin-wandering. Then an O1 search could yield a marginalized-polarization upper limit reaching torque-balance at 100 Hz. Frequencies from 40 to 140 Hz might be probed in equal observing time with 2 × improved detectors.

  7. Active browsing using similarity pyramids

    NASA Astrophysics Data System (ADS)

    Chen, Jau-Yuen; Bouman, Charles A.; Dalton, John C.

    1998-12-01

    In this paper, we describe a new approach to managing large image databases, which we call active browsing. Active browsing integrates relevance feedback into the browsing environment, so that users can modify the database's organization to suit the desired task. Our method is based on a similarity pyramid data structure, which hierarchically organizes the database, so that it can be efficiently browsed. At coarse levels, the similarity pyramid allows users to view the database as large clusters of similar images. Alternatively, users can 'zoom into' finer levels to view individual images. We discuss relevance feedback for the browsing process, and argue that it is fundamentally different from relevance feedback for more traditional search-by-query tasks. We propose two fundamental operations for active browsing: pruning and reorganization. Both of these operations depend on a user-defined relevance set, which represents the image or set of images desired by the user. We present statistical methods for accurately pruning the database, and we propose a new 'worm hole' distance metric for reorganizing the database, so that members of the relevance set are grouped together.

  8. A SETI experiment. [Search for Extra Terrestrial Intelligence

    NASA Technical Reports Server (NTRS)

    Mclaughlin, W. I.

    1986-01-01

    In order to increase the probability of contact in the search for extraterrestrial intelligence (SETI), it has been proposed to search more intensively in certain regions of the electromagnetic spectrum ('the water hole'). The present paper describes a similar narrowing of the search in the time domain. Application of this strategy results in the SETI experiments searching for signals from the Tau Ceti system late in 1986 and early in 1987, and from the Epsilon Eridani system in mid 1988.

  9. High-acceleration cable deployment

    NASA Technical Reports Server (NTRS)

    Barns, C. E.; Canning, T. N.; Gin, B.; King, R. W.; Murphy, J. P.

    1980-01-01

    Prototype high-acceleration umbilical-cable deployment allows electrical communication between above-ground instrumentation and ballistic projectile below surface. Cable deployment is made up of forebody and afterbody. Foreboy can be separated from afterbody by rocket, or they can be fired as unit at target that stops afterbody on impact (forebody would continue, deploying cable). Similar design could be used in study of sea ice and in other surface-penetration studies.

  10. A similarity-based data warehousing environment for medical images.

    PubMed

    Teixeira, Jefferson William; Annibal, Luana Peixoto; Felipe, Joaquim Cezar; Ciferri, Ricardo Rodrigues; Ciferri, Cristina Dutra de Aguiar

    2015-11-01

    A core issue of the decision-making process in the medical field is to support the execution of analytical (OLAP) similarity queries over images in data warehousing environments. In this paper, we focus on this issue. We propose imageDWE, a non-conventional data warehousing environment that enables the storage of intrinsic features taken from medical images in a data warehouse and supports OLAP similarity queries over them. To comply with this goal, we introduce the concept of perceptual layer, which is an abstraction used to represent an image dataset according to a given feature descriptor in order to enable similarity search. Based on this concept, we propose the imageDW, an extended data warehouse with dimension tables specifically designed to support one or more perceptual layers. We also detail how to build an imageDW and how to load image data into it. Furthermore, we show how to process OLAP similarity queries composed of a conventional predicate and a similarity search predicate that encompasses the specification of one or more perceptual layers. Moreover, we introduce an index technique to improve the OLAP query processing over images. We carried out performance tests over a data warehouse environment that consolidated medical images from exams of several modalities. The results demonstrated the feasibility and efficiency of our proposed imageDWE to manage images and to process OLAP similarity queries. The results also demonstrated that the use of the proposed index technique guaranteed a great improvement in query processing. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Search for neutrino emission from microquasars with the ANTARES telescope

    NASA Astrophysics Data System (ADS)

    Galatà, S.

    2012-12-01

    Neutrino telescopes are nowadays exploring a new window of observation on the high energy universe and may shed light on the longstanding problem regarding the origin of cosmic rays. The ANTARES neutrino telescope is located underwater 40 km offshore from the Southern coast of France, on a plateau at 2475 m depth. Since 2007 it observes the high energy (>100 GeV) neutrino sky looking for cosmic neutrino sources. Among the candidate neutrino emitters are microquasars, i.e. galactic X-ray binaries exhibiting relativistic jets, which may accelerate hadrons thus producing neutrinos, under certain conditions. These sources are also variable in time and undergo X-ray or gamma ray outburst that can be related to the acceleration of relativistic particles witnessed by their radio emission. These events can provide a trigger to the neutrino search, with the advantage of drastically reducing the atmospheric neutrino background. A search for neutrino emission from microquasar during outbursts is presented based on the data collected by ANTARES between 2007 and 2010. Upper limits are shown and compared with the predictions.

  12. Prior knowledge of category size impacts visual search.

    PubMed

    Wu, Rachel; McGee, Brianna; Echiverri, Chelsea; Zinszer, Benjamin D

    2018-03-30

    Prior research has shown that category search can be similar to one-item search (as measured by the N2pc ERP marker of attentional selection) for highly familiar, smaller categories (e.g., letters and numbers) because the finite set of items in a category can be grouped into one unit to guide search. Other studies have shown that larger, more broadly defined categories (e.g., healthy food) also can elicit N2pc components during category search, but the amplitude of these components is typically attenuated. Two experiments investigated whether the perceived size of a familiar category impacts category and exemplar search. We presented participants with 16 familiar company logos: 8 from a smaller category (social media companies) and 8 from a larger category (entertainment/recreation manufacturing companies). The ERP results from Experiment 1 revealed that, in a two-item search array, search was more efficient for the smaller category of logos compared to the larger category. In a four-item search array (Experiment 2), where two of the four items were placeholders, search was largely similar between the category types, but there was more attentional capture by nontarget members from the same category as the target for smaller rather than larger categories. These results support a growing literature on how prior knowledge of categories affects attentional selection and capture during visual search. We discuss the implications of these findings in relation to assessing cognitive abilities across the lifespan, given that prior knowledge typically increases with age. © 2018 Society for Psychophysiological Research.

  13. K-t GRAPPA-accelerated 4D flow MRI of liver hemodynamics: influence of different acceleration factors on qualitative and quantitative assessment of blood flow.

    PubMed

    Stankovic, Zoran; Fink, Jury; Collins, Jeremy D; Semaan, Edouard; Russe, Maximilian F; Carr, James C; Markl, Michael; Langer, Mathias; Jung, Bernd

    2015-04-01

    We sought to evaluate the feasibility of k-t parallel imaging for accelerated 4D flow MRI in the hepatic vascular system by investigating the impact of different acceleration factors. k-t GRAPPA accelerated 4D flow MRI of the liver vasculature was evaluated in 16 healthy volunteers at 3T with acceleration factors R = 3, R = 5, and R = 8 (2.0 × 2.5 × 2.4 mm(3), TR = 82 ms), and R = 5 (TR = 41 ms); GRAPPA R = 2 was used as the reference standard. Qualitative flow analysis included grading of 3D streamlines and time-resolved particle traces. Quantitative evaluation assessed velocities, net flow, and wall shear stress (WSS). Significant scan time savings were realized for all acceleration factors compared to standard GRAPPA R = 2 (21-71 %) (p < 0.001). Quantification of velocities and net flow offered similar results between k-t GRAPPA R = 3 and R = 5 compared to standard GRAPPA R = 2. Significantly increased leakage artifacts and noise were seen between standard GRAPPA R = 2 and k-t GRAPPA R = 8 (p < 0.001) with significant underestimation of peak velocities and WSS of up to 31 % in the hepatic arterial system (p <0.05). WSS was significantly underestimated up to 13 % in all vessels of the portal venous system for k-t GRAPPA R = 5, while significantly higher values were observed for the same acceleration with higher temporal resolution in two veins (p < 0.05). k-t acceleration of 4D flow MRI is feasible for liver hemodynamic assessment with acceleration factors R = 3 and R = 5 resulting in a scan time reduction of at least 40 % with similar quantitation of liver hemodynamics compared with GRAPPA R = 2.

  14. [Pain registries and similar data collections : A systematic review].

    PubMed

    Freytag, A; Scriba, B; Kaiser, U; Meißner, W

    2016-12-01

    Registries and similar data collections are a valuable addition to prospective studies as they provide data from real life treatment. In pain medicine only few such data collections exist so far. Aim of the study was to identify German-language registries or similar data collections that record patient-reported and pain-associated outcomes together with other data. A systematic search was carried out, which included the following sources: the data bases PubMed/MEDLINE and Embase, the German Registry for Clinical Trials (DRKS), ClinicalTrials.gov and registry portals known to us. Furthermore, an extended internet search was carried out via Google Scholar. References from personal scientific contacts and from operators of registries were also included. Questionnaires regarding registry items were sent to registry operators. Out of 381 search hits, 37 potentially relevant projects received a questionnaire and 35 answered. From the 35 responders 23 registries or similar data collections fulfilling inclusion criteria could be identified: 5 primarily pain-associated, 3 therapy-associated, 2 population-associated and 13 disease-associated (rheumatism/arthritis 5, joints/spine 4, hernias 1 and cancer 3). The reader obtains contact information on relevant data collections associated with pain, the contents, objectives and the pain assessment instruments applied. This review could give an important impulse for increased networking in health services research on pain. A limitation of the study was that identification of registries was made difficult due to an inconsistent definition and application of the term "registry", incomplete or insufficiently updated registry portals, missing scientific publications as well as two non-responders.

  15. Initiation of combustion in the thermally choked ram accelerator

    NASA Technical Reports Server (NTRS)

    Bruckner, A. P.; Burnham, E. A.; Knowlen, C.; Hertzberg, A.; Bogdanoff, D. W.

    1992-01-01

    The methodology for initiating stable combustion in a ram accelerator operating in the thermally choked mode is presented in this paper. The ram accelerator is a high velocity ramjet-in-tube projectile launcher whose principle of operation is similar to that of an airbreathing ramjet. The subcaliber projectile travels supersonically through a stationary tube filled with a premixed combustible gas mixture. In the thermally choked propulsion mode subsonic combustion takes place behind the base of the projectile and leads to thermal choking, which stabilizes a normal shock system on the projectile, thus producing forward thrust. Projectiles with masses in the 45-90 g range have been accelerated to velocities up to 2650 m/sec in a 38 mm bore, 16 m long accelerator tube. Operation of the ram accelerator is started by injecting the projectile into the accelerator tube at velocities in the 700 - 1300 m/sec range by means of a conventional gas gun. A specially designed obturator, which seals the bore of the gun during this initial acceleration, enters the ram accelerator together with the projectile. The interaction of the obturator with the propellant gas ignites the gas mixture and establishes stable combustion behind the projectile.

  16. Accelerated behavioural development changes fine-scale search behaviour and spatial memory in honey bees (Apis mellifera L.).

    PubMed

    Ushitani, Tomokazu; Perry, Clint J; Cheng, Ken; Barron, Andrew B

    2016-02-01

    Normally, worker honey bees (Apis mellifera) begin foraging when more than 2 weeks old as adults, but if individual bees or the colony is stressed, bees often begin foraging precociously. Here, we examined whether bees that accelerated their behavioural development to begin foraging precociously differed from normal-aged foragers in cognitive performance. We used a social manipulation to generate precocious foragers from small experimental colonies and tested their performance in a free-flight visual reversal learning task, and a test of spatial memory. To assess spatial memory, bees were trained to learn the location of a small sucrose feeder within an array of three landmarks. In tests, the feeder and one landmark were removed and the search behaviour of the bees was recorded. Performance of precocious and normal-aged foragers did not differ in a visual reversal learning task, but the two groups showed a clear difference in spatial memory. Flight behaviour suggested normal-aged foragers were better able to infer the position of the removed landmark and feeder relative to the remaining landmarks than precocious foragers. Previous studies have documented the cognitive decline of old foragers, but this is the first suggestion of a cognitive deficit in young foragers. These data imply that worker honey bees continue their cognitive development during the adult stage. These findings may also help to explain why precocious foragers perform quite poorly as foragers and have a higher than normal loss rate. © 2016. Published by The Company of Biologists Ltd.

  17. RAG-3D: A search tool for RNA 3D substructures

    DOE PAGES

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

    2015-08-24

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

  18. RAG-3D: a search tool for RNA 3D substructures

    PubMed Central

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-01-01

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  19. RAG-3D: A search tool for RNA 3D substructures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

  20. Parallelization of combinatorial search when solving knapsack optimization problem on computing systems based on multicore processors

    NASA Astrophysics Data System (ADS)

    Rahman, P. A.

    2018-05-01

    This scientific paper deals with the model of the knapsack optimization problem and method of its solving based on directed combinatorial search in the boolean space. The offered by the author specialized mathematical model of decomposition of the search-zone to the separate search-spheres and the algorithm of distribution of the search-spheres to the different cores of the multi-core processor are also discussed. The paper also provides an example of decomposition of the search-zone to the several search-spheres and distribution of the search-spheres to the different cores of the quad-core processor. Finally, an offered by the author formula for estimation of the theoretical maximum of the computational acceleration, which can be achieved due to the parallelization of the search-zone to the search-spheres on the unlimited number of the processor cores, is also given.

  1. Microscopy as a statistical, Rényi-Ulam, half-lie game: a new heuristic search strategy to accelerate imaging.

    PubMed

    Drumm, Daniel W; Greentree, Andrew D

    2017-11-07

    Finding a fluorescent target in a biological environment is a common and pressing microscopy problem. This task is formally analogous to the canonical search problem. In ideal (noise-free, truthful) search problems, the well-known binary search is optimal. The case of half-lies, where one of two responses to a search query may be deceptive, introduces a richer, Rényi-Ulam problem and is particularly relevant to practical microscopy. We analyse microscopy in the contexts of Rényi-Ulam games and half-lies, developing a new family of heuristics. We show the cost of insisting on verification by positive result in search algorithms; for the zero-half-lie case bisectioning with verification incurs a 50% penalty in the average number of queries required. The optimal partitioning of search spaces directly following verification in the presence of random half-lies is determined. Trisectioning with verification is shown to be the most efficient heuristic of the family in a majority of cases.

  2. C IV BROAD ABSORPTION LINE ACCELERATION IN SLOAN DIGITAL SKY SURVEY QUASARS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Grier, C. J.; Brandt, W. N.; Trump, J. R.

    2016-06-20

    We present results from the largest systematic investigation of broad absorption line (BAL) acceleration to date. We use spectra of 140 quasars from three Sloan Digital Sky Survey programs to search for global velocity offsets in BALs over timescales of ≈2.5–5.5 years in the quasar rest frame. We carefully select acceleration candidates by requiring monolithic velocity shifts over the entire BAL trough, avoiding BALs with velocity shifts that might be caused by profile variability. The C iv BALs of two quasars show velocity shifts consistent with the expected signatures of BAL acceleration, and the BAL of one quasar shows amore » velocity-shift signature of deceleration. In our two acceleration candidates, we see evidence that the magnitude of the acceleration is not constant over time; the magnitudes of the change in acceleration for both acceleration candidates are difficult to produce with a standard disk-wind model or via geometric projection effects. We measure upper limits to acceleration and deceleration for 76 additional BAL troughs and find that the majority of BALs are stable to within about 3% of their mean velocities. The lack of widespread acceleration/deceleration could indicate that the gas producing most BALs is located at large radii from the central black hole and/or is not currently strongly interacting with ambient material within the host galaxy along our line of sight.« less

  3. Staging and laser acceleration of ions in underdense plasma

    NASA Astrophysics Data System (ADS)

    Ting, Antonio; Hafizi, Bahman; Helle, Michael; Chen, Yu-Hsin; Gordon, Daniel; Kaganovich, Dmitri; Polyanskiy, Mikhail; Pogorelsky, Igor; Babzien, Markus; Miao, Chenlong; Dover, Nicholas; Najmudin, Zulfikar; Ettlinger, Oliver

    2017-03-01

    Accelerating ions from rest in a plasma requires extra considerations because of their heavy mass. Low phase velocity fields or quasi-electrostatic fields are often necessary, either by operating above or near the critical density or by applying other slow wave generating mechanisms. Solid targets have been a favorite and have generated many good results. High density gas targets have also been reported to produce energetic ions. It is interesting to consider acceleration of ions in laser-driven plasma configurations that will potentially allow continuous acceleration in multiple consecutive stages. The plasma will be derived from gaseous targets, producing plasma densities slightly below the critical plasma density (underdense) for the driving laser. Such a plasma is experimentally robust, being repeatable and relatively transparent to externally injected ions from a previous stage. When optimized, multiple stages of this underdense laser plasma acceleration mechanism can progressively accelerate the ions to a high final energy. For a light mass ion such as the proton, relativistic velocities could be reached, making it suitable for further acceleration by high phase velocity plasma accelerators to energies appropriate for High Energy Physics applications. Negatively charged ions such as antiprotons could be similarly accelerated in this multi-staged ion acceleration scheme.

  4. Fast protein tertiary structure retrieval based on global surface shape similarity.

    PubMed

    Sael, Lee; Li, Bin; La, David; Fang, Yi; Ramani, Karthik; Rustamov, Raif; Kihara, Daisuke

    2008-09-01

    Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison. 2008 Wiley-Liss, Inc.

  5. Privacy-Preserving Patient Similarity Learning in a Federated Environment: Development and Analysis.

    PubMed

    Lee, Junghye; Sun, Jimeng; Wang, Fei; Wang, Shuang; Jun, Chi-Hyuck; Jiang, Xiaoqian

    2018-04-13

    There is an urgent need for the development of global analytic frameworks that can perform analyses in a privacy-preserving federated environment across multiple institutions without privacy leakage. A few studies on the topic of federated medical analysis have been conducted recently with the focus on several algorithms. However, none of them have solved similar patient matching, which is useful for applications such as cohort construction for cross-institution observational studies, disease surveillance, and clinical trials recruitment. The aim of this study was to present a privacy-preserving platform in a federated setting for patient similarity learning across institutions. Without sharing patient-level information, our model can find similar patients from one hospital to another. We proposed a federated patient hashing framework and developed a novel algorithm to learn context-specific hash codes to represent patients across institutions. The similarities between patients can be efficiently computed using the resulting hash codes of corresponding patients. To avoid security attack from reverse engineering on the model, we applied homomorphic encryption to patient similarity search in a federated setting. We used sequential medical events extracted from the Multiparameter Intelligent Monitoring in Intensive Care-III database to evaluate the proposed algorithm in predicting the incidence of five diseases independently. Our algorithm achieved averaged area under the curves of 0.9154 and 0.8012 with balanced and imbalanced data, respectively, in κ-nearest neighbor with κ=3. We also confirmed privacy preservation in similarity search by using homomorphic encryption. The proposed algorithm can help search similar patients across institutions effectively to support federated data analysis in a privacy-preserving manner. ©Junghye Lee, Jimeng Sun, Fei Wang, Shuang Wang, Chi-Hyuck Jun, Xiaoqian Jiang. Originally published in JMIR Medical Informatics (http

  6. A measurement of hadron production cross sections for the simulation of accelerator neutrino beams and a search for muon-neutrino to electron-neutrino oscillations in the Δm 2 about equals 1-eV 2 region

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schmitz, David W.

    2008-01-01

    A measurement of hadron production cross-sections for the simulation of accelerator neutrino beams and a search for muon neutrino to electron neutrino oscillations in the Δm 2 ~ 1 eV 2} region. This dissertation presents measurements from two different high energy physics experiments with a very strong connection: the Hadron Production (HARP) experiment located at CERN in Geneva, Switzerland, and the Mini Booster Neutrino Experiment (Mini-BooNE) located at Fermilab in Batavia, Illinois.

  7. Global Image Dissimilarity in Macaque Inferotemporal Cortex Predicts Human Visual Search Efficiency

    PubMed Central

    Sripati, Arun P.; Olson, Carl R.

    2010-01-01

    Finding a target in a visual scene can be easy or difficult depending on the nature of the distractors. Research in humans has suggested that search is more difficult the more similar the target and distractors are to each other. However, it has not yielded an objective definition of similarity. We hypothesized that visual search performance depends on similarity as determined by the degree to which two images elicit overlapping patterns of neuronal activity in visual cortex. To test this idea, we recorded from neurons in monkey inferotemporal cortex (IT) and assessed visual search performance in humans using pairs of images formed from the same local features in different global arrangements. The ability of IT neurons to discriminate between two images was strongly predictive of the ability of humans to discriminate between them during visual search, accounting overall for 90% of the variance in human performance. A simple physical measure of global similarity – the degree of overlap between the coarse footprints of a pair of images – largely explains both the neuronal and the behavioral results. To explain the relation between population activity and search behavior, we propose a model in which the efficiency of global oddball search depends on contrast-enhancing lateral interactions in high-order visual cortex. PMID:20107054

  8. Dense plasma focus (DPF) accelerated non radio isotopic radiological source

    DOEpatents

    Rusnak, Brian; Tang, Vincent

    2017-01-31

    A non-radio-isotopic radiological source using a dense plasma focus (DPF) to produce an intense z-pinch plasma from a gas, such as helium, and which accelerates charged particles, such as generated from the gas or injected from an external source, into a target positioned along an acceleration axis and of a type known to emit ionizing radiation when impinged by the type of accelerated charged particles. In a preferred embodiment, helium gas is used to produce a DPF-accelerated He2+ ion beam to a beryllium target, to produce neutron emission having a similar energy spectrum as a radio-isotopic AmBe neutron source. Furthermore, multiple DPFs may be stacked to provide staged acceleration of charged particles for enhancing energy, tunability, and control of the source.

  9. Fast Depiction Invariant Visual Similarity for Content Based Image Retrieval Based on Data-driven Visual Similarity using Linear Discriminant Analysis

    NASA Astrophysics Data System (ADS)

    Wihardi, Y.; Setiawan, W.; Nugraha, E.

    2018-01-01

    On this research we try to build CBIRS based on Learning Distance/Similarity Function using Linear Discriminant Analysis (LDA) and Histogram of Oriented Gradient (HoG) feature. Our method is invariant to depiction of image, such as similarity of image to image, sketch to image, and painting to image. LDA can decrease execution time compared to state of the art method, but it still needs an improvement in term of accuracy. Inaccuracy in our experiment happen because we did not perform sliding windows search and because of low number of negative samples as natural-world images.

  10. CLAST: CUDA implemented large-scale alignment search tool.

    PubMed

    Yano, Masahiro; Mori, Hiroshi; Akiyama, Yutaka; Yamada, Takuji; Kurokawa, Ken

    2014-12-11

    Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing

  11. Naked singularities as particle accelerators

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Patil, Mandar; Joshi, Pankaj S.

    We investigate here the particle acceleration by naked singularities to arbitrarily high center of mass energies. Recently it has been suggested that black holes could be used as particle accelerators to probe the Planck scale physics. We show that the naked singularities serve the same purpose and probably would do better than their black hole counterparts. We focus on the scenario of a self-similar gravitational collapse starting from a regular initial data, leading to the formation of a globally naked singularity. It is seen that when particles moving along timelike geodesics interact and collide near the Cauchy horizon, the energymore » of collision in the center of mass frame will be arbitrarily high, thus offering a window to Planck scale physics.« less

  12. Sequence search on a supercomputer.

    PubMed

    Gotoh, O; Tagashira, Y

    1986-01-10

    A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base Ver. 1.0 (1) (0.5 M residues) is carried out in a CPU time of 45 sec. About 4 min is required for an exhaustive search of a 1500-base nucleotide sequence against all mammalian sequences (1.2M bases) in Genbank Ver. 29.0. The CPU time is reduced to about a quarter with a faster version.

  13. Optimizing random searches on three-dimensional lattices

    NASA Astrophysics Data System (ADS)

    Yang, Benhao; Yang, Shunkun; Zhang, Jiaquan; Li, Daqing

    2018-07-01

    Search is a universal behavior related to many types of intelligent individuals. While most studies have focused on search in two or infinite-dimensional space, it is still missing how search can be optimized in three-dimensional space. Here we study random searches on three-dimensional (3d) square lattices with periodic boundary conditions, and explore the optimal search strategy with a power-law step length distribution, p(l) ∼l-μ, known as Lévy flights. We find that compared to random searches on two-dimensional (2d) lattices, the optimal exponent μopt on 3d lattices is relatively smaller in non-destructive case and remains similar in destructive case. We also find μopt decreases as the lattice length in z direction increases under high target density. Our findings may help us to understand the role of spatial dimension in search behaviors.

  14. Investigation of longitudinal proton acceleration in exploded targets irradiated by intense short-pulse laser

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gauthier, M.; CEA, DAM, DIF, 91297 Arpajon; Lévy, A.

    2014-01-15

    It was recently shown that a promising way to accelerate protons in the forward direction to high energies is to use under-dense or near-critical density targets instead of solids. Simulations have revealed that the acceleration process depends on the density gradients of the plasma target. Indeed, under certain conditions, the most energetic protons are predicted to be accelerated by a collisionless shock mechanism that significantly increases their energy. We report here the results of a recent experiment dedicated to the study of longitudinal ion acceleration in partially exploded foils using a high intensity (∼5 × 10{sup 18} W/cm{sup 2}) picosecond laser pulse. Wemore » show that protons accelerated using targets having moderate front and rear plasma gradients (up to ∼8 μm gradient length) exhibit similar maximum proton energy and number compared to proton beams that are produced, in similar laser conditions, from solid targets, in the well-known target normal sheath acceleration regime. Particle-In-Cell simulations, performed in the same conditions as the experiment and consistent with the measurements, allow laying a path for further improvement of this acceleration scheme.« less

  15. Role of sugammadex in accelerating postoperative discharge: A meta-analysis.

    PubMed

    Carron, Michele; Zarantonello, Francesco; Lazzarotto, Nadia; Tellaroli, Paola; Ori, Carlo

    2017-06-01

    Sugammadex has been introduced for reversal of neuromuscular blockade (NMB) induced by rocuronium (or vecuronium). Although its efficacy and safety have been established, data are conflicting as to whether it accelerates discharge to the surgical ward compared with neostigmine, which is traditionally used for reversing NMB. The object of this systematic review and meta-analysis was to review the research comparing sugammadex and neostigmine in the context of patient discharge after general anesthesia. Systematic review and meta-analysis. University medical hospital. Five-hundred eighteen patients from six studies were included. A comprehensive search was conducted using PubMed, Web of Science, Google Scholar, and Cochrane Library electronic databases to identify randomized controlled trials written in English. Two reviewers independently selected the studies, extracted data regarding postoperative discharge, and assessed the trials' methodological quality and evidence level. Postoperative discharge time was determined from the operating room (OR) to the postanesthesia care unit (PACU) and from the PACU to the surgical ward. This study was conducted using PRISMA methodology. Time to discharge after NMB reversal with sugammadex or neostigmine. Compared with neostigmine, sugammadex was associated with a significantly faster discharge from the OR to the PACU (mean difference [MD]=22.14min, 95% CI (14.62, 29.67), P<0.0001, I 2 =0%) and from the PACU to the surgical ward (MD=16.95min, 95% CI (0.23, 33.67), P=0.0469, I 2 =98.4%). Similarly, discharge-readiness was shorter for sugammadex than for neostigmine from the OR to the PACU (MD=5.58min, 95% CI (3.03, 8.14), P≤0.0001, I 2 =0%). However, discharge-readiness was similar in both groups for patients moving from the PACU to the surgical ward (MD=-1.10min, 95% CI (-5.69, 3.50), P=0.6394, I 2 =25.3%). Results from this meta-analysis suggest that sugammadex accelerates postoperative discharge of patients after general

  16. Learning context-sensitive shape similarity by graph transduction.

    PubMed

    Bai, Xiang; Yang, Xingwei; Latecki, Longin Jan; Liu, Wenyu; Tu, Zhuowen

    2010-05-01

    Shape similarity and shape retrieval are very important topics in computer vision. The recent progress in this domain has been mostly driven by designing smart shape descriptors for providing better similarity measure between pairs of shapes. In this paper, we provide a new perspective to this problem by considering the existing shapes as a group, and study their similarity measures to the query shape in a graph structure. Our method is general and can be built on top of any existing shape similarity measure. For a given similarity measure, a new similarity is learned through graph transduction. The new similarity is learned iteratively so that the neighbors of a given shape influence its final similarity to the query. The basic idea here is related to PageRank ranking, which forms a foundation of Google Web search. The presented experimental results demonstrate that the proposed approach yields significant improvements over the state-of-art shape matching algorithms. We obtained a retrieval rate of 91.61 percent on the MPEG-7 data set, which is the highest ever reported in the literature. Moreover, the learned similarity by the proposed method also achieves promising improvements on both shape classification and shape clustering.

  17. Abyss or Shelter? On the Relevance of Web Search Engines' Search Results When People Google for Suicide.

    PubMed

    Haim, Mario; Arendt, Florian; Scherr, Sebastian

    2017-02-01

    Despite evidence that suicide rates can increase after suicides are widely reported in the media, appropriate depictions of suicide in the media can help people to overcome suicidal crises and can thus elicit preventive effects. We argue on the level of individual media users that a similar ambivalence can be postulated for search results on online suicide-related search queries. Importantly, the filter bubble hypothesis (Pariser, 2011) states that search results are biased by algorithms based on a person's previous search behavior. In this study, we investigated whether suicide-related search queries, including either potentially suicide-preventive or -facilitative terms, influence subsequent search results. This might thus protect or harm suicidal Internet users. We utilized a 3 (search history: suicide-related harmful, suicide-related helpful, and suicide-unrelated) × 2 (reactive: clicking the top-most result link and no clicking) experimental design applying agent-based testing. While findings show no influences either of search histories or of reactivity on search results in a subsequent situation, the presentation of a helpline offer raises concerns about possible detrimental algorithmic decision-making: Algorithms "decided" whether or not to present a helpline, and this automated decision, then, followed the agent throughout the rest of the observation period. Implications for policy-making and search providers are discussed.

  18. Coastal marsh response to historical and future sea-level acceleration

    USGS Publications Warehouse

    Kirwan, M.; Temmerman, S.

    2009-01-01

    We consider the response of marshland to accelerations in the rate of sea-level rise by utilizing two previously described numerical models of marsh elevation. In a model designed for the Scheldt Estuary (Belgium-SW Netherlands), a feedback between inundation depth and suspended sediment concentrations allows marshes to quickly adjust their elevation to a change in sea-level rise rate. In a model designed for the North Inlet Estuary (South Carolina), a feedback between inundation and vegetation growth allows similar adjustment. Although the models differ in their approach, we find that they predict surprisingly similar responses to sea-level change. Marsh elevations adjust to a step change in the rate of sea-level rise in about 100 years. In the case of a continuous acceleration in the rate of sea-level rise, modeled accretion rates lag behind sea-level rise rates by about 20 years, and never obtain equilibrium. Regardless of the style of acceleration, the models predict approximately 6-14 cm of marsh submergence in response to historical sea-level acceleration, and 3-4 cm of marsh submergence in response to a projected scenario of sea-level rise over the next century. While marshes already low in the tidal frame would be susceptible to these depth changes, our modeling results suggest that factors other than historical sea-level acceleration are more important for observations of degradation in most marshes today.

  19. Search for Stable Strange Quark Matter in Lunar Soil

    NASA Astrophysics Data System (ADS)

    Han, K.; Ashenfelter, J.; Chikanian, A.; Emmet, W.; Finch, L. E.; Heinz, A.; Madsen, J.; Majka, R. D.; Monreal, B.; Sandweiss, J.

    2009-08-01

    We report results from a search for strangelets (small chunks of strange quark matter) in lunar soil using the Yale WNSL accelerator as a mass spectrometer. We have searched over a range in mass from A=42 to A=70amu for nuclear charges 5, 6, 8, 9, and 11. No strangelets were found in the experiment. For strangelets with nuclear charge 8, a concentration in lunar soil higher than 10-16 is excluded at the 95% confidence level. The implied limit on the strangelet flux in cosmic rays is the most sensitive to date for the covered range and is relevant to both recent theoretical flux predictions and a strangelet candidate event found by the AMS-01 experiment.

  20. A spin transfer torque magnetoresistance random access memory-based high-density and ultralow-power associative memory for fully data-adaptive nearest neighbor search with current-mode similarity evaluation and time-domain minimum searching

    NASA Astrophysics Data System (ADS)

    Ma, Yitao; Miura, Sadahiko; Honjo, Hiroaki; Ikeda, Shoji; Hanyu, Takahiro; Ohno, Hideo; Endoh, Tetsuo

    2017-04-01

    A high-density nonvolatile associative memory (NV-AM) based on spin transfer torque magnetoresistive random access memory (STT-MRAM), which achieves highly concurrent and ultralow-power nearest neighbor search with full adaptivity of the template data format, has been proposed and fabricated using the 90 nm CMOS/70 nm perpendicular-magnetic-tunnel-junction hybrid process. A truly compact current-mode circuitry is developed to realize flexibly controllable and high-parallel similarity evaluation, which makes the NV-AM adaptable to any dimensionality and component-bit of template data. A compact dual-stage time-domain minimum searching circuit is also developed, which can freely extend the system for more template data by connecting multiple NM-AM cores without additional circuits for integrated processing. Both the embedded STT-MRAM module and the computing circuit modules in this NV-AM chip are synchronously power-gated to completely eliminate standby power and maximally reduce operation power by only activating the currently accessed circuit blocks. The operations of a prototype chip at 40 MHz are demonstrated by measurement. The average operation power is only 130 µW, and the circuit density is less than 11 µm2/bit. Compared with the latest conventional works in both volatile and nonvolatile approaches, more than 31.3% circuit area reductions and 99.2% power improvements are achieved, respectively. Further power performance analyses are discussed, which verify the special superiority of the proposed NV-AM in low-power and large-memory-based VLSIs.

  1. GEMINI: a computationally-efficient search engine for large gene expression datasets.

    PubMed

    DeFreitas, Timothy; Saddiki, Hachem; Flaherty, Patrick

    2016-02-24

    Low-cost DNA sequencing allows organizations to accumulate massive amounts of genomic data and use that data to answer a diverse range of research questions. Presently, users must search for relevant genomic data using a keyword, accession number of meta-data tag. However, in this search paradigm the form of the query - a text-based string - is mismatched with the form of the target - a genomic profile. To improve access to massive genomic data resources, we have developed a fast search engine, GEMINI, that uses a genomic profile as a query to search for similar genomic profiles. GEMINI implements a nearest-neighbor search algorithm using a vantage-point tree to store a database of n profiles and in certain circumstances achieves an [Formula: see text] expected query time in the limit. We tested GEMINI on breast and ovarian cancer gene expression data from The Cancer Genome Atlas project and show that it achieves a query time that scales as the logarithm of the number of records in practice on genomic data. In a database with 10(5) samples, GEMINI identifies the nearest neighbor in 0.05 sec compared to a brute force search time of 0.6 sec. GEMINI is a fast search engine that uses a query genomic profile to search for similar profiles in a very large genomic database. It enables users to identify similar profiles independent of sample label, data origin or other meta-data information.

  2. Programming and Runtime Support to Blaze FPGA Accelerator Deployment at Datacenter Scale.

    PubMed

    Huang, Muhuan; Wu, Di; Yu, Cody Hao; Fang, Zhenman; Interlandi, Matteo; Condie, Tyson; Cong, Jason

    2016-10-01

    With the end of CPU core scaling due to dark silicon limitations, customized accelerators on FPGAs have gained increased attention in modern datacenters due to their lower power, high performance and energy efficiency. Evidenced by Microsoft's FPGA deployment in its Bing search engine and Intel's 16.7 billion acquisition of Altera, integrating FPGAs into datacenters is considered one of the most promising approaches to sustain future datacenter growth. However, it is quite challenging for existing big data computing systems-like Apache Spark and Hadoop-to access the performance and energy benefits of FPGA accelerators. In this paper we design and implement Blaze to provide programming and runtime support for enabling easy and efficient deployments of FPGA accelerators in datacenters. In particular, Blaze abstracts FPGA accelerators as a service (FaaS) and provides a set of clean programming APIs for big data processing applications to easily utilize those accelerators. Our Blaze runtime implements an FaaS framework to efficiently share FPGA accelerators among multiple heterogeneous threads on a single node, and extends Hadoop YARN with accelerator-centric scheduling to efficiently share them among multiple computing tasks in the cluster. Experimental results using four representative big data applications demonstrate that Blaze greatly reduces the programming efforts to access FPGA accelerators in systems like Apache Spark and YARN, and improves the system throughput by 1.7 × to 3× (and energy efficiency by 1.5× to 2.7×) compared to a conventional CPU-only cluster.

  3. Relations between perceptual and conceptual scope: how global versus local processing fits a focus on similarity versus dissimilarity.

    PubMed

    Förster, Jens

    2009-02-01

    Nine studies showed a bidirectional link (a) between a global processing style and generation of similarities and (b) between a local processing style and generation of dissimilarities. In Experiments 1-4, participants were primed with global versus local perception styles and then asked to work on an allegedly unrelated generation task. Across materials, participants generated more similarities than dissimilarities after global priming, whereas for participants with local priming, the opposite was true. Experiments 5-6 demonstrated a bidirectional link whereby participants who were first instructed to search for similarities attended more to the gestalt of a stimulus than to its details, whereas the reverse was true for those who were initially instructed to search for dissimilarities. Because important psychological variables are correlated with processing styles, in Experiments 7-9, temporal distance, a promotion focus, and high power were predicted and shown to enhance the search for similarities, whereas temporal proximity, a prevention focus, and low power enhanced the search for dissimilarities. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

  4. Survival Processing Enhances Visual Search Efficiency.

    PubMed

    Cho, Kit W

    2018-05-01

    Words rated for their survival relevance are remembered better than when rated using other well-known memory mnemonics. This finding, which is known as the survival advantage effect and has been replicated in many studies, suggests that our memory systems are molded by natural selection pressures. In two experiments, the present study used a visual search task to examine whether there is likewise a survival advantage for our visual systems. Participants rated words for their survival relevance or for their pleasantness before locating that object's picture in a search array with 8 or 16 objects. Although there was no difference in search times among the two rating scenarios when set size was 8, survival processing reduced visual search times when set size was 16. These findings reflect a search efficiency effect and suggest that similar to our memory systems, our visual systems are also tuned toward self-preservation.

  5. Optimization of a Small Scale Linear Reluctance Accelerator

    NASA Astrophysics Data System (ADS)

    Barrera, Thor; Beard, Robby

    2011-11-01

    Reluctance accelerators are extremely promising future methods of transportation. Several problems still plague these devices, most prominently low efficiency. Variables to overcoming efficiency problems are many and difficult to correlate how they affect our accelerator. The study examined several differing variables that present potential challenges in optimizing the efficiency of reluctance accelerators. These include coil and projectile design, power supplies, switching, and the elusive gradient inductance problem. Extensive research in these areas has been performed from computational and theoretical to experimental. Findings show that these parameters share significant similarity to transformer design elements, thus general findings show current optimized parameters the research suggests as a baseline for further research and design. Demonstration of these current findings will be offered at the time of presentation.

  6. The Xenon1T Dark Matter Search Experiment

    NASA Astrophysics Data System (ADS)

    Aprile, Elena

    The worldwide race towards direct dark matter detection in the form of Weakly Interacting Massive Particles (WIMPs) has been dramatically accelerated by the remarkable progress and evolution of liquid xenon time projection chambers (LXeTPCs). With a realistic discovery potential, Xenon100 has already reached a sensitivity of 7 × 10-45 cm2, and continues to accrue data at the Laboratori Nazionali del Gran Sasso (LNGS) in Italy towards its ultimate sensitivity reach at the σ SI ˜ 2 × 10-45 cm2 level for the spin-independent WIMP-nucleon cross-section. To fully explore the favoured parameter space for WIMP dark matter in search of a first robust and statistically significant discovery, or to confirm any hint of a signal from Xenon100, the next phase of the Xenon program will be a detector at the ton scale - Xenon1T. The Xenon1T detector, based on 2.2 ton of LXe viewed by low radioactivity photomultiplier tubes and housed in a water Cherenkov muon veto at LNGS, is presented. With an experimental aim of probing WIMP interaction cross-sections above of order σ SI ˜ 2 × 10-47 cm2 within 2 years of operation, Xenon1T will provide the sensitivity to probe a particularly favourable region of electroweak physics on a timescale compatible with complementary ground and satellite based indirect searches and with accelerator dark matter searches at the LHC. Indeed, for a σ SI ˜ 10-45 cm2 and 100 GeV/c2 WIMP mass, Xenon1T could detect of order 100 events in this exposure, providing statistics for placing significant constraints on the WIMP mass.

  7. Unsupervised Approaches for Post-Processing in Computationally Efficient Waveform-Similarity-Based Earthquake Detection

    NASA Astrophysics Data System (ADS)

    Bergen, K.; Yoon, C. E.; OReilly, O. J.; Beroza, G. C.

    2015-12-01

    Recent improvements in computational efficiency for waveform correlation-based detections achieved by new methods such as Fingerprint and Similarity Thresholding (FAST) promise to allow large-scale blind search for similar waveforms in long-duration continuous seismic data. Waveform similarity search applied to datasets of months to years of continuous seismic data will identify significantly more events than traditional detection methods. With the anticipated increase in number of detections and associated increase in false positives, manual inspection of the detection results will become infeasible. This motivates the need for new approaches to process the output of similarity-based detection. We explore data mining techniques for improved detection post-processing. We approach this by considering similarity-detector output as a sparse similarity graph with candidate events as vertices and similarities as weighted edges. Image processing techniques are leveraged to define candidate events and combine results individually processed at multiple stations. Clustering and graph analysis methods are used to identify groups of similar waveforms and assign a confidence score to candidate detections. Anomaly detection and classification are applied to waveform data for additional false detection removal. A comparison of methods will be presented and their performance will be demonstrated on a suspected induced and non-induced earthquake sequence.

  8. The radial velocity search for extrasolar planets

    NASA Technical Reports Server (NTRS)

    Mcmillan, Robert S.

    1991-01-01

    Radial velocity measurements are being made to search for planets orbiting stars other than the Sun. The reflex acceleration induced on stars by planets can be sensed by measuring the small, slow changes in the line-of-site velocities of stars. To detect these planetary perturbations, the data series must be made on a uniform instrumental scale for as long as it takes a planet to orbit its star. A spectrometer of extreme stability and unprecedented sensitivity to changes in stellar radial velocities was operated.

  9. A hierarchical transition state search algorithm

    NASA Astrophysics Data System (ADS)

    del Campo, Jorge M.; Köster, Andreas M.

    2008-07-01

    A hierarchical transition state search algorithm is developed and its implementation in the density functional theory program deMon2k is described. This search algorithm combines the double ended saddle interpolation method with local uphill trust region optimization. A new formalism for the incorporation of the distance constrain in the saddle interpolation method is derived. The similarities between the constrained optimizations in the local trust region method and the saddle interpolation are highlighted. The saddle interpolation and local uphill trust region optimizations are validated on a test set of 28 representative reactions. The hierarchical transition state search algorithm is applied to an intramolecular Diels-Alder reaction with several internal rotors, which makes automatic transition state search rather challenging. The obtained reaction mechanism is discussed in the context of the experimentally observed product distribution.

  10. Applications of High Intensity Proton Accelerators

    NASA Astrophysics Data System (ADS)

    Raja, Rajendran; Mishra, Shekhar

    2010-06-01

    collider and neutrino factory - summary of working group 2 / J. Galambos, R. Garoby and S. Geer -- Prospects for a very high power CW SRF linac / R. A. Rimmer -- Indian accelerator program for ADS applications / V. C. Sahni and P. Singh -- Ion accelerator activities at VECC (particularly, operating at low temperature) / R. K. Bhandari -- Chinese efforts in high intensity proton accelerators / S. Fu, J. Wang and S. Fang -- ADSR activity in the UK / R. J. Barlow -- ADS development in Japan / K. Kikuchi -- Project-X, SRF, and very large power stations / C. M. Ankenbrandt, R. P. Johnson and M. Popovic -- Power production and ADS / R. Raja -- Experimental neutron source facility based on accelerator driven system / Y. Gohar -- Transmutation mission / W. S. Yang -- Safety performance and issues / J. E. Cahalan -- Spallation target design for accelerator-driven systems / Y. Gohar -- Design considerations for accelerator transmutation of waste system / W. S. Yang -- Japan ADS program / T. Sasa -- Overview of members states' and IAEA activities in the field of Accelerator Driven Systems (ADS) / A. Stanculescu -- Linac for ADS applications - accelerator technologies / R. W. Garnett and R. L. Sheffield -- SRF linacs and accelerator driven sub-critical systems - summary working groups 3 & 4 / J. Delayen -- Production of Actinium-225 via high energy proton induced spallation of Thorium-232 / J. Harvey ... [et al.] -- Search for the electric dipole moment of Radium-225 / R. J. Holt, Z.-T. Lu and R. Mueller -- SRF linac and material science and medicine - summary of working group 5 / J. Nolen, E. Pitcher and H. Kirk.

  11. Prediction of Spacecraft Vibration using Acceleration and Force Envelopes

    NASA Technical Reports Server (NTRS)

    Gordon, Scott; Kaufman, Daniel; Kern, Dennis; Scharton, Terry

    2009-01-01

    The base forces in the GLAST X- and Z-axis sine vibration tests were similar to those derived using generic inputs (from users guide and handbook), but the base forces in the sine test were generally greater than the flight data. Basedrive analyses using envelopes of flight acceleration data provided more accurate predictions of the base force than generic inputs, and as expected, using envelopes of both the flight acceleration and force provided even more accurate predictions The GLAST spacecraft interface accelerations and forces measured during the MECO transient were relatively low in the 60 to 150 Hz regime. One may expect the flight forces measured at the base of various spacecraft to be more dependent on the mass, frequencies, etc. of the spacecraft than are the corresponding interface acceleration data, which may depend more on the launch vehicle configuration.

  12. Visual search for features and conjunctions in development.

    PubMed

    Lobaugh, N J; Cole, S; Rovet, J F

    1998-12-01

    Visual search performance was examined in three groups of children 7 to 12 years of age and in young adults. Colour and orientation feature searches and a conjunction search were conducted. Reaction time (RT) showed expected improvements in processing speed with age. Comparisons of RT's on target-present and target-absent trials were consistent with parallel search on the two feature conditions and with serial search in the conjunction condition. The RT results indicated searches for feature and conjunctions were treated similarly for children and adults. However, the youngest children missed more targets at the largest array sizes, most strikingly in conjunction search. Based on an analysis of speed/accuracy trade-offs, we suggest that low target-distractor discriminability leads to an undersampling of array elements, and is responsible for the high number of misses in the youngest children.

  13. A study on task difficulty and acceleration stress

    NASA Technical Reports Server (NTRS)

    Repperger, D. W.; Rogers, D. B.

    1981-01-01

    The results of two experiments which relate to task difficulty and the effects of environmental stress on tracking performance are discussed and compared to subjective evaluations. The first experiment involved five different sum of sine tracking tasks which humans tracked both in a static condition and under a 5 Gz acceleration stress condition. The second experiment involved similar environmental stress conditions but in this case the tasks were constructed from deterministic functions with specially designed velocity and acceleration profiles. Phase Plane performance analysis was conducted to study potential measures of workload or tracking difficulty.

  14. Effects of acceleration rate on Rayleigh-Taylor instability in elastic-plastic materials

    NASA Astrophysics Data System (ADS)

    Banerjee, Arindam; Polavarapu, Rinosh

    2016-11-01

    The effect of acceleration rate in the elastic-plastic transition stage of Rayleigh-Taylor instability in an accelerated non-Newtonian material is investigated experimentally using a rotating wheel experiment. A non-Newtonian material (mayonnaise) was accelerated at different rates by varying the angular acceleration of a rotating wheel and growth patterns of single mode perturbations with different combinations of amplitude and wavelength were analyzed. Experiments were run at two different acceleration rates to compare with experiments presented in prior years at APS DFD meetings and the peak amplitude responses are captured using a high-speed camera. Similar to the instability acceleration, the elastic-plastic transition acceleration is found to be increasing with increase in acceleration rate for a given amplitude and wavelength. The experimental results will be compared to various analytical strength models and prior experimental studies using Newtonian fluids. Authors acknowledge funding support from Los Alamos National Lab subcontract(370333) and DOE-SSAA Grant (DE-NA0001975).

  15. OrChem - An open source chemistry search engine for Oracle(R).

    PubMed

    Rijnbeek, Mark; Steinbeck, Christoph

    2009-10-22

    Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.

  16. OrChem - An open source chemistry search engine for Oracle®

    PubMed Central

    2009-01-01

    Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521

  17. First muon acceleration using a radio-frequency accelerator

    NASA Astrophysics Data System (ADS)

    Bae, S.; Choi, H.; Choi, S.; Fukao, Y.; Futatsukawa, K.; Hasegawa, K.; Iijima, T.; Iinuma, H.; Ishida, K.; Kawamura, N.; Kim, B.; Kitamura, R.; Ko, H. S.; Kondo, Y.; Li, S.; Mibe, T.; Miyake, Y.; Morishita, T.; Nakazawa, Y.; Otani, M.; Razuvaev, G. P.; Saito, N.; Shimomura, K.; Sue, Y.; Won, E.; Yamazaki, T.

    2018-05-01

    Muons have been accelerated by using a radio-frequency accelerator for the first time. Negative muonium atoms (Mu- ), which are bound states of positive muons (μ+) and two electrons, are generated from μ+'s through the electron capture process in an aluminum degrader. The generated Mu- 's are initially electrostatically accelerated and injected into a radio-frequency quadrupole linac (RFQ). In the RFQ, the Mu- 's are accelerated to 89 keV. The accelerated Mu- 's are identified by momentum measurement and time of flight. This compact muon linac opens the door to various muon accelerator applications including particle physics measurements and the construction of a transmission muon microscope.

  18. SOLAR INTERACTING PROTONS VERSUS INTERPLANETARY PROTONS IN THE CORE PLUS HALO MODEL OF DIFFUSIVE SHOCK ACCELERATION AND STOCHASTIC RE-ACCELERATION

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kocharov, L.; Laitinen, T.; Vainio, R.

    2015-06-10

    With the first observations of solar γ-rays from the decay of pions, the relationship of protons producing ground level enhancements (GLEs) on the Earth to those of similar energies producing the γ-rays on the Sun has been debated. These two populations may be either independent and simply coincident in large flares, or they may be, in fact, the same population stemming from a single accelerating agent and jointly distributed at the Sun and also in space. Assuming the latter, we model a scenario in which particles are accelerated near the Sun in a shock wave with a fraction transported backmore » to the solar surface to radiate, while the remainder is detected at Earth in the form of a GLE. Interplanetary ions versus ions interacting at the Sun are studied for a spherical shock wave propagating in a radial magnetic field through a highly turbulent radial ray (the acceleration core) and surrounding weakly turbulent sector in which the accelerated particles can propagate toward or away from the Sun. The model presented here accounts for both the first-order Fermi acceleration at the shock front and the second-order, stochastic re-acceleration by the turbulence enhanced behind the shock. We find that the re-acceleration is important in generating the γ-radiation and we also find that up to 10% of the particle population can find its way to the Sun as compared to particles escaping to the interplanetary space.« less

  19. When Gravity Fails: Local Search Topology

    NASA Technical Reports Server (NTRS)

    Frank, Jeremy; Cheeseman, Peter; Stutz, John; Lau, Sonie (Technical Monitor)

    1997-01-01

    Local search algorithms for combinatorial search problems frequently encounter a sequence of states in which it is impossible to improve the value of the objective function; moves through these regions, called {\\em plateau moves), dominate the time spent in local search. We analyze and characterize {\\em plateaus) for three different classes of randomly generated Boolean Satisfiability problems. We identify several interesting features of plateaus that impact the performance of local search algorithms. We show that local minima tend to be small but occasionally may be very large. We also show that local minima can be escaped without unsatisfying a large number of clauses, but that systematically searching for an escape route may be computationally expensive if the local minimum is large. We show that plateaus with exits, called benches, tend to be much larger than minima, and that some benches have very few exit states which local search can use to escape. We show that the solutions (i.e. global minima) of randomly generated problem instances form clusters, which behave similarly to local minima. We revisit several enhancements of local search algorithms and explain their performance in light of our results. Finally we discuss strategies for creating the next generation of local search algorithms.

  20. Predicting user click behaviour in search engine advertisements

    NASA Astrophysics Data System (ADS)

    Daryaie Zanjani, Mohammad; Khadivi, Shahram

    2015-10-01

    According to the specific requirements and interests of users, search engines select and display advertisements that match user needs and have higher probability of attracting users' attention based on their previous search history. New objects such as user, advertisement or query cause a deterioration of precision in targeted advertising due to their lack of history. This article surveys this challenge. In the case of new objects, we first extract similar observed objects to the new object and then we use their history as the history of new object. Similarity between objects is measured based on correlation, which is a relation between user and advertisement when the advertisement is displayed to the user. This method is used for all objects, so it has helped us to accurately select relevant advertisements for users' queries. In our proposed model, we assume that similar users behave in a similar manner. We find that users with few queries are similar to new users. We will show that correlation between users and advertisements' keywords is high. Thus, users who pay attention to advertisements' keywords, click similar advertisements. In addition, users who pay attention to specific brand names might have similar behaviours too.

  1. Heavy ion acceleration in the radiation pressure acceleration and breakout afterburner regimes

    NASA Astrophysics Data System (ADS)

    Petrov, G. M.; McGuffey, C.; Thomas, A. G. R.; Krushelnick, K.; Beg, F. N.

    2017-07-01

    We present a theoretical study of heavy ion acceleration from ultrathin (20 nm) gold foil irradiated by high-intensity sub-picosecond lasers. Using two-dimensional particle-in-cell simulations, three laser systems are modeled that cover the range between femtosecond and picosecond pulses. By varying the laser pulse duration we observe a transition from radiation pressure acceleration (RPA) to the relativistic induced transparency (RIT) regime for heavy ions akin to light ions. The underlying physics of beam formation and acceleration is similar for light and heavy ions, however, nuances of the acceleration process make the heavy ions more challenging. A more detailed study involving variation of peak laser intensity I 0 and pulse duration τFWHM revealed that the transition point from RPA to RIT regime depends on the peak laser intensity on target and occurs for pulse duration {τ }{{F}{{W}}{{H}}{{M}}}{{R}{{P}}{{A}}\\to {{R}}{{I}}{{T}}}[{{f}}{{s}}]\\cong 210/\\sqrt{{I}0[{{W}} {{{cm}}}-2]/{10}21}. The most abundant gold ion and charge-to-mass ratio are Au51+ and q/M ≈ 1/4, respectively, half that of light ions. For ultrathin foils, on the order of one skin depth, we established a linear scaling of the maximum energy per nucleon (E/M)max with (q/M)max, which is more favorable than the quadratic one found previously. The numerical simulations predict heavy ion beams with very attractive properties for applications: high directionality (<10° half-angle), high fluxes (>1011 ions sr-1) and energy (>20 MeV/nucleon) from laser systems delivering >20 J of energy on target.

  2. Patient-Centered Tools for Medication Information Search.

    PubMed

    Wilcox, Lauren; Feiner, Steven; Elhadad, Noémie; Vawdrey, David; Tran, Tran H

    2014-05-20

    Recent research focused on online health information seeking highlights a heavy reliance on general-purpose search engines. However, current general-purpose search interfaces do not necessarily provide adequate support for non-experts in identifying suitable sources of health information. Popular search engines have recently introduced search tools in their user interfaces for a range of topics. In this work, we explore how such tools can support non-expert, patient-centered health information search. Scoping the current work to medication-related search, we report on findings from a formative study focused on the design of patient-centered, medication-information search tools. Our study included qualitative interviews with patients, family members, and domain experts, as well as observations of their use of Remedy, a technology probe embodying a set of search tools. Post-operative cardiothoracic surgery patients and their visiting family members used the tools to find information about their hospital medications and were interviewed before and after their use. Domain experts conducted similar search tasks and provided qualitative feedback on their preferences and recommendations for designing these tools. Findings from our study suggest the importance of four valuation principles underlying our tools: credibility, readability, consumer perspective, and topical relevance.

  3. Particle Identification on an FPGA Accelerated Compute Platform for the LHCb Upgrade

    NASA Astrophysics Data System (ADS)

    Fäerber, Christian; Schwemmer, Rainer; Machen, Jonathan; Neufeld, Niko

    2017-07-01

    The current LHCb readout system will be upgraded in 2018 to a “triggerless” readout of the entire detector at the Large Hadron Collider collision rate of 40 MHz. The corresponding bandwidth from the detector down to the foreseen dedicated computing farm (event filter farm), which acts as the trigger, has to be increased by a factor of almost 100 from currently 500 Gb/s up to 40 Tb/s. The event filter farm will preanalyze the data and will select the events on an event by event basis. This will reduce the bandwidth down to a manageable size to write the interesting physics data to tape. The design of such a system is a challenging task, and the reason why different new technologies are considered and have to be investigated for the different parts of the system. For the usage in the event building farm or in the event filter farm (trigger), an experimental field programmable gate array (FPGA) accelerated computing platform is considered and, therefore, tested. FPGA compute accelerators are used more and more in standard servers such as for Microsoft Bing search or Baidu search. The platform we use hosts a general Intel CPU and a high-performance FPGA linked via the high-speed Intel QuickPath Interconnect. An accelerator is implemented on the FPGA. It is very likely that these platforms, which are built, in general, for high-performance computing, are also very interesting for the high-energy physics community. First, the performance results of smaller test cases performed at the beginning are presented. Afterward, a part of the existing LHCb RICH particle identification is tested and is ported to the experimental FPGA accelerated platform. We have compared the performance of the LHCb RICH particle identification running on a normal CPU with the performance of the same algorithm, which is running on the Xeon-FPGA compute accelerator platform.

  4. High Energy Ion Acceleration by Extreme Laser Radiation Pressure

    DTIC Science & Technology

    2017-03-14

    and was published in Nuclear Instruments and Methods A [11]. For similar targets, it was found that by monitoring the divergence of a low- energy ...AFRL-AFOSR-UK-TR-2017-0015 High energy ion acceleration by extreme laser radiation pressure Paul McKenna UNIVERSITY OF STRATHCLYDE VIZ ROYAL COLLEGE...MM-YYYY)   14-03-2017 2. REPORT TYPE  Final 3. DATES COVERED (From - To)  01 May 2013 to 31 Dec 2016 4. TITLE AND SUBTITLE High energy ion acceleration

  5. PARTICLE ACCELERATOR

    DOEpatents

    Teng, L.C.

    1960-01-19

    ABS>A combination of two accelerators, a cyclotron and a ring-shaped accelerator which has a portion disposed tangentially to the cyclotron, is described. Means are provided to transfer particles from the cyclotron to the ring accelerator including a magnetic deflector within the cyclotron, a magnetic shield between the ring accelerator and the cyclotron, and a magnetic inflector within the ring accelerator.

  6. Path integration mediated systematic search: a Bayesian model.

    PubMed

    Vickerstaff, Robert J; Merkle, Tobias

    2012-08-21

    The systematic search behaviour is a backup system that increases the chances of desert ants finding their nest entrance after foraging when the path integrator has failed to guide them home accurately enough. Here we present a mathematical model of the systematic search that is based on extensive behavioural studies in North African desert ants Cataglyphis fortis. First, a simple search heuristic utilising Bayesian inference and a probability density function is developed. This model, which optimises the short-term nest detection probability, is then compared to three simpler search heuristics and to recorded search patterns of Cataglyphis ants. To compare the different searches a method to quantify search efficiency is established as well as an estimate of the error rate in the ants' path integrator. We demonstrate that the Bayesian search heuristic is able to automatically adapt to increasing levels of positional uncertainty to produce broader search patterns, just as desert ants do, and that it outperforms the three other search heuristics tested. The searches produced by it are also arguably the most similar in appearance to the ant's searches. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. The Sweet Spot of a Nonacademic Job Search

    ERIC Educational Resources Information Center

    Lord, Alexandra M.

    2012-01-01

    Because academic culture frowns on Ph.D.'s who consider leaving the ivory tower, most of those who jump ship find themselves at a loss as to where and how to begin a job search. Yet a nonacademic job search is actually quite similar to a standard research project. Both require advance planning, substantial research, collating evidence for an…

  8. SANSparallel: interactive homology search against Uniprot

    PubMed Central

    Somervuo, Panu; Holm, Liisa

    2015-01-01

    Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest. PMID:25855811

  9. The Search for Narrative

    ERIC Educational Resources Information Center

    Fattal, Laura Felleman

    2004-01-01

    Practical and academic, the interrelationship of the visual and performing arts opens unique frontiers to aesthetic pioneers. Divergent in aim from the historic search for similar tonalities between the Synchronists and Stravinsky or atonal musicians of the 1950s-70s and minimalist painters and sculptors, the present use of the visual arts as a…

  10. Programming and Runtime Support to Blaze FPGA Accelerator Deployment at Datacenter Scale

    PubMed Central

    Huang, Muhuan; Wu, Di; Yu, Cody Hao; Fang, Zhenman; Interlandi, Matteo; Condie, Tyson; Cong, Jason

    2017-01-01

    With the end of CPU core scaling due to dark silicon limitations, customized accelerators on FPGAs have gained increased attention in modern datacenters due to their lower power, high performance and energy efficiency. Evidenced by Microsoft’s FPGA deployment in its Bing search engine and Intel’s 16.7 billion acquisition of Altera, integrating FPGAs into datacenters is considered one of the most promising approaches to sustain future datacenter growth. However, it is quite challenging for existing big data computing systems—like Apache Spark and Hadoop—to access the performance and energy benefits of FPGA accelerators. In this paper we design and implement Blaze to provide programming and runtime support for enabling easy and efficient deployments of FPGA accelerators in datacenters. In particular, Blaze abstracts FPGA accelerators as a service (FaaS) and provides a set of clean programming APIs for big data processing applications to easily utilize those accelerators. Our Blaze runtime implements an FaaS framework to efficiently share FPGA accelerators among multiple heterogeneous threads on a single node, and extends Hadoop YARN with accelerator-centric scheduling to efficiently share them among multiple computing tasks in the cluster. Experimental results using four representative big data applications demonstrate that Blaze greatly reduces the programming efforts to access FPGA accelerators in systems like Apache Spark and YARN, and improves the system throughput by 1.7 × to 3× (and energy efficiency by 1.5× to 2.7×) compared to a conventional CPU-only cluster. PMID:28317049

  11. Scene analysis for effective visual search in rough three-dimensional-modeling scenes

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Hu, Xiaopeng

    2016-11-01

    Visual search is a fundamental technology in the computer vision community. It is difficult to find an object in complex scenes when there exist similar distracters in the background. We propose a target search method in rough three-dimensional-modeling scenes based on a vision salience theory and camera imaging model. We give the definition of salience of objects (or features) and explain the way that salience measurements of objects are calculated. Also, we present one type of search path that guides to the target through salience objects. Along the search path, when the previous objects are localized, the search region of each subsequent object decreases, which is calculated through imaging model and an optimization method. The experimental results indicate that the proposed method is capable of resolving the ambiguities resulting from distracters containing similar visual features with the target, leading to an improvement of search speed by over 50%.

  12. Acceleration Modes and Transitions in Pulsed Plasma Accelerators

    NASA Technical Reports Server (NTRS)

    Polzin, Kurt A.; Greve, Christine M.

    2018-01-01

    Pulsed plasma accelerators typically operate by storing energy in a capacitor bank and then discharging this energy through a gas, ionizing and accelerating it through the Lorentz body force. Two plasma accelerator types employing this general scheme have typically been studied: the gas-fed pulsed plasma thruster and the quasi-steady magnetoplasmadynamic (MPD) accelerator. The gas-fed pulsed plasma accelerator is generally represented as a completely transient device discharging in approximately 1-10 microseconds. When the capacitor bank is discharged through the gas, a current sheet forms at the breech of the thruster and propagates forward under a j (current density) by B (magnetic field) body force, entraining propellant it encounters. This process is sometimes referred to as detonation-mode acceleration because the current sheet representation approximates that of a strong shock propagating through the gas. Acceleration of the initial current sheet ceases when either the current sheet reaches the end of the device and is ejected or when the current in the circuit reverses, striking a new current sheet at the breech and depriving the initial sheet of additional acceleration. In the quasi-steady MPD accelerator, the pulse is lengthened to approximately 1 millisecond or longer and maintained at an approximately constant level during discharge. The time over which the transient phenomena experienced during startup typically occur is short relative to the overall discharge time, which is now long enough for the plasma to assume a relatively steady-state configuration. The ionized gas flows through a stationary current channel in a manner that is sometimes referred to as the deflagration-mode of operation. The plasma experiences electromagnetic acceleration as it flows through the current channel towards the exit of the device. A device that had a short pulse length but appeared to operate in a plasma acceleration regime different from the gas-fed pulsed plasma

  13. Accelerated Reader and Its Effect on Fifth-Grade Students' Reading Comprehension

    ERIC Educational Resources Information Center

    Nichols, Jan Shelton

    2013-01-01

    Schools in the United States have been using the Accelerated Reader (AR) program since the mid-1980s. A search of the literature related to the effectiveness of the AR program revealed that many of the studies were conducted more than a decade ago, and a large number of those studies failed to utilize a control group to provide comparative data.…

  14. Search for Hidden Particles (SHiP): a new experiment proposal

    NASA Astrophysics Data System (ADS)

    De Lellis, G.

    2015-06-01

    Searches for new physics with accelerators are being performed at the LHC, looking for high massive particles coupled to matter with ordinary strength. We propose a new experimental facility meant to search for very weakly coupled particles in the few GeV mass domain. The existence of such particles, foreseen in different theoretical models beyond the Standard Model, is largely unexplored from the experimental point of view. A beam dump facility, built at CERN in the north area, using 400 GeV protons is a copious factory of charmed hadrons and could be used to probe the existence of such particles. The beam dump is also an ideal source of tau neutrinos, the less known particle in the Standard Model. In particular, tau anti-neutrinos have not been observed so far. We therefore propose an experiment to search for hidden particles and study tau neutrino physics at the same time.

  15. A link between occupant and vehicle accelerations during common driving tasks.

    PubMed

    Mathias, Anne C; Shibata, Peggy A; Sprague, James K

    2014-01-01

    When evaluating occupant motions during driving tasks, it is desirable to have a well-established correlation between vehicle and occupant accelerations. Therefore, this study demonstrated a methodology to quantify accelerations experienced by the driver of a passenger vehicle and compare them to associated vehicle motions. Acceleration levels were measured at the seat and the driver’s head, cervical spine, and lumbar spine during six non-collision driving tasks. Tasks included mounting a 127 mm (5 in) -high curb, crossing railroad tracks, driving on a rough road, braking heavily from 13.4 m/s (30 mph), having a 89 mm (3.5 in)-diameter roller sequentially pass under two tires, and dropping one tire from a 171-mm (6.75 in) height. The driver experienced peak resultant accelerations of similar magnitudes across all trials. Peak body accelerations were less than 1.2 g, including 0.82 g lumbar acceleration during heavy braking and 0.88 g head acceleration during the curb mount. These preliminary measurements are comparable to or lower than accelerations experienced during non-driving activities such as sitting quickly. This study contributes to the scientific understanding of accelerations experienced by vehicle occupants and demonstrates the potential to relate vehicle and occupant accelerations during common driving activities that do not involve collisions.

  16. Efficient acceleration of neutral atoms in laser produced plasma

    DOE PAGES

    Dalui, M.; Trivikram, T. M.; Colgan, James Patrick; ...

    2017-06-20

    Recent advances in high-intensity laser-produced plasmas have demonstrated their potential as compact charge particle accelerators. Unlike conventional accelerators, transient quasi-static charge separation acceleration fields in laser produced plasmas are highly localized and orders of magnitude larger. Manipulating these ion accelerators, to convert the fast ions to neutral atoms with little change in momentum, transform these to a bright source of MeV atoms. The emittance of the neutral atom beam would be similar to that expected for an ion beam. Since intense laser-produced plasmas have been demonstrated to produce high-brightness-low-emittance beams, it is possible to envisage generation of high-flux, low-emittance, highmore » energy neutral atom beams in length scales of less than a millimeter. Here, we show a scheme where more than 80% of the fast ions are reduced to energetic neutral atoms and demonstrate the feasibility of a high energy neutral atom accelerator that could significantly impact applications in neutral atom lithography and diagnostics.« less

  17. Acceleration of convergence of vector sequences

    NASA Technical Reports Server (NTRS)

    Sidi, A.; Ford, W. F.; Smith, D. A.

    1983-01-01

    A general approach to the construction of convergence acceleration methods for vector sequence is proposed. Using this approach, one can generate some known methods, such as the minimal polynomial extrapolation, the reduced rank extrapolation, and the topological epsilon algorithm, and also some new ones. Some of the new methods are easier to implement than the known methods and are observed to have similar numerical properties. The convergence analysis of these new methods is carried out, and it is shown that they are especially suitable for accelerating the convergence of vector sequences that are obtained when one solves linear systems of equations iteratively. A stability analysis is also given, and numerical examples are provided. The convergence and stability properties of the topological epsilon algorithm are likewise given.

  18. Scaling, Similarity, and the Fourth Paradigm for Hydrology

    NASA Technical Reports Server (NTRS)

    Peters-Lidard, Christa D.; Clark, Martyn; Samaniego, Luis; Verhoest, Niko E. C.; van Emmerik, Tim; Uijlenhoet, Remko; Achieng, Kevin; Franz, Trenton E.; Woods, Ross

    2017-01-01

    In this synthesis paper addressing hydrologic scaling and similarity, we posit that roadblocks in the search for universal laws of hydrology are hindered by our focus on computational simulation (the third paradigm), and assert that it is time for hydrology to embrace a fourth paradigm of data-intensive science. Advances in information-based hydrologic science, coupled with an explosion of hydrologic data and advances in parameter estimation and modelling, have laid the foundation for a data-driven framework for scrutinizing hydrological scaling and similarity hypotheses. We summarize important scaling and similarity concepts (hypotheses) that require testing, describe a mutual information framework for testing these hypotheses, describe boundary condition, state flux, and parameter data requirements across scales to support testing these hypotheses, and discuss some challenges to overcome while pursuing the fourth hydrological paradigm. We call upon the hydrologic sciences community to develop a focused effort towards adopting the fourth paradigm and apply this to outstanding challenges in scaling and similarity.

  19. SA-Search: a web tool for protein structure mining based on a Structural Alphabet

    PubMed Central

    Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

    2004-01-01

    SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search. PMID:15215446

  20. SA-Search: a web tool for protein structure mining based on a Structural Alphabet.

    PubMed

    Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

    2004-07-01

    SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.

  1. Pattern similarity study of functional sites in protein sequences: lysozymes and cystatins

    PubMed Central

    Nakai, Shuryo; Li-Chan, Eunice CY; Dou, Jinglie

    2005-01-01

    Background Although it is generally agreed that topography is more conserved than sequences, proteins sharing the same fold can have different functions, while there are protein families with low sequence similarity. An alternative method for profile analysis of characteristic conserved positions of the motifs within the 3D structures may be needed for functional annotation of protein sequences. Using the approach of quantitative structure-activity relationships (QSAR), we have proposed a new algorithm for postulating functional mechanisms on the basis of pattern similarity and average of property values of side-chains in segments within sequences. This approach was used to search for functional sites of proteins belonging to the lysozyme and cystatin families. Results Hydrophobicity and β-turn propensity of reference segments with 3–7 residues were used for the homology similarity search (HSS) for active sites. Hydrogen bonding was used as the side-chain property for searching the binding sites of lysozymes. The profiles of similarity constants and average values of these parameters as functions of their positions in the sequences could identify both active and substrate binding sites of the lysozyme of Streptomyces coelicolor, which has been reported as a new fold enzyme (Cellosyl). The same approach was successfully applied to cystatins, especially for postulating the mechanisms of amyloidosis of human cystatin C as well as human lysozyme. Conclusion Pattern similarity and average index values of structure-related properties of side chains in short segments of three residues or longer were, for the first time, successfully applied for predicting functional sites in sequences. This new approach may be applicable to studying functional sites in un-annotated proteins, for which complete 3D structures are not yet available. PMID:15904486

  2. Correlation between X-ray flux and rotational acceleration in Vela X-1

    NASA Technical Reports Server (NTRS)

    Deeter, J. E.; Boynton, P. E.; Shibazaki, N.; Hayakawa, S.; Nagase, F.

    1989-01-01

    The results of a search for correlations between X-ray flux and angular acceleration for the accreting binary pulsar Vela X-1 are presented. Results are based on data obtained with the Hakucho satellite during the interval 1982 to 1984. In undertaking this correlation analysis, it was necessary to modify the usual statistical method to deal with conditions imposed by generally unavoidable satellite observing constraints, most notably a mismatch in sampling between the two variables. The results are suggestive of a correlation between flux and the absolute value of the angular acceleration, at a significance level of 96 percent. The implications of the methods and results for future observations and analysis are discussed.

  3. Object recognition based on Google's reverse image search and image similarity

    NASA Astrophysics Data System (ADS)

    Horváth, András.

    2015-12-01

    Image classification is one of the most challenging tasks in computer vision and a general multiclass classifier could solve many different tasks in image processing. Classification is usually done by shallow learning for predefined objects, which is a difficult task and very different from human vision, which is based on continuous learning of object classes and one requires years to learn a large taxonomy of objects which are not disjunct nor independent. In this paper I present a system based on Google image similarity algorithm and Google image database, which can classify a large set of different objects in a human like manner, identifying related classes and taxonomies.

  4. Algorithm for Search and Recovery of the Vertex of Decay in the Hypernuclear Experiment NIS-GIBS at Dubna Nuclotron

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Korotkova, Anna M.; Lukstins, Juris

    2010-01-05

    Search of the decay vertex is an important part of the hypernuclear experiment, carried out of the Dubna nuclotron accelerator. The decay vertex is reconstructed from data from two sets of proportional chambers. The distribution of the vertex of decay of the hypernucleus allows to measure the lifetime of the hypernuclei. Algorithm for searches and automatically calculates the decay vertex has been written.

  5. The CHASE laboratory search for chameleon dark energy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Steffen, Jason H.; /Fermilab

    2010-11-01

    A scalar field is a favorite candidate for the particle responsible for dark energy. However, few theoretical means exist that can simultaneously explain the observed acceleration of the Universe and evade tests of gravity. The chameleon mechanism, whereby the properties of a particle depend upon the local environment, is one possible avenue. We present the results of the Chameleon Afterglow Search (CHASE) experiment, a laboratory probe for chameleon dark energy. CHASE marks a significant improvement other searches for chameleons both in terms of its sensitivity to the photon/chameleon coupling as well as its sensitivity to the classes of chameleon darkmore » energy models and standard power-law models. Since chameleon dark energy is virtually indistinguishable from a cosmological constant, CHASE tests dark energy models in a manner not accessible to astronomical surveys.« less

  6. Interactive searching of facial image databases

    NASA Astrophysics Data System (ADS)

    Nicholls, Robert A.; Shepherd, John W.; Shepherd, Jean

    1995-09-01

    A set of psychological facial descriptors has been devised to enable computerized searching of criminal photograph albums. The descriptors have been used to encode image databased of up to twelve thousand images. Using a system called FACES, the databases are searched by translating a witness' verbal description into corresponding facial descriptors. Trials of FACES have shown that this coding scheme is more productive and efficient than searching traditional photograph albums. An alternative method of searching the encoded database using a genetic algorithm is currenly being tested. The genetic search method does not require the witness to verbalize a description of the target but merely to indicate a degree of similarity between the target and a limited selection of images from the database. The major drawback of FACES is that is requires a manual encoding of images. Research is being undertaken to automate the process, however, it will require an algorithm which can predict human descriptive values. Alternatives to human derived coding schemes exist using statistical classifications of images. Since databases encoded using statistical classifiers do not have an obvious direct mapping to human derived descriptors, a search method which does not require the entry of human descriptors is required. A genetic search algorithm is being tested for such a purpose.

  7. Quality of anaesthesia-related information accessed via Internet searches.

    PubMed

    Caron, S; Berton, J; Beydon, L

    2007-08-01

    We conducted a study to examine the quality and stability of information available from the Internet on four anaesthesia-related topics. In January 2006, we searched using four key words (porphyria, scleroderma, transfusion risk, and epidural analgesia risk) with five search engines (Google, HotBot, AltaVista, Excite, and Yahoo). We used a published scoring system (NetScoring) to evaluate the first 15 sites identified by each of these 20 searches. We also used a simple four-point scale to assess the first 100 sites in the Google search on one of our four topics ('epidural analgesia risk'). In November 2006, we conducted a second evaluation, using three search engines (Google, AltaVista, and Yahoo) with 14 synonyms for 'epidural analgesia risk'. The five search engines performed similarly. NetScoring scores were lower for transfusion risk (P < 0.001). One or more high-quality sites was identified consistently among the first 15 sites in each search. Quality scored using the simple scale correlated closely with medical content and design by NetScoring and with the number of references (P < 0.05). Synonyms of 'epidural analgesia risk' yielded similar results. The quality of accessed information improved somewhat over the 11 month period with Yahoo and AltaVista, but declined with Google. The Internet is a valuable tool for obtaining medical information, but the quality of websites varies between different topics. A simple rating scale may facilitate the quality scoring on individual websites. Differences in precise search terms used for a given topic did not appear to affect the quality of the information obtained.

  8. Patient-Centered Tools for Medication Information Search

    PubMed Central

    Wilcox, Lauren; Feiner, Steven; Elhadad, Noémie; Vawdrey, David; Tran, Tran H.

    2016-01-01

    Recent research focused on online health information seeking highlights a heavy reliance on general-purpose search engines. However, current general-purpose search interfaces do not necessarily provide adequate support for non-experts in identifying suitable sources of health information. Popular search engines have recently introduced search tools in their user interfaces for a range of topics. In this work, we explore how such tools can support non-expert, patient-centered health information search. Scoping the current work to medication-related search, we report on findings from a formative study focused on the design of patient-centered, medication-information search tools. Our study included qualitative interviews with patients, family members, and domain experts, as well as observations of their use of Remedy, a technology probe embodying a set of search tools. Post-operative cardiothoracic surgery patients and their visiting family members used the tools to find information about their hospital medications and were interviewed before and after their use. Domain experts conducted similar search tasks and provided qualitative feedback on their preferences and recommendations for designing these tools. Findings from our study suggest the importance of four valuation principles underlying our tools: credibility, readability, consumer perspective, and topical relevance. PMID:28163972

  9. Airy Wave Packets Accelerating in Space-Time

    NASA Astrophysics Data System (ADS)

    Kondakci, H. Esat; Abouraddy, Ayman F.

    2018-04-01

    Although diffractive spreading is an unavoidable feature of all wave phenomena, certain waveforms can attain propagation invariance. A lesser-explored strategy for achieving optical self-similar propagation exploits the modification of the spatiotemporal field structure when observed in reference frames moving at relativistic speeds. For such an observer, it is predicted that the associated Lorentz boost can bring to a halt the axial dynamics of a wave packet of an arbitrary profile. This phenomenon is particularly striking in the case of a self-accelerating beam—such as an Airy beam—whose peak normally undergoes a transverse displacement upon free propagation. Here we synthesize an acceleration-free Airy wave packet that travels in a straight line by deforming its spatiotemporal spectrum to reproduce the impact of a Lorentz boost. The roles of the axial spatial coordinate and time are swapped, leading to "time diffraction" manifested in self-acceleration observed in the propagating Airy wave-packet frame.

  10. Effect of acoustic coupling on power-law flame acceleration in spherical confinement

    NASA Astrophysics Data System (ADS)

    Akkerman, V'yacheslav; Law, Chung K.

    2013-01-01

    A model describing acoustically-generated parametric instability in a spherical chamber is developed for quasi-one-dimensional, low-Mach number flames. We demonstrate how sound waves generated by a centrally-ignited, outwardly-propagating accelerating flamefront can be incorporated into an existing theory of self-similar flame acceleration in free space [V. Akkerman, C. K. Law, and V. Bychkov, "Self-similar accelerative propagation of expanding wrinkled flames and explosion triggering," Phys. Rev. E 83, 026305 (2011)], 10.1103/PhysRevE.83.026305. Being reflected from the chamber wall, flame-generated acoustics interact with the flamefront and the attendant hydrodynamic flamefront cellular instability. This in turn affects the subsequent flame morphology and propagation speed. It is shown that the acoustics modify the power-law flame acceleration, concomitantly facilitating or inhibiting the transition to detonation in confinement, which allows reconciliation of a discrepancy in experimental measurements of different groups.

  11. Efficacy of low-level laser therapy in accelerating tooth movement, preventing relapse and managing acute pain during orthodontic treatment in humans: a systematic review.

    PubMed

    Sonesson, Mikael; De Geer, Emelie; Subraian, Jaqueline; Petrén, Sofia

    2016-07-07

    Recently low-level laser therapy (LLLT) has been proposed to improve orthodontic treatment. The aims of this systematic review were to investigate the scientific evidence to support applications of LLLT: (a) to accelerate tooth movement, (b) to prevent orthodontic relapse and (c) to modulate acute pain, during treatment with fixed appliances in children and young adults. To ensure a systematic literature approach, this systematic review was conducted to Goodman's four step model. Three databases were searched (Medline, Cochrane Controlled Clinical Trials Register and Scitation), using predetermined search terms. The quality of evidence was rated according to the GRADE system. The search identified 244 articles, 16 of which fulfilled the inclusion criteria: three on acceleration of tooth movement by LLLT and 13 on LLLT modulation of acute pain. No study on LLLT for prevention of relapse was identified. The selected studies reported promising results for LLLT; elevated acceleration of tooth movement and lower pain scores, than controls. With respect to method, there were wide variations in type of laser techniques. The quality of evidence supporting LLLT to accelerate orthodontic tooth movement is very low and low with respect to modulate acute pain. No studies met the inclusion criteria for evaluating LLLT to limit relapse. The results highlight the need for high quality research, with consistency in study design, to determine whether LLLT can enhance fixed appliance treatment in children and young adults.

  12. A New Method for Measuring Text Similarity in Learning Management Systems Using WordNet

    ERIC Educational Resources Information Center

    Alkhatib, Bassel; Alnahhas, Ammar; Albadawi, Firas

    2014-01-01

    As text sources are getting broader, measuring text similarity is becoming more compelling. Automatic text classification, search engines and auto answering systems are samples of applications that rely on text similarity. Learning management systems (LMS) are becoming more important since electronic media is getting more publicly available. As…

  13. Covariant Uniform Acceleration

    NASA Astrophysics Data System (ADS)

    Friedman, Yaakov; Scarr, Tzvi

    2013-04-01

    We derive a 4D covariant Relativistic Dynamics Equation. This equation canonically extends the 3D relativistic dynamics equation , where F is the 3D force and p = m0γv is the 3D relativistic momentum. The standard 4D equation is only partially covariant. To achieve full Lorentz covariance, we replace the four-force F by a rank 2 antisymmetric tensor acting on the four-velocity. By taking this tensor to be constant, we obtain a covariant definition of uniformly accelerated motion. This solves a problem of Einstein and Planck. We compute explicit solutions for uniformly accelerated motion. The solutions are divided into four Lorentz-invariant types: null, linear, rotational, and general. For null acceleration, the worldline is cubic in the time. Linear acceleration covariantly extends 1D hyperbolic motion, while rotational acceleration covariantly extends pure rotational motion. We use Generalized Fermi-Walker transport to construct a uniformly accelerated family of inertial frames which are instantaneously comoving to a uniformly accelerated observer. We explain the connection between our approach and that of Mashhoon. We show that our solutions of uniformly accelerated motion have constant acceleration in the comoving frame. Assuming the Weak Hypothesis of Locality, we obtain local spacetime transformations from a uniformly accelerated frame K' to an inertial frame K. The spacetime transformations between two uniformly accelerated frames with the same acceleration are Lorentz. We compute the metric at an arbitrary point of a uniformly accelerated frame. We obtain velocity and acceleration transformations from a uniformly accelerated system K' to an inertial frame K. We introduce the 4D velocity, an adaptation of Horwitz and Piron s notion of "off-shell." We derive the general formula for the time dilation between accelerated clocks. We obtain a formula for the angular velocity of a uniformly accelerated object. Every rest point of K' is uniformly accelerated, and

  14. Electron acceleration by a focused laser pulse in a static magnetic field

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Huang Shihua; Wu Fengmin; Zhao Xianghao

    2007-12-15

    The model given by K. P. Singh [Phys. Rev. E 69, 056410 (2004)] for vacuum laser acceleration in a static magnetic field is revisited by including the effects of diffraction and the longitudinal electric field of a focused laser beam. Compared with a similar model without a static magnetic field, a simulation shows that electrons can gain much more net energy in this model even using the fifth-order corrected equations for the field of a focused laser beam. The acceleration mechanism and the acceleration efficiency are also investigated.

  15. Secular Acceleration of Barnard's Star

    NASA Astrophysics Data System (ADS)

    Bartlett, Jennifer L.; Ianna, P. A.

    2009-01-01

    Barnard's Star should have significant secular acceleration because it lies close to the Sun and has the highest known proper motion along with a large radial velocity. It will pass within about 1.4 pc in another 9,750 years. Secular changes in proper motion and radial velocity are essentially the Coriolis and centrifugal accelerations, respectively, arising from use of a rotating coordinate system defined by the Sun-star radius vector. Although stellar space velocities measured with respect to the Sun are essentially constant, these perspective effects arise with changing distance and viewing angle. Hipparcos-2 plus Nidever et al. (2002) predict a perspective change in the proper motion of 1.285±0.006 mas yr-2 for Barnard's Star. Recent analysis of 900+ photographic plates between 1968 and 1998 with the 26.25-in (0.67-m) McCormick refractor detected a secular acceleration of 1.25±0.04 mas yr-2, which agrees with the predicted value within the measurement errors. Earlier, Benedict et al. (1999) measured its secular acceleration to be 1.2±0.2 mas yr-2 using 3 years of HST FGS observations. Similarly, a perspective change in radial velocity of 4.50±0.01 m s-1 yr-1 can be predicted for Barnard's Star. Kürster et al. (2003) detected variations in their observations of it that are largely attributable to secular acceleration along the line of sight with some contribution from stellar activity. Although secular acceleration effects have been limited for past studies of stellar motions, they can be significant for observations extending over decades or for high-precision measurements required to detect extrasolar planets. Future studies will need to consider this factor for the nearest stars and for those with large proper motions or radial velocities. NSF grant AST 98-20711; Litton Marine Systems; Peninsula Community Foundation Levinson Fund; UVa Governor's Fellowship, Dean's F&A Fellowship, and Graduate School of Arts and Sciences; and, US Naval Observatory

  16. Cosmic acceleration in a dust only universe via energy-momentum powered gravity

    NASA Astrophysics Data System (ADS)

    Akarsu, Özgür; Katırcı, Nihan; Kumar, Suresh

    2018-01-01

    We propose a modified theory of gravitation constructed by the addition of the term f (Tμ νTμ ν) to the Einstein-Hilbert action, and elaborate a particular case f (Tμ νTμ ν)=α (Tμ νTμ ν)η, where α and η are real constants, dubbed energy-momentum powered gravity (EMPG). We search for viable cosmologies arising from EMPG, especially in the context of the late-time accelerated expansion of the Universe. We investigate the ranges of the EMPG parameters (α ,η ) on theoretical as well as observational grounds leading to the late-time acceleration of the Universe with pressureless matter only, while keeping the successes of standard general relativity at early times. We find that η =0 corresponds to the Λ CDM model, whereas η ≠0 leads to a w CDM -type model. However, the underlying physics of the EMPG model is entirely different in the sense that the energy in the EMPG Universe is sourced by pressureless matter only. Moreover, the energy of the pressureless matter is not conserved, namely, in general it does not dilute as ρ ∝a-3 with the expansion of the Universe. Finally, we constrain the parameters of an EMPG-based cosmology with a recent compilation of 28 Hubble parameter measurements, and find that this model describes an evolution of the Universe similar to that in the Λ CDM model. We briefly discuss that EMPG can be unified with Starobinsky gravity to describe the complete history of the Universe including the inflationary era.

  17. Analyzing radial acceleration with a smartphone acceleration sensor

    NASA Astrophysics Data System (ADS)

    Vogt, Patrik; Kuhn, Jochen

    2013-03-01

    This paper continues the sequence of experiments using the acceleration sensor of smartphones (for description of the function and the use of the acceleration sensor, see Ref. 1) within this column, in this case for analyzing the radial acceleration.

  18. Influence of inter-item symmetry in visual search.

    PubMed

    Roggeveen, Alexa B; Kingstone, Alan; Enns, James T

    2004-01-01

    Does visual search involve a serial inspection of individual items (Feature Integration Theory) or are items grouped and segregated prior to their consideration as a possible target (Attentional Engagement Theory)? For search items defined by motion and shape there is strong support for prior grouping (Kingstone and Bischof, 1999). The present study tested for grouping based on inter-item shape symmetry. Results showed that target-distractor symmetry strongly influenced search whereas distractor-distractor symmetry influenced search more weakly. This indicates that static shapes are evaluated for similarity to one another prior to their explicit identification as 'target' or 'distractor'. Possible reasons for the unequal contributions of target-distractor and distractor-distractor relations are discussed.

  19. SANSparallel: interactive homology search against Uniprot.

    PubMed

    Somervuo, Panu; Holm, Liisa

    2015-07-01

    Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values

    PubMed Central

    Baldi, Pierre

    2010-01-01

    As repositories of chemical molecules continue to expand and become more open, it becomes increasingly important to develop tools to search them efficiently and assess the statistical significance of chemical similarity scores. Here we develop a general framework for understanding, modeling, predicting, and approximating the distribution of chemical similarity scores and its extreme values in large databases. The framework can be applied to different chemical representations and similarity measures but is demonstrated here using the most common binary fingerprints with the Tanimoto similarity measure. After introducing several probabilistic models of fingerprints, including the Conditional Gaussian Uniform model, we show that the distribution of Tanimoto scores can be approximated by the distribution of the ratio of two correlated Normal random variables associated with the corresponding unions and intersections. This remains true also when the distribution of similarity scores is conditioned on the size of the query molecules in order to derive more fine-grained results and improve chemical retrieval. The corresponding extreme value distributions for the maximum scores are approximated by Weibull distributions. From these various distributions and their analytical forms, Z-scores, E-values, and p-values are derived to assess the significance of similarity scores. In addition, the framework allows one to predict also the value of standard chemical retrieval metrics, such as Sensitivity and Specificity at fixed thresholds, or ROC (Receiver Operating Characteristic) curves at multiple thresholds, and to detect outliers in the form of atypical molecules. Numerous and diverse experiments carried in part with large sets of molecules from the ChemDB show remarkable agreement between theory and empirical results. PMID:20540577

  1. A reproducible accelerated in vitro release testing method for PLGA microspheres.

    PubMed

    Shen, Jie; Lee, Kyulim; Choi, Stephanie; Qu, Wen; Wang, Yan; Burgess, Diane J

    2016-02-10

    The objective of the present study was to develop a discriminatory and reproducible accelerated in vitro release method for long-acting PLGA microspheres with inner structure/porosity differences. Risperidone was chosen as a model drug. Qualitatively and quantitatively equivalent PLGA microspheres with different inner structure/porosity were obtained using different manufacturing processes. Physicochemical properties as well as degradation profiles of the prepared microspheres were investigated. Furthermore, in vitro release testing of the prepared risperidone microspheres was performed using the most common in vitro release methods (i.e., sample-and-separate and flow through) for this type of product. The obtained compositionally equivalent risperidone microspheres had similar drug loading but different inner structure/porosity. When microsphere particle size appeared similar, porous risperidone microspheres showed faster microsphere degradation and drug release compared with less porous microspheres. Both in vitro release methods investigated were able to differentiate risperidone microsphere formulations with differences in porosity under real-time (37 °C) and accelerated (45 °C) testing conditions. Notably, only the accelerated USP apparatus 4 method showed good reproducibility for highly porous risperidone microspheres. These results indicated that the accelerated USP apparatus 4 method is an appropriate fast quality control tool for long-acting PLGA microspheres (even with porous structures). Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Folksonomical P2P File Sharing Networks Using Vectorized KANSEI Information as Search Tags

    NASA Astrophysics Data System (ADS)

    Ohnishi, Kei; Yoshida, Kaori; Oie, Yuji

    We present the concept of folksonomical peer-to-peer (P2P) file sharing networks that allow participants (peers) to freely assign structured search tags to files. These networks are similar to folksonomies in the present Web from the point of view that users assign search tags to information distributed over a network. As a concrete example, we consider an unstructured P2P network using vectorized Kansei (human sensitivity) information as structured search tags for file search. Vectorized Kansei information as search tags indicates what participants feel about their files and is assigned by the participant to each of their files. A search query also has the same form of search tags and indicates what participants want to feel about files that they will eventually obtain. A method that enables file search using vectorized Kansei information is the Kansei query-forwarding method, which probabilistically propagates a search query to peers that are likely to hold more files having search tags that are similar to the query. The similarity between the search query and the search tags is measured in terms of their dot product. The simulation experiments examine if the Kansei query-forwarding method can provide equal search performance for all peers in a network in which only the Kansei information and the tendency with respect to file collection are different among all of the peers. The simulation results show that the Kansei query forwarding method and a random-walk-based query forwarding method, for comparison, work effectively in different situations and are complementary. Furthermore, the Kansei query forwarding method is shown, through simulations, to be superior to or equal to the random-walk based one in terms of search speed.

  3. Different predictors of multiple-target search accuracy between nonprofessional and professional visual searchers.

    PubMed

    Biggs, Adam T; Mitroff, Stephen R

    2014-01-01

    Visual search, locating target items among distractors, underlies daily activities ranging from critical tasks (e.g., looking for dangerous objects during security screening) to commonplace ones (e.g., finding your friends in a crowded bar). Both professional and nonprofessional individuals conduct visual searches, and the present investigation is aimed at understanding how they perform similarly and differently. We administered a multiple-target visual search task to both professional (airport security officers) and nonprofessional participants (members of the Duke University community) to determine how search abilities differ between these populations and what factors might predict accuracy. There were minimal overall accuracy differences, although the professionals were generally slower to respond. However, the factors that predicted accuracy varied drastically between groups; variability in search consistency-how similarly an individual searched from trial to trial in terms of speed-best explained accuracy for professional searchers (more consistent professionals were more accurate), whereas search speed-how long an individual took to complete a search when no targets were present-best explained accuracy for nonprofessional searchers (slower nonprofessionals were more accurate). These findings suggest that professional searchers may utilize different search strategies from those of nonprofessionals, and that search consistency, in particular, may provide a valuable tool for enhancing professional search accuracy.

  4. Community Petascale Project for Accelerator Science and Simulation: Advancing Computational Science for Future Accelerators and Accelerator Technologies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Spentzouris, P.; /Fermilab; Cary, J.

    The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessarymore » accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors. ComPASS is in the first year of executing its plan to develop the next-generation HPC accelerator modeling tools. ComPASS aims to develop an integrated simulation environment that will utilize existing and new accelerator physics modules with petascale capabilities, by employing modern computing and solver technologies. The ComPASS vision is to deliver to accelerator scientists a virtual accelerator and virtual prototyping modeling environment, with the necessary multiphysics, multiscale capabilities. The plan for this development includes delivering accelerator modeling applications appropriate for each stage of the ComPASS software evolution. Such applications are already being used to address challenging problems in accelerator design and optimization. The Com

  5. Trading efficiency for effectiveness in similarity-based indexing for image databases

    NASA Astrophysics Data System (ADS)

    Barros, Julio E.; French, James C.; Martin, Worthy N.; Kelly, Patrick M.

    1995-11-01

    Image databases typically manage feature data that can be viewed as points in a feature space. Some features, however, can be better expressed as a collection of points or described by a probability distribution function (PDF) rather than as a single point. In earlier work we introduced a similarity measure and a method for indexing and searching the PDF descriptions of these items that guarantees an answer equivalent to sequential search. Unfortunately, certain properties of the data can restrict the efficiency of that method. In this paper we extend that work and examine trade-offs between efficiency and answer quality or effectiveness. These trade-offs reduce the amount of work required during a search by reducing the number of undesired items fetched without excluding an excessive number of the desired ones.

  6. Perception of linear acceleration in weightlessness

    NASA Technical Reports Server (NTRS)

    Arrott, Anthony P.; Young, Laurence R.; Merfeld, Daniel M.

    1991-01-01

    Tests of the perception and use of linear acceleration sensory information were performed on the science crews of the Spacelab 1 (SL-1) and D-1 missions using linear 'sleds' in-flight (D-1) and pre-post flight. The time delay between the acceleration step stimulus and the subjective response was consistently reduced during weightlessness, but was neither statistically significant nor of functional importance. Increased variability of responses when going from one environment to the other was apparent from measurements on the first day of the mission and in the first days post-flight. Subjective reports of perceived motion during sinusoidal oscillation in weightlessness were qualitatively similar to reports on earth. In a closed-loop motion nulling task, enhanced performance was observed post-flight in all crewmembers tested in the Y or Z axes.

  7. Perception of linear acceleration in weightlessness

    NASA Technical Reports Server (NTRS)

    Arrott, A. P.; Young, L. R.; Merfeld, D. M.

    1990-01-01

    Tests of the perception and use of linear acceleration sensory information were performed on the science crews of the Spacelab 1 (SL-1) and D-1 missions using linear "sleds" in-flight (D-1) and pre-post flight. The time delay between the acceleration step stimulus and the subjective response was consistently reduced during weightlessness, but was neither statistically significant nor of functional importance. Increased variability of responses when going from one environment to the other was apparent from measurements on the first day of the mission and in the first days post-flight. Subjective reports of perceived motion during sinusoidal oscillation in weightlessness were qualitatively similar to reports on earth. In a closed-loop motion nulling task, enhanced performance was observed post-flight in all crewmembers tested in the Y or Z axes.

  8. Faster sequence homology searches by clustering subsequences.

    PubMed

    Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

    2015-04-15

    Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. We developed a fast homology search method based on database subsequence clustering, and implemented it as GHOSTZ. This method clusters similar subsequences from a database to perform an efficient seed search and ungapped extension by reducing alignment candidates based on triangle inequality. The database subsequence clustering technique achieved an ∼2-fold increase in speed without a large decrease in search sensitivity. When we measured with metagenomic data, GHOSTZ is ∼2.2-2.8 times faster than RAPSearch and is ∼185-261 times faster than BLASTX. The source code is freely available for download at http://www.bi.cs.titech.ac.jp/ghostz/ akiyama@cs.titech.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  9. What Friends Are For: Collaborative Intelligence Analysis and Search

    DTIC Science & Technology

    2014-06-01

    14. SUBJECT TERMS Intelligence Community, information retrieval, recommender systems , search engines, social networks, user profiling, Lucene...improvements over existing search systems . The improvements are shown to be robust to high levels of human error and low similarity between users ...precision NOLH nearly orthogonal Latin hypercubes P@ precision at documents RS recommender systems TREC Text REtrieval Conference USM user

  10. Accelerators, Beams And Physical Review Special Topics - Accelerators And Beams

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Siemann, R.H.; /SLAC

    Accelerator science and technology have evolved as accelerators became larger and important to a broad range of science. Physical Review Special Topics - Accelerators and Beams was established to serve the accelerator community as a timely, widely circulated, international journal covering the full breadth of accelerators and beams. The history of the journal and the innovations associated with it are reviewed.

  11. Commnity Petascale Project for Accelerator Science And Simulation: Advancing Computational Science for Future Accelerators And Accelerator Technologies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Spentzouris, Panagiotis; /Fermilab; Cary, John

    The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessarymore » accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors.« less

  12. Search for CP Violation in Hyperon Decay: $$\\Xi^- / \\bar{\\Xi}^+$$ and $$\\Lambda / \\bar{\\Lambda}$$ (in French)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Leros, Nicolas

    2001-06-01

    The HyperCP(EB71) experiment, performed at the Fermi National Accelerator Laboratory in the United States, provides a primary search for direct OP violation in the decays ofmore » $$\\Xi^-/\\bar{\\Xi}^+$$ and $$\\Lambda/ \\bar{\\Lambda}$$ hyperons....« less

  13. Opportunities for future supernova studies of cosmic acceleration.

    PubMed

    Weller, J; Albrecht, A

    2001-03-05

    We investigate the potential of a future supernova data set, as might be obtained by the proposed SNAP satellite, to discriminate among different "dark energy" theories that describe an accelerating Universe. We find that many such models can be distinguished with a fit to the effective pressure-to-density ratio w of this energy. More models can be distinguished when the effective slope dw/dz of a changing w is also fit, but only if our knowledge of the current mass density Omega(m) is improved. We investigate the use of "fitting functions" to interpret luminosity distance data from supernova searches.

  14. Recent results from the University of Washington's 38 mm ram accelerator

    NASA Technical Reports Server (NTRS)

    De Turenne, J. A.; Chew, G.; Bruckner, A. P.

    1992-01-01

    The ram accelerator is a propulsive device that accelerates projectiles using gasdynamic cycles similar to those which generate thrust in airbreathing ramjets. The projectile, analogous to the centerbody of a ramjet, travels supersonically through a stationary tube containing a gaseous fuel and oxidizer mixture. The projectile itself carries no onboard propellant. A combustion zone follows the projectile and stabilizes the shock structure. The resulting pressure distribution continuously accelerates the projectile. Several modes of ram accelerator operation have been investigated experimentally and theoretically. At velocities below the Chapman-Jouguet (C-J) detonation speed of the propellant mixture, the thermally choked propulsion mode accelerates the projectiles. At projectile velocities between approximately 90 and 110 percent of the C-J speed, a transdetonative propulsion mode occurs. At velocities beyond 110 percent of the C-J speed, projectiles experience superdetonative propulsion. This paper presents recent experimental results from these propulsion modes obtained with the University of Washington's 38-mm bore ram accelerator. Data from investigations with hydrogen diluted-gas mixtures are also introduced.

  15. Quantifying the Search Behaviour of Different Demographics Using Google Correlate

    PubMed Central

    Letchford, Adrian; Preis, Tobias; Moat, Helen Susannah

    2016-01-01

    Vast records of our everyday interests and concerns are being generated by our frequent interactions with the Internet. Here, we investigate how the searches of Google users vary across U.S. states with different birth rates and infant mortality rates. We find that users in states with higher birth rates search for more information about pregnancy, while those in states with lower birth rates search for more information about cats. Similarly, we find that users in states with higher infant mortality rates search for more information about credit, loans and diseases. Our results provide evidence that Internet search data could offer new insight into the concerns of different demographics. PMID:26910464

  16. The Organizational Culture and Structure of Accelerated Schools.

    ERIC Educational Resources Information Center

    Steaffens, Susan; McCarthy, Jane; Putney, LeAnn; Steinhoff, Carl

    This paper describes the organizational culture and structure of five accelerated schools in the Clark County School District in Nevada, focusing on the similarities and differences among these schools. The cultural aspects of the schools under comparison included the guiding principles, the central values, and the learning philosophy, whereas the…

  17. Electron Bulk Acceleration and Thermalization at Earth's Quasiperpendicular Bow Shock.

    PubMed

    Chen, L-J; Wang, S; Wilson, L B; Schwartz, S; Bessho, N; Moore, T; Gershman, D; Giles, B; Malaspina, D; Wilder, F D; Ergun, R E; Hesse, M; Lai, H; Russell, C; Strangeway, R; Torbert, R B; F-Vinas, A; Burch, J; Lee, S; Pollock, C; Dorelli, J; Paterson, W; Ahmadi, N; Goodrich, K; Lavraud, B; Le Contel, O; Khotyaintsev, Yu V; Lindqvist, P-A; Boardsen, S; Wei, H; Le, A; Avanov, L

    2018-06-01

    Electron heating at Earth's quasiperpendicular bow shock has been surmised to be due to the combined effects of a quasistatic electric potential and scattering through wave-particle interaction. Here we report the observation of electron distribution functions indicating a new electron heating process occurring at the leading edge of the shock front. Incident solar wind electrons are accelerated parallel to the magnetic field toward downstream, reaching an electron-ion relative drift speed exceeding the electron thermal speed. The bulk acceleration is associated with an electric field pulse embedded in a whistler-mode wave. The high electron-ion relative drift is relaxed primarily through a nonlinear current-driven instability. The relaxed distributions contain a beam traveling toward the shock as a remnant of the accelerated electrons. Similar distribution functions prevail throughout the shock transition layer, suggesting that the observed acceleration and thermalization is essential to the cross-shock electron heating.

  18. Electron Bulk Acceleration and Thermalization at Earth's Quasiperpendicular Bow Shock

    NASA Astrophysics Data System (ADS)

    Chen, L.-J.; Wang, S.; Wilson, L. B.; Schwartz, S.; Bessho, N.; Moore, T.; Gershman, D.; Giles, B.; Malaspina, D.; Wilder, F. D.; Ergun, R. E.; Hesse, M.; Lai, H.; Russell, C.; Strangeway, R.; Torbert, R. B.; F.-Vinas, A.; Burch, J.; Lee, S.; Pollock, C.; Dorelli, J.; Paterson, W.; Ahmadi, N.; Goodrich, K.; Lavraud, B.; Le Contel, O.; Khotyaintsev, Yu. V.; Lindqvist, P.-A.; Boardsen, S.; Wei, H.; Le, A.; Avanov, L.

    2018-06-01

    Electron heating at Earth's quasiperpendicular bow shock has been surmised to be due to the combined effects of a quasistatic electric potential and scattering through wave-particle interaction. Here we report the observation of electron distribution functions indicating a new electron heating process occurring at the leading edge of the shock front. Incident solar wind electrons are accelerated parallel to the magnetic field toward downstream, reaching an electron-ion relative drift speed exceeding the electron thermal speed. The bulk acceleration is associated with an electric field pulse embedded in a whistler-mode wave. The high electron-ion relative drift is relaxed primarily through a nonlinear current-driven instability. The relaxed distributions contain a beam traveling toward the shock as a remnant of the accelerated electrons. Similar distribution functions prevail throughout the shock transition layer, suggesting that the observed acceleration and thermalization is essential to the cross-shock electron heating.

  19. Searching for periodic sources with LIGO. II. Hierarchical searches

    NASA Astrophysics Data System (ADS)

    Brady, Patrick R.; Creighton, Teviet

    2000-04-01

    The detection of quasi-periodic sources of gravitational waves requires the accumulation of signal to noise over long observation times. This represents the most difficult data analysis problem facing experimenters with detectors such as those at LIGO. If not removed, Earth-motion induced Doppler modulations and intrinsic variations of the gravitational-wave frequency make the signals impossible to detect. These effects can be corrected (removed) using a parametrized model for the frequency evolution. In a previous paper, we introduced such a model and computed the number of independent parameter space points for which corrections must be applied to the data stream in a coherent search. Since this number increases with the observation time, the sensitivity of a search for continuous gravitational-wave signals is computationally bound when data analysis proceeds at a similar rate to data acquisition. In this paper, we extend the formalism developed by Brady et al. [Phys. Rev. D 57, 2101 (1998)], and we compute the number of independent corrections Np(ΔT,N) required for incoherent search strategies. These strategies rely on the method of stacked power spectra-a demodulated time series is divided into N segments of length ΔT, each segment is Fourier transformed, a power spectrum is computed, and the N spectra are summed up. This method is incoherent; phase information is lost from segment to segment. Nevertheless, power from a signal with fixed frequency (in the corrected time series) is accumulated in a single frequency bin, and amplitude signal to noise accumulates as ~N1/4 (assuming the segment length ΔT is held fixed). For fixed available computing power, there are optimal values for N and ΔT which maximize the sensitivity of a search in which data analysis takes a total time NΔT. We estimate that the optimal sensitivity of an all-sky search that uses incoherent stacks is a factor of 2-4 better than achieved using coherent Fourier transforms, assuming the

  20. JSC Search System Usability Case Study

    NASA Technical Reports Server (NTRS)

    Meza, David; Berndt, Sarah

    2014-01-01

    The advanced nature of "search" has facilitated the movement from keyword match to the delivery of every conceivable information topic from career, commerce, entertainment, learning... the list is infinite. At NASA Johnson Space Center (JSC ) the Search interface is an important means of knowledge transfer. By indexing multiple sources between directorates and organizations, the system's potential is culture changing in that through search, knowledge of the unique accomplishments in engineering and science can be seamlessly passed between generations. This paper reports the findings of an initial survey, the first of a four part study to help determine user sentiment on the intranet, or local (JSC) enterprise search environment as well as the larger NASA enterprise. The survey is a means through which end users provide direction on the development and transfer of knowledge by way of the search experience. The ideal is to identify what is working and what needs to be improved from the users' vantage point by documenting: (1) Where users are satisfied/dissatisfied (2) Perceived value of interface components (3) Gaps which cause any disappointment in search experience. The near term goal is it to inform JSC search in order to improve users' ability to utilize existing services and infrastructure to perform tasks with a shortened life cycle. Continuing steps include an agency based focus with modified questions to accomplish a similar purpose

  1. Ultra-High Accelerating Gradients in Radio-Frequency Cryogenic Copper Structures

    NASA Astrophysics Data System (ADS)

    Cahill, Alexander David

    Normal conducting radio-frequency (rf) particle accelerators have many applications, including colliders for high energy physics, high-intensity synchrotron light sources, non-destructive testing for security, and medical radiation therapy. In these applications, the accelerating gradient is an important parameter. Specifically for high energy physics, increasing the accelerating gradient extends the potential energy reach and is viewed as a way to mitigate their considerable cost. Furthermore, a gradient increase will enable for more compact and thus accessible free electron lasers (FELs). The major factor limiting larger accelerating gradients is vacuum rf breakdown. Basic physics of this phenomenon has been extensively studied over the last few decades. During which, the occurrence of rf breakdowns was shown to be probabilistic, and can be characterized by a breakdown rate. The current consensus is that vacuum rf breakdowns are caused by movements of crystal defects induced by periodic mechanical stress. The stress may be caused by pulsed surface heating and large electric fields. A compelling piece of evidence that supports this hypothesis is that accelerating structures constructed from harder materials exhibit larger accelerating gradients for similar breakdown rates. One possible method to increase sustained electric fields in copper cavities is to cool them to temperatures below 77 K, where the rf surface resistance and coefficient of thermal expansion decrease, while the yield strength (which correlates with hardness) and thermal conductivity increase. These changes in material properties at low temperature increases metal hardness and decreases the mechanical stress from exposure to rf electromagnetic fields. To test the validity of the improvement in breakdown rate, experiments were conducted with cryogenic accelerating cavities in the Accelerator Structure Test Area (ASTA) at SLAC National Accelerator Laboratory. A short 11.4 GHz standing wave

  2. How to improve your PubMed/MEDLINE searches: 2. display settings, complex search queries and topic searching.

    PubMed

    Fatehi, Farhad; Gray, Leonard C; Wootton, Richard

    2014-01-01

    The way that PubMed results are displayed can be changed using the Display Settings drop-down menu in the result screen. There are three groups of options: Format, Items per page and Sort by, which allow a good deal of control. The results from several searches can be temporarily stored on the Clipboard. Records of interest can be selected on the results page using check boxes and can then be combined, for example to form a reference list. The Related Citations is a valuable feature of PubMed that can provide a set of similar articles when you have identified a record of interest among the results. You can easily search for RCTs or reviews using the appropriate filters or field tags. If you are interested in clinical articles, rather than basic science or health service research, then the Clinical Queries tool on the PubMed home page can be used to retrieve them.

  3. The Heavy Photon Search beamline and its performance

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Baltzell, N.; Egiyan, H.; Ehrhart, M.

    The Heavy Photon Search (HPS) is an experiment to search for a hidden sector photon, aka a heavy photon or dark photon, in fixed target electroproduction at the Thomas Jefferson National Accelerator Facility (JLab). The HPS experiment searches for the emore » $^+$e$^-$ decay of the heavy photon with bump hunt and detached vertex strategies using a compact, large acceptance forward spectrometer, consisting of a silicon microstrip detector (SVT) for tracking and vertexing, and a PbWO$$_4$$ electromagnetic calorimeter for energy measurement and fast triggering. To achieve large acceptance and good vertexing resolution, the first layer of silicon detectors is placed just 10 cm downstream of the target with the sensor edges only 500 $$\\mu$$m above and below the beam. Placing the SVT in such close proximity to the beam puts stringent requirements on the beam profile and beam position stability. As part of an approved engineering run, HPS took data in 2015 and 2016 at 1.05 GeV and 2.3 GeV beam energies, respectively. This study describes the beam line and its performance during that data taking.« less

  4. The Heavy Photon Search beamline and its performance

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Baltzell, N.; Egiyan, H.; Ehrhart, M.

    The Heavy Photon Search (HPS) is an experiment to search for a hidden sector photon, aka a heavy photon or dark photon, in fixed target electroproduction at the Thomas Jefferson National Accelerator Facility (JLab). The HPS experiment searches for the e+e- decay of the heavy photon with bump hunt and detached vertex strategies using a compact, large acceptance forward spectrometer, consisting of a silicon microstrip detector (SVT) for tracking and vertexing, and a PbWO 4 electromagnetic calorimeter for energy measurement and fast triggering. To achieve large acceptance and good vertexing resolution, the first layer of silicon detectors is placed justmore » 10 cm downstream of the target with the sensor edges only 500 μm above and below the beam. Placing the SVT in such close proximity to the beam puts stringent requirements on the beam profile and beam position stability. As part of an approved engineering run, HPS took data in 2015 and 2016 at 1.05 GeV and 2.3 GeV beam energies, respectively. This paper describes the beam line and its performance during that data taking.« less

  5. The Heavy Photon Search beamline and its performance

    DOE PAGES

    Baltzell, N.; Egiyan, H.; Ehrhart, M.; ...

    2017-07-01

    The Heavy Photon Search (HPS) is an experiment to search for a hidden sector photon, aka a heavy photon or dark photon, in fixed target electroproduction at the Thomas Jefferson National Accelerator Facility (JLab). The HPS experiment searches for the emore » $^+$e$^-$ decay of the heavy photon with bump hunt and detached vertex strategies using a compact, large acceptance forward spectrometer, consisting of a silicon microstrip detector (SVT) for tracking and vertexing, and a PbWO$$_4$$ electromagnetic calorimeter for energy measurement and fast triggering. To achieve large acceptance and good vertexing resolution, the first layer of silicon detectors is placed just 10 cm downstream of the target with the sensor edges only 500 $$\\mu$$m above and below the beam. Placing the SVT in such close proximity to the beam puts stringent requirements on the beam profile and beam position stability. As part of an approved engineering run, HPS took data in 2015 and 2016 at 1.05 GeV and 2.3 GeV beam energies, respectively. This study describes the beam line and its performance during that data taking.« less

  6. Fermilab | Tevatron | Accelerator

    Science.gov Websites

    Leading accelerator technology Accelerator complex Illinois Accelerator Research Center Fermilab temperature. They were used to transfer particles from one part of the Fermilab accelerator complex to another center ring of Fermilab's accelerator complex. Before the Tevatron shut down, it had three primary

  7. Optimum tuned mass damper design using harmony search with comparison of classical methods

    NASA Astrophysics Data System (ADS)

    Nigdeli, Sinan Melih; Bekdaş, Gebrail; Sayin, Baris

    2017-07-01

    As known, tuned mass dampers (TMDs) are added to mechanical systems in order to obtain a good vibration damping. The main aim is to reduce the maximum amplitude at the resonance state. In this study, a metaheuristic algorithm called harmony search employed for the optimum design of TMDs. As the optimization objective, the transfer function of the acceleration of the system with respect to ground acceleration was minimized. The numerical trails were conducted for 4 single degree of freedom systems and the results were compared with classical methods. As a conclusion, the proposed method is feasible and more effective than the other documented methods.

  8. Piezoelectric particle accelerator

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kemp, Mark A.; Jongewaard, Erik N.; Haase, Andrew A.

    2017-08-29

    A particle accelerator is provided that includes a piezoelectric accelerator element, where the piezoelectric accelerator element includes a hollow cylindrical shape, and an input transducer, where the input transducer is disposed to provide an input signal to the piezoelectric accelerator element, where the input signal induces a mechanical excitation of the piezoelectric accelerator element, where the mechanical excitation is capable of generating a piezoelectric electric field proximal to an axis of the cylindrical shape, where the piezoelectric accelerator is configured to accelerate a charged particle longitudinally along the axis of the cylindrical shape according to the piezoelectric electric field.

  9. EDITORIAL: Laser and plasma accelerators Laser and plasma accelerators

    NASA Astrophysics Data System (ADS)

    Bingham, Robert

    2009-02-01

    This special issue on laser and plasma accelerators illustrates the rapid advancement and diverse applications of laser and plasma accelerators. Plasma is an attractive medium for particle acceleration because of the high electric field it can sustain, with studies of acceleration processes remaining one of the most important areas of research in both laboratory and astrophysical plasmas. The rapid advance in laser and accelerator technology has led to the development of terawatt and petawatt laser systems with ultra-high intensities and short sub-picosecond pulses, which are used to generate wakefields in plasma. Recent successes include the demonstration by several groups in 2004 of quasi-monoenergetic electron beams by wakefields in the bubble regime with the GeV energy barrier being reached in 2006, and the energy doubling of the SLAC high-energy electron beam from 42 to 85 GeV. The electron beams generated by the laser plasma driven wakefields have good spatial quality with energies ranging from MeV to GeV. A unique feature is that they are ultra-short bunches with simulations showing that they can be as short as a few femtoseconds with low-energy spread, making these beams ideal for a variety of applications ranging from novel high-brightness radiation sources for medicine, material science and ultrafast time-resolved radiobiology or chemistry. Laser driven ion acceleration experiments have also made significant advances over the last few years with applications in laser fusion, nuclear physics and medicine. Attention is focused on the possibility of producing quasi-mono-energetic ions with energies ranging from hundreds of MeV to GeV per nucleon. New acceleration mechanisms are being studied, including ion acceleration from ultra-thin foils and direct laser acceleration. The application of wakefields or beat waves in other areas of science such as astrophysics and particle physics is beginning to take off, such as the study of cosmic accelerators considered

  10. Similarity solutions of time-dependent relativistic radiation-hydrodynamical plane-parallel flows

    NASA Astrophysics Data System (ADS)

    Fukue, Jun

    2018-04-01

    Similarity solutions are examined for the frequency-integrated relativistic radiation-hydrodynamical flows, which are described by the comoving quantities. The flows are vertical plane-parallel time-dependent ones with a gray opacity coefficient. For adequate boundary conditions, the flows are accelerated in a somewhat homologous manner, but terminate at some singular locus, which originates from the pathological behavior in relativistic radiation moment equations truncated in finite orders.

  11. Similarity solutions of time-dependent relativistic radiation-hydrodynamical plane-parallel flows

    NASA Astrophysics Data System (ADS)

    Fukue, Jun

    2018-06-01

    Similarity solutions are examined for the frequency-integrated relativistic radiation-hydrodynamical flows, which are described by the comoving quantities. The flows are vertical plane-parallel time-dependent ones with a gray opacity coefficient. For adequate boundary conditions, the flows are accelerated in a somewhat homologous manner, but terminate at some singular locus, which originates from the pathological behavior in relativistic radiation moment equations truncated in finite orders.

  12. PISA and Scientific Literacy: Similarities and Differences between the Nordic Countries

    ERIC Educational Resources Information Center

    Kjaernsli, Marit; Lie, Svein

    2004-01-01

    In this paper we have set out to search for similarities and differences between the Nordic countries concerning patterns of competencies defined as scientific literacy in the Programme for International Student Assessment (PISA) study. The first part focuses on gender differences concerning the two types of competencies, understanding of…

  13. Search and Graph Database Technologies for Biomedical Semantic Indexing: Experimental Analysis.

    PubMed

    Segura Bedmar, Isabel; Martínez, Paloma; Carruana Martín, Adrián

    2017-12-01

    Biomedical semantic indexing is a very useful support tool for human curators in their efforts for indexing and cataloging the biomedical literature. The aim of this study was to describe a system to automatically assign Medical Subject Headings (MeSH) to biomedical articles from MEDLINE. Our approach relies on the assumption that similar documents should be classified by similar MeSH terms. Although previous work has already exploited the document similarity by using a k-nearest neighbors algorithm, we represent documents as document vectors by search engine indexing and then compute the similarity between documents using cosine similarity. Once the most similar documents for a given input document are retrieved, we rank their MeSH terms to choose the most suitable set for the input document. To do this, we define a scoring function that takes into account the frequency of the term into the set of retrieved documents and the similarity between the input document and each retrieved document. In addition, we implement guidelines proposed by human curators to annotate MEDLINE articles; in particular, the heuristic that says if 3 MeSH terms are proposed to classify an article and they share the same ancestor, they should be replaced by this ancestor. The representation of the MeSH thesaurus as a graph database allows us to employ graph search algorithms to quickly and easily capture hierarchical relationships such as the lowest common ancestor between terms. Our experiments show promising results with an F1 of 69% on the test dataset. To the best of our knowledge, this is the first work that combines search and graph database technologies for the task of biomedical semantic indexing. Due to its horizontal scalability, ElasticSearch becomes a real solution to index large collections of documents (such as the bibliographic database MEDLINE). Moreover, the use of graph search algorithms for accessing MeSH information could provide a support tool for cataloging MEDLINE

  14. MOST: most-similar ligand based approach to target prediction.

    PubMed

    Huang, Tao; Mi, Hong; Lin, Cheng-Yuan; Zhao, Ling; Zhong, Linda L D; Liu, Feng-Bin; Zhang, Ge; Lu, Ai-Ping; Bian, Zhao-Xiang

    2017-03-11

    Many computational approaches have been used for target prediction, including machine learning, reverse docking, bioactivity spectra analysis, and chemical similarity searching. Recent studies have suggested that chemical similarity searching may be driven by the most-similar ligand. However, the extent of bioactivity of most-similar ligands has been oversimplified or even neglected in these studies, and this has impaired the prediction power. Here we propose the MOst-Similar ligand-based Target inference approach, namely MOST, which uses fingerprint similarity and explicit bioactivity of the most-similar ligands to predict targets of the query compound. Performance of MOST was evaluated by using combinations of different fingerprint schemes, machine learning methods, and bioactivity representations. In sevenfold cross-validation with a benchmark Ki dataset from CHEMBL release 19 containing 61,937 bioactivity data of 173 human targets, MOST achieved high average prediction accuracy (0.95 for pKi ≥ 5, and 0.87 for pKi ≥ 6). Morgan fingerprint was shown to be slightly better than FP2. Logistic Regression and Random Forest methods performed better than Naïve Bayes. In a temporal validation, the Ki dataset from CHEMBL19 were used to train models and predict the bioactivity of newly deposited ligands in CHEMBL20. MOST also performed well with high accuracy (0.90 for pKi ≥ 5, and 0.76 for pKi ≥ 6), when Logistic Regression and Morgan fingerprint were employed. Furthermore, the p values associated with explicit bioactivity were found be a robust index for removing false positive predictions. Implicit bioactivity did not offer this capability. Finally, p values generated with Logistic Regression, Morgan fingerprint and explicit activity were integrated with a false discovery rate (FDR) control procedure to reduce false positives in multiple-target prediction scenario, and the success of this strategy it was demonstrated with a case of fluanisone

  15. The effectiveness of position- and composition-specific gap costs for protein similarity searches.

    PubMed

    Stojmirović, Aleksandar; Gertz, E Michael; Altschul, Stephen F; Yu, Yi-Kuo

    2008-07-01

    The flexibility in gap cost enjoyed by hidden Markov models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately examining the influence of position- and composition-specific gap scores, as well as by comparing the retrieval accuracy of the PSSMs constructed using an iterative procedure to that of the HMMs provided by Pfam and SUPERFAMILY, curated ensembles of multiple alignments. We found that position-specific gap penalties have an advantage over uniform gap costs. We did not explore optimizing distinct uniform gap costs for each query. For Pfam, PSSMs iteratively constructed from seeds based on HMM consensus sequences perform equivalently to HMMs that were adjusted to have constant gap transition probabilities, albeit with much greater variance. We observed no effect of composition-specific gap costs on retrieval performance. These results suggest possible improvements to the PSI-BLAST protein database search program. The scripts for performing evaluations are available upon request from the authors.

  16. Computing Principal Eigenvectors of Large Web Graphs: Algorithms and Accelerations Related to PageRank and HITS

    ERIC Educational Resources Information Center

    Nagasinghe, Iranga

    2010-01-01

    This thesis investigates and develops a few acceleration techniques for the search engine algorithms used in PageRank and HITS computations. PageRank and HITS methods are two highly successful applications of modern Linear Algebra in computer science and engineering. They constitute the essential technologies accounted for the immense growth and…

  17. Use of similarity scoring in the development of oral solid dosage forms.

    PubMed

    Ferreira, Ana P; Olusanmi, Dolapo; Sprockel, Omar; Abebe, Admassu; Nikfar, Faranak; Tobyn, Mike

    2016-12-05

    In the oral solid dosage form space, material physical properties have a strong impact on the behaviour of the formulation during processing. The ability to identify materials with similar characteristics (and thus expected to exhibit similar behaviour) within the company's portfolio can help accelerate drug development by enabling early assessment and prediction of potential challenges associated with the powder properties of a new active pharmaceutical ingredient. Such developments will aid the production of robust dosage forms, in an efficient manner. Similarity scoring metrics are widely used in a number of scientific fields. This study proposes a practical implementation of this methodology within pharmaceutical development. The developed similarity metrics is based on the Mahalanobis distance. Scanning electron microscopy was used to confirm morphological similarity between the reference material and the closest matches identified by the metrics proposed. The results show that the metrics proposed are able to successfully identify material with similar physical properties. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Accelerating artificial intelligence with reconfigurable computing

    NASA Astrophysics Data System (ADS)

    Cieszewski, Radoslaw

    Reconfigurable computing is emerging as an important area of research in computer architectures and software systems. Many algorithms can be greatly accelerated by placing the computationally intense portions of an algorithm into reconfigurable hardware. Reconfigurable computing combines many benefits of both software and ASIC implementations. Like software, the mapped circuit is flexible, and can be changed over the lifetime of the system. Similar to an ASIC, reconfigurable systems provide a method to map circuits into hardware. Reconfigurable systems therefore have the potential to achieve far greater performance than software as a result of bypassing the fetch-decode-execute operations of traditional processors, and possibly exploiting a greater level of parallelism. Such a field, where there is many different algorithms which can be accelerated, is an artificial intelligence. This paper presents example hardware implementations of Artificial Neural Networks, Genetic Algorithms and Expert Systems.

  19. Extending the Search for Muon Neutrinos Coincident with Gamma-Ray Bursts in IceCube Data

    NASA Astrophysics Data System (ADS)

    Aartsen, M. G.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Ahrens, M.; Samarai, I. Al; Altmann, D.; Andeen, K.; Anderson, T.; Ansseau, I.; Anton, G.; Archinger, M.; Argüelles, C.; Auffenberg, J.; Axani, S.; Bai, X.; Barwick, S. W.; Baum, V.; Bay, R.; Beatty, J. J.; Becker Tjus, J.; Becker, K.-H.; BenZvi, S.; Berley, D.; Bernardini, E.; Besson, D. Z.; Binder, G.; Bindig, D.; Blaufuss, E.; Blot, S.; Bohm, C.; Börner, M.; Bos, F.; Bose, D.; Böser, S.; Botner, O.; Braun, J.; Brayeur, L.; Bretz, H.-P.; Bron, S.; Burgman, A.; Carver, T.; Casier, M.; Cheung, E.; Chirkin, D.; Christov, A.; Clark, K.; Classen, L.; Coenders, S.; Collin, G. H.; Conrad, J. M.; Cowen, D. F.; Cross, R.; Day, M.; de André, J. P. A. M.; De Clercq, C.; del Pino Rosendo, E.; Dembinski, H.; De Ridder, S.; Desiati, P.; de Vries, K. D.; de Wasseige, G.; de With, M.; DeYoung, T.; Díaz-Vélez, J. C.; di Lorenzo, V.; Dujmovic, H.; Dumm, J. P.; Dunkman, M.; Eberhardt, B.; Ehrhardt, T.; Eichmann, B.; Eller, P.; Euler, S.; Evenson, P. A.; Fahey, S.; Fazely, A. R.; Feintzeig, J.; Felde, J.; Filimonov, K.; Finley, C.; Flis, S.; Fösig, C.-C.; Franckowiak, A.; Friedman, E.; Fuchs, T.; Gaisser, T. K.; Gallagher, J.; Gerhardt, L.; Ghorbani, K.; Giang, W.; Gladstone, L.; Glauch, T.; Glüsenkamp, T.; Goldschmidt, A.; Gonzalez, J. G.; Grant, D.; Griffith, Z.; Haack, C.; Hallgren, A.; Halzen, F.; Hansen, E.; Hansmann, T.; Hanson, K.; Hebecker, D.; Heereman, D.; Helbing, K.; Hellauer, R.; Hickford, S.; Hignight, J.; Hill, G. C.; Hoffman, K. D.; Hoffmann, R.; Hoshina, K.; Huang, F.; Huber, M.; Hultqvist, K.; In, S.; Ishihara, A.; Jacobi, E.; Japaridze, G. S.; Jeong, M.; Jero, K.; Jones, B. J. P.; Kang, W.; Kappes, A.; Karg, T.; Karle, A.; Katz, U.; Kauer, M.; Keivani, A.; Kelley, J. L.; Kheirandish, A.; Kim, J.; Kim, M.; Kintscher, T.; Kiryluk, J.; Kittler, T.; Klein, S. R.; Kohnen, G.; Koirala, R.; Kolanoski, H.; Konietz, R.; Köpke, L.; Kopper, C.; Kopper, S.; Koskinen, D. J.; Kowalski, M.; Krings, K.; Kroll, M.; Krückl, G.; Krüger, C.; Kunnen, J.; Kunwar, S.; Kurahashi, N.; Kuwabara, T.; Kyriacou, A.; Labare, M.; Lanfranchi, J. L.; Larson, M. J.; Lauber, F.; Lennarz, D.; Lesiak-Bzdak, M.; Leuermann, M.; Lu, L.; Lünemann, J.; Madsen, J.; Maggi, G.; Mahn, K. B. M.; Mancina, S.; Mandelartz, M.; Maruyama, R.; Mase, K.; Maunu, R.; McNally, F.; Meagher, K.; Medici, M.; Meier, M.; Menne, T.; Merino, G.; Meures, T.; Miarecki, S.; Micallef, J.; Momenté, G.; Montaruli, T.; Moulai, M.; Nahnhauer, R.; Naumann, U.; Neer, G.; Niederhausen, H.; Nowicki, S. C.; Nygren, D. R.; Obertacke Pollmann, A.; Olivas, A.; O'Murchadha, A.; Palczewski, T.; Pandya, H.; Pankova, D. V.; Peiffer, P.; Penek, Ö.; Pepper, J. A.; Pérez de los Heros, C.; Pieloth, D.; Pinat, E.; Price, P. B.; Przybylski, G. T.; Quinnan, M.; Raab, C.; Rädel, L.; Rameez, M.; Rawlins, K.; Reimann, R.; Relethford, B.; Relich, M.; Resconi, E.; Rhode, W.; Richman, M.; Riedel, B.; Robertson, S.; Rongen, M.; Rott, C.; Ruhe, T.; Ryckbosch, D.; Rysewyk, D.; Sabbatini, L.; Sanchez Herrera, S. E.; Sandrock, A.; Sandroos, J.; Sarkar, S.; Satalecka, K.; Schlunder, P.; Schmidt, T.; Schoenen, S.; Schöneberg, S.; Schumacher, L.; Seckel, D.; Seunarine, S.; Soldin, D.; Song, M.; Spiczak, G. M.; Spiering, C.; Stachurska, J.; Stanev, T.; Stasik, A.; Stettner, J.; Steuer, A.; Stezelberger, T.; Stokstad, R. G.; Stößl, A.; Ström, R.; Strotjohann, N. L.; Sullivan, G. W.; Sutherland, M.; Taavola, H.; Taboada, I.; Tatar, J.; Tenholt, F.; Ter-Antonyan, S.; Terliuk, A.; Tešić, G.; Tilav, S.; Toale, P. A.; Tobin, M. N.; Toscano, S.; Tosi, D.; Tselengidou, M.; Tung, C. F.; Turcati, A.; Unger, E.; Usner, M.; Vandenbroucke, J.; van Eijndhoven, N.; Vanheule, S.; van Rossem, M.; van Santen, J.; Vehring, M.; Voge, M.; Vogel, E.; Vraeghe, M.; Walck, C.; Wallace, A.; Wallraff, M.; Wandkowsky, N.; Waza, A.; Weaver, Ch.; Weiss, M. J.; Wendt, C.; Westerhoff, S.; Whelan, B. J.; Wickmann, S.; Wiebe, K.; Wiebusch, C. H.; Wille, L.; Williams, D. R.; Wills, L.; Wolf, M.; Wood, T. R.; Woolsey, E.; Woschnagg, K.; Xu, D. L.; Xu, X. W.; Xu, Y.; Yanez, J. P.; Yodh, G.; Yoshida, S.; Zoll, M.; IceCube Collaboration

    2017-07-01

    We present an all-sky search for muon neutrinos produced during the prompt γ-ray emission of 1172 gamma-ray bursts (GRBs) with the IceCube Neutrino Observatory. The detection of these neutrinos would constitute evidence for ultra-high-energy cosmic-ray (UHECR) production in GRBs, as interactions between accelerated protons and the prompt γ-ray field would yield charged pions, which decay to neutrinos. A previously reported search for muon neutrino tracks from northern hemisphere GRBs has been extended to include three additional years of IceCube data. A search for such tracks from southern hemisphere GRBs in five years of IceCube data has been introduced to enhance our sensitivity to the highest energy neutrinos. No significant correlation between neutrino events and observed GRBs is seen in the new data. Combining this result with previous muon neutrino track searches and a search for cascade signature events from all neutrino flavors, we obtain new constraints for single-zone fireball models of GRB neutrino and UHECR production.

  20. The Heavy Photon Search test detector

    DOE PAGES

    Battaglieri, M.; Boyarinov, S.; Bueltmann, S.; ...

    2014-12-17

    The Heavy Photon Search (HPS), an experiment to search for a hidden sector photon in fixed target electroproduction, is preparing for installation at the Thomas Jefferson National Accelerator Facility (JLab) in the Fall of 2014. As the first stage of this project, the HPS Test Run apparatus was constructed and operated in 2012 to demonstrate the experiment's technical feasibility and to confirm that the trigger rates and occupancies are as expected. This paper describes the HPS Test Run apparatus and readout electronics and its performance. In this setting, a heavy photon can be identified as a narrow peak in themore » e⁺e⁻invariant mass spectrum above the trident background or as a narrow invariant mass peak with a decay vertex displaced from the production target, so charged particle tracking and vertexing are needed for its detection. In the HPS Test Run, charged particles are measured with a compact forward silicon microstrip tracker inside a dipole magnet. Electromagnetic showers are detected in a PbW0 4 crystal calorimeter situated behind the magnet, and are used to trigger the experiment and identify electrons and positrons. Both detectors are placed close to the beam line and split top-bottom. This arrangement provides sensitivity to low-mass heavy photons, allows clear passage of the unscattered beam, and avoids the spray of degraded electrons coming from the target. The discrimination between prompt and displaced e⁺e⁻ pairs requires the first layer of silicon sensors be placed only 10 cm downstream of the target. The expected signal is small, and the trident background huge, so the experiment requires very large statistics. In addition, the HPS Test Run utilizes high-rate readout and data acquisition electronics and a fast trigger to exploit the essentially 100% duty cycle of the CEBAF accelerator at JLab.« less

  1. Source-to-accelerator quadrupole matching section for a compact linear accelerator

    NASA Astrophysics Data System (ADS)

    Seidl, P. A.; Persaud, A.; Ghiorso, W.; Ji, Q.; Waldron, W. L.; Lal, A.; Vinayakumar, K. B.; Schenkel, T.

    2018-05-01

    Recently, we presented a new approach for a compact radio-frequency (RF) accelerator structure and demonstrated the functionality of the individual components: acceleration units and focusing elements. In this paper, we combine these units to form a working accelerator structure: a matching section between the ion source extraction grids and the RF-acceleration unit and electrostatic focusing quadrupoles between successive acceleration units. The matching section consists of six electrostatic quadrupoles (ESQs) fabricated using 3D-printing techniques. The matching section enables us to capture more beam current and to match the beam envelope to conditions for stable transport in an acceleration lattice. We present data from an integrated accelerator consisting of the source, matching section, and an ESQ doublet sandwiched between two RF-acceleration units.

  2. Electron acceleration behind a wavy dipolarization front

    NASA Astrophysics Data System (ADS)

    Wu, Mingyu; Lu, Quanming; Volwerk, Martin; Nakamura, Rumi; Zhang, Tielong

    2018-02-01

    In this paper, with the in-situ observations from the Time History of Events and Macroscale Interactions during Substorms (THEMIS) probes we report a wavy dipolarization front (DF) event, where the DF has different magnetic structures and electron distributions at different y positions in the Geocentric Solar Magnetospheric (GSM) coordinates. At y ˜2.1RE (RE is the radius of Earth), the DF has a relatively simple structure, which is similar to that of a conventional DF. At y ˜3.0RE, the DF is revealed to have a multiple DF structure, where the plasma exhibits a vortex flow. Such a wavy DF could be the results of the interchange instability. The different structure of such a wavy DF at different sites has a great effect on electron acceleration. Fermi acceleration can occur at the site of the DF with a simple or multiple DF structure, while betatron acceleration as a local process has the contribution to energetic electrons only at the site of the DF with a simple structure.

  3. Design for simultaneous acceleration of stable and unstable beams in a superconducting heavy-ion linear accelerator for RISP

    NASA Astrophysics Data System (ADS)

    Kim, Jongwon; Son, Hyock-Jun; Park, Young-Ho

    2017-11-01

    The post-accelerator of isotope separation on-line (ISOL) system for rare isotope science project (RISP) is a superconducting linear accelerator (SC-linac) with a DC equivalent voltage of around 160 MV. An isotope beam extracted from the ISOL is in a charge state of 1+ and its charge state is increased to n+ by charge breeding with an electron beam ion source (EBIS). The charge breeding takes tens of ms and the pulse width of extracted beam from the EBIS is tens of μs, which operates at up to 30 Hz. Consequently a large portion of radio frequency (rf) time of the post SC-linac is unused. The post-linac is equipped also with an electron cyclotron resonance (ECR) ion source for stable ion acceleration. Thanks to the large phase acceptance of SC-linac, it is possible to accelerate simultaneously both stable and radioisotope ions with a similar charge to mass ratio by sharing rf time. This operation scheme is implemented for RISP with the addition of an electric chopper and magnetic kickers. The facility will be capable of providing the users of the ISOL and in-flight fragmentation (IF) systems with different beams simultaneously, which would help nuclear science users in obtaining a beam time as high-precision measurements often need long hours.

  4. Discomfort during lateral acceleration: influence of seat cushion and backrest.

    PubMed

    Beard, George F; Griffin, Michael J

    2013-07-01

    Lateral acceleration causes discomfort but how the discomfort depends on the frequency of acceleration or characteristics of seating is poorly understood. Using magnitude estimation, twelve male subjects rated the discomfort caused by lateral oscillation at eight frequencies (0.2-1.0 Hz) across four seating conditions (a rigid seat and a train seat, both with and without backrests). Discomfort increased with increasing frequency of lateral acceleration in a similar manner for all four seating conditions. However, at all frequencies and with both seats there was less discomfort when sitting with backrest support than without. Least discomfort occurred on the train seat with backrest and greatest discomfort on the rigid seat without backrest. Current standards predict an additive effect of backrest on vibration discomfort, but the findings show that low frequency lateral acceleration can cause less discomfort when sitting with a backrest than when sitting on the same seat without a backrest. Copyright © 2012 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  5. Microdroplets Accelerate Ring Opening of Epoxides

    NASA Astrophysics Data System (ADS)

    Lai, Yin-Hung; Sathyamoorthi, Shyam; Bain, Ryan M.; Zare, Richard N.

    2018-05-01

    The nucleophilic opening of an epoxide is a classic organic reaction that has widespread utility in both academic and industrial applications. We have studied the reaction of limonene oxide with morpholine to form 1-methyl-2-morpholino-4-(prop-1-en-2-yl) cyclohexan-1-ol in bulk solution and in electrosprayed microdroplets with a 1:1 v/ v water/methanol solvent system. We find that even after 90 min at room temperature, there is no product detected by nuclear magnetic resonance spectroscopy in bulk solution whereas in room-temperature microdroplets (2-3 μm in diameter), the yield is already 0.5% in a flight time of 1 ms as observed by mass spectrometry. This constitutes a rate acceleration of 105 in the microdroplet environment, if we assume that as much as 5% of product is formed in bulk after 90 min of reaction time. We examine how the reaction rate depends on droplet size, solvent composition, sheath gas pressure, and applied voltage. These factors profoundly influence the extent of reaction. This dramatic acceleration is not limited to just one system. We have also found that the nucleophilic opening of cis-stilbene oxide by morpholine is similarly accelerated. Such large acceleration factors in reaction rates suggest the use of microdroplets for ring opening of epoxides in other systems, which may have practical significance if such a procedure could be scaled. [Figure not available: see fulltext.

  6. NASA's GeneLab Phase II: Federated Search and Data Discovery

    NASA Technical Reports Server (NTRS)

    Berrios, Daniel C.; Costes, Sylvain V.; Tran, Peter B.

    2017-01-01

    GeneLab is currently being developed by NASA to accelerate 'open science' biomedical research in support of the human exploration of space and the improvement of life on earth. Phase I of the four-phase GeneLab Data Systems (GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics and proteomics ('omics') data from biomedical research of space environments. The focus of development of the GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

  7. NASAs GeneLab Phase II: Federated Search and Data Discovery

    NASA Technical Reports Server (NTRS)

    Berrios, Daniel C.; Costes, Sylvain; Tran, Peter

    2017-01-01

    GeneLab is currently being developed by NASA to accelerate open science biomedical research in support of the human exploration of space and the improvement of life on earth. Phase I of the four-phase GeneLab Data Systems (GLDS) project emphasized capabilities for submission, curation, search, and retrieval of genomics, transcriptomics and proteomics (omics) data from biomedical research of space environments. The focus of development of the GLDS for Phase II has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

  8. Accelerated in vitro release testing of implantable PLGA microsphere/PVA hydrogel composite coatings

    PubMed Central

    Shen, Jie; Burgess, Diane J.

    2011-01-01

    Dexamethasone loaded poly(lactic-co-glycolic acid) (PLGA) microsphere/PVA hydrogel composites have been investigated as an outer drug-eluting coating for implantable devices such as glucose sensors to counter negative tissue responses to implants. The objective of this study was to develop a discriminatory, accelerated in vitro release testing method for this drug-eluting coating using United States Pharmacopeia (USP) apparatus 4. Polymer degradation and drug release kinetics were investigated under “real-time” and accelerated conditions (i.e. extreme pH, hydro-alcoholic solutions and elevated temperatures). Compared to “real-time” conditions, the initial burst and lag phases were similar using hydro-alcoholic solutions and extreme pH conditions, while the secondary apparent zero-order release phase was slightly accelerated. Elevated temperatures resulted in a significant acceleration of dexamethasone release. The accelerated release data were able to predict “real-time” release when applying the Arrhenius equation. Microsphere batches with faster and slower release profiles were investigated under “real-time” and elevated temperature (60°C) conditions to determine the discriminatory ability of the method. The results demonstrated both the feasibility and the discriminatory ability of this USP apparatus 4 method for in vitro release testing of drug loaded PLGA microsphere/PVA hydrogel composites. This method may be appropriate for similar drug/device combination products and drug delivery systems. PMID:22016033

  9. Accelerated in vitro release testing of implantable PLGA microsphere/PVA hydrogel composite coatings.

    PubMed

    Shen, Jie; Burgess, Diane J

    2012-01-17

    Dexamethasone loaded poly(lactic-co-glycolic acid) (PLGA) microsphere/PVA hydrogel composites have been investigated as an outer drug-eluting coating for implantable devices such as glucose sensors to counter negative tissue responses to implants. The objective of this study was to develop a discriminatory, accelerated in vitro release testing method for this drug-eluting coating using United States Pharmacopeia (USP) apparatus 4. Polymer degradation and drug release kinetics were investigated under "real-time" and accelerated conditions (i.e. extreme pH, hydro-alcoholic solutions and elevated temperatures). Compared to "real-time" conditions, the initial burst and lag phases were similar using hydro-alcoholic solutions and extreme pH conditions, while the secondary apparent zero-order release phase was slightly accelerated. Elevated temperatures resulted in a significant acceleration of dexamethasone release. The accelerated release data were able to predict "real-time" release when applying the Arrhenius equation. Microsphere batches with faster and slower release profiles were investigated under "real-time" and elevated temperature (60°C) conditions to determine the discriminatory ability of the method. The results demonstrated both the feasibility and the discriminatory ability of this USP apparatus 4 method for in vitro release testing of drug loaded PLGA microsphere/PVA hydrogel composites. This method may be appropriate for similar drug/device combination products and drug delivery systems. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Can Accelerators Accelerate Learning?

    NASA Astrophysics Data System (ADS)

    Santos, A. C. F.; Fonseca, P.; Coelho, L. F. S.

    2009-03-01

    The 'Young Talented' education program developed by the Brazilian State Funding Agency (FAPERJ) [1] makes it possible for high-schools students from public high schools to perform activities in scientific laboratories. In the Atomic and Molecular Physics Laboratory at Federal University of Rio de Janeiro (UFRJ), the students are confronted with modern research tools like the 1.7 MV ion accelerator. Being a user-friendly machine, the accelerator is easily manageable by the students, who can perform simple hands-on activities, stimulating interest in physics, and getting the students close to modern laboratory techniques.

  11. Preliminary OARE absolute acceleration measurements on STS-50

    NASA Technical Reports Server (NTRS)

    Blanchard, Robert C.; Nicholson, John Y.; Ritter, James

    1993-01-01

    On-orbit Orbital Acceleration Research Experiment (OARE) data on STS-50 was examined in detail during a 2-day time period. Absolute acceleration levels were derived at the OARE location, the orbiter center-of-gravity, and at the STS-50 spacelab Crystal Growth Facility. The tri-axial OARE raw acceleration measurements (i.e., telemetered data) during the interval were filtered using a sliding trimmed mean filter in order to remove large acceleration spikes (e.g., thrusters) and reduce the noise. Twelve OARE measured biases in each acceleration channel during the 2-day interval were analyzed and applied to the filtered data. Similarly, the in situ measured x-axis scale factors in the sensor's most sensitive range were also analyzed and applied to the data. Due to equipment problem(s) on this flight, both y- and z- axis sensitive range scale factors were determined in a separate process (using the OARE maneuver data) and subsequently applied to the data. All known significant low-frequency corrections at the OARE location (i.e., both vertical and horizontal gravity-gradient, and rotational effects) were removed from the filtered data in order to produce the acceleration components at the orbiter's center-of-gravity, which are the aerodynamic signals along each body axes. Results indicate that there is a force of unknown origin being applied to the Orbiter in addition to the aerodynamic forces. The OARE instrument and all known gravitational and electromagnetic forces were reexamined, but none produce the observed effect. Thus, it is tentatively concluded that the Orbiter is creating the environment observed.

  12. Insights: Talent Searches from Parents' Perspectives

    ERIC Educational Resources Information Center

    Willis, Mariam

    2012-01-01

    Talent Searches offer an opportunity for gifted children to experience learning on prestigious college campuses around the nation, and as importantly, an opportunity to form relationships with like-minded, similar-age peers. Few opportunities open doors for intellectual, social, and emotional growth in gifted children as efficiently as…

  13. Timing and searching millisecond pulsars in globular clusters

    NASA Astrophysics Data System (ADS)

    D'Amico, Nichi; Possenti, Andrea; Manchester, Dick; Johnston, Simon; Kramer, Michael; Sarkissian, John; Lyne, Andrew; Burgay, Marta; Corongiu, Alessandro; Camilo, Fernando; Bailes, Matthew

    2009-10-01

    Timing the dozen pulsars discovered in P303 is ensuring high quality results: (a) the peculiarities (in position or projected acceleration) of all the 5 millisecond pulsars in NGC6752 suggested the presence of non thermal dynamics in the core, perhaps due to black-holes of intermediate mass; (b) the eclipsing pulsar in NGC6397 is a stereotype for studying the late evolution of exotic binaries. We propose to continue our timing project focusing mostly on NGC6752 at 20cm (in order to measure additional parameters useful to constrain the existence of a black-hole) and NGC6397 at 10cm (for studying the eclipse region and the orbital secular evolution). We also request time for performing pilot observations for a new deeper than ever search for millisecond pulsars in a subset of suitable clusters. This revamped search (as well as the requested timing observations) will exploit the new back-ends (APSR and DFB4) now available at Parkes.

  14. Timing and searching millisecond pulsars in globular clusters

    NASA Astrophysics Data System (ADS)

    D'Amico, Nichi; Possenti, Andrea; Manchester, Dick; Johnston, Simon; Kramer, Michael; Sarkissian, John; Lyne, Andrew; Burgay, Marta; Corongiu, Alessandro; Camilo, Fernando; Bailes, Matthew; van Straten, Willem

    2010-04-01

    Timing the dozen pulsars discovered in P303 is ensuring high quality results: (a) the peculiarities (in position or projected acceleration) of all the 5 millisecond pulsars in NGC6752 suggested the presence of non thermal dynamics in the core, perhaps due to black-holes of intermediate mass; (b) the eclipsing pulsar in NGC6397 is a stereotype for studying the late evolution of exotic binaries. We propose to continue our timing project focusing mostly on NGC6752 at 20cm (in order to measure additional parameters useful to constrain the existence of a black-hole) and NGC6397 at 10cm (for studying the eclipse region and the orbital secular evolution). We also request time for performing observations for a new deeper than ever search for millisecond pulsars in a subset of suitable clusters. This revamped search (as well as the requested timing observations) will exploit the new back-ends (APSR and DFB4) now available at Parkes.

  15. Accelerations in Flight

    NASA Technical Reports Server (NTRS)

    Doolittle, J H

    1925-01-01

    This work on accelerometry was done at McCook Field for the purpose of continuing the work done by other investigators and obtaining the accelerations which occur when a high-speed pursuit airplane is subjected to the more common maneuvers. The accelerations obtained in suddenly pulling out of a dive with well-balanced elevators are shown to be within 3 or 4 per cent of the theoretically possible accelerations. The maximum acceleration which a pilot can withstand depends upon the length of time the acceleration is continued. It is shown that he experiences no difficulty under the instantaneous accelerations as high as 7.8 G., but when under accelerations in excess of 4.5 G., continued for several seconds, he quickly loses his faculties.

  16. Particle Acceleration in Active Galactic Nuclei

    NASA Technical Reports Server (NTRS)

    Miller, James A.

    1997-01-01

    The high efficiency of energy generation inferred from radio observations of quasars and X-ray observations of Seyfert active galactic nuclei (AGNs) is apparently achieved only by the gravitational conversion of the rest mass energy of accreting matter onto supermassive black holes. Evidence for the acceleration of particles to high energies by a central engine is also inferred from observations of apparent superluminal motion in flat spectrum, core-dominated radio sources. This phenomenon is widely attributed to the ejection of relativistic bulk plasma from the nuclei of active galaxies, and accounts for the existence of large scale radio jets and lobes at large distances from the central regions of radio galaxies. Reports of radio jets and superluminal motion from galactic black hole candidate X-ray sources indicate that similar processes are operating in these sources. Observations of luminous, rapidly variable high-energy radiation from active galactic nuclei (AGNs) with the Compton Gamma Ray Observatory show directly that particles are accelerated to high energies in a compact environment. The mechanisms which transform the gravitational potential energy of the infalling matter into nonthermal particle energy in galactic black hole candidates and AGNs are not conclusively identified, although several have been proposed. These include direct acceleration by static electric fields (resulting from, for example, magnetic reconnection), shock acceleration, and energy extraction from the rotational energy of Kerr black holes. The dominant acceleration mechanism(s) operating in the black hole environment can only be determined, of course, by a comparison of model predictions with observations. The purpose of the work proposed for this grant was to investigate stochastic particle acceleration through resonant interactions with plasma waves that populate the magnetosphere surrounding an accreting black hole. Stochastic acceleration has been successfully applied to the

  17. Visual search for verbal material in patients with obsessive-compulsive disorder.

    PubMed

    Botta, Fabiano; Vibert, Nicolas; Harika-Germaneau, Ghina; Frasca, Mickaël; Rigalleau, François; Fakra, Eric; Ros, Christine; Rouet, Jean-François; Ferreri, Florian; Jaafari, Nematollah

    2018-06-01

    This study aimed at investigating attentional mechanisms in obsessive-compulsive disorder (OCD) by analysing how visual search processes are modulated by normal and obsession-related distracting information in OCD patients and whether these modulations differ from those observed in healthy people. OCD patients were asked to search for a target word within distractor words that could be orthographically similar to the target, semantically related to the target, semantically related to the most typical obsessions/compulsions observed in OCD patients, or unrelated to the target. Patients' performance and eye movements were compared with those of individually matched healthy controls. In controls, the distractors that were visually similar to the target mostly captured attention. Conversely, patients' attention was captured equally by all kinds of distractor words, whatever their similarity with the target, except obsession-related distractors that attracted patients' attention less than the other distractors. OCD had a major impact on the mostly subliminal mechanisms that guide attention within the search display, but had much less impact on the distractor rejection processes that take place when a distractor is fixated. Hence, visual search in OCD is characterized by abnormal subliminal, but not supraliminal, processing of obsession-related information and by an impaired ability to inhibit task-irrelevant inputs. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. Fuzzy measures on the Gene Ontology for gene product similarity.

    PubMed

    Popescu, Mihail; Keller, James M; Mitchell, Joyce A

    2006-01-01

    One of the most important objects in bioinformatics is a gene product (protein or RNA). For many gene products, functional information is summarized in a set of Gene Ontology (GO) annotations. For these genes, it is reasonable to include similarity measures based on the terms found in the GO or other taxonomy. In this paper, we introduce several novel measures for computing the similarity of two gene products annotated with GO terms. The fuzzy measure similarity (FMS) has the advantage that it takes into consideration the context of both complete sets of annotation terms when computing the similarity between two gene products. When the two gene products are not annotated by common taxonomy terms, we propose a method that avoids a zero similarity result. To account for the variations in the annotation reliability, we propose a similarity measure based on the Choquet integral. These similarity measures provide extra tools for the biologist in search of functional information for gene products. The initial testing on a group of 194 sequences representing three proteins families shows a higher correlation of the FMS and Choquet similarities to the BLAST sequence similarities than the traditional similarity measures such as pairwise average or pairwise maximum.

  19. Semantic Clustering of Search Engine Results

    PubMed Central

    Soliman, Sara Saad; El-Sayed, Maged F.; Hassan, Yasser F.

    2015-01-01

    This paper presents a novel approach for search engine results clustering that relies on the semantics of the retrieved documents rather than the terms in those documents. The proposed approach takes into consideration both lexical and semantics similarities among documents and applies activation spreading technique in order to generate semantically meaningful clusters. This approach allows documents that are semantically similar to be clustered together rather than clustering documents based on similar terms. A prototype is implemented and several experiments are conducted to test the prospered solution. The result of the experiment confirmed that the proposed solution achieves remarkable results in terms of precision. PMID:26933673

  20. Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

    DOE PAGES

    Yim, Won Cheol; Cushman, John C.

    2017-07-22

    Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

  1. Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yim, Won Cheol; Cushman, John C.

    Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

  2. CUDAMPF: a multi-tiered parallel framework for accelerating protein sequence search in HMMER on CUDA-enabled GPU.

    PubMed

    Jiang, Hanyu; Ganesan, Narayan

    2016-02-27

    HMMER software suite is widely used for analysis of homologous protein and nucleotide sequences with high sensitivity. The latest version of hmmsearch in HMMER 3.x, utilizes heuristic-pipeline which consists of MSV/SSV (Multiple/Single ungapped Segment Viterbi) stage, P7Viterbi stage and the Forward scoring stage to accelerate homology detection. Since the latest version is highly optimized for performance on modern multi-core CPUs with SSE capabilities, only a few acceleration attempts report speedup. However, the most compute intensive tasks within the pipeline (viz., MSV/SSV and P7Viterbi stages) still stand to benefit from the computational capabilities of massively parallel processors. A Multi-Tiered Parallel Framework (CUDAMPF) implemented on CUDA-enabled GPUs presented here, offers a finer-grained parallelism for MSV/SSV and Viterbi algorithms. We couple SIMT (Single Instruction Multiple Threads) mechanism with SIMD (Single Instructions Multiple Data) video instructions with warp-synchronism to achieve high-throughput processing and eliminate thread idling. We also propose a hardware-aware optimal allocation scheme of scarce resources like on-chip memory and caches in order to boost performance and scalability of CUDAMPF. In addition, runtime compilation via NVRTC available with CUDA 7.0 is incorporated into the presented framework that not only helps unroll innermost loop to yield upto 2 to 3-fold speedup than static compilation but also enables dynamic loading and switching of kernels depending on the query model size, in order to achieve optimal performance. CUDAMPF is designed as a hardware-aware parallel framework for accelerating computational hotspots within the hmmsearch pipeline as well as other sequence alignment applications. It achieves significant speedup by exploiting hierarchical parallelism on single GPU and takes full advantage of limited resources based on their own performance features. In addition to exceeding performance of other

  3. A Quantum-Based Similarity Method in Virtual Screening.

    PubMed

    Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

    2015-10-02

    One of the most widely-used techniques for ligand-based virtual screening is similarity searching. This study adopted the concepts of quantum mechanics to present as state-of-the-art similarity method of molecules inspired from quantum theory. The representation of molecular compounds in mathematical quantum space plays a vital role in the development of quantum-based similarity approach. One of the key concepts of quantum theory is the use of complex numbers. Hence, this study proposed three various techniques to embed and to re-represent the molecular compounds to correspond with complex numbers format. The quantum-based similarity method that developed in this study depending on complex pure Hilbert space of molecules called Standard Quantum-Based (SQB). The recall of retrieved active molecules were at top 1% and top 5%, and significant test is used to evaluate our proposed methods. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints. Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.

  4. Accelerated magnetic resonance diffusion tensor imaging of the median nerve using simultaneous multi-slice echo planar imaging with blipped CAIPIRINHA.

    PubMed

    Filli, Lukas; Piccirelli, Marco; Kenkel, David; Boss, Andreas; Manoliu, Andrei; Andreisek, Gustav; Bhat, Himanshu; Runge, Val M; Guggenberger, Roman

    2016-06-01

    To investigate the feasibility of MR diffusion tensor imaging (DTI) of the median nerve using simultaneous multi-slice echo planar imaging (EPI) with blipped CAIPIRINHA. After federal ethics board approval, MR imaging of the median nerves of eight healthy volunteers (mean age, 29.4 years; range, 25-32) was performed at 3 T using a 16-channel hand/wrist coil. An EPI sequence (b-value, 1,000 s/mm(2); 20 gradient directions) was acquired without acceleration as well as with twofold and threefold slice acceleration. Fractional anisotropy (FA), mean diffusivity (MD) and quality of nerve tractography (number of tracks, average track length, track homogeneity, anatomical accuracy) were compared between the acquisitions using multivariate ANOVA and the Kruskal-Wallis test. Acquisition time was 6:08 min for standard DTI, 3:38 min for twofold and 2:31 min for threefold acceleration. No differences were found regarding FA (standard DTI: 0.620 ± 0.058; twofold acceleration: 0.642 ± 0.058; threefold acceleration: 0.644 ± 0.061; p ≥ 0.217) and MD (standard DTI: 1.076 ± 0.080 mm(2)/s; twofold acceleration: 1.016 ± 0.123 mm(2)/s; threefold acceleration: 0.979 ± 0.153 mm(2)/s; p ≥ 0.074). Twofold acceleration yielded similar tractography quality compared to standard DTI (p > 0.05). With threefold acceleration, however, average track length and track homogeneity decreased (p = 0.004-0.021). Accelerated DTI of the median nerve is feasible. Twofold acceleration yields similar results to standard DTI. • Standard DTI of the median nerve is limited by its long acquisition time. • Simultaneous multi-slice acquisition is a new technique for accelerated DTI. • Accelerated DTI of the median nerve yields similar results to standard DTI.

  5. Search prefilters to assist in library searching of infrared spectra of automotive clear coats.

    PubMed

    Lavine, Barry K; Fasasi, Ayuba; Mirjankar, Nikhil; White, Collin; Sandercock, Mark

    2015-01-01

    Clear coat searches of the infrared (IR) spectral library of the paint data query (PDQ) forensic database often generate an unusable number of hits that span multiple manufacturers, assembly plants, and years. To improve the accuracy of the hit list, pattern recognition methods have been used to develop search prefilters (i.e., principal component models) that differentiate between similar but non-identical IR spectra of clear coats on the basis of manufacturer (e.g., General Motors, Ford, Chrysler) or assembly plant. A two step procedure to develop these search prefilters was employed. First, the discrete wavelet transform was used to decompose each IR spectrum into wavelet coefficients to enhance subtle but significant features in the spectral data. Second, a genetic algorithm for IR spectral pattern recognition was employed to identify wavelet coefficients characteristic of the manufacturer or assembly plant of the vehicle. Even in challenging trials where the paint samples evaluated were all from the same manufacturer (General Motors) within a limited production year range (2000-2006), the respective assembly plant of the vehicle was correctly identified. Search prefilters to identify assembly plants were successfully validated using 10 blind samples provided by the Royal Canadian Mounted Police (RCMP) as part of a study to populate PDQ to current production years, whereas the search prefilter to discriminate among automobile manufacturers was successfully validated using IR spectra obtained directly from the PDQ database. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. An advanced search engine for patent analytics in medicinal chemistry.

    PubMed

    Pasche, Emilie; Gobeill, Julien; Teodoro, Douglas; Gaudinat, Arnaud; Vishnykova, Dina; Lovis, Christian; Ruch, Patrick

    2012-01-01

    Patent collections contain an important amount of medical-related knowledge, but existing tools were reported to lack of useful functionalities. We present here the development of TWINC, an advanced search engine dedicated to patent retrieval in the domain of health and life sciences. Our tool embeds two search modes: an ad hoc search to retrieve relevant patents given a short query and a related patent search to retrieve similar patents given a patent. Both search modes rely on tuning experiments performed during several patent retrieval competitions. Moreover, TWINC is enhanced with interactive modules, such as chemical query expansion, which is of prior importance to cope with various ways of naming biomedical entities. While the related patent search showed promising performances, the ad-hoc search resulted in fairly contrasted results. Nonetheless, TWINC performed well during the Chemathlon task of the PatOlympics competition and experts appreciated its usability.

  7. Electron bulk acceleration and thermalization at Earth's quasi-perpendicular bow shock

    NASA Astrophysics Data System (ADS)

    Chen, L.-J.; Wang, S.; Wilson, L. B., III; Schwartz, S. J.; Bessho, N.; Moore, T. E.; Gershman, D. J.; Giles, B. L.; Malaspina, D. M.; Wilder, F. D.; Ergun, R. E.; Hesse, M.; Lai, H.; Russell, C. T.; Strangeway, R. J.; Torbert, R. B.; Vinas, A. F.-; Burch, J. L.; Lee, S.; Pollock, C.; Dorelli, J.; Paterson, W. R.; Ahmadi, N.; Goodrich, K. A.; Lavraud, B.; Le Contel, O.; Khotyaintsev, Yu. V.; Lindqvist, P.-A.; Boardsen, S.; Wei, H.; Le, A.; Avanov, L. A.

    2018-05-01

    Electron heating at Earth's quasiperpendicular bow shock has been surmised to be due to the combined effects of a quasistatic electric potential and scattering through wave-particle interaction. Here we report the observation of electron distribution functions indicating a new electron heating process occurring at the leading edge of the shock front. Incident solar wind electrons are accelerated parallel to the magnetic field toward downstream, reaching an electron-ion relative drift speed exceeding the electron thermal speed. The bulk acceleration is associated with an electric field pulse embedded in a whistler-mode wave. The high electron-ion relative drift is relaxed primarily through a nonlinear current-driven instability. The relaxed distributions contain a beam traveling toward the shock as a remnant of the accelerated electrons. Similar distribution functions prevail throughout the shock transition layer, suggesting that the observed acceleration and thermalization is essential to the cross-shock electron heating.

  8. An integrative approach for measuring semantic similarities using gene ontology.

    PubMed

    Peng, Jiajie; Li, Hongxiang; Jiang, Qinghua; Wang, Yadong; Chen, Jin

    2014-01-01

    Gene Ontology (GO) provides rich information and a convenient way to study gene functional similarity, which has been successfully used in various applications. However, the existing GO based similarity measurements have limited functions for only a subset of GO information is considered in each measure. An appropriate integration of the existing measures to take into account more information in GO is demanding. We propose a novel integrative measure called InteGO2 to automatically select appropriate seed measures and then to integrate them using a metaheuristic search method. The experiment results show that InteGO2 significantly improves the performance of gene similarity in human, Arabidopsis and yeast on both molecular function and biological process GO categories. InteGO2 computes gene-to-gene similarities more accurately than tested existing measures and has high robustness. The supplementary document and software are available at http://mlg.hit.edu.cn:8082/.

  9. Query Auto-Completion Based on Word2vec Semantic Similarity

    NASA Astrophysics Data System (ADS)

    Shao, Taihua; Chen, Honghui; Chen, Wanyu

    2018-04-01

    Query auto-completion (QAC) is the first step of information retrieval, which helps users formulate the entire query after inputting only a few prefixes. Regarding the models of QAC, the traditional method ignores the contribution from the semantic relevance between queries. However, similar queries always express extremely similar search intention. In this paper, we propose a hybrid model FS-QAC based on query semantic similarity as well as the query frequency. We choose word2vec method to measure the semantic similarity between intended queries and pre-submitted queries. By combining both features, our experiments show that FS-QAC model improves the performance when predicting the user’s query intention and helping formulate the right query. Our experimental results show that the optimal hybrid model contributes to a 7.54% improvement in terms of MRR against a state-of-the-art baseline using the public AOL query logs.

  10. Curved-line search algorithm for ab initio atomic structure relaxation

    NASA Astrophysics Data System (ADS)

    Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

    2017-09-01

    Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

  11. Accelerated cognitive aging following severe traumatic brain injury: A review.

    PubMed

    Wood, Rodger Ll

    2017-01-01

    The primary objective of this review was to examine relevant clinical and experimental literatures for information on the long-term cognitive impact of serious traumatic brain injury (TBI) with regard to the process of cognitive aging. Online journal databases were queried for studies pertaining to cognitive aging in neurologically healthy populations, as well as the late cognitive effects of serious TBI. Additional studies were identified through searching bibliographies of related publications and using Google search engine. Problems of cognition exhibited by young adults after TBI resemble many cognitive weaknesses of attention deficit and poor working memory that are usually seen in an elderly population who have no neurological history. The current state of the literature provides support for the argument that TBI can result in diminished cognitive reserve which may accelerate the normal process of cognitive decline, leading to premature aging, potentially increasing the risk of dementia.

  12. Searches for magnetic monopoles with IceCube

    NASA Astrophysics Data System (ADS)

    Pollmann, Anna

    2018-01-01

    Particles that carry a magnetic monopole charge are proposed by various theories which go beyond the Standard Model of particle physics. The expected mass of magnetic monopoles varies depending on the theory describing its origin, generally the monopole mass far exceeds those which can be created at accelerators. Magnetic monopoles gain kinetic energy in large scale galactic magnetic fields and, depending on their mass, can obtain relativistic velocities. IceCube is a high energy neutrino detector using the clear ice at the South Pole as a detection medium. As monopoles pass through this ice they produce optical light by a variety of mechanisms. With increasing velocity, they produce light by catalysis of baryon decay, luminescence in the ice associated with electronic excitations, indirect and direct Cherenkov light from the monopole track, and Cherenkov light from cascades induced by pair creation and photonuclear reactions. By searching for this light, current best limits for the monopole flux over a broad range of velocities was achieved using the IceCube detector. A review of these magnetic monopole searches is presented.

  13. A self-similar magnetohydrodynamic model for ball lightnings

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tsui, K. H.

    2006-07-15

    Ball lightning is modeled by magnetohydrodynamic (MHD) equations in two-dimensional spherical geometry with azimuthal symmetry. Dynamic evolutions in the radial direction are described by the self-similar evolution function y(t). The plasma pressure, mass density, and magnetic fields are solved in terms of the radial label {eta}. This model gives spherical MHD plasmoids with axisymmetric force-free magnetic field, and spherically symmetric plasma pressure and mass density, which self-consistently determine the polytropic index {gamma}. The spatially oscillating nature of the radial and meridional field structures indicate embedded regions of closed field lines. These regions are named secondary plasmoids, whereas the overall self-similarmore » spherical structure is named the primary plasmoid. According to this model, the time evolution function allows the primary plasmoid expand outward in two modes. The corresponding ejection of the embedded secondary plasmoids results in ball lightning offering an answer as how they come into being. The first is an accelerated expanding mode. This mode appears to fit plasmoids ejected from thundercloud tops with acceleration to ionosphere seen in high altitude atmospheric observations of sprites and blue jets. It also appears to account for midair high-speed ball lightning overtaking airplanes, and ground level high-speed energetic ball lightning. The second is a decelerated expanding mode, and it appears to be compatible to slowly moving ball lightning seen near ground level. The inverse of this second mode corresponds to an accelerated inward collapse, which could bring ball lightning to an end sometimes with a cracking sound.« less

  14. SU-E-T-512: Electromagnetic Simulations of the Dielectric Wall Accelerator

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Uselmann, A; Mackie, T

    device at low cost. Funding: Morgridge Institute for Research, Madison WI; Conflict of Interest: Dr. Mackie is an investor and board member at CPAC, a company developing compact accelerator designs similar to those discussed in this work, but designs discussed are not directed by CPAC. Funding: Morgridge Institute for Research, Madison WI; Conflict of Interest: Dr. Mackie is an investor and board member at CPAC, a company developing compact accelerator designs similar to those discussed in this work, but designs discussed are not directed by CPAC.« less

  15. Extended Graph-Based Models for Enhanced Similarity Search in Cavbase.

    PubMed

    Krotzky, Timo; Fober, Thomas; Hüllermeier, Eyke; Klebe, Gerhard

    2014-01-01

    To calculate similarities between molecular structures, measures based on the maximum common subgraph are frequently applied. For the comparison of protein binding sites, these measures are not fully appropriate since graphs representing binding sites on a detailed atomic level tend to get very large. In combination with an NP-hard problem, a large graph leads to a computationally demanding task. Therefore, for the comparison of binding sites, a less detailed coarse graph model is used building upon so-called pseudocenters. Consistently, a loss of structural data is caused since many atoms are discarded and no information about the shape of the binding site is considered. This is usually resolved by performing subsequent calculations based on additional information. These steps are usually quite expensive, making the whole approach very slow. The main drawback of a graph-based model solely based on pseudocenters, however, is the loss of information about the shape of the protein surface. In this study, we propose a novel and efficient modeling formalism that does not increase the size of the graph model compared to the original approach, but leads to graphs containing considerably more information assigned to the nodes. More specifically, additional descriptors considering surface characteristics are extracted from the local surface and attributed to the pseudocenters stored in Cavbase. These properties are evaluated as additional node labels, which lead to a gain of information and allow for much faster but still very accurate comparisons between different structures.

  16. Automatic Content Creation for Games to Train Students Distinguishing Similar Chinese Characters

    NASA Astrophysics Data System (ADS)

    Lai, Kwong-Hung; Leung, Howard; Tang, Jeff K. T.

    In learning Chinese, many students often have the problem of mixing up similar characters. This can cause misunderstanding and miscommunication in daily life. It is thus important for students learning the Chinese language to be able to distinguish similar characters and understand their proper usage. In this paper, we propose a game style framework in which the game content in identifying similar Chinese characters in idioms and words is created automatically. Our prior work on analyzing students’ Chinese handwriting can be applied in the similarity measure of Chinese characters. We extend this work by adding the component of radical extraction to speed up the search process. Experimental results show that the proposed method is more accurate and faster in finding more similar Chinese characters compared with the baseline method without considering the radical information.

  17. Compact Plasma Accelerator

    NASA Technical Reports Server (NTRS)

    Foster, John E.

    2004-01-01

    A plasma accelerator has been conceived for both material-processing and spacecraft-propulsion applications. This accelerator generates and accelerates ions within a very small volume. Because of its compactness, this accelerator could be nearly ideal for primary or station-keeping propulsion for spacecraft having masses between 1 and 20 kg. Because this accelerator is designed to generate beams of ions having energies between 50 and 200 eV, it could also be used for surface modification or activation of thin films.

  18. Brain CT image similarity retrieval method based on uncertain location graph.

    PubMed

    Pan, Haiwei; Li, Pengyuan; Li, Qing; Han, Qilong; Feng, Xiaoning; Gao, Linlin

    2014-03-01

    A number of brain computed tomography (CT) images stored in hospitals that contain valuable information should be shared to support computer-aided diagnosis systems. Finding the similar brain CT images from the brain CT image database can effectively help doctors diagnose based on the earlier cases. However, the similarity retrieval for brain CT images requires much higher accuracy than the general images. In this paper, a new model of uncertain location graph (ULG) is presented for brain CT image modeling and similarity retrieval. According to the characteristics of brain CT image, we propose a novel method to model brain CT image to ULG based on brain CT image texture. Then, a scheme for ULG similarity retrieval is introduced. Furthermore, an effective index structure is applied to reduce the searching time. Experimental results reveal that our method functions well on brain CT images similarity retrieval with higher accuracy and efficiency.

  19. Semantic Similarity between Web Documents Using Ontology

    NASA Astrophysics Data System (ADS)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-06-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  20. Semantic Similarity between Web Documents Using Ontology

    NASA Astrophysics Data System (ADS)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-03-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  1. QuickVina: accelerating AutoDock Vina using gradient-based heuristics for global optimization.

    PubMed

    Handoko, Stephanus Daniel; Ouyang, Xuchang; Su, Chinh Tran To; Kwoh, Chee Keong; Ong, Yew Soon

    2012-01-01

    Predicting binding between macromolecule and small molecule is a crucial phase in the field of rational drug design. AutoDock Vina, one of the most widely used docking software released in 2009, uses an empirical scoring function to evaluate the binding affinity between the molecules and employs the iterated local search global optimizer for global optimization, achieving a significantly improved speed and better accuracy of the binding mode prediction compared its predecessor, AutoDock 4. In this paper, we propose further improvement in the local search algorithm of Vina by heuristically preventing some intermediate points from undergoing local search. Our improved version of Vina-dubbed QVina-achieved a maximum acceleration of about 25 times with the average speed-up of 8.34 times compared to the original Vina when tested on a set of 231 protein-ligand complexes while maintaining the optimal scores mostly identical. Using our heuristics, larger number of different ligands can be quickly screened against a given receptor within the same time frame.

  2. Microelectromechanical acceleration-sensing apparatus

    DOEpatents

    Lee, Robb M [Albuquerque, NM; Shul, Randy J [Albuquerque, NM; Polosky, Marc A [Albuquerque, NM; Hoke, Darren A [Albuquerque, NM; Vernon, George E [Rio Rancho, NM

    2006-12-12

    An acceleration-sensing apparatus is disclosed which includes a moveable shuttle (i.e. a suspended mass) and a latch for capturing and holding the shuttle when an acceleration event is sensed above a predetermined threshold level. The acceleration-sensing apparatus provides a switch closure upon sensing the acceleration event and remains latched in place thereafter. Examples of the acceleration-sensing apparatus are provided which are responsive to an acceleration component in a single direction (i.e. a single-sided device) or to two oppositely-directed acceleration components (i.e. a dual-sided device). A two-stage acceleration-sensing apparatus is also disclosed which can sense two acceleration events separated in time. The acceleration-sensing apparatus of the present invention has applications, for example, in an automotive airbag deployment system.

  3. SHORT ACCELERATION TIMES FROM SUPERDIFFUSIVE SHOCK ACCELERATION IN THE HELIOSPHERE

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Perri, S.; Zimbardo, G., E-mail: silvia.perri@fis.unical.it

    2015-12-10

    The analysis of time profiles of particles accelerated at interplanetary shocks allows particle transport properties to be inferred. The frequently observed power-law decay upstream, indeed, implies a superdiffusive particle transport when the level of magnetic field variance does not change as the time interval from the shock front increases. In this context, a superdiffusive shock acceleration (SSA) theory has been developed, allowing us to make predictions of the acceleration times. In this work we estimate for a number of interplanetary shocks, including the solar wind termination shock, the acceleration times for energetic protons in the framework of SSA and wemore » compare the results with the acceleration times predicted by standard diffusive shock acceleration. The acceleration times due to SSA are found to be much shorter than in the classical model, and also shorter than the interplanetary shock lifetimes. This decrease of the acceleration times is due to the scale-free nature of the particle displacements in the framework of superdiffusion. Indeed, very long displacements are possible, increasing the probability for particles far from the front of the shock to return, and short displacements have a high probability of occurrence, increasing the chances for particles close to the front to cross the shock many times.« less

  4. Inertial Mass Viewed as Reaction of the Vacuum to Accelerated Motion

    NASA Technical Reports Server (NTRS)

    Rueda, Alfonso; Haisch, Bernhard

    1999-01-01

    Preliminary analysis of the momentum flux (or of the Poynting vector) of the classical electromagnetic version of the quantum vacuum consisting of zero-point radiation impinging on accelerated objects as viewed by an inertial observer suggests that the resistance to acceleration attributed to inertia may be a force of opposition originating in the vacuum. This analysis avoids the ad hoc modeling of particle-field interaction dynamics used previously by Haisck Rueda and Puthoff (1994) to derive a similar result. This present approach is not dependent upon what happens at the particle point but on how an external observer assesses the kinematical characteristics of the zero-point radiation impinging on the accelerated object. A relativistic form of the equation of motion results from the present analysis.

  5. Examining perceptual and conceptual set biases in multiple-target visual search.

    PubMed

    Biggs, Adam T; Adamo, Stephen H; Dowd, Emma Wu; Mitroff, Stephen R

    2015-04-01

    Visual search is a common practice conducted countless times every day, and one important aspect of visual search is that multiple targets can appear in a single search array. For example, an X-ray image of airport luggage could contain both a water bottle and a gun. Searchers are more likely to miss additional targets after locating a first target in multiple-target searches, which presents a potential problem: If airport security officers were to find a water bottle, would they then be more likely to miss a gun? One hypothetical cause of multiple-target search errors is that searchers become biased to detect additional targets that are similar to a found target, and therefore become less likely to find additional targets that are dissimilar to the first target. This particular hypothesis has received theoretical, but little empirical, support. In the present study, we tested the bounds of this idea by utilizing "big data" obtained from the mobile application Airport Scanner. Multiple-target search errors were substantially reduced when the two targets were identical, suggesting that the first-found target did indeed create biases during subsequent search. Further analyses delineated the nature of the biases, revealing both a perceptual set bias (i.e., a bias to find additional targets with features similar to those of the first-found target) and a conceptual set bias (i.e., a bias to find additional targets with a conceptual relationship to the first-found target). These biases are discussed in terms of the implications for visual-search theories and applications for professional visual searchers.

  6. Mechanism of Facilitated Diffusion during a DNA Search in Crowded Environments.

    PubMed

    Krepel, Dana; Gomez, David; Klumpp, Stefan; Levy, Yaakov

    2016-11-03

    The key feature explaining the rapid recognition of a DNA target site by its protein lies in the combination of one- and three-dimensional (1D and 3D) diffusion, which allows efficient scanning of the many alternative sites. This facilitated diffusion mechanism is expected to be affected by cellular conditions, particularly crowding, given that up to 40% of the total cellular volume may by occupied by macromolecules. Using coarse-grained molecular dynamics and Monte Carlo simulations, we show that the crowding particles can enhance facilitated diffusion and accelerate search kinetics. This effect originates from a trade-off between 3D and 1D diffusion. The 3D diffusion coefficient is lower under crowded conditions, but it has little influence because the excluded volume effect of molecular crowding restricts its use. Largely prevented from using 3D diffusion, the searching protein dramatically increases its use of the hopping search mode, which results in a higher linear diffusion coefficient. The coefficient of linear diffusion also increases under crowded conditions as a result of increased collisions between the crowding particles and the searching protein. Overall, less 3D diffusion coupled with an increase in the use of the hopping and speed of 1D diffusion results in faster search kinetics under crowded conditions. Our study shows that the search kinetics and mechanism are modulated not only by the crowding occupancy but also by the properties of the crowding particles and the salt concentration.

  7. MABE multibeam accelerator

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hasti, D.E.; Ramirez, J.J.; Coleman, P.D.

    1985-01-01

    The Megamp Accelerator and Beam Experiment (MABE) was the technology development testbed for the multiple beam, linear induction accelerator approach for Hermes III, a new 20 MeV, 0.8 MA, 40 ns accelerator being developed at Sandia for gamma-ray simulation. Experimental studies of a high-current, single-beam accelerator (8 MeV, 80 kA), and a nine-beam injector (1.4 MeV, 25 kA/beam) have been completed, and experiments on a nine-beam linear induction accelerator are in progress. A two-beam linear induction accelerator is designed and will be built as a gamma-ray simulator to be used in parallel with Hermes III. The MABE pulsed power systemmore » and accelerator for the multiple beam experiments is described. Results from these experiments and the two-beam design are discussed. 11 refs., 6 figs.« less

  8. Optimal Target Stars in the Search for Life

    NASA Astrophysics Data System (ADS)

    Lingam, Manasvi; Loeb, Abraham

    2018-04-01

    The selection of optimal targets in the search for life represents a highly important strategic issue. In this Letter, we evaluate the benefits of searching for life around a potentially habitable planet orbiting a star of arbitrary mass relative to a similar planet around a Sun-like star. If recent physical arguments implying that the habitability of planets orbiting low-mass stars is selectively suppressed are correct, we find that planets around solar-type stars may represent the optimal targets.

  9. Exploration and Exploitation During Sequential Search

    PubMed Central

    Dam, Gregory; Körding, Konrad

    2012-01-01

    When we learn how to throw darts we adjust how we throw based on where the darts stick. Much of skill learning is computationally similar in that we learn using feedback obtained after the completion of individual actions. We can formalize such tasks as a search problem; among the set of all possible actions, find the action that leads to the highest reward. In such cases our actions have two objectives: we want to best utilize what we already know (exploitation), but we also want to learn to be more successful in the future (exploration). Here we tested how participants learn movement trajectories where feedback is provided as a monetary reward that depends on the chosen trajectory. We mathematically derived the optimal search policy for our experiment using decision theory. The search behavior of participants is well predicted by an ideal searcher model that optimally combines exploration and exploitation. PMID:21585479

  10. Probing electron acceleration and x-ray emission in laser-plasma accelerators

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Thaury, C.; Ta Phuoc, K.; Corde, S.

    2013-06-15

    While laser-plasma accelerators have demonstrated a strong potential in the acceleration of electrons up to giga-electronvolt energies, few experimental tools for studying the acceleration physics have been developed. In this paper, we demonstrate a method for probing the acceleration process. A second laser beam, propagating perpendicular to the main beam, is focused on the gas jet few nanosecond before the main beam creates the accelerating plasma wave. This second beam is intense enough to ionize the gas and form a density depletion, which will locally inhibit the acceleration. The position of the density depletion is scanned along the interaction lengthmore » to probe the electron injection and acceleration, and the betatron X-ray emission. To illustrate the potential of the method, the variation of the injection position with the plasma density is studied.« less

  11. The Collaborative Search by Tag-Based User Profile in Social Media

    PubMed Central

    Li, Xiaodong; Li, Qing

    2014-01-01

    Recently, we have witnessed the popularity and proliferation of social media applications (e.g., Delicious, Flickr, and YouTube) in the web 2.0 era. The rapid growth of user-generated data results in the problem of information overload to users. Facing such a tremendous volume of data, it is a big challenge to assist the users to find their desired data. To attack this critical problem, we propose the collaborative search approach in this paper. The core idea is that similar users may have common interests so as to help users to find their demanded data. Similar research has been conducted on the user log analysis in web search. However, the rapid growth and change of user-generated data in social media require us to discover a brand-new approach to address the unsolved issues (e.g., how to profile users, how to measure the similar users, and how to depict user-generated resources) rather than adopting existing method from web search. Therefore, we investigate various metrics to identify the similar users (user community). Moreover, we conduct the experiment on two real-life data sets by comparing the Collaborative method with the latest baselines. The empirical results show the effectiveness of the proposed approach and validate our observations. PMID:25692176

  12. Shielding analyses for repetitive high energy pulsed power accelerators

    NASA Astrophysics Data System (ADS)

    Jow, H. N.; Rao, D. V.

    Sandia National Laboratories (SNL) designs, tests and operates a variety of accelerators that generate large amounts of high energy Bremsstrahlung radiation over an extended time. Typically, groups of similar accelerators are housed in a large building that is inaccessible to the general public. To facilitate independent operation of each accelerator, test cells are constructed around each accelerator to shield it from the radiation workers occupying surrounding test cells and work-areas. These test cells, about 9 ft. high, are constructed of high density concrete block walls that provide direct radiation shielding. Above the target areas (radiation sources), lead or steel plates are used to minimize skyshine radiation. Space, accessibility and cost considerations impose certain restrictions on the design of these test cells. SNL Health Physics division is tasked to evaluate the adequacy of each test cell design and compare resultant dose rates with the design criteria stated in DOE Order 5480.11. In response, SNL Health Physics has undertaken an intensive effort to assess existing radiation shielding codes and compare their predictions against measured dose rates. This paper provides a summary of the effort and its results.

  13. Objective and subjective measures indicate that orthographically similar words produce a blocking experience.

    PubMed

    Leynes, P Andrew; Brown, Jaime; Landau, Joshua D

    2011-01-01

    Memory blocks are a common experience characterised by inappropriate retrieval of information that impairs memory search processes. In five studies, memory blocks were induced via exposure to orthographically similar words (Smith & Tindell, 1997) while participants reported their subjective experiences to determine whether the memory block effect (MBE) paradigm produces a feeling of being blocked. Experiments 1 and 3 provided evidence that the MBE is associated with more blocked experiences. In Experiments 2 and 4 increased blocking experiences correlated with blocked fragments when the experimental manipulation was disguised, which demonstrates that ratings were not contaminated by demand characteristics. Experiment 5 demonstrated that blocking happens even when there is no study list. Collectively, the subjective retrieval ratings and the objective response data provide converging evidence that exposure to orthographically similar words induces a memory block characterised by an ineffective memory search that perseverates on interfering information.

  14. An MPI + $X$ implementation of contact global search using Kokkos

    DOE PAGES

    Hansen, Glen A.; Xavier, Patrick G.; Mish, Sam P.; ...

    2015-10-05

    This paper describes an approach that seeks to parallelize the spatial search associated with computational contact mechanics. In contact mechanics, the purpose of the spatial search is to find “nearest neighbors,” which is the prelude to an imprinting search that resolves the interactions between the external surfaces of contacting bodies. In particular, we are interested in the contact global search portion of the spatial search associated with this operation on domain-decomposition-based meshes. Specifically, we describe an implementation that combines standard domain-decomposition-based MPI-parallel spatial search with thread-level parallelism (MPI-X) available on advanced computer architectures (those with GPU coprocessors). Our goal ismore » to demonstrate the efficacy of the MPI-X paradigm in the overall contact search. Standard MPI-parallel implementations typically use a domain decomposition of the external surfaces of bodies within the domain in an attempt to efficiently distribute computational work. This decomposition may or may not be the same as the volume decomposition associated with the host physics. The parallel contact global search phase is then employed to find and distribute surface entities (nodes and faces) that are needed to compute contact constraints between entities owned by different MPI ranks without further inter-rank communication. Key steps of the contact global search include computing bounding boxes, building surface entity (node and face) search trees and finding and distributing entities required to complete on-rank (local) spatial searches. To enable source-code portability and performance across a variety of different computer architectures, we implemented the algorithm using the Kokkos hardware abstraction library. While we targeted development towards machines with a GPU accelerator per MPI rank, we also report performance results for OpenMP with a conventional multi-core compute node per rank. Results here demonstrate

  15. A fuzzy-match search engine for physician directories.

    PubMed

    Rastegar-Mojarad, Majid; Kadolph, Christopher; Ye, Zhan; Wall, Daniel; Murali, Narayana; Lin, Simon

    2014-11-04

    A search engine to find physicians' information is a basic but crucial function of a health care provider's website. Inefficient search engines, which return no results or incorrect results, can lead to patient frustration and potential customer loss. A search engine that can handle misspellings and spelling variations of names is needed, as the United States (US) has culturally, racially, and ethnically diverse names. The Marshfield Clinic website provides a search engine for users to search for physicians' names. The current search engine provides an auto-completion function, but it requires an exact match. We observed that 26% of all searches yielded no results. The goal was to design a fuzzy-match algorithm to aid users in finding physicians easier and faster. Instead of an exact match search, we used a fuzzy algorithm to find similar matches for searched terms. In the algorithm, we solved three types of search engine failures: "Typographic", "Phonetic spelling variation", and "Nickname". To solve these mismatches, we used a customized Levenshtein distance calculation that incorporated Soundex coding and a lookup table of nicknames derived from US census data. Using the "Challenge Data Set of Marshfield Physician Names," we evaluated the accuracy of fuzzy-match engine-top ten (90%) and compared it with exact match (0%), Soundex (24%), Levenshtein distance (59%), and fuzzy-match engine-top one (71%). We designed, created a reference implementation, and evaluated a fuzzy-match search engine for physician directories. The open-source code is available at the codeplex website and a reference implementation is available for demonstration at the datamarsh website.

  16. Economic Load Dispatch Using Adaptive Social Acceleration Constant Based Particle Swarm Optimization

    NASA Astrophysics Data System (ADS)

    Jain, N. K.; Nangia, Uma; Jain, Jyoti

    2018-04-01

    In this paper, an Adaptive Social Acceleration Constant based Particle Swarm Optimization (ASACPSO) has been developed which uses the best value of social acceleration constant (Csg). Three formulations of Csg have been used to search for the best value of Csg. These three formulations led to the development of three algorithms-ALDPSO, AELDPSO-I and AELDPSO-II which were implemented for Economic Load Dispatch of IEEE 5 bus, 14 bus and 30 bus systems. The best value of Csg was selected based on the minimum number of Kounts i.e. number of function evaluations required to minimize the function. This value of Csg was directly used in basic PSO algorithm which led to the development of ASACPSO algorithm. ASACPSO was found to converge faster and give more accurate results compared to BPSO for IEEE 5, 14 and 30 bus systems.

  17. Real-time earthquake monitoring using a search engine method.

    PubMed

    Zhang, Jie; Zhang, Haijiang; Chen, Enhong; Zheng, Yi; Kuang, Wenhuan; Zhang, Xiong

    2014-12-04

    When an earthquake occurs, seismologists want to use recorded seismograms to infer its location, magnitude and source-focal mechanism as quickly as possible. If such information could be determined immediately, timely evacuations and emergency actions could be undertaken to mitigate earthquake damage. Current advanced methods can report the initial location and magnitude of an earthquake within a few seconds, but estimating the source-focal mechanism may require minutes to hours. Here we present an earthquake search engine, similar to a web search engine, that we developed by applying a computer fast search method to a large seismogram database to find waveforms that best fit the input data. Our method is several thousand times faster than an exact search. For an Mw 5.9 earthquake on 8 March 2012 in Xinjiang, China, the search engine can infer the earthquake's parameters in <1 s after receiving the long-period surface wave data.

  18. Acceleration and Propagation of Anomalous Cosmic Rays and Near-Relativistic Electrons in the Heliosheath

    NASA Astrophysics Data System (ADS)

    Roelof, E. C.

    2017-12-01

    Voyager 1/2 LECP observations at the termination shock (TS) crossings established that energetic ions (40keV-1MeV) appeared to be locally accelerated "termination shock particles", and since then have exhibited remarkably steady and similar intensities at both spacecraft throughout the heliosheath (HS). On the other hand, the anomalous cosmic rays (ACRs, 4-80 MeV total energy H, He, and O ions) increased more or less steadily across the shock and then gradually peaked years later. All the time in the HS, the ACRs at each spacecraft exhibited a striking "common spectrum", i.e., closely similar intensity histories when ordered by total energy. Near-relativistic electrons (30 keV-1 MeV) exhibited seemingly mutually inconsistent behavior while the two Voyagers transited the shock and HS, with the VGR2 electrons peaking at the shock, but later disappearing for a year (in 2010) and then slowly recovering, as opposed to the less variable VGR1 electrons whose remarkably smooth time history (2008-2012) was very similar to the VGR1 ACRs. Consequently, shock acceleration seems to be operating locally at the TS along with another spatially distributed acceleration/transport mechanism within the HS. The "reservoir" equation (Roelof, AIP Conf. Proc., 1500, 174-179 and 180-184, 2012) offers quantitative explanations for many of these apparently disparate observations. Meso-scale gradients and curvatures in the magnetic field produce transverse transport of energetic particles and (in direct consequence) "transverse compressive" acceleration that relates the fractional rate of momentum d(lnp)/dt=-(1/3)div(Vperp) to the divergence of the component of the plasma velocity transverse to the magnetic field. However, this acceleration rate must compete with the extinction rate of singly-charged ions due to charge exchange with the cold interstellar neutral H-atoms that permeate the HS. The agreement of the Voyager 1/2 LECP observations with the acceleration/extinction processes has

  19. Analysis of flame acceleration in open or vented obstructed pipes

    NASA Astrophysics Data System (ADS)

    Bychkov, Vitaly; Sadek, Jad; Akkerman, V'yacheslav

    2017-01-01

    While flame propagation through obstacles is often associated with turbulence and/or shocks, Bychkov et al. [V. Bychkov et al., Phys. Rev. Lett. 101, 164501 (2008), 10.1103/PhysRevLett.101.164501] have revealed a shockless, conceptually laminar mechanism of extremely fast flame acceleration in semiopen obstructed pipes (one end of a pipe is closed; a flame is ignited at the closed end and propagates towards the open one). The acceleration is devoted to a powerful jet flow produced by delayed combustion in the spaces between the obstacles, with turbulence playing only a supplementary role in this process. In the present work, this formulation is extended to pipes with both ends open in order to describe the recent experiments and modeling by Yanez et al. [J. Yanez et al., arXiv:1208.6453] as well as the simulations by Middha and Hansen [P. Middha and O. R. Hansen, Process Safety Prog. 27, 192 (2008) 10.1002/prs.10242]. It is demonstrated that flames accelerate strongly in open or vented obstructed pipes and the acceleration mechanism is similar to that in semiopen ones (shockless and laminar), although acceleration is weaker in open pipes. Starting with an inviscid approximation, we subsequently incorporate hydraulic resistance (viscous forces) into the analysis for the sake of comparing its role to that of a jet flow driving acceleration. It is shown that hydraulic resistance is actually not required to drive flame acceleration. In contrast, this is a supplementary effect, which moderates acceleration. On the other hand, viscous forces are nevertheless an important effect because they are responsible for the initial delay occurring before the flame acceleration onset, which is observed in the experiments and simulations. Accounting for this effect provides good agreement between the experiments, modeling, and the present theory.

  20. In Search of Speedier Searches.

    ERIC Educational Resources Information Center

    Peterson, Ivars

    1984-01-01

    Methods to make computer searching as simple and efficient as possible have led to the development of various data structures. Data structures specify the items involved in searching and what can be done to them. The nature and advantages of using "self-adjusting" data structures (self-adjusting binary search trees) are discussed. (JN)

  1. Fast correspondences search in anatomical trees

    NASA Astrophysics Data System (ADS)

    dos Santos, Thiago R.; Gergel, Ingmar; Meinzer, Hans-Peter; Maier-Hein, Lena

    2010-03-01

    Registration of multiple medical images commonly comprises the steps feature extraction, correspondences search and transformation computation. In this paper, we present a new method for a fast and pose independent search of correspondences using as features anatomical trees such as the bronchial system in the lungs or the vessel system in the liver. Our approach scores the similarities between the trees' nodes (bifurcations) taking into account both, topological properties extracted from their graph representations and anatomical properties extracted from the trees themselves. The node assignment maximizes the global similarity (sum of the scores of each pair of assigned nodes), assuring that the matches are distributed throughout the trees. Furthermore, the proposed method is able to deal with distortions in the data, such as noise, motion, artifacts, and problems associated with the extraction method, such as missing or false branches. According to an evaluation on swine lung data sets, the method requires less than one second on average to compute the matching and yields a high rate of correct matches compared to state of the art work.

  2. Stochastic acceleration of electrons from multiple uncorrelated plasma waves

    NASA Astrophysics Data System (ADS)

    Gee, David; Michel, Pierre; Wurtele, Jonathan

    2017-10-01

    One-dimensional theory puts a strict limit on the maximum energy attainable by an electron trapped and accelerated by an electron plasma wave (EPW). However, experimental measurements of hot electron distributions accelerated by stimulated Raman scattering (SRS) in ICF experiments typically show a thermal distribution with temperatures of the order of the kinetic energy of the resonant EPW's (Thot mvp2 , where vp is the phase velocity of the EPW's driven by SRS) and no clear cutoff at high energies. In this project, we are investigating conditions under which electrons can be stochastically accelerated by multiple uncorrelated EPW's, such as those generated by incoherent laser speckles in large laser spots like the ones used on NIF ( mm-size), and reproduce distributions similar to those observed in experiments. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.

  3. Full-Text Searching on Major Supermarket Systems: Dialog, Data-Star, and Nexis.

    ERIC Educational Resources Information Center

    Tenopir, Carol; Berglund, Sharon

    1993-01-01

    Examines the similarities, differences, and full-text features of the three most-used online systems for full-text searching in general libraries: DIALOG, Data-Star, and NEXIS. Overlapping databases, unique sources, search features, proximity operators, set building, language enhancement and word equivalencies, and display features are discussed.…

  4. Understanding nature's particle accelerators using high energy gamma-ray survey instruments

    NASA Astrophysics Data System (ADS)

    Abeysekara, Anushka Udara

    Nature's particle accelerators, such as Pulsars, Pulsar Wind Nebulae, Active Galactic Nuclei and Supernova Remnants accelerate charged particles to very high energies that then produce high energy photons. The particle acceleration mechanisms and the high energy photon emission mechanisms are poorly understood phenomena. These mechanisms can be understood either by studying individual sources in detail or, alternatively, using the collective properties of a sample of sources. Recent development of GeV survey instruments, such as Fermi-LAT, and TeV survey instruments, such as Milagro, provides a large sample of high energy gamma-ray flux measurements from galactic and extra-galactic sources. In this thesis I provide constraints on GeV and TeV radiation mechanisms using the X-ray-TeV correlations and GeV-TeV correlations. My data sample was obtained from three targeted searches for extragalactic sources and two targeted search for galactic sources, using the existing Milagro sky maps. The first extragalactic candidate list consists of Fermi-LAT GeV extragalactic sources, and the second extragalactic candidate list consists of TeVCat extragalactic sources that have been detected by Imaging Atmospheric Cerenkov Telescopes (IACTs). In both extragalactic candidate lists Markarian 421 was the only source detected by Milagro. A comparison between the Markarian 421 time-averaged flux, measured by Milagro, and the flux measurements of transient states, measured by IACTs, is discussed. The third extragalactic candidate list is a list of potential TeV emitting BL Lac candidates that was synthesized using X-ray observations of BL Lac objects and a Synchrotron Self-Compton model. Milagro's sensitivity was not sufficient to detect any of those candidates. However, the 95% confidence flux upper limits of those sources were above the predicted flux. Therefore, these results provide evidence to conclude that the Synchrotron Self-Compton model for BL Lac objects is still a viable

  5. Structural texture similarity metrics for image analysis and retrieval.

    PubMed

    Zujovic, Jana; Pappas, Thrasyvoulos N; Neuhoff, David L

    2013-07-01

    We develop new metrics for texture similarity that accounts for human visual perception and the stochastic nature of textures. The metrics rely entirely on local image statistics and allow substantial point-by-point deviations between textures that according to human judgment are essentially identical. The proposed metrics extend the ideas of structural similarity and are guided by research in texture analysis-synthesis. They are implemented using a steerable filter decomposition and incorporate a concise set of subband statistics, computed globally or in sliding windows. We conduct systematic tests to investigate metric performance in the context of "known-item search," the retrieval of textures that are "identical" to the query texture. This eliminates the need for cumbersome subjective tests, thus enabling comparisons with human performance on a large database. Our experimental results indicate that the proposed metrics outperform peak signal-to-noise ratio (PSNR), structural similarity metric (SSIM) and its variations, as well as state-of-the-art texture classification metrics, using standard statistical measures.

  6. Reaching extended length-scales with accelerated dynamics

    NASA Astrophysics Data System (ADS)

    Hubartt, Bradley; Shim, Yunsic; Amar, Jacques

    2012-02-01

    While temperature-accelerated dynamics (TAD) has been quite successful in extending the time-scales for non-equilibrium simulations of small systems, the computational time increases rapidly with system size. One possible solution to this problem, which we refer to as parTAD^1 is to use spatial decomposition combined with our previously developed semi-rigorous synchronous sublattice algorithm^2. However, while such an approach leads to significantly better scaling as a function of system-size, it also artificially limits the size of activated events and is not completely rigorous. Here we discuss progress we have made in developing an alternative approach in which localized saddle-point searches are combined with parallel GPU-based molecular dynamics in order to improve the scaling behavior. By using this method, along with the use of an adaptive method to determine the optimal high-temperature^3, we have been able to significantly increase the range of time- and length-scales over which accelerated dynamics simulations may be carried out. [1] Y. Shim et al, Phys. Rev. B 76, 205439 (2007); ibid, Phys. Rev. Lett. 101, 116101 (2008). [2] Y. Shim and J.G. Amar, Phys. Rev. B 71, 125432 (2005). [3] Y. Shim and J.G. Amar, J. Chem. Phys. 134, 054127 (2011).

  7. Study of the similarity function in Indexing-First-One hashing

    NASA Astrophysics Data System (ADS)

    Lai, Y.-L.; Jin, Z.; Goi, B.-M.; Chai, T.-Y.

    2017-06-01

    The recent proposed Indexing-First-One (IFO) hashing is a latest technique that is particularly adopted for eye iris template protection, i.e. IrisCode. However, IFO employs the measure of Jaccard Similarity (JS) initiated from Min-hashing has yet been adequately discussed. In this paper, we explore the nature of JS in binary domain and further propose a mathematical formulation to generalize the usage of JS, which is subsequently verified by using CASIA v3-Interval iris database. Our study reveals that JS applied in IFO hashing is a generalized version in measure two input objects with respect to Min-Hashing where the coefficient of JS is equal to one. With this understanding, IFO hashing can propagate the useful properties of Min-hashing, i.e. similarity preservation, thus favorable for similarity searching or recognition in binary space.

  8. Sagace: A web-based search engine for biomedical databases in Japan

    PubMed Central

    2012-01-01

    Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816

  9. Exploring the Logic of Mobile Search

    ERIC Educational Resources Information Center

    Westlund, Oscar; Gomez-Barroso, Jose-Luis; Compano, Ramon; Feijoo, Claudio

    2011-01-01

    After more than a decade of development work and hopes, the usage of mobile Internet has finally taken off. Now, we are witnessing the first signs of evidence of what might become the explosion of mobile content and applications that will be shaping the (mobile) Internet of the future. Similar to the wired Internet, search will become very…

  10. Higgsino dark matter or not: Role of disappearing track searches at the LHC and future colliders

    NASA Astrophysics Data System (ADS)

    Fukuda, Hajime; Nagata, Natsumi; Otono, Hidetoshi; Shirai, Satoshi

    2018-06-01

    Higgsino in supersymmetric standard models is known to be a promising candidate for dark matter in the Universe. Its phenomenological property is strongly affected by the gaugino fraction in the Higgsino-like state. If this is sizable, in other words, if gaugino masses are less than O (10) TeV, we may probe the Higgsino dark matter in future non-accelerator experiments such as dark matter direct searches and measurements of electric dipole moments. On the other hand, if gauginos are much heavier, then it is hard to search for Higgsino in these experiments. In this case, due to a lack of gaugino components, the mass difference between the neutral and charged Higgsinos is uniquely determined by electroweak interactions to be around 350 MeV, which makes the heavier charged state rather long-lived, with a decay length of about 1 cm. In this letter, we argue that a charged particle with a flight length of O (1) cm can be probed in disappearing-track searches if we require only two hits in the pixel detector. Even in this case, we can reduce background events with the help of the displaced-vertex reconstruction technique. We study the prospects of this search strategy at the LHC and future colliders for the Higgsino dark matter scenario. It is found that an almost pure Higgsino is indeed within the reach of the future 33 TeV collider experiments. We then discuss that the interplay among collider and non-accelerator experiments plays a crucial role in testing the Higgsino dark matter scenarios. Our strategy for disappearing-track searches can also enlarge the discovery potential of pure wino dark matter as well as other electroweak-charged dark matter candidates.

  11. Semiconductor acceleration sensor

    NASA Astrophysics Data System (ADS)

    Ueyanagi, Katsumichi; Kobayashi, Mitsuo; Goto, Tomoaki

    1996-09-01

    This paper reports a practical semiconductor acceleration sensor especially suited for automotive air bag systems. The acceleration sensor includes four beams arranged in a swastika structure. Two piezoresistors are formed on each beam. These eight piezoresistors constitute a Wheatstone bridge. The swastika structure of the sensing elements, an upper glass plate and a lower glass plate exhibit the squeeze film effect which enhances air dumping, by which the constituent silicon is prevented from breakdown. The present acceleration sensor has the following features. The acceleration force component perpendicular to the sensing direction can be cancelled. The cross-axis sensitivity is less than 3 percent. And, the erroneous offset caused by the differences between the thermal expansion coefficients of the constituent materials can be canceled. The high aspect ratio configuration realized by plasma etching facilitates reducing the dimensions and improving the sensitivity of the acceleration sensor. The present acceleration sensor is 3.9 mm by 3.9 mm in area and 1.2 mm in thickness. The present acceleration sensor can measure from -50 to +50 G with sensitivity of 0.275 mV/G and with non-linearity of less than 1 percent. The acceleration sensor withstands shock of 3000 G.

  12. Effect of Reprocessing and Accelerated Weathering on Impact-Modified Recycled Blend

    NASA Astrophysics Data System (ADS)

    Ramesh, V.; Mohanty, Smita; Biswal, Manoranjan; Nayak, Sanjay K.

    2015-12-01

    Recovery of recycled polycarbonate, acrylonitrile butadiene styrene, high-impact polystyrene, and its blends from waste electrical and electronic equipment plastics products properties were enhanced by the addition of virgin polycarbonate and impact modifier. The optimized blend formulation was processed through five cycles, at processing temperature, 220-240 °C and accelerated weathering up to 700 h. Moreover, the effect of reprocessing and accelerated weathering in the physical properties of the modified blends was investigated by mechanical, thermal, rheological, and morphological studies. The results show that in each reprocessing cycle, the tensile strength and impact strength decreased significantly and the similar behavior has been observed from accelerated weathering. Subsequently, the viscosity decreases and this decrease becomes the effect of thermal and photo-oxidative degradation. This can be correlated with FTIR analysis.

  13. Visual search for object categories is predicted by the representational architecture of high-level visual cortex

    PubMed Central

    Alvarez, George A.; Nakayama, Ken; Konkle, Talia

    2016-01-01

    Visual search is a ubiquitous visual behavior, and efficient search is essential for survival. Different cognitive models have explained the speed and accuracy of search based either on the dynamics of attention or on similarity of item representations. Here, we examined the extent to which performance on a visual search task can be predicted from the stable representational architecture of the visual system, independent of attentional dynamics. Participants performed a visual search task with 28 conditions reflecting different pairs of categories (e.g., searching for a face among cars, body among hammers, etc.). The time it took participants to find the target item varied as a function of category combination. In a separate group of participants, we measured the neural responses to these object categories when items were presented in isolation. Using representational similarity analysis, we then examined whether the similarity of neural responses across different subdivisions of the visual system had the requisite structure needed to predict visual search performance. Overall, we found strong brain/behavior correlations across most of the higher-level visual system, including both the ventral and dorsal pathways when considering both macroscale sectors as well as smaller mesoscale regions. These results suggest that visual search for real-world object categories is well predicted by the stable, task-independent architecture of the visual system. NEW & NOTEWORTHY Here, we ask which neural regions have neural response patterns that correlate with behavioral performance in a visual processing task. We found that the representational structure across all of high-level visual cortex has the requisite structure to predict behavior. Furthermore, when directly comparing different neural regions, we found that they all had highly similar category-level representational structures. These results point to a ubiquitous and uniform representational structure in high

  14. Comparison of PubMed and Google Scholar literature searches.

    PubMed

    Anders, Michael E; Evans, Dennis P

    2010-05-01

    Literature searches are essential to evidence-based respiratory care. To conduct literature searches, respiratory therapists rely on search engines to retrieve information, but there is a dearth of literature on the comparative efficiencies of search engines for researching clinical questions in respiratory care. To compare PubMed and Google Scholar search results for clinical topics in respiratory care to that of a benchmark. We performed literature searches with PubMed and Google Scholar, on 3 clinical topics. In PubMed we used the Clinical Queries search filter. In Google Scholar we used the search filters in the Advanced Scholar Search option. We used the reference list of a related Cochrane Collaboration evidence-based systematic review as the benchmark for each of the search results. We calculated recall (sensitivity) and precision (positive predictive value) with 2 x 2 contingency tables. We compared the results with the chi-square test of independence and Fisher's exact test. PubMed and Google Scholar had similar recall for both overall search results (71% vs 69%) and full-text results (43% vs 51%). PubMed had better precision than Google Scholar for both overall search results (13% vs 0.07%, P < .001) and full-text results (8% vs 0.05%, P < .001). Our results suggest that PubMed searches with the Clinical Queries filter are more precise than with the Advanced Scholar Search in Google Scholar for respiratory care topics. PubMed appears to be more practical to conduct efficient, valid searches for informing evidence-based patient-care protocols, for guiding the care of individual patients, and for educational purposes.

  15. CALIL.JP, a new web service that provides one-stop searching of Japan-wide libraries' collections

    NASA Astrophysics Data System (ADS)

    Yoshimoto, Ryuuji

    Calil.JP is a new free online service that enables federated searching, marshalling and integration of Web-OPAC data on the collections of libraries from around Japan. It offers the search results through user-friendly interface. Developed with a concept of accelerating discovery of fun-to-read books and motivating users to head for libraries, Calil was initially designed mainly for public library users. It now extends to cover university libraries and special libraries. This article presents the Calil's basic capabilities, concept, progress made thus far, and plan for further development as viewed from an engineering development manager.

  16. Pulsar searching and timing with the Parkes telescope

    NASA Astrophysics Data System (ADS)

    Ng, C. W. Y.

    2014-11-01

    Pulsars are highly magnetised, rapidly rotating neutron stars that radiate a beam of coherent radio emission from their magnetic poles. An introduction to the pulsar phenomenology is presented in Chapter 1 of this thesis. The extreme conditions found in and around such compact objects make pulsars fantastic natural laboratories, as their strong gravitational fields provide exclusive insights to a rich variety of fundamental physics and astronomy. The discovery of pulsars is therefore a gateway to new science. An overview of the standard pulsar searching technique is described in Chapter 2, as well as a discussion on notable pulsar searching efforts undertaken thus far with various telescopes. The High Time Resolution Universe (HTRU) Pulsar Survey conducted with the 64-m Parkes radio telescope in Australia forms the bulk of this PhD. In particular, the author has led the search effort of the HTRU low-latitude Galactic plane project part which is introduced in Chapter 3. We discuss the computational challenges arising from the processing of the petabyte-sized survey data. Two new radio interference mitigation techniques are introduced, as well as a partially-coherent segmented acceleration search algorithm which aims to increase our chances of discovering highly-relativistic short-orbit binary systems, covering a parameter space including the potential pulsar-black hole binaries. We show that under a linear acceleration approximation, a ratio of ~0.1 of data length over orbital period results in the highest effectiveness for this search algorithm. Chapter 4 presents the initial results from the HTRU low-latitude Galactic plane survey. From the 37 per cent of data processed thus far, we have re-detected 348 previously known pulsars and discovered a further 47 pulsars. Two of which are fast-spinning pulsars with periods less than 30 ms. PSR J1101-6424 is a millisecond pulsar (MSP) with a heavy white dwarf companion while its short spin period of 5 ms indicates

  17. Rapid acceleration leads to rapid weakening in earthquake-like laboratory experiments

    NASA Astrophysics Data System (ADS)

    Chang, J. C.; Lockner, D. A.; Reches, Z.

    2012-12-01

    We simulated the slip of a fault-patch during a large earthquake by rapidly loading an experimental, ring-shaped fault with energy stored in a spinning flywheel. The flywheel abruptly delivers a finite amount of energy by spinning the fault-patch that spontaneously dissipates the energy without operator intervention. We conducted 42 experiments on Sierra White granite (SWG) samples, and 24 experiments on Kasota dolomite (KD) samples. Each experiment starts by spinning a 225 kg disk-shaped flywheel to a prescribed angular velocity. We refer to this experiment as an "earthquake-like slip-event" (ELSE). The strength-evolution in ELSE experiments is similar to the strength-evolution proposed for earthquake models and observed in stick-slip experiments. Further, we found that ELSE experiments are similar to earthquakes in at least three ways: (1) slip driven by the release of a finite amount of stored energy; (2) pattern of fault strength evolution; and (3) seismically observed values, such as average slip, peak-velocity and rise-time. By assuming that the measured slip, D, in ELSE experiments is equivalent to the average slip during an earthquake, we found that ELSE experiments (D = 0.003-4.6 m) correspond to earthquakes in moment-magnitude range of Mw = 4-8. In ELSE experiments, the critical-slip-distance, dc, has mean values of 2.7 cm and 1.2 cm for SWG and KD, that are much shorter than the 1-10 m in steady-state classical experiments in rotary shear systems. We attribute these dc values, to ELSE loading in which the fault-patch is abruptly loaded by impact with a spinning flywheel. Under this loading, the friction-velocity relations are strikingly different from those under steady-state loading on the same rock samples with the same shear system (Reches and Lockner, Nature, 2010). We further note that the slip acceleration in ELSE evolves systematically with fault strength and wear-rate, and that the dynamic weakening is restricted to the period of intense

  18. Signature energetic analysis of accelerate electron beam after first acceleration station by accelerating stand of Joint Institute for Nuclear Research

    NASA Astrophysics Data System (ADS)

    Sledneva, A. S.; Kobets, V. V.

    2017-06-01

    The linear electron accelerator based on the LINAC - 800 accelerator imported from the Netherland is created at Joint Institute for Nuclear Research in the framework of the project on creation of the Testbed with an electron beam of a linear accelerator with an energy up to 250 MV. Currently two accelerator stations with a 60 MV energy of a beam are put in operation and the work is to put the beam through accelerating section of the third accelerator station. The electron beam with an energy of 23 MeV is used for testing the crystals (BaF2, CsI (native), and LYSO) in order to explore the opportunity to use them in particle detectors in experiments: Muon g-2, Mu2e, Comet, whose preparation requires a detailed study of the detectors properties such as their irradiation by the accelerator beams.

  19. A topic clustering approach to finding similar questions from large question and answer archives.

    PubMed

    Zhang, Wei-Nan; Liu, Ting; Yang, Yang; Cao, Liujuan; Zhang, Yu; Ji, Rongrong

    2014-01-01

    With the blooming of Web 2.0, Community Question Answering (CQA) services such as Yahoo! Answers (http://answers.yahoo.com), WikiAnswer (http://wiki.answers.com), and Baidu Zhidao (http://zhidao.baidu.com), etc., have emerged as alternatives for knowledge and information acquisition. Over time, a large number of question and answer (Q&A) pairs with high quality devoted by human intelligence have been accumulated as a comprehensive knowledge base. Unlike the search engines, which return long lists of results, searching in the CQA services can obtain the correct answers to the question queries by automatically finding similar questions that have already been answered by other users. Hence, it greatly improves the efficiency of the online information retrieval. However, given a question query, finding the similar and well-answered questions is a non-trivial task. The main challenge is the word mismatch between question query (query) and candidate question for retrieval (question). To investigate this problem, in this study, we capture the word semantic similarity between query and question by introducing the topic modeling approach. We then propose an unsupervised machine-learning approach to finding similar questions on CQA Q&A archives. The experimental results show that our proposed approach significantly outperforms the state-of-the-art methods.

  20. Real-time earthquake monitoring using a search engine method

    PubMed Central

    Zhang, Jie; Zhang, Haijiang; Chen, Enhong; Zheng, Yi; Kuang, Wenhuan; Zhang, Xiong

    2014-01-01

    When an earthquake occurs, seismologists want to use recorded seismograms to infer its location, magnitude and source-focal mechanism as quickly as possible. If such information could be determined immediately, timely evacuations and emergency actions could be undertaken to mitigate earthquake damage. Current advanced methods can report the initial location and magnitude of an earthquake within a few seconds, but estimating the source-focal mechanism may require minutes to hours. Here we present an earthquake search engine, similar to a web search engine, that we developed by applying a computer fast search method to a large seismogram database to find waveforms that best fit the input data. Our method is several thousand times faster than an exact search. For an Mw 5.9 earthquake on 8 March 2012 in Xinjiang, China, the search engine can infer the earthquake’s parameters in <1 s after receiving the long-period surface wave data. PMID:25472861

  1. FERMILAB ACCELERATOR R&D PROGRAM TOWARDS INTENSITY FRONTIER ACCELERATORS : STATUS AND PROGRESS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shiltsev, Vladimir

    2016-11-15

    The 2014 P5 report indicated the accelerator-based neutrino and rare decay physics research as a centrepiece of the US domestic HEP program at Fermilab. Operation, upgrade and development of the accelerators for the near- term and longer-term particle physics program at the Intensity Frontier face formidable challenges. Here we discuss key elements of the accelerator physics and technology R&D program toward future multi-MW proton accelerators and present its status and progress. INTENSITY FRONTIER ACCELERATORS

  2. EDITORIAL: Laser and Plasma Accelerators Workshop, Kardamyli, Greece, 2009 Laser and Plasma Accelerators Workshop, Kardamyli, Greece, 2009

    NASA Astrophysics Data System (ADS)

    Bingham, Bob; Muggli, Patric

    2011-01-01

    -resolved radiobiology or chemistry. Such laser-generated beams will form the basis of the fifth generation light sources and will be compact versions of the much more expensive fourth generation XFEL, such as LCLS light sources. Laser-driven ion acceleration is also making rapid headway; one of the goals in these experiments is to produce protons and carbon ions of hundreds of MeV for oncology. These experiments are carried out using solid-target-laser interactions. There is still a number of issues to be resolved in these experiments including the origin of light ions. The paper by Willingale et al addresses this issue and demonstrates that deuteron ions originating from the front surface can gain comparable energies as those from the rear surface. Furthermore, from two-dimensional simulations they show that a proton-rich contamination layer over the surface is detrimental to deuteron ion acceleration from the rear surface but not detrimental to the front surface acceleration mechanism. Studies of different laser polarizations on ion acceleration at the rear surface were reported by Antici et al. It was shown that no real enhancement using a particular polarization was found. At higher radiation intensities, especially with the multi-petawatt lasers being planned, radiation reaction becomes important. This was reported by Chen et al who found that radiation reaction effects on ion acceleration in laser-foil interactions impeded the backward moving electrons, which enhanced the ion acceleration. An interesting new development is the use of ultra-relativistic proton beams to drive plasma wakefields. This is similar to the SLAC electron-beam-driven wakefields. However, unlike the SLAC electron beam, which is of the order of 30 fs long and matches the period of the plasma wave necessary to create the blowout or bubble regime, the ion beam is very much longer. To create shorter ion beams a magnetic compression scheme is investigated in the paper by Caldwell et al, and results for proton

  3. Vestibular afferent responses to linear accelerations in the alert squirrel monkey

    NASA Technical Reports Server (NTRS)

    Somps, Christopher J.; Schor, Robert H.; Tomko, David L.

    1994-01-01

    The spontaneous activity of 40 otolith afferents and 44 canal afferents was recorded in 4 alert, intact squirrel monkeys. Polarization vectors and response properties of otolith afferents were determined during static re-orientations relative to gravity and during Earth-horizontal, sinusoidal, linear oscillations. Canal afferents were tested for sensitivity to linear accelerations. For regular otolith afferents, a significant correlation between upright discharge rate and sensitivity to dynamic acceleration in the horizontal plane was observed. This correlation was not present in irregular units. The sensitivity of otolith afferents to both static tilts and dynamic linear acceleration was much greater in irregularly discharging units than in regularly discharging units. The spontaneous activity and static and dynamic response properties of regularly discharging otolith afferents were similar to those reported in barbiturate-anesthetized squirrel monkeys. Irregular afferents also had similar dynamic response properties when compared to anesthetized monkeys. However, this sample of irregular afferents in alert animals had higher resting discharge rates and greater sensitivity to static tilts. The majority of otolith polarization vectors were oriented near the horizontal in the plane of the utricular maculae; however, directions of maximum sensitivity were different during dynamic and static testing. Canal afferents were not sensitive to static tilts or linear oscillations of the head.

  4. Interrupted Visual Searches Reveal Volatile Search Memory

    ERIC Educational Resources Information Center

    Shen, Y. Jeremy; Jiang, Yuhong V.

    2006-01-01

    This study investigated memory from interrupted visual searches. Participants conducted a change detection search task on polygons overlaid on scenes. Search was interrupted by various disruptions, including unfilled delay, passive viewing of other scenes, and additional search on new displays. Results showed that performance was unaffected by…

  5. Searching for confining hidden valleys at LHCb, ATLAS, and CMS

    NASA Astrophysics Data System (ADS)

    Pierce, Aaron; Shakya, Bibhushan; Tsai, Yuhsin; Zhao, Yue

    2018-05-01

    We explore strategies for probing hidden valley scenarios exhibiting confinement. Such scenarios lead to a moderate multiplicity of light hidden hadrons for generic showering and hadronization similar to QCD. Their decays are typically soft and displaced, making them challenging to probe with traditional LHC searches. We show that the low trigger requirements and excellent track and vertex reconstruction at LHCb provide a favorable environment to search for such signals. We propose novel search strategies in both muonic and hadronic channels. We also study existing ATLAS and CMS searches and compare them with our proposals at LHCb. We find that the reach at LHCb is generically better in the parameter space we consider here, even with optimistic background estimations for ATLAS and CMS searches. We discuss potential modifications at ATLAS and CMS that might make these experiments competitive with the LHCb reach. Our proposed searches can be applied to general hidden valley models as well as exotic Higgs boson decays, such as in twin Higgs models.

  6. Anomalous gravitropic response of Chara rhizoids during enhanced accelerations.

    PubMed

    Braun, M

    1996-07-01

    Centrifugal accelerations of 50-250 g were applied to rhizoids of Chara globularis Thuill. at stimulation angles (alpha) of 5-90 degrees between the acceleration vector and the rhizoid axis. After the start of centrifugation, the statoliths were pressed asymmetrically onto the centrifugal flank of the apical cell wall. In contrast to the well-known bending (by bowing) under 1 g, the rhizoids responded in two distinct phases. Following an initial phase of sharp bending (by bulging), which is similar to the negatively gravitropic response of Chara protonemata, rhizoids stopped bending and, in the second phase, grew straight in directions clearly deviating from the direction of acceleration. These response angles (beta) between the axis of the bent part of the rhizoid and the acceleration vector were strictly correlated with the g-level of acceleration. The higher the acceleration the greater was beta. Except for the sharp bending, the shape and growth rate of the centrifuged rhizoids were not different from those of gravistimulated control rhizoids at 1 g. These results indicate that gravitropic bending of rhizoids during enhanced accelerations (5 degrees < or = alpha < or = 90 degrees) is caused not only by subapical differential flank growth, as it is the case at 1 g, but also by also by the centripetal displacement of the growth centre as was recently discussed for the negative gravitropism of Chara protonemata. A hypothesis for cytoskeletally mediated polar growth is presented based on data from positive gravitropic bending of Chara rhizoids at 1 g and from the anomalous gravitropic bending of rhizoids compared with the negatively gravitropic bending of Chara protonemata. The data obtained are also relevant to a general understanding of graviperception in higher-plant organs.

  7. Representational flexibility and response control in a multistep multilocation search task.

    PubMed

    Zelazo, P D; Reznick, J S; Spinazzola, J

    1998-03-01

    Three experiments were conducted to explore the determinants of 2-year-olds' perseverative errors in a search task. In Experiment 1, children either retrieved an object during a preswitch phase or merely observed a hiding event. Active search produced perseveration on postswitch trials, but mere observation did not. In Experiment 2, similar results were found, even when active search occurred in the absence of observation. Finally, in Experiment 3, children observed a hiding event at 1 location on some pretest trials and simply retrieved an object at a different location on other trials. On test trials, in which an object was hidden at a 3rd location, children tended to search where they had searched previously. Together, the results indicate that active search is required to elicit perseveration, which points to failures of response control rather than representational inflexibility.

  8. Early Acceleration of Mathematics Students and its Effect on Growth in Self-esteem: A Longitudinal Study

    NASA Astrophysics Data System (ADS)

    Ma, Xin

    2002-11-01

    The Longitudinal Study of American Youth (LSAY) database was employed to examine the educational practice of early acceleration of students of mathematics on the development of their self-esteem across the entire secondary grade levels. Students were classified into three different academic categories (gifted, honors, and regular). Results indicated that, in terms of the development of their self-esteem, gifted students benefited from early acceleration, honors students neither benefited nor were harmed by early acceleration, and regular students were harmed by early acceleration. Early acceleration in mathematics promoted significant growth in self-esteem among gifted male students and among gifted, honors, and regular minority students. When students were accelerated, schools showed similar average growth in self-esteem among gifted students and regular students and a large effect of general support for mathematics on the average growth in self-esteem among honors students.

  9. Mechanisms of Plasma Acceleration in Coronal Jets

    NASA Astrophysics Data System (ADS)

    Soto, N.; Reeves, K.; Savcheva, A. S.

    2016-12-01

    Jets are small explosions that occur frequently in the Sun possibly driven by the local reconfiguration of the magnetic field, or reconnection. There are two types of coronal jets: standard jets and blowout jets. The purpose of this project is to determine which mechanisms accelerate plasma in two different jets, one that occurred in January 17, 2015 at the disk of the sun and another in October 24, 2015 at the limb. Two possible acceleration mechanisms are chromospheric evaporation and magnetic acceleration. Using SDO/AIA, Hinode/XRT and IRIS data, we create height-time plots, and calculate the velocities of each wavelength for both jets. We calculate the potential magnetic field of the jet and the general region around it to gain a more detailed understanding of its structure, and determine if the jet is likely to be either a standard or blowout jet. Finally, we calculate the magnetic field strength for different heights along the jet spire, and use differential emission measures to calculate the plasma density. Once we have these two values, we calculate the Alfven speed. When analyzing our results we are looking for certain patterns in our velocities. If the plasma in a jet is accelerated by chromospheric evaporation, we expect the velocities to increase as function of temperature, which is what we observed in the October 24th jet. The magnetic models for this jet also show the Eiffel Tower shaped structure characteristic of standard jets, which tend to have plasma accelerated by this mechanism. On the other hand, if the acceleration mechanism were magnetic acceleration, we would expect the velocities to be similar regardless of temperature. For the January 17th jet, we saw that along the spire, the velocities where approximately 200 km/s in all wavelengths, but the velocities of hot plasma detected at the base were closer to the Alfven speed, which was estimated to be about 2,000 km/s. These observations suggest that the plasma in the January 17th jet is

  10. Caffeine accelerates recovery from general anesthesia

    PubMed Central

    Wang, Qiang; Fong, Robert; Mason, Peggy; Fox, Aaron P.

    2013-01-01

    General anesthetics inhibit neurotransmitter release from both neurons and secretory cells. If inhibition of neurotransmitter release is part of an anesthetic mechanism of action, then drugs that facilitate neurotransmitter release may aid in reversing general anesthesia. Drugs that elevate intracellular cAMP levels are known to facilitate neurotransmitter release. Three cAMP elevating drugs (forskolin, theophylline, and caffeine) were tested; all three drugs reversed the inhibition of neurotransmitter release produced by isoflurane in PC12 cells in vitro. The drugs were tested in isoflurane-anesthetized rats. Animals were injected with either saline or saline containing drug. All three drugs dramatically accelerated recovery from isoflurane anesthesia, but caffeine was most effective. None of the drugs, at the concentrations tested, had significant effects on breathing rates, O2 saturation, heart rate, or blood pressure in anesthetized animals. Caffeine alone was tested on propofol-anesthetized rats where it dramatically accelerated recovery from anesthesia. The ability of caffeine to accelerate recovery from anesthesia for different chemical classes of anesthetics, isoflurane and propofol, opens the possibility that it will do so for all commonly used general anesthetics, although additional studies will be required to determine whether this is in fact the case. Because anesthesia in rodents is thought to be similar to that in humans, these results suggest that caffeine might allow for rapid and uniform emergence from general anesthesia in human patients. PMID:24375022

  11. PubMed related articles: a probabilistic topic-based model for content similarity

    PubMed Central

    Lin, Jimmy; Wilbur, W John

    2007-01-01

    Background We present a probabilistic topic-based model for content similarity called pmra that underlies the related article search feature in PubMed. Whether or not a document is about a particular topic is computed from term frequencies, modeled as Poisson distributions. Unlike previous probabilistic retrieval models, we do not attempt to estimate relevance–but rather our focus is "relatedness", the probability that a user would want to examine a particular document given known interest in another. We also describe a novel technique for estimating parameters that does not require human relevance judgments; instead, the process is based on the existence of MeSH ® in MEDLINE ®. Results The pmra retrieval model was compared against bm25, a competitive probabilistic model that shares theoretical similarities. Experiments using the test collection from the TREC 2005 genomics track shows a small but statistically significant improvement of pmra over bm25 in terms of precision. Conclusion Our experiments suggest that the pmra model provides an effective ranking algorithm for related article search. PMID:17971238

  12. Mobile Visual Search Based on Histogram Matching and Zone Weight Learning

    NASA Astrophysics Data System (ADS)

    Zhu, Chuang; Tao, Li; Yang, Fan; Lu, Tao; Jia, Huizhu; Xie, Xiaodong

    2018-01-01

    In this paper, we propose a novel image retrieval algorithm for mobile visual search. At first, a short visual codebook is generated based on the descriptor database to represent the statistical information of the dataset. Then, an accurate local descriptor similarity score is computed by merging the tf-idf weighted histogram matching and the weighting strategy in compact descriptors for visual search (CDVS). At last, both the global descriptor matching score and the local descriptor similarity score are summed up to rerank the retrieval results according to the learned zone weights. The results show that the proposed approach outperforms the state-of-the-art image retrieval method in CDVS.

  13. The Perth Automated Supernova Search

    NASA Astrophysics Data System (ADS)

    Williams, A. J.

    1997-12-01

    An automated search for supernovae in late spiral galaxies has been established at Perth Observatory, Western Australia. This automated search uses three low-cost PC-clone computers, a liquid nitrogen cooled CCD camera built locally, and a 61-cm telescope automated for the search. The images are all analysed automatically in real-time by routines in Perth Vista, the image processing system ported to the PC architecture for the search system. The telescope control software written for the project, Teljoy, maintains open-loop position accuracy better than 30" of arc after hundreds of jumps over an entire night. Total capital cost to establish and run this supernova search over the seven years of development and operation was around US$30,000. To date, the system has discovered a total of 6 confirmed supernovae, made an independent detection of a seventh, and detected one unconfirmed event assumed to be a supernova. The various software and hardware components of the search system are described in detail, the analysis of the first three years of data is discussed, and results presented. We find a Type Ib/c rate of 0.43 +/- 0.43 SNu, and a Type IIP rate of 0.86 +/- 0.49 SNu, where SNu are 'supernova units', expressed in supernovae per 10^10 solar blue luminosity galaxy per century. These values are for a Hubble constant of 75 km/s per Mpc, and scale as (H0/75)^2. The small number of discoveries has left large statistical uncertainties, but our strategy of frequent observations has reduced systematic errors - altering detection threshold or peak supernova luminosity by +/- 0.5 mag changes estimated rates by only around 20%. Similarly, adoption of different light curve templates for Type Ia and Type IIP supernovae has a minimal effect on the final statistics (2% and 4% change, respectively).

  14. A Full-Text-Based Search Engine for Finding Highly Matched Documents Across Multiple Categories

    NASA Technical Reports Server (NTRS)

    Nguyen, Hung D.; Steele, Gynelle C.

    2016-01-01

    This report demonstrates the full-text-based search engine that works on any Web-based mobile application. The engine has the capability to search databases across multiple categories based on a user's queries and identify the most relevant or similar. The search results presented here were found using an Android (Google Co.) mobile device; however, it is also compatible with other mobile phones.

  15. Race, self-selection, and the job search process.

    PubMed

    Pager, Devah; Pedulla, David S

    2015-01-01

    While existing research has documented persistent barriers facing African-American job seekers, far less research has questioned how job seekers respond to this reality. Do minorities self-select into particular segments of the labor market to avoid discrimination? Such questions have remained unanswered due to the lack of data available on the positions to which job seekers apply. Drawing on two original data sets with application-specific information, we find little evidence that blacks target or avoid particular job types. Rather, blacks cast a wider net in their search than similarly situated whites, including a greater range of occupational categories and characteristics in their pool of job applications. Additionally, we show that perceptions of discrimination are associated with increased search breadth, suggesting that broad search among African-Americans represents an adaptation to labor market discrimination. Together these findings provide novel evidence on the role of race and self-selection in the job search process.

  16. Illinois Accelerator Research Center

    DOE PAGES

    Kroc, Thomas K.; Cooper, Charlie A.

    2017-10-26

    The Illinois Accelerator Research Center (IARC) hosts a new accelerator development program at Fermi National Accelerator Laboratory. IARC provides access to Fermi's state-of-the-art facilities and technologies for research, development and industrialization of particle accelerator technology. In addition to facilitating access to available existing Fermi infrastructure, the IARC Campus has a dedicated 36,000 ft2 heavy assembly building (HAB) with all the infrastructure needed to develop, commission and operate new accelerators. Connected to the HAB is a 47,000 ft Office, Technology and Engineering (OTE) building, paid for by the state, that has office, meeting, and light technical space. The OTE building, whichmore » contains the Accelerator Physics Center, and nearby Accelerator and Technical divisions provide IARC collaborators with unique access to world class expertise in a wide array of accelerator technologies. Finally, at IARC scientists and engineers from Fermilab and academia work side by side with industrial partners to develop breakthroughs in accelerator science and translate them into applications for the nation's health, wealth and security.« less

  17. Illinois Accelerator Research Center

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kroc, Thomas K.; Cooper, Charlie A.

    The Illinois Accelerator Research Center (IARC) hosts a new accelerator development program at Fermi National Accelerator Laboratory. IARC provides access to Fermi's state-of-the-art facilities and technologies for research, development and industrialization of particle accelerator technology. In addition to facilitating access to available existing Fermi infrastructure, the IARC Campus has a dedicated 36,000 ft2 heavy assembly building (HAB) with all the infrastructure needed to develop, commission and operate new accelerators. Connected to the HAB is a 47,000 ft Office, Technology and Engineering (OTE) building, paid for by the state, that has office, meeting, and light technical space. The OTE building, whichmore » contains the Accelerator Physics Center, and nearby Accelerator and Technical divisions provide IARC collaborators with unique access to world class expertise in a wide array of accelerator technologies. Finally, at IARC scientists and engineers from Fermilab and academia work side by side with industrial partners to develop breakthroughs in accelerator science and translate them into applications for the nation's health, wealth and security.« less

  18. Illinois Accelerator Research Center

    NASA Astrophysics Data System (ADS)

    Kroc, Thomas K.; Cooper, Charlie A.

    The Illinois Accelerator Research Center (IARC) hosts a new accelerator development program at Fermi National Accelerator Laboratory. IARC provides access to Fermi's state-of-the-art facilities and technologies for research, development and industrialization of particle accelerator technology. In addition to facilitating access to available existing Fermi infrastructure, the IARC Campus has a dedicated 36,000 ft2 Heavy Assembly Building (HAB) with all the infrastructure needed to develop, commission and operate new accelerators. Connected to the HAB is a 47,000 ft2 Office, Technology and Engineering (OTE) building, paid for by the state, that has office, meeting, and light technical space. The OTE building, which contains the Accelerator Physics Center, and nearby Accelerator and Technical divisions provide IARC collaborators with unique access to world class expertise in a wide array of accelerator technologies. At IARC scientists and engineers from Fermilab and academia work side by side with industrial partners to develop breakthroughs in accelerator science and translate them into applications for the nation's health, wealth and security.

  19. Mapping the Color Space of Saccadic Selectivity in Visual Search

    ERIC Educational Resources Information Center

    Xu, Yun; Higgins, Emily C.; Xiao, Mei; Pomplun, Marc

    2007-01-01

    Color coding is used to guide attention in computer displays for such critical tasks as baggage screening or air traffic control. It has been shown that a display object attracts more attention if its color is more similar to the color for which one is searching. However, what does "similar" precisely mean? Can we predict the amount of attention…

  20. Marked Acceleration of Atherosclerosis following Lactobacillus casei induced Coronary Arteritis in a Mouse Model of Kawasaki Disease

    PubMed Central

    Chen, Shuang; Lee, Young Ho; Crother, Timothy R.; Fishbein, Michael; Zhang, Wenxuan; Yilmaz, Atilla; Shimada, Kenichi; Schulte, Danica J; Lehman, Thomas J.A.; Shah, Prediman K.; Arditi, Moshe

    2012-01-01

    Objective To investigate if Lactobacillus casei cell wall extract (LCWE)-induced Kawasaki Disease (KD) accelerates atherosclerosis in hypercholesterolemic mice. Method and Resuslts Apoe−/− or Ldlr−/− mice were injected with LCWE (KD mice) or PBS, fed high fat diet for 8 weeks, and atherosclerotic lesions in aortic sinuses (AS), arch (AC) and whole aorta were assessed. KD mice had larger, more complex aortic lesions with abundant collagen, and both extracellular and intracellular lipid and foam cells, compared to lesions in control mice despite similar cholesterol levels. Both Apoe−/− KD and Ldlr−/− KD mice showed dramatic acceleration in atherosclerosis vs. controls, with increases in en face aortic atherosclerosis and plaque size in both the AS and AC plaques. Accelerated atherosclerosis was associated with increased circulating IL-12p40, IFN-γ, TNF-α, and increased macrophage, DC, and T cell recruitment in lesions. Furthermore, daily injections of the IL-1Ra, which inhibits LCWE induced KD vasculitis, prevented the acceleration of atherosclerosis. Conclusions Our results suggest an important pathophysiologic link between coronary arteritis/vasculitis in the KD mouse model and subsequent atherosclerotic acceleration, supporting the concept that a similar relation may also be present in KD patients. These results also suggest that KD in childhood may predispose to accelerated and early atherosclerosis as adults. PMID:22628430

  1. Application of multivariable search techniques to the optimization of airfoils in a low speed nonlinear inviscid flow field

    NASA Technical Reports Server (NTRS)

    Hague, D. S.; Merz, A. W.

    1975-01-01

    Multivariable search techniques are applied to a particular class of airfoil optimization problems. These are the maximization of lift and the minimization of disturbance pressure magnitude in an inviscid nonlinear flow field. A variety of multivariable search techniques contained in an existing nonlinear optimization code, AESOP, are applied to this design problem. These techniques include elementary single parameter perturbation methods, organized search such as steepest-descent, quadratic, and Davidon methods, randomized procedures, and a generalized search acceleration technique. Airfoil design variables are seven in number and define perturbations to the profile of an existing NACA airfoil. The relative efficiency of the techniques are compared. It is shown that elementary one parameter at a time and random techniques compare favorably with organized searches in the class of problems considered. It is also shown that significant reductions in disturbance pressure magnitude can be made while retaining reasonable lift coefficient values at low free stream Mach numbers.

  2. Accelerated test design

    NASA Technical Reports Server (NTRS)

    Mcdermott, P. P.

    1980-01-01

    The design of an accelerated life test program for electric batteries is discussed. A number of observations and suggestions on the procedures and objectives for conducting an accelerated life test program are presented. Equations based on nonlinear regression analysis for predicting the accelerated life test parameters are discussed.

  3. Effect law of Damage Characteristics of Rock Similar Material with Pre-Existing Cracks

    NASA Astrophysics Data System (ADS)

    Li, S. G.; Cheng, X. Y.; Liu, C.

    2017-11-01

    In order to further study the failure mechanism for rock similar materials, this study established the damage model based on accumulative AE events, investigated the damage characteristics for rock similar material samples with pre-existing cracks of varying width under uniaxial compression load. The equipment used in this study is the self-developed YYW-II strain controlled unconfined compression apparatus and the PCIE-8 acoustic emission (AE) monitoring system. The influences of the width of the pre-existing cracks to the damage characteristics of rock similar materials are analyzed. Results show that, (1) the damage model can better describe the damage characteristics of rock similar materials; (2) the tested samples have three stages during failure: initial damage stage, stable development of damage stage, and accelerated development of damage stage; (3) with the width of pre-existing cracks vary from 3mm to 5mm, the damage of rock similar materials increases gradually. The outcomes of this study provided additional values to the research of the failure mechanism for geotechnical similar material models.

  4. Routine development of objectively derived search strategies.

    PubMed

    Hausner, Elke; Waffenschmidt, Siw; Kaiser, Thomas; Simon, Michael

    2012-02-29

    Over the past few years, information retrieval has become more and more professionalized, and information specialists are considered full members of a research team conducting systematic reviews. Research groups preparing systematic reviews and clinical practice guidelines have been the driving force in the development of search strategies, but open questions remain regarding the transparency of the development process and the available resources. An empirically guided approach to the development of a search strategy provides a way to increase transparency and efficiency. Our aim in this paper is to describe the empirically guided development process for search strategies as applied by the German Institute for Quality and Efficiency in Health Care (Institut für Qualität und Wirtschaftlichkeit im Gesundheitswesen, or "IQWiG"). This strategy consists of the following steps: generation of a test set, as well as the development, validation and standardized documentation of the search strategy. We illustrate our approach by means of an example, that is, a search for literature on brachytherapy in patients with prostate cancer. For this purpose, a test set was generated, including a total of 38 references from 3 systematic reviews. The development set for the generation of the strategy included 25 references. After application of textual analytic procedures, a strategy was developed that included all references in the development set. To test the search strategy on an independent set of references, the remaining 13 references in the test set (the validation set) were used. The validation set was also completely identified. Our conclusion is that an objectively derived approach similar to that used in search filter development is a feasible way to develop and validate reliable search strategies. Besides creating high-quality strategies, the widespread application of this approach will result in a substantial increase in the transparency of the development process of

  5. An absence of neutrinos associated with cosmic-ray acceleration in γ-ray bursts

    NASA Astrophysics Data System (ADS)

    Abbasi, R.; Abdou, Y.; Abu-Zayyad, T.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Altmann, D.; Andeen, K.; Auffenberg, J.; Bai, X.; Baker, M.; Barwick, S. W.; Bay, R.; Bazo Alba, J. L.; Beattie, K.; Beatty, J. J.; Bechet, S.; Becker, J. K.; Becker, K.-H.; Bell, M.; Benabderrahmane, M. L.; Benzvi, S.; Berdermann, J.; Berghaus, P.; Berley, D.; Bernardini, E.; Bertrand, D.; Besson, D. Z.; Bindig, D.; Bissok, M.; Blaufuss, E.; Blumenthal, J.; Boersma, D. J.; Bohm, C.; Bose, D.; Böser, S.; Botner, O.; Brayeur, L.; Brown, A. M.; Buitink, S.; Caballero-Mora, K. S.; Carson, M.; Casier, M.; Chirkin, D.; Christy, B.; Clevermann, F.; Cohen, S.; Colnard, C.; Cowen, D. F.; Cruz Silva, A. H.; D'Agostino, M. V.; Danninger, M.; Daughhetee, J.; Davis, J. C.; de Clercq, C.; Degner, T.; Descamps, F.; Desiati, P.; de Vries-Uiterweerd, G.; Deyoung, T.; Díaz-Vélez, J. C.; Dierckxsens, M.; Dreyer, J.; Dumm, J. P.; Dunkman, M.; Eisch, J.; Ellsworth, R. W.; Engdegård, O.; Euler, S.; Evenson, P. A.; Fadiran, O.; Fazely, A. R.; Fedynitch, A.; Feintzeig, J.; Feusels, T.; Filimonov, K.; Finley, C.; Fischer-Wasels, T.; Flis, S.; Franckowiak, A.; Franke, R.; Gaisser, T. K.; Gallagher, J.; Gerhardt, L.; Gladstone, L.; Glüsenkamp, T.; Goldschmidt, A.; Goodman, J. A.; Góra, D.; Grant, D.; Griesel, T.; Groß, A.; Grullon, S.; Gurtner, M.; Ha, C.; Haj Ismail, A.; Hallgren, A.; Halzen, F.; Han, K.; Hanson, K.; Heereman, D.; Heinen, D.; Helbing, K.; Hellauer, R.; Hickford, S.; Hill, G. C.; Hoffman, K. D.; Hoffmann, B.; Homeier, A.; Hoshina, K.; Huelsnitz, W.; Hülβ, J.-P.; Hulth, P. O.; Hultqvist, K.; Hussain, S.; Ishihara, A.; Jacobi, E.; Jacobsen, J.; Japaridze, G. S.; Johansson, H.; Kappes, A.; Karg, T.; Karle, A.; Kiryluk, J.; Kislat, F.; Klein, S. R.; Köhne, J.-H.; Kohnen, G.; Kolanoski, H.; Köpke, L.; Kopper, S.; Koskinen, D. J.; Kowalski, M.; Kowarik, T.; Krasberg, M.; Kroll, G.; Kunnen, J.; Kurahashi, N.; Kuwabara, T.; Labare, M.; Laihem, K.; Landsman, H.; Larson, M. J.; Lauer, R.; Lünemann, J.; Madsen, J.; Marotta, A.; Maruyama, R.; Mase, K.; Matis, H. S.; Meagher, K.; Merck, M.; Mészáros, P.; Meures, T.; Miarecki, S.; Middell, E.; Milke, N.; Miller, J.; Montaruli, T.; Morse, R.; Movit, S. M.; Nahnhauer, R.; Nam, J. W.; Naumann, U.; Nowicki, S. C.; Nygren, D. R.; Odrowski, S.; Olivas, A.; Olivo, M.; O'Murchadha, A.; Panknin, S.; Paul, L.; Pérez de Los Heros, C.; Piegsa, A.; Pieloth, D.; Posselt, J.; Price, P. B.; Przybylski, G. T.; Rawlins, K.; Redl, P.; Resconi, E.; Rhode, W.; Ribordy, M.; Richman, M.; Riedel, B.; Rizzo, A.; Rodrigues, J. P.; Rothmaier, F.; Rott, C.; Ruhe, T.; Rutledge, D.; Ruzybayev, B.; Ryckbosch, D.; Sander, H.-G.; Santander, M.; Sarkar, S.; Schatto, K.; Schmidt, T.; Schöneberg, S.; Schönwald, A.; Schukraft, A.; Schulte, L.; Schultes, A.; Schulz, O.; Schunck, M.; Seckel, D.; Semburg, B.; Seo, S. H.; Sestayo, Y.; Seunarine, S.; Silvestri, A.; Smith, M. W. E.; Spiczak, G. M.; Spiering, C.; Stamatikos, M.; Stanev, T.; Stezelberger, T.; Stokstad, R. G.; Stößl, A.; Strahler, E. A.; Ström, R.; Stüer, M.; Sullivan, G. W.; Taavola, H.; Taboada, I.; Tamburro, A.; Ter-Antonyan, S.; Tilav, S.; Toale, P. A.; Toscano, S.; Tosi, D.; van Eijndhoven, N.; van Overloop, A.; van Santen, J.; Vehring, M.; Voge, M.; Walck, C.; Waldenmaier, T.; Wallraff, M.; Walter, M.; Wasserman, R.; Weaver, Ch.; Wendt, C.; Westerhoff, S.; Whitehorn, N.; Wiebe, K.; Wiebusch, C. H.; Williams, D. R.; Wischnewski, R.; Wissing, H.; Wolf, M.; Wood, T. R.; Woschnagg, K.; Xu, C.; Xu, D. L.; Xu, X. W.; Yanez, J. P.; Yodh, G.; Yoshida, S.; Zarzhitsky, P.; Zoll, M.; IceCube Collaboration

    2012-04-01

    Very energetic astrophysical events are required to accelerate cosmic rays to above 1018electronvolts. GRBs (γ-ray bursts) have been proposed as possible candidate sources. In the GRB `fireball' model, cosmic-ray acceleration should be accompanied by neutrinos produced in the decay of charged pions created in interactions between the high-energy cosmic-ray protons and γ-rays. Previous searches for such neutrinos found none, but the constraints were weak because the sensitivity was at best approximately equal to the predicted flux. Here we report an upper limit on the flux of energetic neutrinos associated with GRBs that is at least a factor of 3.7 below the predictions. This implies either that GRBs are not the only sources of cosmic rays with energies exceeding 1018electronvolts or that the efficiency of neutrino production is much lower than has been predicted.

  6. Self-mapping the longitudinal field structure of a nonlinear plasma accelerator cavity

    DOE PAGES

    Clayton, C. E.; Adli, E.; Allen, J.; ...

    2016-08-16

    The preservation of emittance of the accelerating beam is the next challenge for plasma-based accelerators envisioned for future light sources and colliders. The field structure of a highly nonlinear plasma wake is potentially suitable for this purpose but has not been yet measured. Here we show that the longitudinal variation of the fields in a nonlinear plasma wakefield accelerator cavity produced by a relativistic electron bunch can be mapped using the bunch itself as a probe. We find that, for much of the cavity that is devoid of plasma electrons, the transverse force is constant longitudinally to within ±3% (r.m.s.).more » Moreover, comparison of experimental data and simulations has resulted in mapping of the longitudinal electric field of the unloaded wake up to 83 GV m –1 to a similar degree of accuracy. Lastly, these results bode well for high-gradient, high-efficiency acceleration of electron bunches while preserving their emittance in such a cavity.« less

  7. Self-mapping the longitudinal field structure of a nonlinear plasma accelerator cavity

    PubMed Central

    Clayton, C. E.; Adli, E.; Allen, J.; An, W.; Clarke, C. I.; Corde, S.; Frederico, J.; Gessner, S.; Green, S. Z.; Hogan, M. J.; Joshi, C.; Litos, M.; Lu, W.; Marsh, K. A.; Mori, W. B.; Vafaei-Najafabadi, N.; Xu, X.; Yakimenko, V.

    2016-01-01

    The preservation of emittance of the accelerating beam is the next challenge for plasma-based accelerators envisioned for future light sources and colliders. The field structure of a highly nonlinear plasma wake is potentially suitable for this purpose but has not been yet measured. Here we show that the longitudinal variation of the fields in a nonlinear plasma wakefield accelerator cavity produced by a relativistic electron bunch can be mapped using the bunch itself as a probe. We find that, for much of the cavity that is devoid of plasma electrons, the transverse force is constant longitudinally to within ±3% (r.m.s.). Moreover, comparison of experimental data and simulations has resulted in mapping of the longitudinal electric field of the unloaded wake up to 83 GV m−1 to a similar degree of accuracy. These results bode well for high-gradient, high-efficiency acceleration of electron bunches while preserving their emittance in such a cavity. PMID:27527569

  8. Plasma inverse transition acceleration

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xie, Ming

    It can be proved fundamentally from the reciprocity theorem with which the electromagnetism is endowed that corresponding to each spontaneous process of radiation by a charged particle there is an inverse process which defines a unique acceleration mechanism, from Cherenkov radiation to inverse Cherenkov acceleration (ICA) [1], from Smith-Purcell radiation to inverse Smith-Purcell acceleration (ISPA) [2], and from undulator radiation to inverse undulator acceleration (IUA) [3]. There is no exception. Yet, for nearly 30 years after each of the aforementioned inverse processes has been clarified for laser acceleration, inverse transition acceleration (ITA), despite speculation [4], has remained the least understood,more » and above all, no practical implementation of ITA has been found, until now. Unlike all its counterparts in which phase synchronism is established one way or the other such that a particle can continuously gain energy from an acceleration wave, the ITA to be discussed here, termed plasma inverse transition acceleration (PITA), operates under fundamentally different principle. As a result, the discovery of PITA has been delayed for decades, waiting for a conceptual breakthrough in accelerator physics: the principle of alternating gradient acceleration [5, 6, 7, 8, 9, 10]. In fact, PITA was invented [7, 8] as one of several realizations of the new principle.« less

  9. Multipactor Physics, Acceleration, and Breakdown in Dielectric-Loaded Accelerating Structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fischer, Richard P.; Gold, Steven H.

    2016-07-01

    The objective of this 3-year program is to study the physics issues associated with rf acceleration in dielectric-loaded accelerating (DLA) structures, with a focus on the key issue of multipactor loading, which has been found to cause very significant rf power loss in DLA structures whenever the rf pulsewidth exceeds the multipactor risetime (~10 ns). The experiments are carried out in the X-band magnicon laboratory at the Naval Research Laboratory (NRL) in collaboration with Argonne National Laboratory (ANL) and Euclid Techlabs LLC, who develop the test structures with support from the DoE SBIR program. There are two main elements inmore » the research program: (1) high-power tests of DLA structures using the magnicon output (20 MW @11.4 GHz), and (2) tests of electron acceleration in DLA structures using relativistic electrons from a compact X-band accelerator. The work during this period has focused on a study of the use of an axial magnetic field to suppress multipactor in DLA structures, with several new high power tests carried out at NRL, and on preparation of the accelerator for the electron acceleration experiments.« less

  10. Seasonal trends in sleep-disordered breathing: evidence from Internet search engine query data.

    PubMed

    Ingram, David G; Matthews, Camilla K; Plante, David T

    2015-03-01

    The primary aim of the current study was to test the hypothesis that there is a seasonal component to snoring and obstructive sleep apnea (OSA) through the use of Google search engine query data. Internet search engine query data were retrieved from Google Trends from January 2006 to December 2012. Monthly normalized search volume was obtained over that 7-year period in the USA and Australia for the following search terms: "snoring" and "sleep apnea". Seasonal effects were investigated by fitting cosinor regression models. In addition, the search terms "snoring children" and "sleep apnea children" were evaluated to examine seasonal effects in pediatric populations. Statistically significant seasonal effects were found using cosinor analysis in both USA and Australia for "snoring" (p < 0.00001 for both countries). Similarly, seasonal patterns were observed for "sleep apnea" in the USA (p = 0.001); however, cosinor analysis was not significant for this search term in Australia (p = 0.13). Seasonal patterns for "snoring children" and "sleep apnea children" were observed in the USA (p = 0.002 and p < 0.00001, respectively), with insufficient search volume to examine these search terms in Australia. All searches peaked in the winter or early spring in both countries, with the magnitude of seasonal effect ranging from 5 to 50 %. Our findings indicate that there are significant seasonal trends for both snoring and sleep apnea internet search engine queries, with a peak in the winter and early spring. Further research is indicated to determine the mechanisms underlying these findings, whether they have clinical impact, and if they are associated with other comorbid medical conditions that have similar patterns of seasonal exacerbation.

  11. Induction linear accelerators

    NASA Astrophysics Data System (ADS)

    Birx, Daniel

    1992-03-01

    Among the family of particle accelerators, the Induction Linear Accelerator is the best suited for the acceleration of high current electron beams. Because the electromagnetic radiation used to accelerate the electron beam is not stored in the cavities but is supplied by transmission lines during the beam pulse it is possible to utilize very low Q (typically<10) structures and very large beam pipes. This combination increases the beam breakup limited maximum currents to of order kiloamperes. The micropulse lengths of these machines are measured in 10's of nanoseconds and duty factors as high as 10-4 have been achieved. Until recently the major problem with these machines has been associated with the pulse power drive. Beam currents of kiloamperes and accelerating potentials of megavolts require peak power drives of gigawatts since no energy is stored in the structure. The marriage of liner accelerator technology and nonlinear magnetic compressors has produced some unique capabilities. It now appears possible to produce electron beams with average currents measured in amperes, peak currents in kiloamperes and gradients exceeding 1 MeV/meter, with power efficiencies approaching 50%. The nonlinear magnetic compression technology has replaced the spark gap drivers used on earlier accelerators with state-of-the-art all-solid-state SCR commutated compression chains. The reliability of these machines is now approaching 1010 shot MTBF. In the following paper we will briefly review the historical development of induction linear accelerators and then discuss the design considerations.

  12. ION ACCELERATOR

    DOEpatents

    Bell, J.S.

    1959-09-15

    An arrangement for the drift tubes in a linear accelerator is described whereby each drift tube acts to shield the particles from the influence of the accelerating field and focuses the particles passing through the tube. In one embodiment the drift tube is splii longitudinally into quadrants supported along the axis of the accelerator by webs from a yoke, the quadrants. webs, and yoke being of magnetic material. A magnetic focusing action is produced by energizing a winding on each web to set up a magnetic field between adjacent quadrants. In the other embodiment the quadrants are electrically insulated from each other and have opposite polarity voltages on adjacent quadrants to provide an electric focusing fleld for the particles, with the quadrants spaced sufficienily close enough to shield the particles within the tube from the accelerating electric field.

  13. Schooling in Times of Acceleration

    ERIC Educational Resources Information Center

    Buddeberg, Magdalena; Hornberg, Sabine

    2017-01-01

    Modern societies are characterised by forms of acceleration, which influence social processes. Sociologist Hartmut Rosa has systematised temporal structures by focusing on three categories of social acceleration: technical acceleration, acceleration of social change, and acceleration of the pace of life. All three processes of acceleration are…

  14. Impact Accelerations of Barefoot and Shod Running.

    PubMed

    Thompson, M; Seegmiller, J; McGowan, C P

    2016-05-01

    During the ground contact phase of running, the body's mass is rapidly decelerated resulting in forces that propagate through the musculoskeletal system. The repetitive attenuation of these impact forces is thought to contribute to overuse injuries. Modern running shoes are designed to reduce impact forces, with the goal to minimize running related overuse injuries. Additionally, the fore/mid foot strike pattern that is adopted by most individuals when running barefoot may reduce impact force transmission. The aim of the present study was to compare the effects of the barefoot running form (fore/mid foot strike & decreased stride length) and running shoes on running kinetics and impact accelerations. 10 healthy, physically active, heel strike runners ran in 3 conditions: shod, barefoot and barefoot while heel striking, during which 3-dimensional motion analysis, ground reaction force and accelerometer data were collected. Shod running was associated with increased ground reaction force and impact peak magnitudes, but decreased impact accelerations, suggesting that the midsole of running shoes helps to attenuate impact forces. Barefoot running exhibited a similar decrease in impact accelerations, as well as decreased impact peak magnitude, which appears to be due to a decrease in stride length and/or a more plantarflexed position at ground contact. © Georg Thieme Verlag KG Stuttgart · New York.

  15. Dynamic search and working memory in social recall.

    PubMed

    Hills, Thomas T; Pachur, Thorsten

    2012-01-01

    What are the mechanisms underlying search in social memory (e.g., remembering the people one knows)? Do the search mechanisms involve dynamic local-to-global transitions similar to semantic search, and are these transitions governed by the general control of attention, associated with working memory span? To find out, we asked participants to recall individuals from their personal social networks and measured each participant's working memory capacity. Additionally, participants provided social-category and contact-frequency information about the recalled individuals as well as information about the social proximity among the recalled individuals. On the basis of these data, we tested various computational models of memory search regarding their ability to account for the patterns in which participants recalled from social memory. Although recall patterns showed clustering based on social categories, models assuming dynamic transitions between representations cued by social proximity and frequency information predicted participants' recall patterns best-no additional explanatory power was gained from social-category information. Moreover, individual differences in the time between transitions were positively correlated with differences in working memory capacity. These results highlight the role of social proximity in structuring social memory and elucidate the role of working memory for maintaining search criteria during search within that structure.

  16. Accelerated increase in plant species richness on mountain summits is linked to warming.

    PubMed

    Steinbauer, Manuel J; Grytnes, John-Arvid; Jurasinski, Gerald; Kulonen, Aino; Lenoir, Jonathan; Pauli, Harald; Rixen, Christian; Winkler, Manuela; Bardy-Durchhalter, Manfred; Barni, Elena; Bjorkman, Anne D; Breiner, Frank T; Burg, Sarah; Czortek, Patryk; Dawes, Melissa A; Delimat, Anna; Dullinger, Stefan; Erschbamer, Brigitta; Felde, Vivian A; Fernández-Arberas, Olatz; Fossheim, Kjetil F; Gómez-García, Daniel; Georges, Damien; Grindrud, Erlend T; Haider, Sylvia; Haugum, Siri V; Henriksen, Hanne; Herreros, María J; Jaroszewicz, Bogdan; Jaroszynska, Francesca; Kanka, Robert; Kapfer, Jutta; Klanderud, Kari; Kühn, Ingolf; Lamprecht, Andrea; Matteodo, Magali; di Cella, Umberto Morra; Normand, Signe; Odland, Arvid; Olsen, Siri L; Palacio, Sara; Petey, Martina; Piscová, Veronika; Sedlakova, Blazena; Steinbauer, Klaus; Stöckli, Veronika; Svenning, Jens-Christian; Teppa, Guido; Theurillat, Jean-Paul; Vittoz, Pascal; Woodin, Sarah J; Zimmermann, Niklaus E; Wipf, Sonja

    2018-04-01

    Globally accelerating trends in societal development and human environmental impacts since the mid-twentieth century 1-7 are known as the Great Acceleration and have been discussed as a key indicator of the onset of the Anthropocene epoch 6 . While reports on ecological responses (for example, changes in species range or local extinctions) to the Great Acceleration are multiplying 8, 9 , it is unknown whether such biotic responses are undergoing a similar acceleration over time. This knowledge gap stems from the limited availability of time series data on biodiversity changes across large temporal and geographical extents. Here we use a dataset of repeated plant surveys from 302 mountain summits across Europe, spanning 145 years of observation, to assess the temporal trajectory of mountain biodiversity changes as a globally coherent imprint of the Anthropocene. We find a continent-wide acceleration in the rate of increase in plant species richness, with five times as much species enrichment between 2007 and 2016 as fifty years ago, between 1957 and 1966. This acceleration is strikingly synchronized with accelerated global warming and is not linked to alternative global change drivers. The accelerating increases in species richness on mountain summits across this broad spatial extent demonstrate that acceleration in climate-induced biotic change is occurring even in remote places on Earth, with potentially far-ranging consequences not only for biodiversity, but also for ecosystem functioning and services.

  17. Demeter, persephone, and the search for emergence in agent-based models.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    North, M. J.; Howe, T. R.; Collier, N. T.

    2006-01-01

    In Greek mythology, the earth goddess Demeter was unable to find her daughter Persephone after Persephone was abducted by Hades, the god of the underworld. Demeter is said to have embarked on a long and frustrating, but ultimately successful, search to find her daughter. Unfortunately, long and frustrating searches are not confined to Greek mythology. In modern times, agent-based modelers often face similar troubles when searching for agents that are to be to be connected to one another and when seeking appropriate target agents while defining agent behaviors. The result is a 'search for emergence' in that many emergent ormore » potentially emergent behaviors in agent-based models of complex adaptive systems either implicitly or explicitly require search functions. This paper considers a new nested querying approach to simplifying such agent-based modeling and multi-agent simulation search problems.« less

  18. Single particles accelerate final stages of capillary break-up

    NASA Astrophysics Data System (ADS)

    Lindner, Anke; Fiscina, Jorge Eduardo; Wagner, Christian

    2015-06-01

    Droplet formation of suspensions is present in many industrial and technological processes such as coating and food engineering. Whilst the finite-time singularity of the minimum neck diameter in capillary break-up of simple liquids can be described by well-known self-similarity solutions, the pinching of non-Brownian suspension depends in a complex way on the particle dynamics in the thinning thread. Here we focus on the very dilute regime where the filament contains only isolated beads to identify the physical mechanisms leading to the pronounced acceleration of the filament thinning observed. This accelerated regime is characterized by an asymmetric shape of the filament with an enhanced curvature that depends on the size and the spatial distribution of the particles within the capillary thread.

  19. ACCELERATION AND THE GIFTED.

    ERIC Educational Resources Information Center

    GIBSON, ARTHUR R.; STEPHANS, THOMAS M.

    ACCELERATION OF PUPILS AND SUBJECTS IS CONSIDERED A MEANS OF EDUCATING THE ACADEMICALLY GIFTED STUDENT. FIVE INTRODUCTORY ARTICLES PROVIDE A FRAMEWORK FOR THINKING ABOUT ACCELERATION. FIVE PROJECT REPORTS OF ACCELERATED PROGRAMS IN OHIO ARE INCLUDED. ACCELERATION IS NOW BEING REGARDED MORE FAVORABLY THAN FORMERLY, BECAUSE METHODS HAVE BEEN…

  20. Conventional and Accelerated-Solvent Extractions of Green Tea (Camellia sinensis) for Metabolomics-based Chemometrics

    PubMed Central

    Kellogg, Joshua J.; Wallace, Emily D.; Graf, Tyler N.; Oberlies, Nicholas H.; Cech, Nadja B.

    2018-01-01

    Metabolomics has emerged as an important analytical technique for multiple applications. The value of information obtained from metabolomics analysis depends on the degree to which the entire metabolome is present and the reliability of sample treatment to ensure reproducibility across the study. The purpose of this study was to compare methods of preparing complex botanical extract samples prior to metabolomics profiling. Two extraction methodologies, accelerated solvent extraction and a conventional solvent maceration, were compared using commercial green tea [Camellia sinensis (L.) Kuntze (Theaceae)] products as a test case. The accelerated solvent protocol was first evaluated to ascertain critical factors influencing extraction using a D-optimal experimental design study. The accelerated solvent and conventional extraction methods yielded similar metabolite profiles for the green tea samples studied. The accelerated solvent extraction yielded higher total amounts of extracted catechins, was more reproducible, and required less active bench time to prepare the samples. This study demonstrates the effectiveness of accelerated solvent as an efficient methodology for metabolomics studies. PMID:28787673