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Sample records for quantum database search

  1. An efficient quantum search engine on unsorted database

    NASA Astrophysics Data System (ADS)

    Lu, Songfeng; Zhang, Yingyu; Liu, Fang

    2013-10-01

    We consider the problem of finding one or more desired items out of an unsorted database. Patel has shown that if the database permits quantum queries, then mere digitization is sufficient for efficient search for one desired item. The algorithm, called factorized quantum search algorithm, presented by him can locate the desired item in an unsorted database using O() queries to factorized oracles. But the algorithm requires that all the attribute values must be distinct from each other. In this paper, we discuss how to make a database satisfy the requirements, and present a quantum search engine based on the algorithm. Our goal is achieved by introducing auxiliary files for the attribute values that are not distinct, and converting every complex query request into a sequence of calls to factorized quantum search algorithm. The query complexity of our algorithm is O() for most cases.

  2. Online Database Searching Workbook.

    ERIC Educational Resources Information Center

    Littlejohn, Alice C.; Parker, Joan M.

    Designed primarily for use by first-time searchers, this workbook provides an overview of online searching. Following a brief introduction which defines online searching, databases, and database producers, five steps in carrying out a successful search are described: (1) identifying the main concepts of the search statement; (2) selecting a…

  3. Quantum Search and Beyond

    DTIC Science & Technology

    2008-07-02

    solution of certain problems for which the communication needs do not dominate. A similar situation prevails in the quantum world. Quantum teleportation and...REPORT Quantum Search and Beyond 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: Ten years ago, the quantum search algorithm was designed to provide a way...P.O. Box 12211 Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS quantum searching - partial quantum searching, fixed-point quantum

  4. Quantum Search in Hilbert Space

    NASA Technical Reports Server (NTRS)

    Zak, Michail

    2003-01-01

    A proposed quantum-computing algorithm would perform a search for an item of information in a database stored in a Hilbert-space memory structure. The algorithm is intended to make it possible to search relatively quickly through a large database under conditions in which available computing resources would otherwise be considered inadequate to perform such a task. The algorithm would apply, more specifically, to a relational database in which information would be stored in a set of N complex orthonormal vectors, each of N dimensions (where N can be exponentially large). Each vector would constitute one row of a unitary matrix, from which one would derive the Hamiltonian operator (and hence the evolutionary operator) of a quantum system. In other words, all the stored information would be mapped onto a unitary operator acting on a quantum state that would represent the item of information to be retrieved. Then one could exploit quantum parallelism: one could pose all search queries simultaneously by performing a quantum measurement on the system. In so doing, one would effectively solve the search problem in one computational step. One could exploit the direct- and inner-product decomposability of the unitary matrix to make the dimensionality of the memory space exponentially large by use of only linear resources. However, inasmuch as the necessary preprocessing (the mapping of the stored information into a Hilbert space) could be exponentially expensive, the proposed algorithm would likely be most beneficial in applications in which the resources available for preprocessing were much greater than those available for searching.

  5. Relativistic quantum private database queries

    NASA Astrophysics Data System (ADS)

    Sun, Si-Jia; Yang, Yu-Guang; Zhang, Ming-Ou

    2015-04-01

    Recently, Jakobi et al. (Phys Rev A 83, 022301, 2011) suggested the first practical private database query protocol (J-protocol) based on the Scarani et al. (Phys Rev Lett 92, 057901, 2004) quantum key distribution protocol. Unfortunately, the J-protocol is just a cheat-sensitive private database query protocol. In this paper, we present an idealized relativistic quantum private database query protocol based on Minkowski causality and the properties of quantum information. Also, we prove that the protocol is secure in terms of the user security and the database security.

  6. Critically damped quantum search.

    PubMed

    Mizel, Ari

    2009-04-17

    Although measurement and unitary processes can accomplish any quantum evolution in principle, thinking in terms of dissipation and damping can be powerful. We propose a modification of Grover's algorithm in which the idea of damping plays a natural role. Remarkably, we find that there is a critical damping value that divides between the quantum O(sqrt[N]) and classical O(N) search regimes. In addition, by allowing the damping to vary in a fashion we describe, one obtains a fixed-point quantum search algorithm in which ignorance of the number of targets increases the number of oracle queries only by a factor of 1.5.

  7. Begin: Online Database Searching Now!

    ERIC Educational Resources Information Center

    Lodish, Erica K.

    1986-01-01

    Because of the increasing importance of online databases, school library media specialists are encouraged to introduce students to online searching. Four books that would help media specialists gain a basic background are reviewed and it is noted that although they are very technical, they can be adapted to individual needs. (EM)

  8. Fixed-point quantum search.

    PubMed

    Grover, Lov K

    2005-10-07

    The quantum search algorithm consists of an iterative sequence of selective inversions and diffusion type operations, as a result of which it is able to find a state with desired properties (target state) in an unsorted database of size N in only sqrt[N] queries. This is achieved by designing the iterative transformations in a way that each iteration results in a small rotation of the state vector in a two-dimensional Hilbert space that includes the target state; if we choose the right number of iterative steps, we will stop just at the target state. This Letter shows that by replacing the selective inversions by selective phase shifts of pi/3, the algorithm preferentially converges to the target state irrespective of the step size or number of iterations. This feature leads to robust search algorithms and also to new schemes for quantum control and error correction.

  9. Quantum Error Correction Protects Quantum Search Algorithms Against Decoherence.

    PubMed

    Botsinis, Panagiotis; Babar, Zunaira; Alanis, Dimitrios; Chandra, Daryus; Nguyen, Hung; Ng, Soon Xin; Hanzo, Lajos

    2016-12-07

    When quantum computing becomes a wide-spread commercial reality, Quantum Search Algorithms (QSA) and especially Grover's QSA will inevitably be one of their main applications, constituting their cornerstone. Most of the literature assumes that the quantum circuits are free from decoherence. Practically, decoherence will remain unavoidable as is the Gaussian noise of classic circuits imposed by the Brownian motion of electrons, hence it may have to be mitigated. In this contribution, we investigate the effect of quantum noise on the performance of QSAs, in terms of their success probability as a function of the database size to be searched, when decoherence is modelled by depolarizing channels' deleterious effects imposed on the quantum gates. Moreover, we employ quantum error correction codes for limiting the effects of quantum noise and for correcting quantum flips. More specifically, we demonstrate that, when we search for a single solution in a database having 4096 entries using Grover's QSA at an aggressive depolarizing probability of 10(-3), the success probability of the search is 0.22 when no quantum coding is used, which is improved to 0.96 when Steane's quantum error correction code is employed. Finally, apart from Steane's code, the employment of Quantum Bose-Chaudhuri-Hocquenghem (QBCH) codes is also considered.

  10. Quantum Error Correction Protects Quantum Search Algorithms Against Decoherence

    NASA Astrophysics Data System (ADS)

    Botsinis, Panagiotis; Babar, Zunaira; Alanis, Dimitrios; Chandra, Daryus; Nguyen, Hung; Ng, Soon Xin; Hanzo, Lajos

    2016-12-01

    When quantum computing becomes a wide-spread commercial reality, Quantum Search Algorithms (QSA) and especially Grover’s QSA will inevitably be one of their main applications, constituting their cornerstone. Most of the literature assumes that the quantum circuits are free from decoherence. Practically, decoherence will remain unavoidable as is the Gaussian noise of classic circuits imposed by the Brownian motion of electrons, hence it may have to be mitigated. In this contribution, we investigate the effect of quantum noise on the performance of QSAs, in terms of their success probability as a function of the database size to be searched, when decoherence is modelled by depolarizing channels’ deleterious effects imposed on the quantum gates. Moreover, we employ quantum error correction codes for limiting the effects of quantum noise and for correcting quantum flips. More specifically, we demonstrate that, when we search for a single solution in a database having 4096 entries using Grover’s QSA at an aggressive depolarizing probability of 10‑3, the success probability of the search is 0.22 when no quantum coding is used, which is improved to 0.96 when Steane’s quantum error correction code is employed. Finally, apart from Steane’s code, the employment of Quantum Bose-Chaudhuri-Hocquenghem (QBCH) codes is also considered.

  11. Quantum Error Correction Protects Quantum Search Algorithms Against Decoherence

    PubMed Central

    Botsinis, Panagiotis; Babar, Zunaira; Alanis, Dimitrios; Chandra, Daryus; Nguyen, Hung; Ng, Soon Xin; Hanzo, Lajos

    2016-01-01

    When quantum computing becomes a wide-spread commercial reality, Quantum Search Algorithms (QSA) and especially Grover’s QSA will inevitably be one of their main applications, constituting their cornerstone. Most of the literature assumes that the quantum circuits are free from decoherence. Practically, decoherence will remain unavoidable as is the Gaussian noise of classic circuits imposed by the Brownian motion of electrons, hence it may have to be mitigated. In this contribution, we investigate the effect of quantum noise on the performance of QSAs, in terms of their success probability as a function of the database size to be searched, when decoherence is modelled by depolarizing channels’ deleterious effects imposed on the quantum gates. Moreover, we employ quantum error correction codes for limiting the effects of quantum noise and for correcting quantum flips. More specifically, we demonstrate that, when we search for a single solution in a database having 4096 entries using Grover’s QSA at an aggressive depolarizing probability of 10−3, the success probability of the search is 0.22 when no quantum coding is used, which is improved to 0.96 when Steane’s quantum error correction code is employed. Finally, apart from Steane’s code, the employment of Quantum Bose-Chaudhuri-Hocquenghem (QBCH) codes is also considered. PMID:27924865

  12. Searching NCBI Databases Using Entrez.

    PubMed

    Gibney, Gretchen; Baxevanis, Andreas D

    2011-10-01

    One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two basic protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An alternate protocol builds upon the first basic protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The support protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

  13. Searching NCBI databases using Entrez.

    PubMed

    Baxevanis, Andreas D

    2008-12-01

    One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An Alternate Protocol builds upon the first Basic Protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The Support Protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

  14. Searching NCBI databases using Entrez.

    PubMed

    Gibney, Gretchen; Baxevanis, Andreas D

    2011-06-01

    One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two basic protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An alternate protocol builds upon the first basic protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The support protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

  15. Database Search Engines: Paradigms, Challenges and Solutions.

    PubMed

    Verheggen, Kenneth; Martens, Lennart; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

    2016-01-01

    The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engines is demonstrated using the freely available SearchGUI interface. This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact.

  16. Library Instruction and Online Database Searching.

    ERIC Educational Resources Information Center

    Mercado, Heidi

    1999-01-01

    Reviews changes in online database searching in academic libraries. Topics include librarians conducting all searches; the advent of end-user searching and the need for user instruction; compact disk technology; online public catalogs; the Internet; full text databases; electronic information literacy; user education and the remote library user;…

  17. Online Database Searching in Smaller Public Libraries.

    ERIC Educational Resources Information Center

    Roose, Tina

    1983-01-01

    Online database searching experiences of nine Illinois public libraries--Arlington Heights, Deerfield, Elk Grove Village, Evanston, Glenview, Northbrook, Schaumburg Township, Waukegan, Wilmette--are discussed, noting search costs, user charges, popular databases, library acquisition, interaction with users, and staff training. Three sources are…

  18. Using volume holograms to search digital databases

    NASA Astrophysics Data System (ADS)

    Burr, Geoffrey W.; Maltezos, George; Grawert, Felix; Kobras, Sebastian; Hanssen, Holger; Coufal, Hans J.

    2002-01-01

    Holographic data storage offers the potential for simultaneous search of an entire database by performing multiple optical correlations between stored data pages and a search argument. This content-addressable retrieval produces one analog correlation score for each stored volume hologram. We have previously developed fuzzy encoding techniques for this fast parallel search, and holographically searched a small database with high fidelity. We recently showed that such systems can be configured to produce true inner-products, and proposed an architecture in which massively-parallel searches could be implemented. However, the speed advantage over conventional electronic search provided by parallelism brings with it the possibility of erroneous search results, since these analog correlation scores are subject to various noise sources. We show that the fidelity of such an optical search depends not only on the usual holographic storage signal-to-noise factors (such as readout power, diffraction efficiency, and readout speed), but also on the particular database query being made. In effect, the presence of non-matching database records with nearly the same correlation score as the targeted matching records reduces the speed advantage of the parallel search. Thus for any given fidelity target, the performance improvement offered by a content-addressable holographic storage can vary from query to query even within the same database.

  19. 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.

  20. Searching gene and protein sequence databases.

    PubMed

    Barsalou, T; Brutlag, D L

    1991-01-01

    A large-scale effort to map and sequence the human genome is now under way. Crucial to the success of this research is a group of computer programs that analyze and compare data on molecular sequences. This article describes the classic algorithms for similarity searching and sequence alignment. Because good performance of these algorithms is critical to searching very large and growing databases, we analyze the running times of the algorithms and discuss recent improvements in this area.

  1. Efficient search and retrieval in biometric databases

    NASA Astrophysics Data System (ADS)

    Mhatre, Amit J.; Palla, Srinivas; Chikkerur, Sharat; Govindaraju, Venu

    2005-03-01

    Biometric identification has emerged as a reliable means of controlling access to both physical and virtual spaces. Fingerprints, face and voice biometrics are being increasingly used as alternatives to passwords, PINs and visual verification. In spite of the rapid proliferation of large-scale databases, the research has thus far been focused only on accuracy within small databases. In larger applications, response time and retrieval efficiency also become important in addition to accuracy. Unlike structured information such as text or numeric data that can be sorted, biometric data does not have any natural sorting order. Therefore indexing and binning of biometric databases represents a challenging problem. We present results using parallel combination of multiple biometrics to bin the database. Using hand geometry and signature features we show that the search space can be reduced to just 5% of the entire database.

  2. Multi-Database Searching in Forensic Psychology.

    ERIC Educational Resources Information Center

    Piotrowski, Chris; Perdue, Robert W.

    Traditional library skills have been augmented since the introduction of online computerized database services. Because of the complexity of the field, forensic psychology can benefit enormously from the application of comprehensive bibliographic search strategies. The study reported here demonstrated the bibliographic results obtained when a…

  3. Searching Across the International Space Station Databases

    NASA Technical Reports Server (NTRS)

    Maluf, David A.; McDermott, William J.; Smith, Ernest E.; Bell, David G.; Gurram, Mohana

    2007-01-01

    Data access in the enterprise generally requires us to combine data from different sources and different formats. It is advantageous thus to focus on the intersection of the knowledge across sources and domains; keeping irrelevant knowledge around only serves to make the integration more unwieldy and more complicated than necessary. A context search over multiple domain is proposed in this paper to use context sensitive queries to support disciplined manipulation of domain knowledge resources. The objective of a context search is to provide the capability for interrogating many domain knowledge resources, which are largely semantically disjoint. The search supports formally the tasks of selecting, combining, extending, specializing, and modifying components from a diverse set of domains. This paper demonstrates a new paradigm in composition of information for enterprise applications. In particular, it discusses an approach to achieving data integration across multiple sources, in a manner that does not require heavy investment in database and middleware maintenance. This lean approach to integration leads to cost-effectiveness and scalability of data integration with an underlying schemaless object-relational database management system. This highly scalable, information on demand system framework, called NX-Search, which is an implementation of an information system built on NETMARK. NETMARK is a flexible, high-throughput open database integration framework for managing, storing, and searching unstructured or semi-structured arbitrary XML and HTML used widely at the National Aeronautics Space Administration (NASA) and industry.

  4. Searching the NCBI databases using Entrez.

    PubMed

    Baxevanis, Andreas D

    2006-03-01

    One of the most widely-used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An Alternate Protocol builds upon the first Basic Protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The Support Protocol reviews how to save frequently-issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

  5. Searching the NCBI databases using Entrez.

    PubMed

    Baxevanis, Andreas D

    2006-11-01

    One of the most widely-used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An Alternate Protocol builds upon the first Basic Protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The Support Protocol reviews how to save frequently-issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

  6. Audio stream classification for multimedia database search

    NASA Astrophysics Data System (ADS)

    Artese, M.; Bianco, S.; Gagliardi, I.; Gasparini, F.

    2013-03-01

    Search and retrieval of huge archives of Multimedia data is a challenging task. A classification step is often used to reduce the number of entries on which to perform the subsequent search. In particular, when new entries of the database are continuously added, a fast classification based on simple threshold evaluation is desirable. In this work we present a CART-based (Classification And Regression Tree [1]) classification framework for audio streams belonging to multimedia databases. The database considered is the Archive of Ethnography and Social History (AESS) [2], which is mainly composed of popular songs and other audio records describing the popular traditions handed down generation by generation, such as traditional fairs, and customs. The peculiarities of this database are that it is continuously updated; the audio recordings are acquired in unconstrained environment; and for the non-expert human user is difficult to create the ground truth labels. In our experiments, half of all the available audio files have been randomly extracted and used as training set. The remaining ones have been used as test set. The classifier has been trained to distinguish among three different classes: speech, music, and song. All the audio files in the dataset have been previously manually labeled into the three classes above defined by domain experts.

  7. Multiparty Quantum Key Agreement Based on Quantum Search Algorithm

    PubMed Central

    Cao, Hao; Ma, Wenping

    2017-01-01

    Quantum key agreement is an important topic that the shared key must be negotiated equally by all participants, and any nontrivial subset of participants cannot fully determine the shared key. To date, the embed modes of subkey in all the previously proposed quantum key agreement protocols are based on either BB84 or entangled states. The research of the quantum key agreement protocol based on quantum search algorithms is still blank. In this paper, on the basis of investigating the properties of quantum search algorithms, we propose the first quantum key agreement protocol whose embed mode of subkey is based on a quantum search algorithm known as Grover’s algorithm. A novel example of protocols with 5 – party is presented. The efficiency analysis shows that our protocol is prior to existing MQKA protocols. Furthermore it is secure against both external attack and internal attacks. PMID:28332610

  8. Multiparty Quantum Key Agreement Based on Quantum Search Algorithm.

    PubMed

    Cao, Hao; Ma, Wenping

    2017-03-23

    Quantum key agreement is an important topic that the shared key must be negotiated equally by all participants, and any nontrivial subset of participants cannot fully determine the shared key. To date, the embed modes of subkey in all the previously proposed quantum key agreement protocols are based on either BB84 or entangled states. The research of the quantum key agreement protocol based on quantum search algorithms is still blank. In this paper, on the basis of investigating the properties of quantum search algorithms, we propose the first quantum key agreement protocol whose embed mode of subkey is based on a quantum search algorithm known as Grover's algorithm. A novel example of protocols with 5 - party is presented. The efficiency analysis shows that our protocol is prior to existing MQKA protocols. Furthermore it is secure against both external attack and internal attacks.

  9. Multiparty Quantum Key Agreement Based on Quantum Search Algorithm

    NASA Astrophysics Data System (ADS)

    Cao, Hao; Ma, Wenping

    2017-03-01

    Quantum key agreement is an important topic that the shared key must be negotiated equally by all participants, and any nontrivial subset of participants cannot fully determine the shared key. To date, the embed modes of subkey in all the previously proposed quantum key agreement protocols are based on either BB84 or entangled states. The research of the quantum key agreement protocol based on quantum search algorithms is still blank. In this paper, on the basis of investigating the properties of quantum search algorithms, we propose the first quantum key agreement protocol whose embed mode of subkey is based on a quantum search algorithm known as Grover’s algorithm. A novel example of protocols with 5 – party is presented. The efficiency analysis shows that our protocol is prior to existing MQKA protocols. Furthermore it is secure against both external attack and internal attacks.

  10. Quantum Private Comparison Based on Quantum Search Algorithm

    NASA Astrophysics Data System (ADS)

    Zhang, Wei-Wei; Li, Dan; Song, Ting-Ting; Li, Yan-Bing

    2013-05-01

    We propose two quantum private comparison protocols based on quantum search algorithm with the help of a semi-honest third party. Our protocols utilize the properties of quantum search algorithm, the unitary operations, and the single-particle measurements. The security of our protocols is discussed with respect to both the outsider attack and the participant attack. There is no information leaked about the private information and the comparison result, even the third party cannot know these information.

  11. Two Quantum Direct Communication Protocols Based on Quantum Search Algorithm

    NASA Astrophysics Data System (ADS)

    Xu, Shu-Jiang; Chen, Xiu-Bo; Wang, Lian-Hai; Niu, Xin-Xin; Yang, Yi-Xian

    2015-07-01

    Based on the properties of two-qubit Grover's quantum search algorithm, we propose two quantum direct communication protocols, including a deterministic secure quantum communication and a quantum secure direct communication protocol. Secret messages can be directly sent from the sender to the receiver by using two-qubit unitary operations and the single photon measurement with one of the proposed protocols. Theoretical analysis shows that the security of the proposed protocols can be highly ensured.

  12. WAIS Searching of the Current Contents Database

    NASA Astrophysics Data System (ADS)

    Banholzer, P.; Grabenstein, M. E.

    The Homer E. Newell Memorial Library of NASA's Goddard Space Flight Center is developing capabilities to permit Goddard personnel to access electronic resources of the Library via the Internet. The Library's support services contractor, Maxima Corporation, and their subcontractor, SANAD Support Technologies have recently developed a World Wide Web Home Page (http://www-library.gsfc.nasa.gov) to provide the primary means of access. The first searchable database to be made available through the HomePage to Goddard employees is Current Contents, from the Institute for Scientific Information (ISI). The initial implementation includes coverage of articles from the last few months of 1992 to present. These records are augmented with abstracts and references, and often are more robust than equivalent records in bibliographic databases that currently serve the astronomical community. Maxima/SANAD selected Wais Incorporated's WAIS product with which to build the interface to Current Contents. This system allows access from Macintosh, IBM PC, and Unix hosts, which is an important feature for Goddard's multiplatform environment. The forms interface is structured to allow both fielded (author, article title, journal name, id number, keyword, subject term, and citation) and unfielded WAIS searches. The system allows a user to: Retrieve individual journal article records. Retrieve Table of Contents of specific issues of journals. Connect to articles with similar subject terms or keywords. Connect to other issues of the same journal in the same year. Browse journal issues from an alphabetical list of indexed journal names.

  13. The Database Dilemma: Online Search Strategies in Nursing.

    ERIC Educational Resources Information Center

    Fried, Ava K.; And Others

    1989-01-01

    Describes a study that compared the coverage of the nursing profession, subject heading specificity, and ease of retrieval of the MEDLINE and Nursing & Allied Health (CINAHL) online databases. The strengths and weaknesses of each database are discussed and hints for searching on both databases are provided. (four references) (CLB)

  14. Online Bibliographic Searching in the Humanities Databases: An Introduction.

    ERIC Educational Resources Information Center

    Suresh, Raghini S.

    Numerous easily accessible databases cover almost every subject area in the humanities. The principal database resources in the humanities are described. There are two major database vendors for humanities information: BRS (Bibliographic Retrieval Services) and DIALOG Information Services, Inc. As an introduction to online searching, this article…

  15. Modernizing quantum annealing using local searches

    NASA Astrophysics Data System (ADS)

    Chancellor, Nicholas

    2017-02-01

    I describe how real quantum annealers may be used to perform local (in state space) searches around specified states, rather than the global searches traditionally implemented in the quantum annealing algorithm (QAA). Such protocols will have numerous advantages over simple quantum annealing. By using such searches the effect of problem mis-specification can be reduced, as only energy differences between the searched states will be relevant. The QAA is an analogue of simulated annealing, a classical numerical technique which has now been superseded. Hence, I explore two strategies to use an annealer in a way which takes advantage of modern classical optimization algorithms. Specifically, I show how sequential calls to quantum annealers can be used to construct analogues of population annealing and parallel tempering which use quantum searches as subroutines. The techniques given here can be applied not only to optimization, but also to sampling. I examine the feasibility of these protocols on real devices and note that implementing such protocols should require minimal if any change to the current design of the flux qubit-based annealers by D-Wave Systems Inc. I further provide proof-of-principle numerical experiments based on quantum Monte Carlo that demonstrate simple examples of the discussed techniques.

  16. Quantum walk search through potential barriers

    NASA Astrophysics Data System (ADS)

    Wong, Thomas G.

    2016-12-01

    An ideal quantum walk transitions from one vertex to another with perfect fidelity, but in physical systems, the particle may be hindered by potential energy barriers. Then the particle has some amplitude of tunneling through the barriers, and some amplitude of staying put. We investigate the algorithmic consequence of such barriers for the quantum walk formulation of Grover’s algorithm. We prove that the failure amplitude must scale as O(1/\\sqrt{N}) for search to retain its quantum O(\\sqrt{N}) runtime; otherwise, it searches in classical O(N) time. Thus searching larger ‘databases’ requires increasingly reliable hop operations or error correction. This condition holds for both discrete- and continuous-time quantum walks.

  17. Search for New Quantum Algorithms

    DTIC Science & Technology

    2006-05-01

    Topological computing for beginners, (slide presentation), Lecture Notes for Chapter 9 - Physics 219 - Quantum Computation. (http...14 II.A.8. A QHS algorithm for Feynman integrals ......................................................18 II.A.9. Non-abelian QHS algorithms -- A...idea is that NOT all environmentally entangling transformations are equally likely. In particular, for spatially separated physical quantum

  18. Multiple Database Searching: Techniques and Pitfalls

    ERIC Educational Resources Information Center

    Hawkins, Donald T.

    1978-01-01

    Problems involved in searching multiple data bases are discussed including indexing differences, overlap among data bases, variant spellings, and elimination of duplicate items from search output. Discussion focuses on CA Condensates, Inspec, and Metadex data bases. (J PF)

  19. Searching the ASRS Database Using QUORUM Keyword Search, Phrase Search, Phrase Generation, and Phrase Discovery

    NASA Technical Reports Server (NTRS)

    McGreevy, Michael W.; Connors, Mary M. (Technical Monitor)

    2001-01-01

    To support Search Requests and Quick Responses at the Aviation Safety Reporting System (ASRS), four new QUORUM methods have been developed: keyword search, phrase search, phrase generation, and phrase discovery. These methods build upon the core QUORUM methods of text analysis, modeling, and relevance-ranking. QUORUM keyword search retrieves ASRS incident narratives that contain one or more user-specified keywords in typical or selected contexts, and ranks the narratives on their relevance to the keywords in context. QUORUM phrase search retrieves narratives that contain one or more user-specified phrases, and ranks the narratives on their relevance to the phrases. QUORUM phrase generation produces a list of phrases from the ASRS database that contain a user-specified word or phrase. QUORUM phrase discovery finds phrases that are related to topics of interest. Phrase generation and phrase discovery are particularly useful for finding query phrases for input to QUORUM phrase search. The presentation of the new QUORUM methods includes: a brief review of the underlying core QUORUM methods; an overview of the new methods; numerous, concrete examples of ASRS database searches using the new methods; discussion of related methods; and, in the appendices, detailed descriptions of the new methods.

  20. Adiabatic Quantum Search in Open Systems.

    PubMed

    Wild, Dominik S; Gopalakrishnan, Sarang; Knap, Michael; Yao, Norman Y; Lukin, Mikhail D

    2016-10-07

    Adiabatic quantum algorithms represent a promising approach to universal quantum computation. In isolated systems, a key limitation to such algorithms is the presence of avoided level crossings, where gaps become extremely small. In open quantum systems, the fundamental robustness of adiabatic algorithms remains unresolved. Here, we study the dynamics near an avoided level crossing associated with the adiabatic quantum search algorithm, when the system is coupled to a generic environment. At zero temperature, we find that the algorithm remains scalable provided the noise spectral density of the environment decays sufficiently fast at low frequencies. By contrast, higher order scattering processes render the algorithm inefficient at any finite temperature regardless of the spectral density, implying that no quantum speedup can be achieved. Extensions and implications for other adiabatic quantum algorithms will be discussed.

  1. Adiabatic Quantum Search in Open Systems

    NASA Astrophysics Data System (ADS)

    Wild, Dominik S.; Gopalakrishnan, Sarang; Knap, Michael; Yao, Norman Y.; Lukin, Mikhail D.

    2016-10-01

    Adiabatic quantum algorithms represent a promising approach to universal quantum computation. In isolated systems, a key limitation to such algorithms is the presence of avoided level crossings, where gaps become extremely small. In open quantum systems, the fundamental robustness of adiabatic algorithms remains unresolved. Here, we study the dynamics near an avoided level crossing associated with the adiabatic quantum search algorithm, when the system is coupled to a generic environment. At zero temperature, we find that the algorithm remains scalable provided the noise spectral density of the environment decays sufficiently fast at low frequencies. By contrast, higher order scattering processes render the algorithm inefficient at any finite temperature regardless of the spectral density, implying that no quantum speedup can be achieved. Extensions and implications for other adiabatic quantum algorithms will be discussed.

  2. Quantum search algorithms on a regular lattice

    SciTech Connect

    Hein, Birgit; Tanner, Gregor

    2010-07-15

    Quantum algorithms for searching for one or more marked items on a d-dimensional lattice provide an extension of Grover's search algorithm including a spatial component. We demonstrate that these lattice search algorithms can be viewed in terms of the level dynamics near an avoided crossing of a one-parameter family of quantum random walks. We give approximations for both the level splitting at the avoided crossing and the effectively two-dimensional subspace of the full Hilbert space spanning the level crossing. This makes it possible to give the leading order behavior for the search time and the localization probability in the limit of large lattice size including the leading order coefficients. For d=2 and d=3, these coefficients are calculated explicitly. Closed form expressions are given for higher dimensions.

  3. Is Library Database Searching a Language Learning Activity?

    ERIC Educational Resources Information Center

    Bordonaro, Karen

    2010-01-01

    This study explores how non-native speakers of English think of words to enter into library databases when they begin the process of searching for information in English. At issue is whether or not language learning takes place when these students use library databases. Language learning in this study refers to the use of strategies employed by…

  4. Chemical Substructure Searching: Comparing Three Commercially Available Databases.

    ERIC Educational Resources Information Center

    Wagner, A. Ben

    1986-01-01

    Compares the differences in coverage and utility of three substructure databases--Chemical Abstracts, Index Chemicus, and Chemical Information System's Nomenclature Search System. The differences between Chemical Abstracts with two different vendors--STN International and Questel--are described and a summary guide for choosing between databases is…

  5. Searching the PASCAL database - A user's perspective

    NASA Technical Reports Server (NTRS)

    Jack, Robert F.

    1989-01-01

    The operation of PASCAL, a bibliographic data base covering broad subject areas in science and technology, is discussed. The data base includes information from about 1973 to the present, including topics in engineering, chemistry, physics, earth science, environmental science, biology, psychology, and medicine. Data from 1986 to the present may be searched using DIALOG. The procedures and classification codes for searching PASCAL are presented. Examples of citations retrieved from the data base are given and suggestions are made concerning when to use PASCAL.

  6. Exhaustive Database Searching for Amino Acid Mutations in Proteomes

    SciTech Connect

    Hyatt, Philip Douglas; Pan, Chongle

    2012-01-01

    Amino acid mutations in proteins can be found by searching tandem mass spectra acquired in shotgun proteomics experiments against protein sequences predicted from genomes. Traditionally, unconstrained searches for amino acid mutations have been accomplished by using a sequence tagging approach that combines de novo sequencing with database searching. However, this approach is limited by the performance of de novo sequencing. The Sipros algorithm v2.0 was developed to perform unconstrained database searching using high-resolution tandem mass spectra by exhaustively enumerating all single non-isobaric mutations for every residue in a protein database. The performance of Sipros for amino acid mutation identification exceeded that of an established sequence tagging algorithm, Inspect, based on benchmarking results from a Rhodopseudomonas palustris proteomics dataset. To demonstrate the viability of the algorithm for meta-proteomics, Sipros was used to identify amino acid mutations in a natural microbial community in acid mine drainage.

  7. Private database queries based on counterfactual quantum key distribution

    NASA Astrophysics Data System (ADS)

    Zhang, Jia-Li; Guo, Fen-Zhuo; Gao, Fei; Liu, Bin; Wen, Qiao-Yan

    2013-08-01

    Based on the fundamental concept of quantum counterfactuality, we propose a protocol to achieve quantum private database queries, which is a theoretical study of how counterfactuality can be employed beyond counterfactual quantum key distribution (QKD). By adding crucial detecting apparatus to the device of QKD, the privacy of both the distrustful user and the database owner can be guaranteed. Furthermore, the proposed private-database-query protocol makes full use of the low efficiency in the counterfactual QKD, and by adjusting the relevant parameters, the protocol obtains excellent flexibility and extensibility.

  8. Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

    PubMed

    Deutsch, Eric W; Sun, Zhi; Campbell, David S; Binz, Pierre-Alain; Farrah, Terry; Shteynberg, David; Mendoza, Luis; Omenn, Gilbert S; Moritz, Robert L

    2016-11-04

    The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances-a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ∼20,000 primary isoforms plus contaminants to a very large database that includes almost all nonredundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the

  9. The Effects of Search Tool Type and Cognitive Style on Performance during Hypermedia Database Searches.

    ERIC Educational Resources Information Center

    Leader, Lars F.; Klein, James D.

    1996-01-01

    Describes a study that investigated the effects of search tools and learner cognitive styles on performance in searches for information within a hypermedia database. Students in a university English-as-a-Second-Language program were assigned to one of four treatment groups, and results show a significant interaction between search tool and…

  10. Searching Harvard Business Review Online. . . Lessons in Searching a Full Text Database.

    ERIC Educational Resources Information Center

    Tenopir, Carol

    1985-01-01

    This article examines the Harvard Business Review Online (HBRO) database (bibliographic description fields, abstracts, extracted information, full text, subject descriptors) and reports on 31 sample HBRO searches conducted in Bibliographic Retrieval Services to test differences between searching full text and searching bibliographic record. Sample…

  11. Quantum search simulation with Wolfram Mathematica

    NASA Astrophysics Data System (ADS)

    Prokopenya, Alexander N.

    2016-09-01

    We consider Grover's algorithm of quantum search for one or several integers out of N = 2n, where n is a number of quantum bits in the memory register. There is a black-box or subroutine containing information about hidden integers and it can easily recognize these integers but we do not know which ones out of N they are. To find the hidden items we can do no better with a classical computer than to apply the subroutine repeatedly to all possible integers until we hit on the special one and in the worst case we have to repeat this procedure N times. We have analyzed the Grover algorithm carefully and showed that it enables to speed up this search quadratically, although its realization requires to know a number of hidden items. The lower bound for the probability of successful solving the search problem has been obtained. The validity of the results was demonstrated by simulation of the Grover search algorithm using the package QuantumCircuit written in the Wolfram Mathematica language.

  12. Coherence depletion in the Grover quantum search algorithm

    NASA Astrophysics Data System (ADS)

    Shi, Hai-Long; Liu, Si-Yuan; Wang, Xiao-Hui; Yang, Wen-Li; Yang, Zhan-Ying; Fan, Heng

    2017-03-01

    We investigate the role of quantum coherence depletion (QCD) in the Grover search algorithm (GA) by using several typical measures of quantum coherence and quantum correlations. By using the relative entropy of coherence measure (Cr), we show that the success probability depends on the QCD. The same phenomenon is also found by using the l1 norm of coherence measure (Cl1).In the limit case, the cost performance is defined to characterize the behavior about QCD in enhancing the success probability of GA, which is only related to the number of searcher items and the scale of the database, regardless of using Cr or Cl 1. In the generalized Grover search algorithm (GGA), the QCD for a class of states increases with the required optimal measurement time. In comparison, the quantification of other quantum correlations in GA, such as pairwise entanglement, multipartite entanglement, pairwise discord, and genuine multipartite discord, cannot be directly related to the success probability or the optimal measurement time. Additionally, we do not detect pairwise nonlocality or genuine tripartite nonlocality in GA since Clauser-Horne-Shimony-Holt inequality and Svetlichny's inequality are not violated.

  13. Fixed-point adiabatic quantum search

    NASA Astrophysics Data System (ADS)

    Dalzell, Alexander M.; Yoder, Theodore J.; Chuang, Isaac L.

    2017-01-01

    Fixed-point quantum search algorithms succeed at finding one of M target items among N total items even when the run time of the algorithm is longer than necessary. While the famous Grover's algorithm can search quadratically faster than a classical computer, it lacks the fixed-point property—the fraction of target items must be known precisely to know when to terminate the algorithm. Recently, Yoder, Low, and Chuang [Phys. Rev. Lett. 113, 210501 (2014), 10.1103/PhysRevLett.113.210501] gave an optimal gate-model search algorithm with the fixed-point property. Previously, it had been discovered by Roland and Cerf [Phys. Rev. A 65, 042308 (2002), 10.1103/PhysRevA.65.042308] that an adiabatic quantum algorithm, operating by continuously varying a Hamiltonian, can reproduce the quadratic speedup of gate-model Grover search. We ask, can an adiabatic algorithm also reproduce the fixed-point property? We show that the answer depends on what interpolation schedule is used, so as in the gate model, there are both fixed-point and non-fixed-point versions of adiabatic search, only some of which attain the quadratic quantum speedup. Guided by geometric intuition on the Bloch sphere, we rigorously justify our claims with an explicit upper bound on the error in the adiabatic approximation. We also show that the fixed-point adiabatic search algorithm can be simulated in the gate model with neither loss of the quadratic Grover speedup nor of the fixed-point property. Finally, we discuss natural uses of fixed-point algorithms such as preparation of a relatively prime state and oblivious amplitude amplification.

  14. Forensic utilization of familial searches in DNA databases.

    PubMed

    Gershaw, Cassandra J; Schweighardt, Andrew J; Rourke, Linda C; Wallace, Margaret M

    2011-01-01

    DNA evidence is widely recognized as an invaluable tool in the process of investigation and identification, as well as one of the most sought after types of evidence for presentation to a jury. In the United States, the development of state and federal DNA databases has greatly impacted the forensic community by creating an efficient, searchable system that can be used to eliminate or include suspects in an investigation based on matching DNA profiles - the profile already in the database to the profile of the unknown sample in evidence. Recent changes in legislation have begun to allow for the possibility to expand the parameters of DNA database searches, taking into account the possibility of familial searches. This article discusses prospective positive outcomes of utilizing familial DNA searches and acknowledges potential negative outcomes, thereby presenting both sides of this very complicated, rapidly evolving situation.

  15. Complementary use of the SciSearch database for improved biomedical information searching.

    PubMed Central

    Brown, C M

    1998-01-01

    The use of at least two complementary online biomedical databases is generally considered critical for biomedical scientists seeking to keep fully abreast of recent research developments as well as to retrieve the highest number of relevant citations possible. Although the National Library of Medicine's MEDLINE is usually the database of choice, this paper illustrates the benefits of using another database, the Institute for Scientific Information's SciSearch, when conducting a biomedical information search. When a simple query about red wine consumption and coronary artery disease was posed simultaneously in both MEDLINE and SciSearch, a greater number of relevant citations were retrieved through SciSearch. This paper also provides suggestions for carrying out a comprehensive biomedical literature search in a rapid and efficient manner by using SciSearch in conjunction with MEDLINE. PMID:9549014

  16. Molecule database framework: a framework for creating database applications with chemical structure search capability

    PubMed Central

    2013-01-01

    Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was

  17. The LAILAPS search engine: relevance ranking in life science databases.

    PubMed

    Lange, Matthias; Spies, Karl; Bargsten, Joachim; Haberhauer, Gregor; Klapperstück, Matthias; Leps, Michael; Weinel, Christian; Wünschiers, Röbbe; Weissbach, Mandy; Stein, Jens; Scholz, Uwe

    2010-01-15

    Search engines and retrieval systems are popular tools at a life science desktop. The manual inspection of hundreds of database entries, that reflect a life science concept or fact, is a time intensive daily work. Hereby, not the number of query results matters, but the relevance does. In this paper, we present the LAILAPS search engine for life science databases. The concept is to combine a novel feature model for relevance ranking, a machine learning approach to model user relevance profiles, ranking improvement by user feedback tracking and an intuitive and slim web user interface, that estimates relevance rank by tracking user interactions. Queries are formulated as simple keyword lists and will be expanded by synonyms. Supporting a flexible text index and a simple data import format, LAILAPS can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. With a set of features, extracted from each database hit in combination with user relevance preferences, a neural network predicts user specific relevance scores. Using expert knowledge as training data for a predefined neural network or using users own relevance training sets, a reliable relevance ranking of database hits has been implemented. In this paper, we present the LAILAPS system, the concepts, benchmarks and use cases. LAILAPS is public available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.

  18. Content-Based Search on a Database of Geometric Models: Identifying Objects of Similar Shape

    SciTech Connect

    XAVIER, PATRICK G.; HENRY, TYSON R.; LAFARGE, ROBERT A.; MEIRANS, LILITA; RAY, LAWRENCE P.

    2001-11-01

    The Geometric Search Engine is a software system for storing and searching a database of geometric models. The database maybe searched for modeled objects similar in shape to a target model supplied by the user. The database models are generally from CAD models while the target model may be either a CAD model or a model generated from range data collected from a physical object. This document describes key generation, database layout, and search of the database.

  19. Generalized Jaynes-Cummings model as a quantum search algorithm

    SciTech Connect

    Romanelli, A.

    2009-07-15

    We propose a continuous time quantum search algorithm using a generalization of the Jaynes-Cummings model. In this model the states of the atom are the elements among which the algorithm realizes the search, exciting resonances between the initial and the searched states. This algorithm behaves like Grover's algorithm; the optimal search time is proportional to the square root of the size of the search set and the probability to find the searched state oscillates periodically in time. In this frame, it is possible to reinterpret the usual Jaynes-Cummings model as a trivial case of the quantum search algorithm.

  20. Are Bibliographic Management Software Search Interfaces Reliable?: A Comparison between Search Results Obtained Using Database Interfaces and the EndNote Online Search Function

    ERIC Educational Resources Information Center

    Fitzgibbons, Megan; Meert, Deborah

    2010-01-01

    The use of bibliographic management software and its internal search interfaces is now pervasive among researchers. This study compares the results between searches conducted in academic databases' search interfaces versus the EndNote search interface. The results show mixed search reliability, depending on the database and type of search…

  1. Feature selection in validating mass spectrometry database search results.

    PubMed

    Fang, Jianwen; Dong, Yinghua; Williams, Todd D; Lushington, Gerald H

    2008-02-01

    Tandem mass spectrometry (MS/MS) combined with protein database searching has been widely used in protein identification. A validation procedure is generally required to reduce the number of false positives. Advanced tools using statistical and machine learning approaches may provide faster and more accurate validation than manual inspection and empirical filtering criteria. In this study, we use two feature selection algorithms based on random forest and support vector machine to identify peptide properties that can be used to improve validation models. We demonstrate that an improved model based on an optimized set of features reduces the number of false positives by 58% relative to the model which used only search engine scores, at the same sensitivity score of 0.8. In addition, we develop classification models based on the physicochemical properties and protein sequence environment of these peptides without using search engine scores. The performance of the best model based on the support vector machine algorithm is at 0.8 AUC, 0.78 accuracy, and 0.7 specificity, suggesting a reasonably accurate classification. The identified properties important to fragmentation and ionization can be either used in independent validation tools or incorporated into peptide sequencing and database search algorithms to improve existing software programs.

  2. Enriching Great Britain's National Landslide Database by searching newspaper archives

    NASA Astrophysics Data System (ADS)

    Taylor, Faith E.; Malamud, Bruce D.; Freeborough, Katy; Demeritt, David

    2015-11-01

    Our understanding of where landslide hazard and impact will be greatest is largely based on our knowledge of past events. Here, we present a method to supplement existing records of landslides in Great Britain by searching an electronic archive of regional newspapers. In Great Britain, the British Geological Survey (BGS) is responsible for updating and maintaining records of landslide events and their impacts in the National Landslide Database (NLD). The NLD contains records of more than 16,500 landslide events in Great Britain. Data sources for the NLD include field surveys, academic articles, grey literature, news, public reports and, since 2012, social media. We aim to supplement the richness of the NLD by (i) identifying additional landslide events, (ii) acting as an additional source of confirmation of events existing in the NLD and (iii) adding more detail to existing database entries. This is done by systematically searching the Nexis UK digital archive of 568 regional newspapers published in the UK. In this paper, we construct a robust Boolean search criterion by experimenting with landslide terminology for four training periods. We then apply this search to all articles published in 2006 and 2012. This resulted in the addition of 111 records of landslide events to the NLD over the 2 years investigated (2006 and 2012). We also find that we were able to obtain information about landslide impact for 60-90% of landslide events identified from newspaper articles. Spatial and temporal patterns of additional landslides identified from newspaper articles are broadly in line with those existing in the NLD, confirming that the NLD is a representative sample of landsliding in Great Britain. This method could now be applied to more time periods and/or other hazards to add richness to databases and thus improve our ability to forecast future events based on records of past events.

  3. Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses.

    PubMed

    Park, Heejin; Bae, Junwoo; Kim, Hyunwoo; Kim, Sangok; Kim, Hokeun; Mun, Dong-Gi; Joh, Yoonsung; Lee, Wonyeop; Chae, Sehyun; Lee, Sanghyuk; Kim, Hark Kyun; Hwang, Daehee; Lee, Sang-Won; Paek, Eunok

    2014-12-01

    In proteogenomic analysis, construction of a compact, customized database from mRNA-seq data and a sensitive search of both reference and customized databases are essential to accurately determine protein abundances and structural variations at the protein level. However, these tasks have not been systematically explored, but rather performed in an ad-hoc fashion. Here, we present an effective method for constructing a compact database containing comprehensive sequences of sample-specific variants--single nucleotide variants, insertions/deletions, and stop-codon mutations derived from Exome-seq and RNA-seq data. It, however, occupies less space by storing variant peptides, not variant proteins. We also present an efficient search method for both customized and reference databases. The separate searches of the two databases increase the search time, and a unified search is less sensitive to identify variant peptides due to the smaller size of the customized database, compared to the reference database, in the target-decoy setting. Our method searches the unified database once, but performs target-decoy validations separately. Experimental results show that our approach is as fast as the unified search and as sensitive as the separate searches. Our customized database includes mutation information in the headers of variant peptides, thereby facilitating the inspection of peptide-spectrum matches.

  4. Fast and accurate database searches with MS-GF+Percolator.

    PubMed

    Granholm, Viktor; Kim, Sangtae; Navarro, José C F; Sjölund, Erik; Smith, Richard D; Käll, Lukas

    2014-02-07

    One can interpret fragmentation spectra stemming from peptides in mass-spectrometry-based proteomics experiments using so-called database search engines. Frequently, one also runs post-processors such as Percolator to assess the confidence, infer unique peptides, and increase the number of identifications. A recent search engine, MS-GF+, has shown promising results, due to a new and efficient scoring algorithm. However, MS-GF+ provides few statistical estimates about the peptide-spectrum matches, hence limiting the biological interpretation. Here, we enabled Percolator processing for MS-GF+ output and observed an increased number of identified peptides for a wide variety of data sets. In addition, Percolator directly reports p values and false discovery rate estimates, such as q values and posterior error probabilities, for peptide-spectrum matches, peptides, and proteins, functions that are useful for the whole proteomics community.

  5. Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search.

    PubMed

    Shortreed, Michael R; Wenger, Craig D; Frey, Brian L; Sheynkman, Gloria M; Scalf, Mark; Keller, Mark P; Attie, Alan D; Smith, Lloyd M

    2015-11-06

    Bottom-up proteomics database search algorithms used for peptide identification cannot comprehensively identify post-translational modifications (PTMs) in a single-pass because of high false discovery rates (FDRs). A new approach to database searching enables global PTM (G-PTM) identification by exclusively looking for curated PTMs, thereby avoiding the FDR penalty experienced during conventional variable modification searches. We identified over 2200 unique, high-confidence modified peptides comprising 26 different PTM types in a single-pass database search.

  6. The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.

    PubMed

    Cherry, J Michael

    2015-12-02

    At the core of the Saccharomyces Genome Database (SGD) are chromosomal features that encode a product. These include protein-coding genes and major noncoding RNA genes, such as tRNA and rRNA genes. The basic entry point into SGD is a gene or open-reading frame name that leads directly to the locus summary information page. A keyword describing function, phenotype, selective condition, or text from abstracts will also provide a door into the SGD. A DNA or protein sequence can be used to identify a gene or a chromosomal region using BLAST. Protein and DNA sequence identifiers, PubMed and NCBI IDs, author names, and function terms are also valid entry points. The information in SGD has been gathered and is maintained by a group of scientific biocurators and software developers who are devoted to providing researchers with up-to-date information from the published literature, connections to all the major research resources, and tools that allow the data to be explored. All the collected information cannot be represented or summarized for every possible question; therefore, it is necessary to be able to search the structured data in the database. This protocol describes the YeastMine tool, which provides an advanced search capability via an interactive tool. The SGD also archives results from microarray expression experiments, and a strategy designed to explore these data using the SPELL (Serial Pattern of Expression Levels Locator) tool is provided.

  7. Grover's search algorithm with an entangled database state

    NASA Astrophysics Data System (ADS)

    Alsing, Paul M.; McDonald, Nathan

    2011-05-01

    Grover's oracle based unstructured search algorithm is often stated as "given a phone number in a directory, find the associated name." More formally, the problem can be stated as "given as input a unitary black box Uf for computing an unknown function f:{0,1}n ->{0,1}find x=x0 an element of {0,1}n such that f(x0) =1, (and zero otherwise). The crucial role of the externally supplied oracle Uf (whose inner workings are unknown to the user) is to change the sign of the solution 0 x , while leaving all other states unaltered. Thus, Uf depends on the desired solution x0. This paper examines an amplitude amplification algorithm in which the user encodes the directory (e.g. names and telephone numbers) into an entangled database state, which at a later time can be queried on one supplied component entry (e.g. a given phone number t0) to find the other associated unknown component (e.g. name x0). For N=2n names x with N associated phone numbers t , performing amplitude amplification on a subspace of size N of the total space of size N2 produces the desired state 0 0 x t in √N steps. We discuss how and why sequential (though not concurrent parallel) searches can be performed on multiple database states. Finally, we show how this procedure can be generalized to databases with more than two correlated lists (e.g. x t s r ...).

  8. Accelerating chemical database searching using graphics processing units.

    PubMed

    Liu, Pu; Agrafiotis, Dimitris K; Rassokhin, Dmitrii N; Yang, Eric

    2011-08-22

    The utility of chemoinformatics systems depends on the accurate computer representation and efficient manipulation of chemical compounds. In such systems, a small molecule is often digitized as a large fingerprint vector, where each element indicates the presence/absence or the number of occurrences of a particular structural feature. Since in theory the number of unique features can be exceedingly large, these fingerprint vectors are usually folded into much shorter ones using hashing and modulo operations, allowing fast "in-memory" manipulation and comparison of molecules. There is increasing evidence that lossless fingerprints can substantially improve retrieval performance in chemical database searching (substructure or similarity), which have led to the development of several lossless fingerprint compression algorithms. However, any gains in storage and retrieval afforded by compression need to be weighed against the extra computational burden required for decompression before these fingerprints can be compared. Here we demonstrate that graphics processing units (GPU) can greatly alleviate this problem, enabling the practical application of lossless fingerprints on large databases. More specifically, we show that, with the help of a ~$500 ordinary video card, the entire PubChem database of ~32 million compounds can be searched in ~0.2-2 s on average, which is 2 orders of magnitude faster than a conventional CPU. If multiple query patterns are processed in batch, the speedup is even more dramatic (less than 0.02-0.2 s/query for 1000 queries). In the present study, we use the Elias gamma compression algorithm, which results in a compression ratio as high as 0.097.

  9. Comparison Study of Overlap among 21 Scientific Databases in Searching Pesticide Information.

    ERIC Educational Resources Information Center

    Meyer, Daniel E.; And Others

    1983-01-01

    Evaluates overlapping coverage of 21 scientific databases used in 10 online pesticide searches in an attempt to identify minimum number of databases needed to generate 90 percent of unique, relevant citations for given search. Comparison of searches combined under given pesticide usage (herbicide, fungicide, insecticide) is discussed. Nine…

  10. Cycloquest: Identification of cyclopeptides via database search of their mass spectra against genome databases

    PubMed Central

    Mohimani, Hosein; Liu, Wei-Ting; Mylne, Joshua S.; Poth, Aaron G.; Colgrave, Michelle L.; Tran, Dat; Selsted, Michael E.; Dorrestein, Pieter C.; Pevzner, Pavel A.

    2011-01-01

    Hundreds of ribosomally synthesized cyclopeptides have been isolated from all domains of life, the vast majority having been reported in the last 15 years. Studies of cyclic peptides have highlighted their exceptional potential both as stable drug scaffolds and as biomedicines in their own right. Despite this, computational techniques for cyclopeptide identification are still in their infancy, with many such peptides remaining uncharacterized. Tandem mass spectrometry has occupied a niche role in cyclopeptide identification, taking over from traditional techniques such as nuclear magnetic resonance spectroscopy (NMR). MS/MS studies require only picogram quantities of peptide (compared to milligrams for NMR studies) and are applicable to complex samples, abolishing the requirement for time-consuming chromatographic purification. While database search tools such as Sequest and Mascot have become standard tools for the MS/MS identification of linear peptides, they are not applicable to cyclopeptides, due to the parent mass shift resulting from cyclization, and different fragmentation pattern of cyclic peptides. In this paper, we describe the development of a novel database search methodology to aid in the identification of cyclopeptides by mass spectrometry, and evaluate its utility in identifying two peptide rings from Helianthus annuus, a bacterial cannibalism factor from Bacillus subtilis, and a θ-defensin from Rhesus macaque. PMID:21851130

  11. Nested Quantum Search and NP-Complete Problem

    NASA Technical Reports Server (NTRS)

    Williams, C.; Cerf, N. J.; Grover, L. K.

    1998-01-01

    A quantum algorithm is known that solves an unstructured search problem in a number of iterations of order square-root of d, where d is the dimension of the search space, whereas any classical algorithm scales as O(d).

  12. Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics.

    PubMed

    Refsgaard, Jan C; Munk, Stephanie; Jensen, Lars J

    2016-01-01

    Advances in mass spectrometric instrumentation in the past 15 years have resulted in an explosion in the raw data yield from typical phosphoproteomics workflows. This poses the challenge of confidently identifying peptide sequences, localizing phosphosites to proteins and quantifying these from the vast amounts of raw data. This task is tackled by computational tools implementing algorithms that match the experimental data to databases, providing the user with lists for downstream analysis. Several platforms for such automated interpretation of mass spectrometric data have been developed, each having strengths and weaknesses that must be considered for the individual needs. These are reviewed in this chapter. Equally critical for generating highly confident output datasets is the application of sound statistical criteria to limit the inclusion of incorrect peptide identifications from database searches. Additionally, careful filtering and use of appropriate statistical tests on the output datasets affects the quality of all downstream analyses and interpretation of the data. Our considerations and general practices on these aspects of phosphoproteomics data processing are presented here.

  13. Quantum algorithms for the ordered search problem via semidefinite programming

    SciTech Connect

    Childs, Andrew M.; Landahl, Andrew J.; Parrilo, Pablo A.

    2007-03-15

    One of the most basic computational problems is the task of finding a desired item in an ordered list of N items. While the best classical algorithm for this problem uses log{sub 2} N queries to the list, a quantum computer can solve the problem using a constant factor fewer queries. However, the precise value of this constant is unknown. By characterizing a class of quantum query algorithms for the ordered search problem in terms of a semidefinite program, we find quantum algorithms for small instances of the ordered search problem. Extending these algorithms to arbitrarily large instances using recursion, we show that there is an exact quantum ordered search algorithm using 4 log{sub 605} N{approx_equal}0.433 log{sub 2} N queries, which improves upon the previously best known exact algorithm.

  14. The Use of AJAX in Searching a Bibliographic Database: A Case Study of the Italian Biblioteche Oggi Database

    ERIC Educational Resources Information Center

    Cavaleri, Piero

    2008-01-01

    Purpose: The purpose of this paper is to describe the use of AJAX for searching the Biblioteche Oggi database of bibliographic records. Design/methodology/approach: The paper is a demonstration of how bibliographic database single page interfaces allow the implementation of more user-friendly features for social and collaborative tasks. Findings:…

  15. Automated searching for quantum subsystem codes

    SciTech Connect

    Crosswhite, Gregory M.; Bacon, Dave

    2011-02-15

    Quantum error correction allows for faulty quantum systems to behave in an effectively error-free manner. One important class of techniques for quantum error correction is the class of quantum subsystem codes, which are relevant both to active quantum error-correcting schemes as well as to the design of self-correcting quantum memories. Previous approaches for investigating these codes have focused on applying theoretical analysis to look for interesting codes and to investigate their properties. In this paper we present an alternative approach that uses computational analysis to accomplish the same goals. Specifically, we present an algorithm that computes the optimal quantum subsystem code that can be implemented given an arbitrary set of measurement operators that are tensor products of Pauli operators. We then demonstrate the utility of this algorithm by performing a systematic investigation of the quantum subsystem codes that exist in the setting where the interactions are limited to two-body interactions between neighbors on lattices derived from the convex uniform tilings of the plane.

  16. Multiparty controlled quantum secure direct communication based on quantum search algorithm

    NASA Astrophysics Data System (ADS)

    Kao, Shih-Hung; Hwang, Tzonelih

    2013-12-01

    In this study, a new controlled quantum secure direct communication (CQSDC) protocol using the quantum search algorithm as the encoding function is proposed. The proposed protocol is based on the multi-particle Greenberger-Horne-Zeilinger entangled state and the one-step quantum transmission strategy. Due to the one-step transmission of qubits, the proposed protocol can be easily extended to a multi-controller environment, and is also free from the Trojan horse attacks. The analysis shows that the use of quantum search algorithm in the construction of CQSDC appears very promising.

  17. Adiabatic quantum algorithm for search engine ranking.

    PubMed

    Garnerone, Silvano; Zanardi, Paolo; Lidar, Daniel A

    2012-06-08

    We propose an adiabatic quantum algorithm for generating a quantum pure state encoding of the PageRank vector, the most widely used tool in ranking the relative importance of internet pages. We present extensive numerical simulations which provide evidence that this algorithm can prepare the quantum PageRank state in a time which, on average, scales polylogarithmically in the number of web pages. We argue that the main topological feature of the underlying web graph allowing for such a scaling is the out-degree distribution. The top-ranked log(n) entries of the quantum PageRank state can then be estimated with a polynomial quantum speed-up. Moreover, the quantum PageRank state can be used in "q-sampling" protocols for testing properties of distributions, which require exponentially fewer measurements than all classical schemes designed for the same task. This can be used to decide whether to run a classical update of the PageRank.

  18. Adiabatic Quantum Algorithm for Search Engine Ranking

    NASA Astrophysics Data System (ADS)

    Garnerone, Silvano; Zanardi, Paolo; Lidar, Daniel A.

    2012-06-01

    We propose an adiabatic quantum algorithm for generating a quantum pure state encoding of the PageRank vector, the most widely used tool in ranking the relative importance of internet pages. We present extensive numerical simulations which provide evidence that this algorithm can prepare the quantum PageRank state in a time which, on average, scales polylogarithmically in the number of web pages. We argue that the main topological feature of the underlying web graph allowing for such a scaling is the out-degree distribution. The top-ranked log⁡(n) entries of the quantum PageRank state can then be estimated with a polynomial quantum speed-up. Moreover, the quantum PageRank state can be used in “q-sampling” protocols for testing properties of distributions, which require exponentially fewer measurements than all classical schemes designed for the same task. This can be used to decide whether to run a classical update of the PageRank.

  19. Automated Search for new Quantum Experiments

    NASA Astrophysics Data System (ADS)

    Krenn, Mario; Malik, Mehul; Fickler, Robert; Lapkiewicz, Radek; Zeilinger, Anton

    2016-03-01

    Quantum mechanics predicts a number of, at first sight, counterintuitive phenomena. It therefore remains a question whether our intuition is the best way to find new experiments. Here, we report the development of the computer algorithm Melvin which is able to find new experimental implementations for the creation and manipulation of complex quantum states. Indeed, the discovered experiments extensively use unfamiliar and asymmetric techniques which are challenging to understand intuitively. The results range from the first implementation of a high-dimensional Greenberger-Horne-Zeilinger state, to a vast variety of experiments for asymmetrically entangled quantum states—a feature that can only exist when both the number of involved parties and dimensions is larger than 2. Additionally, new types of high-dimensional transformations are found that perform cyclic operations. Melvin autonomously learns from solutions for simpler systems, which significantly speeds up the discovery rate of more complex experiments. The ability to automate the design of a quantum experiment can be applied to many quantum systems and allows the physical realization of quantum states previously thought of only on paper.

  20. Towards computational improvement of DNA database indexing and short DNA query searching.

    PubMed

    Stojanov, Done; Koceski, Sašo; Mileva, Aleksandra; Koceska, Nataša; Bande, Cveta Martinovska

    2014-09-03

    In order to facilitate and speed up the search of massive DNA databases, the database is indexed at the beginning, employing a mapping function. By searching through the indexed data structure, exact query hits can be identified. If the database is searched against an annotated DNA query, such as a known promoter consensus sequence, then the starting locations and the number of potential genes can be determined. This is particularly relevant if unannotated DNA sequences have to be functionally annotated. However, indexing a massive DNA database and searching an indexed data structure with millions of entries is a time-demanding process. In this paper, we propose a fast DNA database indexing and searching approach, identifying all query hits in the database, without having to examine all entries in the indexed data structure, limiting the maximum length of a query that can be searched against the database. By applying the proposed indexing equation, the whole human genome could be indexed in 10 hours on a personal computer, under the assumption that there is enough RAM to store the indexed data structure. Analysing the methodology proposed by Reneker, we observed that hits at starting positions [Formula: see text] are not reported, if the database is searched against a query shorter than [Formula: see text] nucleotides, such that [Formula: see text] is the length of the DNA database words being mapped and [Formula: see text] is the length of the query. A solution of this drawback is also presented.

  1. Optimal state discrimination and unstructured search in nonlinear quantum mechanics

    NASA Astrophysics Data System (ADS)

    Childs, Andrew M.; Young, Joshua

    2016-02-01

    Nonlinear variants of quantum mechanics can solve tasks that are impossible in standard quantum theory, such as perfectly distinguishing nonorthogonal states. Here we derive the optimal protocol for distinguishing two states of a qubit using the Gross-Pitaevskii equation, a model of nonlinear quantum mechanics that arises as an effective description of Bose-Einstein condensates. Using this protocol, we present an algorithm for unstructured search in the Gross-Pitaevskii model, obtaining an exponential improvement over a previous algorithm of Meyer and Wong. This result establishes a limitation on the effectiveness of the Gross-Pitaevskii approximation. More generally, we demonstrate similar behavior under a family of related nonlinearities, giving evidence that the ability to quickly discriminate nonorthogonal states and thereby solve unstructured search is a generic feature of nonlinear quantum mechanics.

  2. (Sub)structure Searches in Databases Containing Generic Chemical Structure Representations.

    ERIC Educational Resources Information Center

    Schoch-Grubler, Ursula

    1990-01-01

    Reviews three database systems available for searching generic chemical structure representations: (1) Derwent's Chemical Code System; (2) IDC's Gremas System; and (3) Derwent's Markush DARC System. Various types of searches are described, features desirable to users are discussed, and comparison searches are described that measured recall and…

  3. Searching Databases without Query-Building Aids: Implications for Dyslexic Users

    ERIC Educational Resources Information Center

    Berget, Gerd; Sandnes, Frode Eika

    2015-01-01

    Introduction: Few studies document the information searching behaviour of users with cognitive impairments. This paper therefore addresses the effect of dyslexia on information searching in a database with no tolerance for spelling errors and no query-building aids. The purpose was to identify effective search interface design guidelines that…

  4. Medical Students' Personal Knowledge, Searching Proficiency, and Database Use in Problem Solving.

    ERIC Educational Resources Information Center

    Wildemuth, Barbara M.; And Others

    1995-01-01

    Discusses the relationship between personal knowledge in a domain and online searching proficiency in that domain, and the relationship between searching proficiency and database-assisted problem-solving performance based on a study of medical students. Search results, selection of terms, and efficiency were found to be related to problem-solving…

  5. Adaptive search in mobile peer-to-peer databases

    NASA Technical Reports Server (NTRS)

    Wolfson, Ouri (Inventor); Xu, Bo (Inventor)

    2010-01-01

    Information is stored in a plurality of mobile peers. The peers communicate in a peer to peer fashion, using a short-range wireless network. Occasionally, a peer initiates a search for information in the peer to peer network by issuing a query. Queries and pieces of information, called reports, are transmitted among peers that are within a transmission range. For each search additional peers are utilized, wherein these additional peers search and relay information on behalf of the originator of the search.

  6. On the complexity of search for keys in quantum cryptography

    NASA Astrophysics Data System (ADS)

    Molotkov, S. N.

    2016-03-01

    The trace distance is used as a security criterion in proofs of security of keys in quantum cryptography. Some authors doubted that this criterion can be reduced to criteria used in classical cryptography. The following question has been answered in this work. Let a quantum cryptography system provide an ɛ-secure key such that ½‖ρ XE - ρ U ⊗ ρ E ‖1 < ɛ, which will be repeatedly used in classical encryption algorithms. To what extent does the ɛ-secure key reduce the number of search steps (guesswork) as compared to the use of ideal keys? A direct relation has been demonstrated between the complexity of the complete consideration of keys, which is one of the main security criteria in classical systems, and the trace distance used in quantum cryptography. Bounds for the minimum and maximum numbers of search steps for the determination of the actual key have been presented.

  7. Laplacian versus adjacency matrix in quantum walk search

    NASA Astrophysics Data System (ADS)

    Wong, Thomas G.; Tarrataca, Luís; Nahimov, Nikolay

    2016-10-01

    A quantum particle evolving by Schrödinger's equation contains, from the kinetic energy of the particle, a term in its Hamiltonian proportional to Laplace's operator. In discrete space, this is replaced by the discrete or graph Laplacian, which gives rise to a continuous-time quantum walk. Besides this natural definition, some quantum walk algorithms instead use the adjacency matrix to effect the walk. While this is equivalent to the Laplacian for regular graphs, it is different for non-regular graphs and is thus an inequivalent quantum walk. We algorithmically explore this distinction by analyzing search on the complete bipartite graph with multiple marked vertices, using both the Laplacian and adjacency matrix. The two walks differ qualitatively and quantitatively in their required jumping rate, runtime, sampling of marked vertices, and in what constitutes a natural initial state. Thus the choice of the Laplacian or adjacency matrix to effect the walk has important algorithmic consequences.

  8. Searching the expressed sequence tag (EST) databases: panning for genes.

    PubMed

    Jongeneel, C V

    2000-02-01

    The genomes of living organisms contain many elements, including genes coding for proteins. The portions of the genes expressed as mature mRNA, collectively known as the transcriptome, represent only a small part of the genome. The expressed sequence tag (EST) databases contain an increasingly large part of the transcriptome of many species. For this reason, these databases are probably the most abundant source of new coding sequences available today. However, the raw data deposited in the EST databases are to a large extent unorganised, unannotated, redundant and of relatively low quality. This paper reviews some of the characteristics of the EST data, and the methods that can be used to find novel protein sequences within them. It also documents a collection of databases, software and web sites that can be useful to biologists interested in mining the EST databases over the Internet, or in establishing a local environment for such analyses.

  9. Content Evaluation of Textual CD-ROM and Web Databases. Database Searching Series.

    ERIC Educational Resources Information Center

    Jacso, Peter

    This book provides guidelines for evaluating a variety of database types, including abstracting and indexing, directory, full-text, and page-image databases available in online and/or CD-ROM formats. The book discusses the purpose and techniques of comparing and evaluating the most important characteristics of textual databases, such as their…

  10. Algorithms for database-dependent search of MS/MS data.

    PubMed

    Matthiesen, Rune

    2013-01-01

    The frequent used bottom-up strategy for identification of proteins and their associated modifications generate nowadays typically thousands of MS/MS spectra that normally are matched automatically against a protein sequence database. Search engines that take as input MS/MS spectra and a protein sequence database are referred as database-dependent search engines. Many programs both commercial and freely available exist for database-dependent search of MS/MS spectra and most of the programs have excellent user documentation. The aim here is therefore to outline the algorithm strategy behind different search engines rather than providing software user manuals. The process of database-dependent search can be divided into search strategy, peptide scoring, protein scoring, and finally protein inference. Most efforts in the literature have been put in to comparing results from different software rather than discussing the underlining algorithms. Such practical comparisons can be cluttered by suboptimal implementation and the observed differences are frequently caused by software parameters settings which have not been set proper to allow even comparison. In other words an algorithmic idea can still be worth considering even if the software implementation has been demonstrated to be suboptimal. The aim in this chapter is therefore to split the algorithms for database-dependent searching of MS/MS data into the above steps so that the different algorithmic ideas become more transparent and comparable. Most search engines provide good implementations of the first three data analysis steps mentioned above, whereas the final step of protein inference are much less developed for most search engines and is in many cases performed by an external software. The final part of this chapter illustrates how protein inference is built into the VEMS search engine and discusses a stand-alone program SIR for protein inference that can import a Mascot search result.

  11. Federated or cached searches: providing expected performance from multiple invasive species databases

    USGS Publications Warehouse

    Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

    2011-01-01

    Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

  12. Federated or cached searches: Providing expected performance from multiple invasive species databases

    NASA Astrophysics Data System (ADS)

    Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

    2011-06-01

    Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

  13. Faster quantum searching with almost any diffusion operator

    NASA Astrophysics Data System (ADS)

    Tulsi, Avatar

    2015-05-01

    Grover's search algorithm drives a quantum system from an initial state |s > to a desired final state |t > by using selective phase inversions of these two states. Earlier, we studied a generalization of Grover's algorithm that relaxes the assumption of the efficient implementation of Is, the selective phase inversion of the initial state, also known as a diffusion operator. This assumption is known to become a serious handicap in cases of physical interest. Our general search algorithm works with almost any diffusion operator Ds with the only restriction of having |s > as one of its eigenstates. The price that we pay for using any operator is an increase in the number of oracle queries by a factor of O (B ) , where B is a characteristic of the eigenspectrum of Ds and can be large in some situations. Here we show that by using a quantum Fourier transform, we can regain the optimal query complexity of Grover's algorithm without losing the freedom of using any diffusion operator for quantum searching. However, the total number of operators required by the algorithm is still O (B ) times more than that of Grover's algorithm. So our algorithm offers an advantage only if the oracle operator is computationally more expensive than the diffusion operator, which is true in most search problems.

  14. Use of Composite Protein Database including Search Result Sequences for Mass Spectrometric Analysis of Cell Secretome

    PubMed Central

    Shin, Jihye; Kim, Gamin; Kabir, Mohammad Humayun; Park, Seong Jun; Lee, Seoung Taek; Lee, Cheolju

    2015-01-01

    Mass spectrometric (MS) data of human cell secretomes are usually run through the conventional human database for identification. However, the search may result in false identifications due to contamination of the secretome with fetal bovine serum (FBS) proteins. To overcome this challenge, here we provide a composite protein database including human as well as 199 FBS protein sequences for MS data search of human cell secretomes. Searching against the human-FBS database returned more reliable results with fewer false-positive and false-negative identifications compared to using either a human only database or a human-bovine database. Furthermore, the improved results validated our strategy without complex experiments like SILAC. We expect our strategy to improve the accuracy of human secreted protein identification and to also add value for general use. PMID:25822838

  15. Using the Turning Research Into Practice (TRIP) database: how do clinicians really search?*

    PubMed Central

    Meats, Emma; Brassey, Jon; Heneghan, Carl; Glasziou, Paul

    2007-01-01

    Objectives: Clinicians and patients are increasingly accessing information through Internet searches. This study aimed to examine clinicians' current search behavior when using the Turning Research Into Practice (TRIP) database to examine search engine use and the ways it might be improved. Methods: A Web log analysis was undertaken of the TRIP database—a meta-search engine covering 150 health resources including MEDLINE, The Cochrane Library, and a variety of guidelines. The connectors for terms used in searches were studied, and observations were made of 9 users' search behavior when working with the TRIP database. Results: Of 620,735 searches, most used a single term, and 12% (n = 75,947) used a Boolean operator: 11% (n = 69,006) used “AND” and 0.8% (n = 4,941) used “OR.” Of the elements of a well-structured clinical question (population, intervention, comparator, and outcome), the population was most commonly used, while fewer searches included the intervention. Comparator and outcome were rarely used. Participants in the observational study were interested in learning how to formulate better searches. Conclusions: Web log analysis showed most searches used a single term and no Boolean operators. Observational study revealed users were interested in conducting efficient searches but did not always know how. Therefore, either better training or better search interfaces are required to assist users and enable more effective searching. PMID:17443248

  16. Techniques for searching the CINAHL database using the EBSCO interface.

    PubMed

    Lawrence, Janna C

    2007-04-01

    The cumulative index to Nursing and Allied Health Literature (CINAHL) is a useful research tool for accessing articles of interest to nurses and health care professionals. More than 2,800 journals are indexed by CINAHL and can be searched easily using assigned subject headings. Detailed instructions about conducting, combining, and saving searches in CINAHL are provided in this article. Establishing an account at EBSCO further allows a nurse to save references and searches and to receive e-mail alerts when new articles on a topic of interest are published.

  17. Increasing number of databases searched in systematic reviews and meta-analyses between 1994 and 2014

    PubMed Central

    Lam, Michael T.; McDiarmid, Mary

    2016-01-01

    Objectives The purpose of this study was to determine whether the number of bibliographic databases used to search the health sciences literature in individual systematic reviews (SRs) and meta-analyses (MAs) changed over a twenty-year period related to the official 1995 launch of the Cochrane Database of Systematic Reviews (CDSR). Methods Ovid MEDLINE was searched using a modified version of a strategy developed by the Scottish Intercollegiate Guidelines Network to identify SRs and MAs. Records from 3 milestone years were searched: the year immediately preceding (1994) and 1 (2004) and 2 (2014) decades following the CDSR launch. Records were sorted with randomization software. Abstracts or full texts of the records were examined to identify database usage until 100 relevant records were identified from each of the 3 years. Results The mean and median number of bibliographic databases searched in 1994, 2004, and 2014 were 1.62 and 1, 3.34 and 3, and 3.73 and 4, respectively. Studies that searched only 1 database decreased over the 3 milestone years (60% in 1994, 28% in 2004, and 10% in 2014). Conclusions The number of bibliographic databases searched in individual SRs and MAs increased from 1994 to 2014. PMID:27822149

  18. SledgeHMMER: a web server for batch searching the Pfam database.

    PubMed

    Chukkapalli, Giridhar; Guda, Chittibabu; Subramaniam, Shankar

    2004-07-01

    The SledgeHMMER web server is intended for genome-scale searching of the Pfam database without having to install this database and the HMMER software locally. The server implements a parallelized version of hmmpfam, the program used for searching the Pfam HMM database. Pfam search results have been calculated for the entire Swiss-Prot and TrEmbl database sequences (approximately 1.2 million) on 256 processors of IA64-based teragrid machines. The Pfam database can be searched in local, glocal or merged mode, using either gathering or E-value thresholds. Query sequences are first matched against the pre-calculated entries to retrieve results, and those without matches are processed through a new search process. Results are emailed in a space-delimited tabular format upon completion of the search. While most other Pfam-searching web servers set a limit of one sequence per query, this server processes batch sequences with no limit on the number of input sequences. The web server and downloadable data are accessible from http://SledgeHmmer.sdsc.edu.

  19. Dialog's Knowledge Index and BRS/After Dark: Database Searching on Personal Computers.

    ERIC Educational Resources Information Center

    Tenopir, Carol

    1983-01-01

    Describes two new bibliographic information services being marketed to microcomputer owners by DIALOG, Inc. and Bibliographic Retrieval Services to allow access to databases at low rates during evening hours. Subject focus, selection of a database, search strategies employed on each system are discussed, and the two services are compared. (EJS)

  20. STEPS: A Grid Search Methodology for Optimized Peptide Identification Filtering of MS/MS Database Search Results

    SciTech Connect

    Piehowski, Paul D.; Petyuk, Vladislav A.; Sandoval, John D.; Burnum, Kristin E.; Kiebel, Gary R.; Monroe, Matthew E.; Anderson, Gordon A.; Camp, David G.; Smith, Richard D.

    2013-03-01

    For bottom-up proteomics there are a wide variety of database searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection - referred to as STEPS - utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types.

  1. Searching for Controlled Trials of Complementary and Alternative Medicine: A Comparison of 15 Databases

    PubMed Central

    Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

    2011-01-01

    This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE records—these were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases. PMID:19468052

  2. InfoTrac's SearchBank Databases: Business Information and More.

    ERIC Educational Resources Information Center

    Mehta, Usha; Goodman, Beth

    1997-01-01

    Describes the InfoTrac SearchBank based on experiences at the University of Nevada, Reno, libraries where the service is available through the online catalog. Highlights include remote access through the Internet; indexing and abstracting; full-text access to 460 journal titles; a powerful search engine; and business-oriented databases.…

  3. Extending the Role of the Corporate Library: Corporate Database Applications Using BRS/Search Software.

    ERIC Educational Resources Information Center

    Lammert, Diana

    1993-01-01

    Describes the McKenna Information Center's application of BRS/SEARCH, information retrieval software, as part of its services to Kennmetal Inc., its parent company. Features and uses of the software, including commands, custom searching, menu-driven interfaces, preparing reports, and designing databases are covered. Nine examples of software…

  4. Social Work Literature Searching: Current Issues with Databases and Online Search Engines

    ERIC Educational Resources Information Center

    McGinn, Tony; Taylor, Brian; McColgan, Mary; McQuilkan, Janice

    2016-01-01

    Objectives: To compare the performance of a range of search facilities; and to illustrate the execution of a comprehensive literature search for qualitative evidence in social work. Context: Developments in literature search methods and comparisons of search facilities help facilitate access to the best available evidence for social workers.…

  5. Efficiency of 22 online databases in the search for physicochemical, toxicological and ecotoxicological information on chemicals.

    PubMed

    Guerbet, Michel; Guyodo, Gaetan

    2002-03-01

    The objective of this study was to evaluate the efficiency of 22 free online databases that could be used for an exhaustive search of physicochemical, toxicological and/or ecotoxicological information about various chemicals. Twenty-two databases with free access on the Internet were referenced. We then selected 27 major physicochemical, toxicological and ecotoxicological criteria and 14 compounds belonging to seven different chemical classes which were used to interrogate all the databases. Two indices were successively calculated to evaluate the efficiency with taking or not taking account of their specialization. More than 50% of the 22 databases 'knew' all of the 14 chemicals, but the quantity of information provided is very different from one to the other and most are poorly documented. Two categories clearly appear with specialized and non-specialized databases. The HSDB database is the most efficient general database to be searched first, because it is well documented for most of the 27 criteria. However, some specialized databases (i.e. EXTOXNET, SOLVEDB, etc.) must be searched secondarily to find additional information.

  6. MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

    PubMed

    Wang, Yingfeng; Kora, Guruprasad; Bowen, Benjamin P; Pan, Chongle

    2014-10-07

    A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here, we present the open-source MIDAS algorithm (Metabolite Identification via Database Searching). To evaluate a metabolite-spectrum match (MSM), MIDAS first enumerates possible fragments from a metabolite by systematic bond dissociation, then calculates the plausibility of the fragments based on their fragmentation pathways, and finally scores the MSM to assess how well the experimental MS/MS spectrum from collision-induced dissociation (CID) is explained by the metabolite's predicted CID MS/MS spectrum. MIDAS was designed to search high-resolution tandem mass spectra acquired on time-of-flight or Orbitrap mass spectrometer against a metabolite database in an automated and high-throughput manner. The accuracy of metabolite identification by MIDAS was benchmarked using four sets of standard tandem mass spectra from MassBank. On average, for 77% of original spectra and 84% of composite spectra, MIDAS correctly ranked the true compounds as the first MSMs out of all MetaCyc metabolites as decoys. MIDAS correctly identified 46% more original spectra and 59% more composite spectra at the first MSMs than an existing database-searching algorithm, MetFrag. MIDAS was showcased by searching a published real-world measurement of a metabolome from Synechococcus sp. PCC 7002 against the MetaCyc metabolite database. MIDAS identified many metabolites missed in the previous study. MIDAS identifications should be considered only as candidate metabolites, which need to be confirmed using standard compounds. To facilitate manual validation, MIDAS provides annotated spectra for MSMs and labels observed mass spectral peaks with predicted fragments. The database searching and manual validation can be performed online at http://midas.omicsbio.org.

  7. Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database.

    SciTech Connect

    Quock, D. E. R.; Cianciarulo, M. B.; APS Engineering Support Division; Purdue Univ.

    2007-01-01

    The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, the necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.

  8. A search algorithm for quantum state engineering and metrology

    NASA Astrophysics Data System (ADS)

    Knott, P. A.

    2016-07-01

    In this paper we present a search algorithm that finds useful optical quantum states which can be created with current technology. We apply the algorithm to the field of quantum metrology with the goal of finding states that can measure a phase shift to a high precision. Our algorithm efficiently produces a number of novel solutions: we find experimentally ready schemes to produce states that show significant improvements over the state-of-the-art, and can measure with a precision that beats the shot noise limit by over a factor of 4. Furthermore, these states demonstrate a robustness to moderate/high photon losses, and we present a conceptually simple measurement scheme that saturates the Cramér-Rao bound.

  9. The LAILAPS search engine: a feature model for relevance ranking in life science databases.

    PubMed

    Lange, Matthias; Spies, Karl; Colmsee, Christian; Flemming, Steffen; Klapperstück, Matthias; Scholz, Uwe

    2010-03-25

    Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.

  10. CLIP: similarity searching of 3D databases using clique detection.

    PubMed

    Rhodes, Nicholas; Willett, Peter; Calvet, Alain; Dunbar, James B; Humblet, Christine

    2003-01-01

    This paper describes a program for 3D similarity searching, called CLIP (for Candidate Ligand Identification Program), that uses the Bron-Kerbosch clique detection algorithm to find those structures in a file that have large structures in common with a target structure. Structures are characterized by the geometric arrangement of pharmacophore points and the similarity between two structures calculated using modifications of the Simpson and Tanimoto association coefficients. This modification takes into account the fact that a distance tolerance is required to ensure that pairs of interatomic distances can be regarded as equivalent during the clique-construction stage of the matching algorithm. Experiments with HIV assay data demonstrate the effectiveness and the efficiency of this approach to virtual screening.

  11. Practical Quantum Private Database Queries Based on Passive Round-Robin Differential Phase-shift Quantum Key Distribution

    NASA Astrophysics Data System (ADS)

    Li, Jian; Yang, Yu-Guang; Chen, Xiu-Bo; Zhou, Yi-Hua; Shi, Wei-Min

    2016-08-01

    A novel quantum private database query protocol is proposed, based on passive round-robin differential phase-shift quantum key distribution. Compared with previous quantum private database query protocols, the present protocol has the following unique merits: (i) the user Alice can obtain one and only one key bit so that both the efficiency and security of the present protocol can be ensured, and (ii) it does not require to change the length difference of the two arms in a Mach-Zehnder interferometer and just chooses two pulses passively to interfere with so that it is much simpler and more practical. The present protocol is also proved to be secure in terms of the user security and database security.

  12. Practical Quantum Private Database Queries Based on Passive Round-Robin Differential Phase-shift Quantum Key Distribution.

    PubMed

    Li, Jian; Yang, Yu-Guang; Chen, Xiu-Bo; Zhou, Yi-Hua; Shi, Wei-Min

    2016-08-19

    A novel quantum private database query protocol is proposed, based on passive round-robin differential phase-shift quantum key distribution. Compared with previous quantum private database query protocols, the present protocol has the following unique merits: (i) the user Alice can obtain one and only one key bit so that both the efficiency and security of the present protocol can be ensured, and (ii) it does not require to change the length difference of the two arms in a Mach-Zehnder interferometer and just chooses two pulses passively to interfere with so that it is much simpler and more practical. The present protocol is also proved to be secure in terms of the user security and database security.

  13. Practical Quantum Private Database Queries Based on Passive Round-Robin Differential Phase-shift Quantum Key Distribution

    PubMed Central

    Li, Jian; Yang, Yu-Guang; Chen, Xiu-Bo; Zhou, Yi-Hua; Shi, Wei-Min

    2016-01-01

    A novel quantum private database query protocol is proposed, based on passive round-robin differential phase-shift quantum key distribution. Compared with previous quantum private database query protocols, the present protocol has the following unique merits: (i) the user Alice can obtain one and only one key bit so that both the efficiency and security of the present protocol can be ensured, and (ii) it does not require to change the length difference of the two arms in a Mach-Zehnder interferometer and just chooses two pulses passively to interfere with so that it is much simpler and more practical. The present protocol is also proved to be secure in terms of the user security and database security. PMID:27539654

  14. Development and Validation of Search Filters to Identify Articles on Family Medicine in Online Medical Databases.

    PubMed

    Pols, David H J; Bramer, Wichor M; Bindels, Patrick J E; van de Laar, Floris A; Bohnen, Arthur M

    2015-01-01

    Physicians and researchers in the field of family medicine often need to find relevant articles in online medical databases for a variety of reasons. Because a search filter may help improve the efficiency and quality of such searches, we aimed to develop and validate search filters to identify research studies of relevance to family medicine. Using a new and objective method for search filter development, we developed and validated 2 search filters for family medicine. The sensitive filter had a sensitivity of 96.8% and a specificity of 74.9%. The specific filter had a specificity of 97.4% and a sensitivity of 90.3%. Our new filters should aid literature searches in the family medicine field. The sensitive filter may help researchers conducting systematic reviews, whereas the specific filter may help family physicians find answers to clinical questions at the point of care when time is limited.

  15. A formulation of a matrix sparsity approach for the quantum ordered search algorithm

    NASA Astrophysics Data System (ADS)

    Parmar, Jupinder; Rahman, Saarim; Thiara, Jaskaran

    One specific subset of quantum algorithms is Grovers Ordered Search Problem (OSP), the quantum counterpart of the classical binary search algorithm, which utilizes oracle functions to produce a specified value within an ordered database. Classically, the optimal algorithm is known to have a log2N complexity; however, Grovers algorithm has been found to have an optimal complexity between the lower bound of ((lnN‑1)/π≈0.221log2N) and the upper bound of 0.433log2N. We sought to lower the known upper bound of the OSP. With Farhi et al. MITCTP 2815 (1999), arXiv:quant-ph/9901059], we see that the OSP can be resolved into a translational invariant algorithm to create quantum query algorithm restraints. With these restraints, one can find Laurent polynomials for various k — queries — and N — database sizes — thus finding larger recursive sets to solve the OSP and effectively reducing the upper bound. These polynomials are found to be convex functions, allowing one to make use of convex optimization to find an improvement on the known bounds. According to Childs et al. [Phys. Rev. A 75 (2007) 032335], semidefinite programming, a subset of convex optimization, can solve the particular problem represented by the constraints. We were able to implement a program abiding to their formulation of a semidefinite program (SDP), leading us to find that it takes an immense amount of storage and time to compute. To combat this setback, we then formulated an approach to improve results of the SDP using matrix sparsity. Through the development of this approach, along with an implementation of a rudimentary solver, we demonstrate how matrix sparsity reduces the amount of time and storage required to compute the SDP — overall ensuring further improvements will likely be made to reach the theorized lower bound.

  16. Vehicle-triggered video compression/decompression for fast and efficient searching in large video databases

    NASA Astrophysics Data System (ADS)

    Bulan, Orhan; Bernal, Edgar A.; Loce, Robert P.; Wu, Wencheng

    2013-03-01

    Video cameras are widely deployed along city streets, interstate highways, traffic lights, stop signs and toll booths by entities that perform traffic monitoring and law enforcement. The videos captured by these cameras are typically compressed and stored in large databases. Performing a rapid search for a specific vehicle within a large database of compressed videos is often required and can be a time-critical life or death situation. In this paper, we propose video compression and decompression algorithms that enable fast and efficient vehicle or, more generally, event searches in large video databases. The proposed algorithm selects reference frames (i.e., I-frames) based on a vehicle having been detected at a specified position within the scene being monitored while compressing a video sequence. A search for a specific vehicle in the compressed video stream is performed across the reference frames only, which does not require decompression of the full video sequence as in traditional search algorithms. Our experimental results on videos captured in a local road show that the proposed algorithm significantly reduces the search space (thus reducing time and computational resources) in vehicle search tasks within compressed video streams, particularly those captured in light traffic volume conditions.

  17. A Bayesian network approach to the database search problem in criminal proceedings

    PubMed Central

    2012-01-01

    Background The ‘database search problem’, that is, the strengthening of a case - in terms of probative value - against an individual who is found as a result of a database search, has been approached during the last two decades with substantial mathematical analyses, accompanied by lively debate and centrally opposing conclusions. This represents a challenging obstacle in teaching but also hinders a balanced and coherent discussion of the topic within the wider scientific and legal community. This paper revisits and tracks the associated mathematical analyses in terms of Bayesian networks. Their derivation and discussion for capturing probabilistic arguments that explain the database search problem are outlined in detail. The resulting Bayesian networks offer a distinct view on the main debated issues, along with further clarity. Methods As a general framework for representing and analyzing formal arguments in probabilistic reasoning about uncertain target propositions (that is, whether or not a given individual is the source of a crime stain), this paper relies on graphical probability models, in particular, Bayesian networks. This graphical probability modeling approach is used to capture, within a single model, a series of key variables, such as the number of individuals in a database, the size of the population of potential crime stain sources, and the rarity of the corresponding analytical characteristics in a relevant population. Results This paper demonstrates the feasibility of deriving Bayesian network structures for analyzing, representing, and tracking the database search problem. The output of the proposed models can be shown to agree with existing but exclusively formulaic approaches. Conclusions The proposed Bayesian networks allow one to capture and analyze the currently most well-supported but reputedly counter-intuitive and difficult solution to the database search problem in a way that goes beyond the traditional, purely formulaic expressions

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

    PubMed Central

    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 PMID:26719890

  19. Searching for quantum optimal controls under severe constraints

    SciTech Connect

    Riviello, Gregory; Tibbetts, Katharine Moore; Brif, Constantin; Long, Ruixing; Wu, Re-Bing; Ho, Tak-San; Rabitz, Herschel

    2015-04-06

    The success of quantum optimal control for both experimental and theoretical objectives is connected to the topology of the corresponding control landscapes, which are free from local traps if three conditions are met: (1) the quantum system is controllable, (2) the Jacobian of the map from the control field to the evolution operator is of full rank, and (3) there are no constraints on the control field. This paper investigates how the violation of assumption (3) affects gradient searches for globally optimal control fields. The satisfaction of assumptions (1) and (2) ensures that the control landscape lacks fundamental traps, but certain control constraints can still prevent successful optimization of the objective. Using optimal control simulations, we show that the most severe field constraints are those that limit essential control resources, such as the number of control variables, the control duration, and the field strength. Proper management of these resources is an issue of great practical importance for optimization in the laboratory. For each resource, we show that constraints exceeding quantifiable limits can introduce artificial traps to the control landscape and prevent gradient searches from reaching a globally optimal solution. These results demonstrate that careful choice of relevant control parameters helps to eliminate artificial traps and facilitate successful optimization.

  20. Searching for quantum optimal controls under severe constraints

    DOE PAGES

    Riviello, Gregory; Tibbetts, Katharine Moore; Brif, Constantin; ...

    2015-04-06

    The success of quantum optimal control for both experimental and theoretical objectives is connected to the topology of the corresponding control landscapes, which are free from local traps if three conditions are met: (1) the quantum system is controllable, (2) the Jacobian of the map from the control field to the evolution operator is of full rank, and (3) there are no constraints on the control field. This paper investigates how the violation of assumption (3) affects gradient searches for globally optimal control fields. The satisfaction of assumptions (1) and (2) ensures that the control landscape lacks fundamental traps, butmore » certain control constraints can still prevent successful optimization of the objective. Using optimal control simulations, we show that the most severe field constraints are those that limit essential control resources, such as the number of control variables, the control duration, and the field strength. Proper management of these resources is an issue of great practical importance for optimization in the laboratory. For each resource, we show that constraints exceeding quantifiable limits can introduce artificial traps to the control landscape and prevent gradient searches from reaching a globally optimal solution. These results demonstrate that careful choice of relevant control parameters helps to eliminate artificial traps and facilitate successful optimization.« less

  1. Support Vector Machines for Improved Peptide Identification from Tandem Mass Spectrometry Database Search

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.

    2009-05-06

    Accurate identification of peptides is a current challenge in mass spectrometry (MS) based proteomics. The standard approach uses a search routine to compare tandem mass spectra to a database of peptides associated with the target organism. These database search routines yield multiple metrics associated with the quality of the mapping of the experimental spectrum to the theoretical spectrum of a peptide. The structure of these results make separating correct from false identifications difficult and has created a false identification problem. Statistical confidence scores are an approach to battle this false positive problem that has led to significant improvements in peptide identification. We have shown that machine learning, specifically support vector machine (SVM), is an effective approach to separating true peptide identifications from false ones. The SVM-based peptide statistical scoring method transforms a peptide into a vector representation based on database search metrics to train and validate the SVM. In practice, following the database search routine, a peptides is denoted in its vector representation and the SVM generates a single statistical score that is then used to classify presence or absence in the sample

  2. Planning for End-User Database Searching: Drexel and the Mac: A User-Consistent Interface.

    ERIC Educational Resources Information Center

    LaBorie, Tim; Donnelly, Leslie

    Drexel University instituted a microcomputing program in 1984 which required all freshmen to own Apple Macintosh microcomputers. All students were taught database searching on the BRS (Bibliographic Retrieval Services) system as part of the freshman humanities curriculum, and the university library was chosen as the site to house continuing…

  3. Parallel database search and prime factorization with magnonic holographic memory devices

    SciTech Connect

    Khitun, Alexander

    2015-12-28

    In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

  4. Successful Keyword Searching: Initiating Research on Popular Topics Using Electronic Databases.

    ERIC Educational Resources Information Center

    MacDonald, Randall M.; MacDonald, Susan Priest

    Students are using electronic resources more than ever before to locate information for assignments. Without the proper search terms, results are incomplete, and students are frustrated. Using the keywords, key people, organizations, and Web sites provided in this book and compiled from the most commonly used databases, students will be able to…

  5. Toward a public analysis database for LHC new physics searches using M ADA NALYSIS 5

    NASA Astrophysics Data System (ADS)

    Dumont, B.; Fuks, B.; Kraml, S.; Bein, S.; Chalons, G.; Conte, E.; Kulkarni, S.; Sengupta, D.; Wymant, C.

    2015-02-01

    We present the implementation, in the MadAnalysis 5 framework, of several ATLAS and CMS searches for supersymmetry in data recorded during the first run of the LHC. We provide extensive details on the validation of our implementations and propose to create a public analysis database within this framework.

  6. An Interactive Iterative Method for Electronic Searching of Large Literature Databases

    ERIC Educational Resources Information Center

    Hernandez, Marco A.

    2013-01-01

    PubMed® is an on-line literature database hosted by the U.S. National Library of Medicine. Containing over 21 million citations for biomedical literature--both abstracts and full text--in the areas of the life sciences, behavioral studies, chemistry, and bioengineering, PubMed® represents an important tool for researchers. PubMed® searches return…

  7. Sports Information Online: Searching the SPORT Database and Tips for Finding Sports Medicine Information Online.

    ERIC Educational Resources Information Center

    Janke, Richard V.; And Others

    1988-01-01

    The first article describes SPORT, a database providing international coverage of athletics and physical education, and compares it to other online services in terms of coverage, thesauri, possible search strategies, and actual usage. The second article reviews available online information on sports medicine. (CLB)

  8. Parallel database search and prime factorization with magnonic holographic memory devices

    NASA Astrophysics Data System (ADS)

    Khitun, Alexander

    2015-12-01

    In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

  9. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  10. Systematic reviews and meta-analyses of traditional chinese medicine must search chinese databases to reduce language bias.

    PubMed

    Wu, Xin-Yin; Tang, Jin-Ling; Mao, Chen; Yuan, Jin-Qiu; Qin, Ying; Chung, Vincent C H

    2013-01-01

    Systematic reviews (SRs) that fail to search non-English databases may miss relevant studies and cause selection bias. The bias may be particularly severe in SRs of traditional Chinese medicine (TCM) as most randomized controlled trials (RCT) in TCM are published and accessible only in Chinese. In this study we investigated how often Chinese databases were not searched in SRs of TCM, how many trials were missed, and whether a bias may occur if Chinese databases were not searched. We searched 5 databases in English and 3 in Chinese for RCTs of Chinese herbal medicine for coronary artery disease and found that 96.64% (115/119) eligible studies could be identified only from Chinese databases. In a random sample of 80 Cochrane reviews on TCM, we found that Chinese databases were only searched in 43 or 53.75%, in which almost all the included studies were identified from Chinese databases. We also compared SRs of the same topic and found that they may draw a different conclusion if Chinese databases were not searched. In conclusion, an overwhelmingly high percentage of eligible trials on TCM could only be identified in Chinese databases. Reviewers in TCM are suggested to search Chinese databases to reduce potential selection bias.

  11. Studying Gene Expression: Database Searches and Promoter Fusions to Investigate Transcriptional Regulation in Bacteria†

    PubMed Central

    Martinez-Vaz, Betsy M.; Makarevitch, Irina; Stensland, Shane

    2010-01-01

    A laboratory project was designed to illustrate how to search biological databases and utilize the information provided by these resources to investigate transcriptional regulation in Escherichia coli. The students searched several databases (NCBI Genomes, RegulonDB and EcoCyc) to learn about gene function, regulation, and the organization of transcriptional units. A fluorometer and GFP promoter fusions were used to obtain fluorescence data and measure changes in transcriptional activity. The class designed and performed experiments to investigate the regulation of genes necessary for biosynthesis of amino acids and how expression is affected by environmental signals and transcriptional regulators. Assessment data showed that this activity enhanced students’ knowledge of databases, reporter genes and transcriptional regulation. PMID:23653697

  12. MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines

    PubMed Central

    Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I.; Marcotte, Edward M.

    2011-01-01

    Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for all possible PSMs and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for all detected proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses. PMID:21488652

  13. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

    PubMed

    Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I; Marcotte, Edward M

    2011-07-01

    Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for every possible PSM and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for most proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses.

  14. Quantum computers and unstructured search: finding and counting items with an arbitrarily entangled initial state

    NASA Astrophysics Data System (ADS)

    Carlini, A.; Hosoya, A.

    2001-02-01

    Grover's quantum algorithm for an unstructured search problem and the COUNT algorithm by Brassard et al. are generalized to the case when the initial state is arbitrarily and maximally entangled. This ansatz might be relevant with quantum subroutines, when the computational qubits and the environment are coupled, and in general when the control over the quantum system is partial.

  15. Multimedia explorer: image database, image proxy-server and search-engine.

    PubMed Central

    Frankewitsch, T.; Prokosch, U.

    1999-01-01

    Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval. PMID:10566463

  16. Searching via walking: How to find a marked clique of a complete graph using quantum walks

    SciTech Connect

    Hillery, Mark; Reitzner, Daniel; Buzek, Vladimir

    2010-06-15

    We show how a quantum walk can be used to find a marked edge or a marked complete subgraph of a complete graph. We employ a version of a quantum walk, the scattering walk, which lends itself to experimental implementation. The edges are marked by adding elements to them that impart a specific phase shift to the particle as it enters or leaves the edge. If the complete graph has N vertices and the subgraph has K vertices, the particle becomes localized on the subgraph in O(N/K) steps. This leads to a quantum search that is quadratically faster than a corresponding classical search. We show how to implement the quantum walk using a quantum circuit and a quantum oracle, which allows us to specify the resources needed for a quantitative comparison of the efficiency of classical and quantum searches--the number of oracle calls.

  17. Quantum search algorithm tailored to clause-satisfaction problems

    NASA Astrophysics Data System (ADS)

    Tulsi, Avatar

    2015-05-01

    Many important computer science problems can be reduced to the clause-satisfaction problem. We are given n Boolean variables xk and m clauses cj where each clause is a function of values of some xk. We want to find an assignment i of xk for which all m clauses are satisfied. Let fj(i ) be a binary function, which is 1 if the j th clause is satisfied by the assignment i , else fj(i ) =0 . Then the solution is r for which f (i =r )=1 , where f (i ) is the and function of all fj(i ) . In quantum computing, Grover's algorithm can be used to find r . A crucial component of this algorithm is the selective phase inversion Ir of the solution state encoding r . Ir is implemented by computing f (i ) for all i in superposition which requires computing and of all m binary functions fj(i ) . Hence there must be coupling between the computation circuits for each fj(i ) . In this paper, we present an alternative quantum search algorithm which relaxes the requirement of such couplings. Hence it offers implementation advantages for clause-satisfaction problems.

  18. A Novel Concept for the Search and Retrieval of the Derwent Markush Resource Database.

    PubMed

    Barth, Andreas; Stengel, Thomas; Litterst, Edwin; Kraut, Hans; Matuszczyk, Henry; Ailer, Franz; Hajkowski, Steve

    2016-05-23

    The representation of and search for generic chemical structures (Markush) remains a continuing challenge. Several research groups have addressed this problem, and over time a limited number of practical solutions have been proposed. Today there are two large commercial providers of Markush databases: Chemical Abstracts Service (CAS) and Thomson Reuters. The Thomson Reuters "Derwent" Markush database is currently offered via the online services Questel and STN and as a data feed for in-house use. The aim of this paper is to briefly review the existing Markush systems (databases plus search engines) and to describe our new approach for the implementation of the Derwent Markush Resource on STN. Our new approach demonstrates the integration of the Derwent Markush Resource database into the existing chemistry-focused STN platform without loss of detail. This provides compatibility with other structure and Markush databases on STN and at the same time makes it possible to deploy the specific features and functions of the Derwent approach. It is shown that the different Markush languages developed by CAS and Derwent can be combined into a single general Markush description. In this concept the generic nodes are grouped together in a unique hierarchy where all chemical elements and fragments can be integrated. As a consequence, both systems are searchable using a single structure query. Moreover, the presented concept could serve as a promising starting point for a common generalized description of Markush structures.

  19. Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

    PubMed

    Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

    2016-01-01

    Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

  20. Searching molecular structure databases with tandem mass spectra using CSI:FingerID

    PubMed Central

    Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

    2015-01-01

    Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543

  1. Discovery of novel mesangial cell proliferation inhibitors using a three-dimensional database searching method.

    PubMed

    Kurogi, Y; Miyata, K; Okamura, T; Hashimoto, K; Tsutsumi, K; Nasu, M; Moriyasu, M

    2001-07-05

    A three-dimensional pharmacophore model of mesangial cell (MC) proliferation inhibitors was generated from a training set of 4-(diethoxyphosphoryl)methyl-N-(3-phenyl-[1,2,4]thiadiazol-5-yl)benzamide, 2, and its derivatives using the Catalyst/HIPHOP software program. On the basis of the in vitro MC proliferation inhibitory activity, a pharmacophore model was generated as seven features consisting of two hydrophobic regions, two hydrophobic aromatic regions, and three hydrogen bond acceptors. Using this model as a three-dimensional query to search the Maybridge database, structurally novel 41 compounds were identified. The evaluation of MC proliferation inhibitory activity using available samples from the 41 identified compounds exhibited over 50% inhibitory activity at the 100 nM range. Interestingly, the newly identified compounds by the 3D database searching method exhibited the reduced inhibition of normal proximal tubular epithelial cell proliferation compared to a training set of compounds.

  2. BioSCAN: a network sharable computational resource for searching biosequence databases.

    PubMed

    Singh, R K; Hoffman, D L; Tell, S G; White, C T

    1996-06-01

    We describe a network sharable, interactive computational tool for rapid and sensitive search and analysis of biomolecular sequence databases such as GenBank, GenPept, Protein Identification Resource, and SWISS-PROT. The resource is accessible via the World Wide Web using popular client software such as Mosaic and Netscape. The client software is freely available on a number of computing platforms including Macintosh, IBM-PC, and Unix workstations.

  3. Rapid identification of anonymous subjects in large criminal databases: problems and solutions in IAFIS III/FBI subject searches

    NASA Astrophysics Data System (ADS)

    Kutzleb, C. D.

    1997-02-01

    The high incidence of recidivism (repeat offenders) in the criminal population makes the use of the IAFIS III/FBI criminal database an important tool in law enforcement. The problems and solutions employed by IAFIS III/FBI criminal subject searches are discussed for the following topics: (1) subject search selectivity and reliability; (2) the difficulty and limitations of identifying subjects whose anonymity may be a prime objective; (3) database size, search workload, and search response time; (4) techniques and advantages of normalizing the variability in an individual's name and identifying features into identifiable and discrete categories; and (5) the use of database demographics to estimate the likelihood of a match between a search subject and database subjects.

  4. Doubling the success of quantum walk search using internal-state measurements

    NASA Astrophysics Data System (ADS)

    Prūsis, Krišjānis; Vihrovs, Jevgēnijs; Wong, Thomas G.

    2016-11-01

    In typical discrete-time quantum walk algorithms, one measures the position of the walker while ignoring its internal spin/coin state. Rather than neglecting the information in this internal state, we show that additionally measuring it doubles the success probability of many quantum spatial search algorithms. For example, this allows Grover's unstructured search problem to be solved with certainty, rather than with probability 1/2 if only the walker's position is measured, so the additional measurement yields a search algorithm that is twice as fast as without it, on average. Thus the internal state of discrete-time quantum walks holds valuable information that can be utilized to improve algorithms. Furthermore, we determine conditions for which spatial search problems on regular graphs are amenable to this doubling of the success probability, and this involves diagrammatically analyzing search using degenerate perturbation theory and deriving a useful formula for how the quantum walk acts in its reduced subspace.

  5. A hybrid approach for addressing ring flexibility in 3D database searching.

    PubMed

    Sadowski, J

    1997-01-01

    A hybrid approach for flexible 3D database searching is presented that addresses the problem of ring flexibility. It combines the explicit storage of up to 25 multiple conformations of rings, with up to eight atoms, generated by the 3D structure generator CORINA with the power of a torsional fitting technique implemented in the 3D database system UNITY. A comparison with the original UNITY approach, using a database with about 130,000 entries and five different pharmacophore queries, was performed. The hybrid approach scored, on an average, 10-20% more hits than the reference run. Moreover, specific problems with unrealistic hit geometries produced by the original approach can be excluded. In addition, the influence of the maximum number of ring conformations per molecule was investigated. An optimal number of 10 conformations per molecule is recommended.

  6. Practical private database queries based on a quantum-key-distribution protocol

    SciTech Connect

    Jakobi, Markus; Simon, Christoph; Gisin, Nicolas; Bancal, Jean-Daniel; Branciard, Cyril; Walenta, Nino; Zbinden, Hugo

    2011-02-15

    Private queries allow a user, Alice, to learn an element of a database held by a provider, Bob, without revealing which element she is interested in, while limiting her information about the other elements. We propose to implement private queries based on a quantum-key-distribution protocol, with changes only in the classical postprocessing of the key. This approach makes our scheme both easy to implement and loss tolerant. While unconditionally secure private queries are known to be impossible, we argue that an interesting degree of security can be achieved by relying on fundamental physical principles instead of unverifiable security assumptions in order to protect both the user and the database. We think that the scope exists for such practical private queries to become another remarkable application of quantum information in the footsteps of quantum key distribution.

  7. Fast multiresolution search algorithm for optimal retrieval in large multimedia databases

    NASA Astrophysics Data System (ADS)

    Song, Byung C.; Kim, Myung J.; Ra, Jong Beom

    1999-12-01

    Most of the content-based image retrieval systems require a distance computation for each candidate image in the database. As a brute-force approach, the exhaustive search can be employed for this computation. However, this exhaustive search is time-consuming and limits the usefulness of such systems. Thus, there is a growing demand for a fast algorithm which provides the same retrieval results as the exhaustive search. In this paper, we prose a fast search algorithm based on a multi-resolution data structure. The proposed algorithm computes the lower bound of distance at each level and compares it with the latest minimum distance, starting from the low-resolution level. Once it is larger than the latest minimum distance, we can exclude the candidates without calculating the full- resolution distance. By doing this, we can dramatically reduce the total computational complexity. It is noticeable that the proposed fast algorithm provides not only the same retrieval results as the exhaustive search, but also a faster searching ability than existing fast algorithms. For additional performance improvement, we can easily combine the proposed algorithm with existing tree-based algorithms. The algorithm can also be used for the fast matching of various features such as luminance histograms, edge images, and local binary partition textures.

  8. A grammar based methodology for structural motif finding in ncRNA database search.

    PubMed

    Quest, Daniel; Tapprich, William; Ali, Hesham

    2007-01-01

    In recent years, sequence database searching has been conducted through local alignment heuristics, pattern-matching, and comparison of short statistically significant patterns. While these approaches have unlocked many clues as to sequence relationships, they are limited in that they do not provide context-sensitive searching capabilities (e.g. considering pseudoknots, protein binding positions, and complementary base pairs). Stochastic grammars (hidden Markov models HMMs and stochastic context-free grammars SCFG) do allow for flexibility in terms of local context, but the context comes at the cost of increased computational complexity. In this paper we introduce a new grammar based method for searching for RNA motifs that exist within a conserved RNA structure. Our method constrains computational complexity by using a chain of topology elements. Through the use of a case study we present the algorithmic approach and benchmark our approach against traditional methods.

  9. Pharmacophore modeling and three-dimensional database searching for drug design using catalyst.

    PubMed

    Kurogi, Y; Güner, O F

    2001-07-01

    Perceiving a pharmacophore is the first essential step towards understanding the interaction between a receptor and a ligand. Once a pharmacophore is established, a beneficial use of it is 3D database searching to retrieve novel compounds that would match the pharmacophore, without necessarily duplicating the topological features of known active compounds (hence remain independent of existing patents). As the 3D searching technology has evolved over the years, it has been effectively used for lead optimization, combinatorial library focusing, as well as virtual high-throughput screening. Clearly established as one of the successful computational tools in rational drug design, we present in this review article a brief history of the evolution of this technology and detailed algorithms of Catalyst, the latest 3D searching software to be released. We also provide brief summary of published successes with this technology, including two recent patent applications.

  10. Searching via walking: How to find a marked clique of a complete graph using quantum walks

    NASA Astrophysics Data System (ADS)

    Hillery, Mark; Reitzner, Daniel; Bužek, Vladimír

    2010-06-01

    We show how a quantum walk can be used to find a marked edge or a marked complete subgraph of a complete graph. We employ a version of a quantum walk, the scattering walk, which lends itself to experimental implementation. The edges are marked by adding elements to them that impart a specific phase shift to the particle as it enters or leaves the edge. If the complete graph has N vertices and the subgraph has K vertices, the particle becomes localized on the subgraph in O(N/K) steps. This leads to a quantum search that is quadratically faster than a corresponding classical search. We show how to implement the quantum walk using a quantum circuit and a quantum oracle, which allows us to specify the resources needed for a quantitative comparison of the efficiency of classical and quantum searches—the number of oracle calls.

  11. The effect of wild card designations and rare alleles in forensic DNA database searches.

    PubMed

    Tvedebrink, Torben; Bright, Jo-Anne; Buckleton, John S; Curran, James M; Morling, Niels

    2015-05-01

    Forensic DNA databases are powerful tools used for the identification of persons of interest in criminal investigations. Typically, they consist of two parts: (1) a database containing DNA profiles of known individuals and (2) a database of DNA profiles associated with crime scenes. The risk of adventitious or chance matches between crimes and innocent people increases as the number of profiles within a database grows and more data is shared between various forensic DNA databases, e.g. from different jurisdictions. The DNA profiles obtained from crime scenes are often partial because crime samples may be compromised in quantity or quality. When an individual's profile cannot be resolved from a DNA mixture, ambiguity is introduced. A wild card, F, may be used in place of an allele that has dropped out or when an ambiguous profile is resolved from a DNA mixture. Variant alleles that do not correspond to any marker in the allelic ladder or appear above or below the extent of the allelic ladder range are assigned the allele designation R for rare allele. R alleles are position specific with respect to the observed/unambiguous allele. The F and R designations are made when the exact genotype has not been determined. The F and R designation are treated as wild cards for searching, which results in increased chance of adventitious matches. We investigated the probability of adventitious matches given these two types of wild cards.

  12. General Quantum Meet-in-the-Middle Search Algorithm Based on Target Solution of Fixed Weight

    NASA Astrophysics Data System (ADS)

    Fu, Xiang-Qun; Bao, Wan-Su; Wang, Xiang; Shi, Jian-Hong

    2016-10-01

    Similar to the classical meet-in-the-middle algorithm, the storage and computation complexity are the key factors that decide the efficiency of the quantum meet-in-the-middle algorithm. Aiming at the target vector of fixed weight, based on the quantum meet-in-the-middle algorithm, the algorithm for searching all n-product vectors with the same weight is presented, whose complexity is better than the exhaustive search algorithm. And the algorithm can reduce the storage complexity of the quantum meet-in-the-middle search algorithm. Then based on the algorithm and the knapsack vector of the Chor-Rivest public-key crypto of fixed weight d, we present a general quantum meet-in-the-middle search algorithm based on the target solution of fixed weight, whose computational complexity is \\sumj = 0d {(O(\\sqrt {Cn - k + 1d - j }) + O(C_kj log C_k^j))} with Σd i =0 Ck i memory cost. And the optimal value of k is given. Compared to the quantum meet-in-the-middle search algorithm for knapsack problem and the quantum algorithm for searching a target solution of fixed weight, the computational complexity of the algorithm is lower. And its storage complexity is smaller than the quantum meet-in-the-middle-algorithm. Supported by the National Basic Research Program of China under Grant No. 2013CB338002 and the National Natural Science Foundation of China under Grant No. 61502526

  13. The Use of Research Electronic Data Capture (REDCap) Software to Create a Database of Librarian-Mediated Literature Searches

    PubMed Central

    LYON, JENNIFER A.; GARCIA-MILIAN, ROLANDO; NORTON, HANNAH F.; TENNANT, MICHELE R.

    2015-01-01

    Expert-mediated literature searching, a keystone service in biomedical librarianship, would benefit significantly from regular methodical review. This paper describes the novel use of Research Electronic Data Capture (REDCap) software to create a database of literature searches conducted at a large academic health sciences library. An archive of paper search requests was entered into REDCap, and librarians now prospectively enter records for current searches. Having search data readily available allows librarians to reuse search strategies and track their workload. In aggregate, this data can help guide practice and determine priorities by identifying users’ needs, tracking librarian effort, and focusing librarians’ continuing education. PMID:25023012

  14. Effects of dissipation on an adiabatic quantum search algorithm

    NASA Astrophysics Data System (ADS)

    de Vega, Inés; Bañuls, Mari Carmen; Pérez, A.

    2010-12-01

    According to recent studies (Amin et al 2008 Phys. Rev. Lett. 100 060503), the effect of a thermal bath may improve the performance of a quantum adiabatic search algorithm. In this paper, we compare the effects of such a thermal environment on the algorithm performance with those of a structured environment similar to the one encountered in systems coupled to an electromagnetic field that exists within a photonic crystal. Whereas for all the parameter regimes explored here, the algorithm performance is worsened by contact with a thermal environment, the picture appears to be different when one considers a structured environment. In this case we show that by tuning the environment parameters to certain regimes, the algorithm performance can actually be improved with respect to the closed system case. Additionally, the relevance of considering the dissipation rates as complex quantities is discussed in both cases. More specifically, we find that the imaginary part of the rates cannot be neglected with the usual argument that it simply amounts to an energy shift and in fact influences crucially the system dynamics.

  15. Searching for patterns in remote sensing image databases using neural networks

    NASA Technical Reports Server (NTRS)

    Paola, Justin D.; Schowengerdt, Robert A.

    1995-01-01

    We have investigated a method, based on a successful neural network multispectral image classification system, of searching for single patterns in remote sensing databases. While defining the pattern to search for and the feature to be used for that search (spectral, spatial, temporal, etc.) is challenging, a more difficult task is selecting competing patterns to train against the desired pattern. Schemes for competing pattern selection, including random selection and human interpreted selection, are discussed in the context of an example detection of dense urban areas in Landsat Thematic Mapper imagery. When applying the search to multiple images, a simple normalization method can alleviate the problem of inconsistent image calibration. Another potential problem, that of highly compressed data, was found to have a minimal effect on the ability to detect the desired pattern. The neural network algorithm has been implemented using the PVM (Parallel Virtual Machine) library and nearly-optimal speedups have been obtained that help alleviate the long process of searching through imagery.

  16. Data Analysis Provenance: Use Case for Exoplanet Search in CoRoT Database

    NASA Astrophysics Data System (ADS)

    de Souza, L.; Salete Marcon Gomes Vaz, M.; Emílio, M.; Ferreira da Rocha, J. C.; Janot Pacheco, E.; Carlos Boufleur, R.

    2012-09-01

    CoRoT (COnvection Rotation and Planetary Transits) is a mission led by the French national space agency CNES, in collaboration with Austria, Spain, Germany, Belgium and Brazil. The mission priority is dedicated to exoplanet search and stellar seismology. CoRoT light curves database became public after one year of their delivery to the CoRoT Co-Is, following the CoRoT data policy. The CoRoT archive contains thousands of light curves in FITS format. Several exoplanet search algorithms require detrend algorithms to remove both stellar and instrumental signal, improving the chance to detect a transit. Different detrend and transit detection algorithms can be applied to the same database. Tracking the origin of the information and how the data was derived in each level in the data analysis process is essential to allow sharing, reuse, reprocessing and further analysis. This work aims at applying a formalized and codified knowledge model by means of domain ontology. It allows to enrich the data analysis with semantic and standardization. It holds the provenance information in the database for a posteriori recovers by humans or software agents.

  17. Exploring Multidisciplinary Data Sets through Database Driven Search Capabilities and Map-Based Web Services

    NASA Astrophysics Data System (ADS)

    O'Hara, S.; Ferrini, V.; Arko, R.; Carbotte, S. M.; Leung, A.; Bonczkowski, J.; Goodwillie, A.; Ryan, W. B.; Melkonian, A. K.

    2008-12-01

    Relational databases containing geospatially referenced data enable the construction of robust data access pathways that can be customized to suit the needs of a diverse user community. Web-based search capabilities driven by radio buttons and pull-down menus can be generated on-the-fly leveraging the power of the relational database and providing specialists a means of discovering specific data and data sets. While these data access pathways are sufficient for many scientists, map-based data exploration can also be an effective means of data discovery and integration by allowing users to rapidly assess the spatial co- registration of several data types. We present a summary of data access tools currently provided by the Marine Geoscience Data System (www.marine-geo.org) that are intended to serve a diverse community of users and promote data integration. Basic search capabilities allow users to discover data based on data type, device type, geographic region, research program, expedition parameters, personnel and references. In addition, web services are used to create database driven map interfaces that provide live access to metadata and data files.

  18. EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities

    PubMed Central

    Hsin, Kun-Yi; Morgan, Hugh P.; Shave, Steven R.; Hinton, Andrew C.; Taylor, Paul; Walkinshaw, Malcolm D.

    2011-01-01

    We present the relational database EDULISS (EDinburgh University Ligand Selection System), which stores structural, physicochemical and pharmacophoric properties of small molecules. The database comprises a collection of over 4 million commercially available compounds from 28 different suppliers. A user-friendly web-based interface for EDULISS (available at http://eduliss.bch.ed.ac.uk/) has been established providing a number of data-mining possibilities. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for unique compound recognition, especially for a large scale database, is demonstrated by making use of small subgroups of the descriptors. Many of the shape and distance descriptors are held as pre-calculated bit strings permitting fast and efficient similarity and pharmacophore searches which can be used to identify families of related compounds for biological testing. Two ligand searching applications are given to demonstrate how EDULISS can be used to extract families of molecules with selected structural and biophysical features. PMID:21051336

  19. A neotropical Miocene pollen database employing image-based search and semantic modeling1

    PubMed Central

    Han, Jing Ginger; Cao, Hongfei; Barb, Adrian; Punyasena, Surangi W.; Jaramillo, Carlos; Shyu, Chi-Ren

    2014-01-01

    • Premise of the study: Digital microscopic pollen images are being generated with increasing speed and volume, producing opportunities to develop new computational methods that increase the consistency and efficiency of pollen analysis and provide the palynological community a computational framework for information sharing and knowledge transfer. • Methods: Mathematical methods were used to assign trait semantics (abstract morphological representations) of the images of neotropical Miocene pollen and spores. Advanced database-indexing structures were built to compare and retrieve similar images based on their visual content. A Web-based system was developed to provide novel tools for automatic trait semantic annotation and image retrieval by trait semantics and visual content. • Results: Mathematical models that map visual features to trait semantics can be used to annotate images with morphology semantics and to search image databases with improved reliability and productivity. Images can also be searched by visual content, providing users with customized emphases on traits such as color, shape, and texture. • Discussion: Content- and semantic-based image searches provide a powerful computational platform for pollen and spore identification. The infrastructure outlined provides a framework for building a community-wide palynological resource, streamlining the process of manual identification, analysis, and species discovery. PMID:25202648

  20. Associative memory model for searching an image database by image snippet

    NASA Astrophysics Data System (ADS)

    Khan, Javed I.; Yun, David Y.

    1994-09-01

    This paper presents an associative memory called an multidimensional holographic associative computing (MHAC), which can be potentially used to perform feature based image database query using image snippet. MHAC has the unique capability to selectively focus on specific segments of a query frame during associative retrieval. As a result, this model can perform search on the basis of featural significance described by a subset of the snippet pixels. This capability is critical for visual query in image database because quite often the cognitive index features in the snippet are statistically weak. Unlike, the conventional artificial associative memories, MHAC uses a two level representation and incorporates additional meta-knowledge about the reliability status of segments of information it receives and forwards. In this paper we present the analysis of focus characteristics of MHAC.

  1. Average probability that a "cold hit" in a DNA database search results in an erroneous attribution.

    PubMed

    Song, Yun S; Patil, Anand; Murphy, Erin E; Slatkin, Montgomery

    2009-01-01

    We consider a hypothetical series of cases in which the DNA profile of a crime-scene sample is found to match a known profile in a DNA database (i.e., a "cold hit"), resulting in the identification of a suspect based only on genetic evidence. We show that the average probability that there is another person in the population whose profile matches the crime-scene sample but who is not in the database is approximately 2(N - d)p(A), where N is the number of individuals in the population, d is the number of profiles in the database, and p(A) is the average match probability (AMP) for the population. The AMP is estimated by computing the average of the probabilities that two individuals in the population have the same profile. We show further that if a priori each individual in the population is equally likely to have left the crime-scene sample, then the average probability that the database search attributes the crime-scene sample to a wrong person is (N - d)p(A).

  2. rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

    PubMed Central

    Hahn, Lars; Leimeister, Chris-André; Morgenstern, Burkhard

    2016-01-01

    Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don’t-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/ PMID:27760124

  3. SAM: String-based sequence search algorithm for mitochondrial DNA database queries

    PubMed Central

    Röck, Alexander; Irwin, Jodi; Dür, Arne; Parsons, Thomas; Parson, Walther

    2011-01-01

    The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA. This convention requires recommendations for standardized sequence alignment that is known to vary between scientific disciplines, even between laboratories. As a consequence, database searches that are vital for the interpretation of mtDNA data can suffer from biased results when query and database haplotypes are annotated differently. In the forensic context that would usually lead to underestimation of the absolute and relative frequencies. To address this issue we introduce SAM, a string-based search algorithm that converts query and database sequences to position-free nucleotide strings and thus eliminates the possibility that identical sequences will be missed in a database query. The mere application of a BLAST algorithm would not be a sufficient remedy as it uses a heuristic approach and does not address properties specific to mtDNA, such as phylogenetically stable but also rapidly evolving insertion and deletion events. The software presented here provides additional flexibility to incorporate phylogenetic data, site-specific mutation rates, and other biologically relevant information that would refine the interpretation of mitochondrial DNA data. The manuscript is accompanied by freeware and example data sets that can be used to evaluate the new software (http://stringvalidation.org). PMID:21056022

  4. Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies.

    PubMed

    Blakeley, Paul; Overton, Ian M; Hubbard, Simon J

    2012-11-02

    Proteogenomics has the potential to advance genome annotation through high quality peptide identifications derived from mass spectrometry experiments, which demonstrate a given gene or isoform is expressed and translated at the protein level. This can advance our understanding of genome function, discovering novel genes and gene structure that have not yet been identified or validated. Because of the high-throughput shotgun nature of most proteomics experiments, it is essential to carefully control for false positives and prevent any potential misannotation. A number of statistical procedures to deal with this are in wide use in proteomics, calculating false discovery rate (FDR) and posterior error probability (PEP) values for groups and individual peptide spectrum matches (PSMs). These methods control for multiple testing and exploit decoy databases to estimate statistical significance. Here, we show that database choice has a major effect on these confidence estimates leading to significant differences in the number of PSMs reported. We note that standard target:decoy approaches using six-frame translations of nucleotide sequences, such as assembled transcriptome data, apparently underestimate the confidence assigned to the PSMs. The source of this error stems from the inflated and unusual nature of the six-frame database, where for every target sequence there exists five "incorrect" targets that are unlikely to code for protein. The attendant FDR and PEP estimates lead to fewer accepted PSMs at fixed thresholds, and we show that this effect is a product of the database and statistical modeling and not the search engine. A variety of approaches to limit database size and remove noncoding target sequences are examined and discussed in terms of the altered statistical estimates generated and PSMs reported. These results are of importance to groups carrying out proteogenomics, aiming to maximize the validation and discovery of gene structure in sequenced genomes

  5. The Relationship between Searches Performed in Online Databases and the Number of Full-Text Articles Accessed: Measuring the Interaction between Database and E-Journal Collections

    ERIC Educational Resources Information Center

    Lamothe, Alain R.

    2011-01-01

    The purpose of this paper is to report the results of a quantitative analysis exploring the interaction and relationship between the online database and electronic journal collections at the J. N. Desmarais Library of Laurentian University. A very strong relationship exists between the number of searches and the size of the online database…

  6. MHC-I ligand discovery using targeted database searches of mass spectrometry data: Implications for T cell immunotherapies.

    PubMed

    Murphy, John Patrick; Konda, Prathyusha; Kowalewski, Daniel J; Schuster, Heiko; Clements, Derek; Kim, Youra; Cohen, Alejandro Martin; Sharif, Tanveer; Nielsen, Morten; Stevanović, Stefan; Lee, Patrick W; Gujar, Shashi

    2017-02-28

    Class I major histocompatibility complex I (MHC-I)-bound peptide ligands dictate the activation and specificity of CD8+ T-cells, and thus are important for devising T cell immunotherapies. In recent times, advances in mass spectrometry (MS) have enabled the precise identification of these MHC-I peptides wherein MS spectra are compared against a reference proteome. Unfortunately, matching these spectra to reference proteome databases is hindered by inflated search spaces attributed to a lack of enzyme restriction in the searches, limiting the efficiency with which MHC ligands are discovered. Here, we offer a solution to this problem whereby we developed a targeted database search approach, and accompanying tool SpectMHC, that is based on a priori-predicted MHC-I peptides. We first validated the approach using mass spectrometry data from 2 different allotype-specific mouse antibodies for the C57BL/6 mouse background. We then developed allotype-specific HLA databases to search previously published MS datasets of human peripheral blood mononuclear cells (PBMCs). Using this targeted search strategy improved peptide identifications for both mouse and human ligandomes by greater than two-fold and is superior to traditional "no enzyme" searches of reference proteomes. Our novel targeted database search promises to uncover otherwise missed novel T cell epitopes of therapeutic potential.

  7. Quantum exhaustive key search with simplified-DES as a case study.

    PubMed

    Almazrooie, Mishal; Samsudin, Azman; Abdullah, Rosni; Mutter, Kussay N

    2016-01-01

    To evaluate the security of a symmetric cryptosystem against any quantum attack, the symmetric algorithm must be first implemented on a quantum platform. In this study, a quantum implementation of a classical block cipher is presented. A quantum circuit for a classical block cipher of a polynomial size of quantum gates is proposed. The entire work has been tested on a quantum mechanics simulator called libquantum. First, the functionality of the proposed quantum cipher is verified and the experimental results are compared with those of the original classical version. Then, quantum attacks are conducted by using Grover's algorithm to recover the secret key. The proposed quantum cipher is used as a black box for the quantum search. The quantum oracle is then queried over the produced ciphertext to mark the quantum state, which consists of plaintext and key qubits. The experimental results show that for a key of n-bit size and key space of N such that [Formula: see text], the key can be recovered in [Formula: see text] computational steps.

  8. Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

    PubMed Central

    Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

    2016-01-01

    Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs. PMID:27929431

  9. Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science.

    PubMed

    Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

    2016-12-06

    Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

  10. Real-Time Ligand Binding Pocket Database Search Using Local Surface Descriptors

    PubMed Central

    Chikhi, Rayan; Sael, Lee; Kihara, Daisuke

    2010-01-01

    Due to the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of a particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two dimensional pseudo-Zernike moments or the 3D Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark study employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed. PMID:20455259

  11. Fine-grained Database Field Search Using Attribute-Based Encryption for E-Healthcare Clouds.

    PubMed

    Guo, Cheng; Zhuang, Ruhan; Jie, Yingmo; Ren, Yizhi; Wu, Ting; Choo, Kim-Kwang Raymond

    2016-11-01

    An effectively designed e-healthcare system can significantly enhance the quality of access and experience of healthcare users, including facilitating medical and healthcare providers in ensuring a smooth delivery of services. Ensuring the security of patients' electronic health records (EHRs) in the e-healthcare system is an active research area. EHRs may be outsourced to a third-party, such as a community healthcare cloud service provider for storage due to cost-saving measures. Generally, encrypting the EHRs when they are stored in the system (i.e. data-at-rest) or prior to outsourcing the data is used to ensure data confidentiality. Searchable encryption (SE) scheme is a promising technique that can ensure the protection of private information without compromising on performance. In this paper, we propose a novel framework for controlling access to EHRs stored in semi-trusted cloud servers (e.g. a private cloud or a community cloud). To achieve fine-grained access control for EHRs, we leverage the ciphertext-policy attribute-based encryption (CP-ABE) technique to encrypt tables published by hospitals, including patients' EHRs, and the table is stored in the database with the primary key being the patient's unique identity. Our framework can enable different users with different privileges to search on different database fields. Differ from previous attempts to secure outsourcing of data, we emphasize the control of the searches of the fields within the database. We demonstrate the utility of the scheme by evaluating the scheme using datasets from the University of California, Irvine.

  12. Designing novel nicotinic agonists by searching a database of molecular shapes

    NASA Astrophysics Data System (ADS)

    Sheridan, Robert P.; Venkataraghavan, R.

    1987-10-01

    We introduce an approach by which novel ligands can be designed for a receptor if a pharmacophore geometry has been established and the receptor-bound conformations of other ligands are known. We use the shape-matching method of Kuntz et al. [J. Mol. Biol., 161 (1982) 269-288] to search a database of molecular shapes for those molecules which can fit inside the combined volume of the known ligands and which have interatomic distances compatible with the pharmacophore geometry. Some of these molecules are then modified by interactive modeling techniques to better match the chemical properties of the known ligands. Our shape database (about 5000 candidate molecules) is derived from a subset of the Cambridge Crystallographic Database [Allen et al., Acta Crystallogr., Sect. B,35 (1979) 2331-2339]. We show, as an example, how several novel designs for nicotinic agonists can be derived by this approach, given a pharmacophore model derived from known agonists [Sheridan et al., J. Med. Chem., 29 (1986) 889-906]. This report complements our previous report [DesJarlais et al., J. Med. Chem., in press], which introduced a similar method for designing ligands when the structure of the receptor is known.

  13. ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.

    PubMed

    Rognes, T

    2001-04-01

    There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of this technology. The new algorithm initially exploits parallelism to perform a very rapid computation of the exact optimal ungapped alignment score for all diagonals in the alignment matrix. Then, a novel heuristic is employed to compute an approximate score of a gapped alignment by combining the scores of several diagonals. This approximate score is used to select the most interesting database sequences for a subsequent Smith-Waterman alignment, which is also parallelised. The resulting method represents a substantial improvement compared to existing heuristics. The sensitivity and specificity of ParAlign was found to be as good as Smith-Waterman implementations when the same method for computing the statistical significance of the matches was used. In terms of speed, only the significantly less sensitive NCBI BLAST 2 program was found to outperform the new approach. Online searches are available at http://dna.uio.no/search/

  14. Seismic Search Engine: A distributed database for mining large scale seismic data

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Vaidya, S.; Kuzma, H. A.

    2009-12-01

    The International Monitoring System (IMS) of the CTBTO collects terabytes worth of seismic measurements from many receiver stations situated around the earth with the goal of detecting underground nuclear testing events and distinguishing them from other benign, but more common events such as earthquakes and mine blasts. The International Data Center (IDC) processes and analyzes these measurements, as they are collected by the IMS, to summarize event detections in daily bulletins. Thereafter, the data measurements are archived into a large format database. Our proposed Seismic Search Engine (SSE) will facilitate a framework for data exploration of the seismic database as well as the development of seismic data mining algorithms. Analogous to GenBank, the annotated genetic sequence database maintained by NIH, through SSE, we intend to provide public access to seismic data and a set of processing and analysis tools, along with community-generated annotations and statistical models to help interpret the data. SSE will implement queries as user-defined functions composed from standard tools and models. Each query is compiled and executed over the database internally before reporting results back to the user. Since queries are expressed with standard tools and models, users can easily reproduce published results within this framework for peer-review and making metric comparisons. As an illustration, an example query is “what are the best receiver stations in East Asia for detecting events in the Middle East?” Evaluating this query involves listing all receiver stations in East Asia, characterizing known seismic events in that region, and constructing a profile for each receiver station to determine how effective its measurements are at predicting each event. The results of this query can be used to help prioritize how data is collected, identify defective instruments, and guide future sensor placements.

  15. Integration of first-principles methods and crystallographic database searches for new ferroelectrics: Strategies and explorations

    NASA Astrophysics Data System (ADS)

    Bennett, Joseph W.; Rabe, Karin M.

    2012-11-01

    In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb1/2Mn1/2)O3 as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb2O4; and (3) ferroelectric semiconductors with formula M2P2(S,Se)6. A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties.

  16. Internet programs for drawing moth pheromone analogs and searching literature database.

    PubMed

    Byers, John A

    2002-04-01

    An Internet web page is described for organizing and analyzing information about lepidopteran sex pheromone components. Hypertext markup language (HTML) with JavaScript program code is used to draw moth pheromone analogs by combining GIF bitmap images for viewing by web browsers such as Netscape or Microsoft Intemet Explorer. Straight-chain hydrocarbons of 5-22 carbons with epoxides or unsaturated positions of E or Z geometrical configuration with several altemative functional groups can be drawn by simply checking menu bars or checkboxes representing chain length, E/Z unsaturation points, epoxide position and chirality, and optional functional groups. The functional group can be an aldehyde, alcohol, or ester of formate, acetate, propionate, or butyrate. The program is capable of drawing several million structures and naming them [e.g., (E,E)-8,10-dodecadien-1-ol and abbreviated as E8E10-12:OH]. A Java applet program run from the same page searches forthe presently drawn structure in an intemal database compiled from the Pherolist, and if the component is found, provides a textarea display of the families and species using the component. Links are automatically specified for drawn components if found in the Pherolist web site (maintained by H. Am). Windowed links can also be made to two other JavaScript programs that allow searches of a web site database with over 5900 research citations on lepidopteran semiochemicals and a calculator of vapor pressures of some moth sex pheromone analogs at a specified temperature. Various evolutionary and biosynthetic aspects are discussed in regard to the diversity of moth sex pheromone components.

  17. Proteomics of Soil and Sediment: Protein Identification by De Novo Sequencing of Mass Spectra Complements Traditional Database Searching

    NASA Astrophysics Data System (ADS)

    Miller, S.; Rizzo, A. I.; Waldbauer, J.

    2014-12-01

    Proteomics has the potential to elucidate the metabolic pathways and taxa responsible for in situ biogeochemical transformations. However, low rates of protein identification from high resolution mass spectra have been a barrier to the development of proteomics in complex environmental samples. Much of the difficulty lies in the computational challenge of linking mass spectra to their corresponding proteins. Traditional database search methods for matching peptide sequences to mass spectra are often inadequate due to the complexity of environmental proteomes and the large database search space, as we demonstrate with soil and sediment proteomes generated via a range of extraction methods. One alternative to traditional database searching is de novo sequencing, which identifies peptide sequences without the need for a database. BLAST can then be used to match de novo sequences to similar genetic sequences. Assigning confidence to putative identifications has been one hurdle for the implementation of de novo sequencing. We found that accurate de novo sequences can be screened by quality score and length. Screening criteria are verified by comparing the results of de novo sequencing and traditional database searching for well-characterized proteomes from simple biological systems. The BLAST hits of screened sequences are interrogated for taxonomic and functional information. We applied de novo sequencing to organic topsoil and marine sediment proteomes. Peak-rich proteomes, which can result from various extraction techniques, yield thousands of high-confidence protein identifications, an improvement over previous proteomic studies of soil and sediment. User-friendly software tools for de novo metaproteomics analysis have been developed. This "De Novo Analysis" Pipeline is also a faster method of data analysis than constructing a tailored sequence database for traditional database searching.

  18. Proteomics of Soil and Sediment: Protein Identification by De Novo Sequencing of Mass Spectra Complements Traditional Database Searching

    NASA Astrophysics Data System (ADS)

    Miller, S.; Rizzo, A. I.; Waldbauer, J.

    2015-12-01

    Proteomics has the potential to elucidate the metabolic pathways and taxa responsible for in situ biogeochemical transformations. However, low rates of protein identification from high resolution mass spectra have been a barrier to the development of proteomics in complex environmental samples. Much of the difficulty lies in the computational challenge of linking mass spectra to their corresponding proteins. Traditional database search methods for matching peptide sequences to mass spectra are often inadequate due to the complexity of environmental proteomes and the large database search space, as we demonstrate with soil and sediment proteomes generated via a range of extraction methods. One alternative to traditional database searching is de novo sequencing, which identifies peptide sequences without the need for a database. BLAST can then be used to match de novo sequences to similar genetic sequences. Assigning confidence to putative identifications has been one hurdle for the implementation of de novo sequencing. We found that accurate de novo sequences can be screened by quality score and length. Screening criteria are verified by comparing the results of de novo sequencing and traditional database searching for well-characterized proteomes from simple biological systems. The BLAST hits of screened sequences are interrogated for taxonomic and functional information. We applied de novo sequencing to organic topsoil and marine sediment proteomes. Peak-rich proteomes, which can result from various extraction techniques, yield thousands of high-confidence protein identifications, an improvement over previous proteomic studies of soil and sediment. User-friendly software tools for de novo metaproteomics analysis have been developed. This "De Novo Analysis" Pipeline is also a faster method of data analysis than constructing a tailored sequence database for traditional database searching.

  19. webPRC: the Profile Comparer for alignment-based searching of public domain databases.

    PubMed

    Brandt, Bernd W; Heringa, Jaap

    2009-07-01

    Profile-profile methods are well suited to detect remote evolutionary relationships between protein families. Profile Comparer (PRC) is an existing stand-alone program for scoring and aligning hidden Markov models (HMMs), which are based on multiple sequence alignments. Since PRC compares profile HMMs instead of sequences, it can be used to find distant homologues. For this purpose, PRC is used by, for example, the CATH and Pfam-domain databases. As PRC is a profile comparer, it only reports profile HMM alignments and does not produce multiple sequence alignments. We have developed webPRC server, which makes it straightforward to search for distant homologues or similar alignments in a number of domain databases. In addition, it provides the results both as multiple sequence alignments and aligned HMMs. Furthermore, the user can view the domain annotation, evaluate the PRC hits with the Jalview multiple alignment editor and generate logos from the aligned HMMs or the aligned multiple alignments. Thus, this server assists in detecting distant homologues with PRC as well as in evaluating and using the results. The webPRC interface is available at http://www.ibi.vu.nl/programs/prcwww/.

  20. Neuron-Miner: An Advanced Tool for Morphological Search and Retrieval in Neuroscientific Image Databases.

    PubMed

    Conjeti, Sailesh; Mesbah, Sepideh; Negahdar, Mohammadreza; Rautenberg, Philipp L; Zhang, Shaoting; Navab, Nassir; Katouzian, Amin

    2016-10-01

    The steadily growing amounts of digital neuroscientific data demands for a reliable, systematic, and computationally effective retrieval algorithm. In this paper, we present Neuron-Miner, which is a tool for fast and accurate reference-based retrieval within neuron image databases. The proposed algorithm is established upon hashing (search and retrieval) technique by employing multiple unsupervised random trees, collectively called as Hashing Forests (HF). The HF are trained to parse the neuromorphological space hierarchically and preserve the inherent neuron neighborhoods while encoding with compact binary codewords. We further introduce the inverse-coding formulation within HF to effectively mitigate pairwise neuron similarity comparisons, thus allowing scalability to massive databases with little additional time overhead. The proposed hashing tool has superior approximation of the true neuromorphological neighborhood with better retrieval and ranking performance in comparison to existing generalized hashing methods. This is exhaustively validated by quantifying the results over 31266 neuron reconstructions from Neuromorpho.org dataset curated from 147 different archives. We envisage that finding and ranking similar neurons through reference-based querying via Neuron Miner would assist neuroscientists in objectively understanding the relationship between neuronal structure and function for applications in comparative anatomy or diagnosis.

  1. A method for fast database search for all k-nucleotide repeats.

    PubMed Central

    Benson, G; Waterman, M S

    1994-01-01

    A significant portion of DNA consists of repeating patterns of various sizes, from very small (one, two and three nucleotides) to very large (over 300 nucleotides). Although the functions of these repeating regions are not well understood, they appear important for understanding the expression, regulation and evolution of DNA. For example, increases in the number of trinucleotide repeats have been associated with human genetic disease, including Fragile-X mental retardation and Huntington's disease. Repeats are also useful as a tool in mapping and identifying DNA; the number of copies of a particular pattern at a site is often variable among individuals (polymorphic) and is therefore helpful in locating genes via linkage studies and also in providing DNA fingerprints of individuals. The number of repeating regions is unknown as is the distribution of pattern sizes. It would be useful to search for such regions in the DNA database in order that they may be studied more fully. The DNA database currently consists of approximately 150 million basepairs and is growing exponentially. Therefore, any program to look for repeats must be efficient and fast. In this paper, we present some new techniques that are useful in recognizing repeating patterns and describe a new program for rapidly detecting repeat regions in the DNA database where the basic unit of the repeat has size up to 32 nucleotides. It is our hope that the examples in this paper will illustrate the unrealized diversity of repeats in DNA and that the program we have developed will be a useful tool for locating new and interesting repeats. PMID:7984436

  2. MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites.

    PubMed

    Golovin, Adel; Dimitropoulos, Dimitris; Oldfield, Tom; Rachedi, Abdelkrim; Henrick, Kim

    2005-01-01

    The three-dimensional environments of ligand binding sites have been derived from the parsing and loading of the PDB entries into a relational database. For each bound molecule the biological assembly of the quaternary structure has been used to determine all contact residues and a fast interactive search and retrieval system has been developed. Prosite pattern and short sequence search options are available together with a novel graphical query generator for inter-residue contacts. The database and its query interface are accessible from the Internet through a web server located at: http://www.ebi.ac.uk/msd-srv/msdsite.

  3. 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

  4. 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.

  5. Renormalization group for a continuous-time quantum search in finite dimensions

    NASA Astrophysics Data System (ADS)

    Li, Shanshan; Boettcher, Stefan

    2017-03-01

    We consider the quantum search problem with a continuous-time quantum walk for networks characterized by a finite spectral dimension ds of the network Laplacian. For general networks of fractal (integer or noninteger) dimension df, for which in general df≠ds , it suggests that it is ds that determines the computational complexity of the quantum search. Our results continue those of A. M. Childs and J. Goldstone [Phys. Rev. A 70, 022314 (2004), 10.1103/PhysRevA.70.022314] for lattices of integer dimension, where d =df=ds . Thus, we find for general fractals that the Grover limit of quantum search can be obtained whenever ds>4 . This complements the recent discussion of mean-field (i.e., ds→∞ ) networks by S. Chakraborty et al. [Phys. Rev. Lett. 116, 100501 (2016), 10.1103/PhysRevLett.116.100501] showing that for all those networks, spatial search by quantum walk is optimal.

  6. Performing private database queries in a real-world environment using a quantum protocol

    NASA Astrophysics Data System (ADS)

    Chan, Philip; Lucio-Martinez, Itzel; Mo, Xiaofan; Simon, Christoph; Tittel, Wolfgang

    2014-06-01

    In the well-studied cryptographic primitive 1-out-of-N oblivious transfer, a user retrieves a single element from a database of size N without the database learning which element was retrieved. While it has previously been shown that a secure implementation of 1-out-of-N oblivious transfer is impossible against arbitrarily powerful adversaries, recent research has revealed an interesting class of private query protocols based on quantum mechanics in a cheat sensitive model. Specifically, a practical protocol does not need to guarantee that the database provider cannot learn what element was retrieved if doing so carries the risk of detection. The latter is sufficient motivation to keep a database provider honest. However, none of the previously proposed protocols could cope with noisy channels. Here we present a fault-tolerant private query protocol, in which the novel error correction procedure is integral to the security of the protocol. Furthermore, we present a proof-of-concept demonstration of the protocol over a deployed fibre.

  7. Performing private database queries in a real-world environment using a quantum protocol

    PubMed Central

    Chan, Philip; Lucio-Martinez, Itzel; Mo, Xiaofan; Simon, Christoph; Tittel, Wolfgang

    2014-01-01

    In the well-studied cryptographic primitive 1-out-of-N oblivious transfer, a user retrieves a single element from a database of size N without the database learning which element was retrieved. While it has previously been shown that a secure implementation of 1-out-of-N oblivious transfer is impossible against arbitrarily powerful adversaries, recent research has revealed an interesting class of private query protocols based on quantum mechanics in a cheat sensitive model. Specifically, a practical protocol does not need to guarantee that the database provider cannot learn what element was retrieved if doing so carries the risk of detection. The latter is sufficient motivation to keep a database provider honest. However, none of the previously proposed protocols could cope with noisy channels. Here we present a fault-tolerant private query protocol, in which the novel error correction procedure is integral to the security of the protocol. Furthermore, we present a proof-of-concept demonstration of the protocol over a deployed fibre. PMID:24913129

  8. Q-Learning-Based Adjustable Fixed-Phase Quantum Grover Search Algorithm

    NASA Astrophysics Data System (ADS)

    Guo, Ying; Shi, Wensha; Wang, Yijun; Hu, Jiankun

    2017-02-01

    We demonstrate that the rotation phase can be suitably chosen to increase the efficiency of the phase-based quantum search algorithm, leading to a dynamic balance between iterations and success probabilities of the fixed-phase quantum Grover search algorithm with Q-learning for a given number of solutions. In this search algorithm, the proposed Q-learning algorithm, which is a model-free reinforcement learning strategy in essence, is used for performing a matching algorithm based on the fraction of marked items λ and the rotation phase α. After establishing the policy function α = π(λ), we complete the fixed-phase Grover algorithm, where the phase parameter is selected via the learned policy. Simulation results show that the Q-learning-based Grover search algorithm (QLGA) enables fewer iterations and gives birth to higher success probabilities. Compared with the conventional Grover algorithms, it avoids the optimal local situations, thereby enabling success probabilities to approach one.

  9. Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database

    PubMed Central

    2007-01-01

    We present a novel protein structure database search tool, 3D-BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, robust statistical basis, and effective and reliable search capabilities) and employs a kappa-alpha (κ, α) plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity. PMID:17335583

  10. Complementary Value of Databases for Discovery of Scholarly Literature: A User Survey of Online Searching for Publications in Art History

    ERIC Educational Resources Information Center

    Nemeth, Erik

    2010-01-01

    Discovery of academic literature through Web search engines challenges the traditional role of specialized research databases. Creation of literature outside academic presses and peer-reviewed publications expands the content for scholarly research within a particular field. The resulting body of literature raises the question of whether scholars…

  11. Searching for NEO precoveries in the PS1 and MPC databases

    NASA Astrophysics Data System (ADS)

    Weryk, Robert J.; Wainscoat, Richard J.

    2016-10-01

    The Pan-STARRS (PS1) survey telescope, operated by the University of Hawai`i, covers the sky north of -49 degrees declination with its seven square degree field-of-view. Described in detail by Wainscoat et al. (2015), it has become the leading telescope for new Near Earth Object (NEO) discoveries. In 2015, it found almost half of the new Near Earth Asteroids, as well as half of the new comets.Observations of potential NEOs must be followed up before they can be confirmed and announced as new discoveries, and we are dependent on the follow-up capabilities of other telescopes for this. However, not every NEO candidate is immediately followed up and linked into a well established orbit, possibly due to the fact that smaller bodies may not be visible at current instrument sensitivity limits for very long, or that their predicted orbits are too uncertain so follow-up telescopes look in the wrong location. But in certain cases, these objects may have been observed during previous lunations.We present a method to search for precovery detections in both the PS1 database, and the Isolated Tracklet File (ITF) provided by the Minor Planet Center (MPC). This file contains over 12 million detections mostly from the large surveys, which are not associated with any known objects. We demonstrate that multi-tracklet linkages for both known and unknown objects may be found in these databases, including detections for both NEOs and non-NEOs which often appear on the MPC's NEO Confirmation Page.[1] Wainscoat, R. et al., IAU Symposium 318, editors S. Chesley and R. Jedicke (2015)

  12. Introducing a New Interface for the Online MagIC Database by Integrating Data Uploading, Searching, and Visualization

    NASA Astrophysics Data System (ADS)

    Jarboe, N.; Minnett, R.; Constable, C.; Koppers, A. A.; Tauxe, L.

    2013-12-01

    The Magnetics Information Consortium (MagIC) is dedicated to supporting the paleomagnetic, geomagnetic, and rock magnetic communities through the development and maintenance of an online database (http://earthref.org/MAGIC/), data upload and quality control, searches, data downloads, and visualization tools. While MagIC has completed importing some of the IAGA paleomagnetic databases (TRANS, PINT, PSVRL, GPMDB) and continues to import others (ARCHEO, MAGST and SECVR), further individual data uploading from the community contributes a wealth of easily-accessible rich datasets. Previously uploading of data to the MagIC database required the use of an Excel spreadsheet using either a Mac or PC. The new method of uploading data utilizes an HTML 5 web interface where the only computer requirement is a modern browser. This web interface will highlight all errors discovered in the dataset at once instead of the iterative error checking process found in the previous Excel spreadsheet data checker. As a web service, the community will always have easy access to the most up-to-date and bug free version of the data upload software. The filtering search mechanism of the MagIC database has been changed to a more intuitive system where the data from each contribution is displayed in tables similar to how the data is uploaded (http://earthref.org/MAGIC/search/). Searches themselves can be saved as a permanent URL, if desired. The saved search URL could then be used as a citation in a publication. When appropriate, plots (equal area, Zijderveld, ARAI, demagnetization, etc.) are associated with the data to give the user a quicker understanding of the underlying dataset. The MagIC database will continue to evolve to meet the needs of the paleomagnetic, geomagnetic, and rock magnetic communities.

  13. Low-Mode Conformational Search Method with Semiempirical Quantum Mechanical Calculations: Application to Enantioselective Organocatalysis.

    PubMed

    Kamachi, Takashi; Yoshizawa, Kazunari

    2016-02-22

    A conformational search program for finding low-energy conformations of large noncovalent complexes has been developed. A quantitatively reliable semiempirical quantum mechanical PM6-DH+ method, which is able to accurately describe noncovalent interactions at a low computational cost, was employed in contrast to conventional conformational search programs in which molecular mechanical methods are usually adopted. Our approach is based on the low-mode method whereby an initial structure is perturbed along one of its low-mode eigenvectors to generate new conformations. This method was applied to determine the most stable conformation of transition state for enantioselective alkylation by the Maruoka and cinchona alkaloid catalysts and Hantzsch ester hydrogenation of imines by chiral phosphoric acid. Besides successfully reproducing the previously reported most stable DFT conformations, the conformational search with the semiempirical quantum mechanical calculations newly discovered a more stable conformation at a low computational cost.

  14. MassMatrix: A Database Search Program for Rapid Characterization of Proteins and Peptides from Tandem Mass Spectrometry Data

    PubMed Central

    Xu, Hua; Freitas, Michael A.

    2009-01-01

    MassMatrix is a program that matches tandem mass spectra with theoretical peptide sequences derived from a protein database. The program uses a mass accuracy sensitive probabilistic score model to rank peptide matches. The tandem mass spectrometry search software was evaluated by use of a high mass accuracy data set and its results compared with those from Mascot, SEQUEST, X!Tandem, and OMSSA. For the high mass accuracy data, MassMatrix provided better sensitivity than Mascot, SEQUEST, X!Tandem, and OMSSA for a given specificity and the percentage of false positives was 2%. More importantly all manually validated true positives corresponded to a unique peptide/spectrum match. The presence of decoy sequence and additional variable post-translational modifications did not significantly affect the results from the high mass accuracy search. MassMatrix performs well when compared with Mascot, SEQUEST, X!Tandem, and OMSSA with regard to search time. MassMatrix was also run on a distributed memory clusters and achieved search speeds of ~100,000 spectra per hour when searching against a complete human database with 8 variable modifications. The algorithm is available for public searches at http://www.massmatrix.net. PMID:19235167

  15. Search for a border between classical and quantum worlds

    NASA Astrophysics Data System (ADS)

    Alicki, Robert

    2002-03-01

    The effects of environmental decoherence on a mass-center position of a body consisting of many atoms are studied using a kind of linear quantum Boltzmann equation. It is shown that under realistic laboratory conditions these effects can be essentially eliminated for dust particles containing 1015 atoms. However, the initial velocity distribution and certain geometrical conditions make standard interference-type measurements extremally difficult beyond the nanometer scale. The results are illustrated by the analysis of the recent experiments involving fullerenes. Applications of decoherence effects to precise monitoring of environment or to separation of molecules are suggested.

  16. A Nonhomogeneous Cuckoo Search Algorithm Based on Quantum Mechanism for Real Parameter Optimization.

    PubMed

    Cheung, Ngaam J; Ding, Xue-Ming; Shen, Hong-Bin

    2017-02-01

    Cuckoo search (CS) algorithm is a nature-inspired search algorithm, in which all the individuals have identical search behaviors. However, this simple homogeneous search behavior is not always optimal to find the potential solution to a special problem, and it may trap the individuals into local regions leading to premature convergence. To overcome the drawback, this paper presents a new variant of CS algorithm with nonhomogeneous search strategies based on quantum mechanism to enhance search ability of the classical CS algorithm. Featured contributions in this paper include: 1) quantum-based strategy is developed for nonhomogeneous update laws and 2) we, for the first time, present a set of theoretical analyses on CS algorithm as well as the proposed algorithm, respectively, and conclude a set of parameter boundaries guaranteeing the convergence of the CS algorithm and the proposed algorithm. On 24 benchmark functions, we compare our method with five existing CS-based methods and other ten state-of-the-art algorithms. The numerical results demonstrate that the proposed algorithm is significantly better than the original CS algorithm and the rest of compared methods according to two nonparametric tests.

  17. SPLICE: A program to assemble partial query solutions from three-dimensional database searches into novel ligands

    NASA Astrophysics Data System (ADS)

    Ho, Chris M. W.; Marshall, Garland R.

    1993-12-01

    SPLICE is a program that processes partial query solutions retrieved from 3D, structural databases to generate novel, aggregate ligands. It is designed to interface with the database searching program FOUNDATION, which retrieves fragments containing any combination of a user-specified minimum number of matching query elements. SPLICE eliminates aspects of structures that are physically incapable of binding within the active site. Then, a systematic rule-based procedure is performed upon the remaining fragments to ensure receptor complementarity. All modifications are automated and remain transparent to the user. Ligands are then assembled by linking components into composite structures through overlapping bonds. As a control experiment, FOUNDATION and SPLICE were used to reconstruct a know HIV-1 protease inhibitor after it had been fragmented, reoriented, and added to a sham database of fifty different small molecules. To illustrate the capabilities of this program, a 3D search query containing the pharmacophoric elements of an aspartic proteinase-inhibitor crystal complex was searched using FOUNDATION against a subset of the Cambridge Structural Database. One hundred thirty-one compounds were retrieved, each containing any combination of at least four query elements. Compounds were automatically screened and edited for receptor complementarity. Numerous combinations of fragments were discovered that could be linked to form novel structures, containing a greater number of pharmacophoric elements than any single retrieved fragment.

  18. Microwave experiments simulating quantum search and directed transport in artificial graphene.

    PubMed

    Böhm, Julian; Bellec, Matthieu; Mortessagne, Fabrice; Kuhl, Ulrich; Barkhofen, Sonja; Gehler, Stefan; Stöckmann, Hans-Jürgen; Foulger, Iain; Gnutzmann, Sven; Tanner, Gregor

    2015-03-20

    A series of quantum search algorithms have been proposed recently providing an algebraic speedup compared to classical search algorithms from N to √N, where N is the number of items in the search space. In particular, devising searches on regular lattices has become popular in extending Grover's original algorithm to spatial searching. Working in a tight-binding setup, it could be demonstrated, theoretically, that a search is possible in the physically relevant dimensions 2 and 3 if the lattice spectrum possesses Dirac points. We present here a proof of principle experiment implementing wave search algorithms and directed wave transport in a graphene lattice arrangement. The idea is based on bringing localized search states into resonance with an extended lattice state in an energy region of low spectral density-namely, at or near the Dirac point. The experiment is implemented using classical waves in a microwave setup containing weakly coupled dielectric resonators placed in a honeycomb arrangement, i.e., artificial graphene. Furthermore, we investigate the scaling behavior experimentally using linear chains.

  19. Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin.

    PubMed

    Good, Andrew C

    2007-10-01

    With readily available CPU power and copious disk storage, it is now possible to undertake rapid comparison of 3D properties derived from explicit ligand overlay experiments. With this in mind, shape software tools originally devised in the 1990s are revisited, modified and applied to the problem of ligand database shape comparison. The utility of Connolly surface data is highlighted using the program MAKESITE, which leverages surface normal data to a create ligand shape cast. This cast is applied directly within DOCK, allowing the program to be used unmodified as a shape searching tool. In addition, DOCK has undergone multiple modifications to create a dedicated ligand shape comparison tool KIN. Scoring has been altered to incorporate the original incarnation of Gaussian function derived shape description based on STO-3G atomic electron density. In addition, a tabu-like search refinement has been added to increase search speed by removing redundant starting orientations produced during clique matching. The ability to use exclusion regions, again based on Gaussian shape overlap, has also been integrated into the scoring function. The use of both DOCK with MAKESITE and KIN in database screening mode is illustrated using a published ligand shape virtual screening template. The advantages of using a clique-driven search paradigm are highlighted, including shape optimization within a pharmacophore constrained framework, and easy incorporation of additional scoring function modifications. The potential for further development of such methods is also discussed.

  20. Preparing College Students To Search Full-Text Databases: Is Instruction Necessary?

    ERIC Educational Resources Information Center

    Riley, Cheryl; Wales, Barbara

    Full-text databases allow Central Missouri State University's clients to access some of the serials that libraries have had to cancel due to escalating subscription costs; EbscoHost, the subject of this study, is one such database. The database is available free to all Missouri residents. A survey was designed consisting of 21 questions intended…

  1. Searching for first-degree familial relationships in California's offender DNA database: validation of a likelihood ratio-based approach.

    PubMed

    Myers, Steven P; Timken, Mark D; Piucci, Matthew L; Sims, Gary A; Greenwald, Michael A; Weigand, James J; Konzak, Kenneth C; Buoncristiani, Martin R

    2011-11-01

    A validation study was performed to measure the effectiveness of using a likelihood ratio-based approach to search for possible first-degree familial relationships (full-sibling and parent-child) by comparing an evidence autosomal short tandem repeat (STR) profile to California's ∼1,000,000-profile State DNA Index System (SDIS) database. Test searches used autosomal STR and Y-STR profiles generated for 100 artificial test families. When the test sample and the first-degree relative in the database were characterized at the 15 Identifiler(®) (Applied Biosystems(®), Foster City, CA) STR loci, the search procedure included 96% of the fathers and 72% of the full-siblings. When the relative profile was limited to the 13 Combined DNA Index System (CODIS) core loci, the search procedure included 93% of the fathers and 61% of the full-siblings. These results, combined with those of functional tests using three real families, support the effectiveness of this tool. Based upon these results, the validated approach was implemented as a key, pragmatic and demonstrably practical component of the California Department of Justice's Familial Search Program. An investigative lead created through this process recently led to an arrest in the Los Angeles Grim Sleeper serial murders.

  2. Hadamard NMR spectroscopy for two-dimensional quantum information processing and parallel search algorithms.

    PubMed

    Gopinath, T; Kumar, Anil

    2006-12-01

    Hadamard spectroscopy has earlier been used to speed-up multi-dimensional NMR experiments. In this work, we speed-up the two-dimensional quantum computing scheme, by using Hadamard spectroscopy in the indirect dimension, resulting in a scheme which is faster and requires the Fourier transformation only in the direct dimension. Two and three qubit quantum gates are implemented with an extra observer qubit. We also use one-dimensional Hadamard spectroscopy for binary information storage by spatial encoding and implementation of a parallel search algorithm.

  3. Colloquium: Herbertsmithite and the search for the quantum spin liquid

    NASA Astrophysics Data System (ADS)

    Norman, M. R.

    2016-10-01

    Quantum spin liquids form a novel class of matter where, despite the existence of strong exchange interactions, spins do not order down to the lowest measured temperature. Typically, these occur in lattices that act to frustrate the appearance of magnetism. In two dimensions, the classic example is the kagome lattice composed of corner sharing triangles. There are a variety of minerals whose transition metal ions form such a lattice. Hence, a number of them have been studied and were then subsequently synthesized in order to obtain more pristine samples. Of particular note was the report in 2005 by Dan Nocera's group of the synthesis of herbertsmithite, composed of a lattice of copper ions sitting on a kagome lattice, which indeed does not order down to the lowest measured temperature despite the existence of a large exchange interaction of 17 meV. Over the past decade, this material has been extensively studied, yielding a number of intriguing surprises that have in turn motivated a resurgence of interest in the theoretical study of the spin 1 /2 Heisenberg model on a kagome lattice. This Colloquium reviews these developments and then discusses potential future directions, both experimental and theoretical, as well as the challenge of doping these materials with the hope that this could lead to the discovery of novel topological and superconducting phases.

  4. Millennial Students' Mental Models of Search: Implications for Academic Librarians and Database Developers

    ERIC Educational Resources Information Center

    Holman, Lucy

    2011-01-01

    Today's students exhibit generational differences in the way they search for information. Observations of first-year students revealed a proclivity for simple keyword or phrases searches with frequent misspellings and incorrect logic. Although no students had strong mental models of search mechanisms, those with stronger models did construct more…

  5. Comparative Recall and Precision of Simple and Expert Searches in Google Scholar and Eight Other Databases

    ERIC Educational Resources Information Center

    Walters, William H.

    2011-01-01

    This study evaluates the effectiveness of simple and expert searches in Google Scholar (GS), EconLit, GEOBASE, PAIS, POPLINE, PubMed, Social Sciences Citation Index, Social Sciences Full Text, and Sociological Abstracts. It assesses the recall and precision of 32 searches in the field of later-life migration: nine simple keyword searches and 23…

  6. Subspace projection method for unstructured searches with noisy quantum oracles using a signal-based quantum emulation device

    NASA Astrophysics Data System (ADS)

    La Cour, Brian R.; Ostrove, Corey I.

    2017-01-01

    This paper describes a novel approach to solving unstructured search problems using a classical, signal-based emulation of a quantum computer. The classical nature of the representation allows one to perform subspace projections in addition to the usual unitary gate operations. Although bandwidth requirements will limit the scale of problems that can be solved by this method, it can nevertheless provide a significant computational advantage for problems of limited size. In particular, we find that, for the same number of noisy oracle calls, the proposed subspace projection method provides a higher probability of success for finding a solution than does an single application of Grover's algorithm on the same device.

  7. HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks

    PubMed Central

    Dai, Xinbin; Li, Jun; Liu, Tingsong; Zhao, Patrick Xuechun

    2016-01-01

    The biological networks controlling plant signal transduction, metabolism and gene regulation are composed of not only tens of thousands of genes, compounds, proteins and RNAs but also the complicated interactions and co-ordination among them. These networks play critical roles in many fundamental mechanisms, such as plant growth, development and environmental response. Although much is known about these complex interactions, the knowledge and data are currently scattered throughout the published literature, publicly available high-throughput data sets and third-party databases. Many ‘unknown’ yet important interactions among genes need to be mined and established through extensive computational analysis. However, exploring these complex biological interactions at the network level from existing heterogeneous resources remains challenging and time-consuming for biologists. Here, we introduce HRGRN, a graph search-empowered integrative database of Arabidopsis signal transduction, metabolism and gene regulatory networks. HRGRN utilizes Neo4j, which is a highly scalable graph database management system, to host large-scale biological interactions among genes, proteins, compounds and small RNAs that were either validated experimentally or predicted computationally. The associated biological pathway information was also specially marked for the interactions that are involved in the pathway to facilitate the investigation of cross-talk between pathways. Furthermore, HRGRN integrates a series of graph path search algorithms to discover novel relationships among genes, compounds, RNAs and even pathways from heterogeneous biological interaction data that could be missed by traditional SQL database search methods. Users can also build subnetworks based on known interactions. The outcomes are visualized with rich text, figures and interactive network graphs on web pages. The HRGRN database is freely available at http://plantgrn.noble.org/hrgrn/. PMID:26657893

  8. Deterministic quantum-public-key encryption: Forward search attack and randomization

    NASA Astrophysics Data System (ADS)

    Nikolopoulos, Georgios M.; Ioannou, Lawrence M.

    2009-04-01

    In the classical setting, public-key encryption requires randomness in order to be secure against a forward search attack, whereby an adversary compares the encryption of a guess of the secret message with the encryption of the actual secret message. We show that this is also true in the information-theoretic setting—where the public keys are quantum systems—by defining and giving an example of a forward search attack for any deterministic quantum-public-key bit-encryption scheme. However, unlike in the classical setting, we show that any such deterministic scheme can be used as a black box to build a randomized bit-encryption scheme that is no longer susceptible to this attack.

  9. A quantum-behaved evolutionary algorithm based on the Bloch spherical search

    NASA Astrophysics Data System (ADS)

    Li, Panchi

    2014-04-01

    In order to enhance the optimization ability of the quantum evolutionary algorithms, a new quantum-behaved evolutionary algorithm is proposed. In this algorithm, the search mechanism is established based on the Bloch sphere. First, the individuals are expressed by qubits described on the Bloch sphere, then the rotation axis is established by Pauli matrixes, and the evolution search is realized by rotating qubits on the Bloch sphere about the rotating axis. In order to avoid premature convergence, the mutation of individuals is achieved by the Hadamard gates. Such rotation can make the current qubit approximate the target qubit along with the great circle on the Bloch sphere, which can accelerate optimization process. Taking the function extreme value optimization as an example, the experimental results show that the proposed algorithm is obviously superior to other similar algorithms.

  10. Feasibility of LC/TOFMS and elemental database searching as a spectral library for pesticides in food.

    PubMed

    Thurman, E Michael; Ferrer, Imma; Malato, Octavio; Fernández-Alba, Amadeo Rodriguez

    2006-11-01

    Traditionally, the screening of unknown pesticides in food has been accomplished by GC/MS methods using conventional library-searching routines. However, many of the new polar and thermally labile pesticides are more readily and easily analysed by LC/MS methods and no searchable libraries currently exist (with the exception of some user libraries, which are limited). Therefore, there is a need for LC/MS libraries that can detect pesticides and their degradation products. This paper reports an identification scheme using a combination of LC/MS time-of-flight (accurate mass) and an Access database of 350 pesticides that are amenable to positive ion electrospray. The approach differs from conventional library searching of fragment ions. The concept consists of three parts: (1) initial screening of possible pesticides in actual market-place fruit extracts (apple and orange) using accurate mass and generating an accurate mass via an automatic ion-extraction routine, (2) searching the Access database manually for screening identification of a pesticide, and (3) identification of the suspected compound by accurate mass of at least one fragment ion and comparison of retention time with an actual standard. Imazalil and iprodione were identified in apples and thiabendazole in oranges using this database approach.

  11. A continued search for transient events in the COBE DMR database simultaneous with cosmic gamma-ray bursts

    NASA Astrophysics Data System (ADS)

    Stacy, J. Gregory; Jackson, Peter D.; Bontekoe, Tj. Romke; Winkler, Christoph

    1996-08-01

    We report on the status of our ongoing project to search the database of the COBE Differential Microwave Radiometer (DMR) experiment for transient signals at microwave wavelengths simultaneous with cosmic gamma-ray bursts (GRBs). To date we have carried out a complete search of the DMR database using burst positions taken from the original BATSE 1B catalog for the eight-month period of overlap (May-December 1991) corresponding to the first public release of COBE data. We are currently repeating our original search of the COBE DMR database using the revised burst positions of the newly-released BATSE 3B catalog. Using BATSE 1B positions, at least two apparent simultaneous observations of GRBs by the COBE DMR occurred in 1991, along with a number of ``near misses'' within 30 seconds in time. At present, only upper limits to burst microwave emission are indicated. Even in the event of a non-detection of a GRB by the COBE DMR, unprecedented observational limits will still be obtained, constraining the predictions of the many theoretical models proposed to explain the origin of GRBs.

  12. A Multivariate Mixture Model to Estimate the Accuracy of Glycosaminoglycan Identifications Made by Tandem Mass Spectrometry (MS/MS) and Database Search.

    PubMed

    Chiu, Yulun; Schliekelman, Paul; Orlando, Ron; Sharp, Joshua S

    2017-02-01

    We present a statistical model to estimate the accuracy of derivatized heparin and heparan sulfate (HS) glycosaminoglycan (GAG) assignments to tandem mass (MS/MS) spectra made by the first published database search application, GAG-ID. Employing a multivariate expectation-maximization algorithm, this statistical model distinguishes correct from ambiguous and incorrect database search results when computing the probability that heparin/HS GAG assignments to spectra are correct based upon database search scores. Using GAG-ID search results for spectra generated from a defined mixture of 21 synthesized tetrasaccharide sequences as well as seven spectra of longer defined oligosaccharides, we demonstrate that the computed probabilities are accurate and have high power to discriminate between correctly, ambiguously, and incorrectly assigned heparin/HS GAGs. This analysis makes it possible to filter large MS/MS database search results with predictable false identification error rates.

  13. Highly charged ions for atomic clocks, quantum information, and search for α variation.

    PubMed

    Safronova, M S; Dzuba, V A; Flambaum, V V; Safronova, U I; Porsev, S G; Kozlov, M G

    2014-07-18

    We propose 10 highly charged ions as candidates for the development of next generation atomic clocks, quantum information, and search for α variation. They have long-lived metastable states with transition wavelengths to the ground state between 170-3000 nm, relatively simple electronic structure, stable isotopes, and high sensitivity to α variation (e.g., Sm(14+), Pr(10+), Sm(13+), Nd(10+)). We predict their properties crucial for the experimental exploration and highlight particularly attractive systems for these applications.

  14. Digital cloning: identification of human cDNAs homologous to novel kinases through expressed sequence tag database searching.

    PubMed

    Chen, H C; Kung, H J; Robinson, D

    1998-01-01

    Identification of novel kinases based on their sequence conservation within kinase catalytic domain has relied so far on two major approaches, low-stringency hybridization of cDNA libraries, and PCR method using degenerate primers. Both of these approaches at times are technically difficult and time-consuming. We have developed a procedure that can significantly reduce the time and effort involved in searching for novel kinases and increase the sensitivity of the analysis. This procedure exploits the computer analysis of a vast resource of human cDNA sequences represented in the expressed sequence tag (EST) database. Seventeen novel human cDNA clones showing significant homology to serine/threonine kinases, including STE-20, CDK- and YAK-related family kinases, were identified by searching EST database. Further sequence analysis of these novel kinases obtained either directly from EST clones or from PCR-RACE products confirmed their identity as protein kinases. Given the rapid accumulation of the EST database and the advent of powerful computer analysis software, this approach provides a fast, sensitive, and economical way to identify novel kinases as well as other genes from EST database.

  15. Effect of cleavage enzyme, search algorithm and decoy database on mass spectrometric identification of wheat gluten proteins.

    PubMed

    Vensel, William H; Dupont, Frances M; Sloane, Stacia; Altenbach, Susan B

    2011-07-01

    While tandem mass spectrometry (MS/MS) is routinely used to identify proteins from complex mixtures, certain types of proteins present unique challenges for MS/MS analyses. The major wheat gluten proteins, gliadins and glutenins, are particularly difficult to distinguish by MS/MS. Each of these groups contains many individual proteins with similar sequences that include repetitive motifs rich in proline and glutamine. These proteins have few cleavable tryptic sites, often resulting in only one or two tryptic peptides that may not provide sufficient information for identification. Additionally, there are less than 14,000 complete protein sequences from wheat in the current NCBInr release. In this paper, MS/MS methods were optimized for the identification of the wheat gluten proteins. Chymotrypsin and thermolysin as well as trypsin were used to digest the proteins and the collision energy was adjusted to improve fragmentation of chymotryptic and thermolytic peptides. Specialized databases were constructed that included protein sequences derived from contigs from several assemblies of wheat expressed sequence tags (ESTs), including contigs assembled from ESTs of the cultivar under study. Two different search algorithms were used to interrogate the database and the results were analyzed and displayed using a commercially available software package (Scaffold). We examined the effect of protein database content and size on the false discovery rate. We found that as database size increased above 30,000 sequences there was a decrease in the number of proteins identified. Also, the type of decoy database influenced the number of proteins identified. Using three enzymes, two search algorithms and a specialized database allowed us to greatly increase the number of detected peptides and distinguish proteins within each gluten protein group.

  16. Search for quantum size effects in ultrathin epitaxial metallic films

    NASA Astrophysics Data System (ADS)

    Badoz, P. A.; D'Avitaya, F. Arnaud; Rosencher, E.

    In order to investigate quantum size effects in ultrathin metal films, tunneling spectroscopy measurements have been performed in the epitaxial CoSi2/Si system, with a metal thickness ranging from 1000 Å down to 35 A, i.e. a few de Broglie wavelengths of electrons in CoSi 2. The resulting spectra show extremely rich sets of features, the origin of which are investigated. The peaks observed at low energy (-100 meV, +100 meV) are thickness independent and attributed to phonon emission by hot electrons. The peaks observed at higher energy (up to 600 meV) are thickness dependent but their physical origin is not yet fully ascertained. The absence of unambiguous electron quantization effects in these epitaxial films is discussed and tentatively attributed to small thickness fluctuations (of the order of a few monolayers), which tend to blur the quantization of the electronic energies. Nous avons étudié les effets de quantification électronique dans les films métalliques minces par spectroscopie tunnel des jonctions CoSi2/Si épitaxiées, pour des épaisseurs de film métallique variant de 1000 ? 35 A, i.e. quelques longueurs d'ondes de de Broglie des électrons dans le CoSi 2. Les spectres obtenus montrent un ensemble de structures extrêmement riche dont nous discutons l'origine physique. Les pics observés à faible énergie (-100 meV, + 100 meV) sont indépendants de I'épaisseur du film de CoSi2, et attribués à l'émission de phonons par les électrons chauds dans le silicium. L'origine des pics observés à plus forte énergie (jusqu'à 600 meV) et dont la position dépend de l'épaisseur du film, est encore incomplètement comprise. Nous discutons l'absence d'effets clairement reliés à la quantification du gaz d'électrons bidimensionnel dans ces films épitaxiés: celle-ci pourrait provenir de faibles fluctuations d'épaisseur (quelques monocouches) qui tendent à brouiller la quantification des énergies électroniques.

  17. Systematic Dimensionality Reduction for Quantum Walks: Optimal Spatial Search and Transport on Non-Regular Graphs

    NASA Astrophysics Data System (ADS)

    Novo, Leonardo; Chakraborty, Shantanav; Mohseni, Masoud; Neven, Hartmut; Omar, Yasser

    2015-09-01

    Continuous time quantum walks provide an important framework for designing new algorithms and modelling quantum transport and state transfer problems. Often, the graph representing the structure of a problem contains certain symmetries that confine the dynamics to a smaller subspace of the full Hilbert space. In this work, we use invariant subspace methods, that can be computed systematically using the Lanczos algorithm, to obtain the reduced set of states that encompass the dynamics of the problem at hand without the specific knowledge of underlying symmetries. First, we apply this method to obtain new instances of graphs where the spatial quantum search algorithm is optimal: complete graphs with broken links and complete bipartite graphs, in particular, the star graph. These examples show that regularity and high-connectivity are not needed to achieve optimal spatial search. We also show that this method considerably simplifies the calculation of quantum transport efficiencies. Furthermore, we observe improved efficiencies by removing a few links from highly symmetric graphs. Finally, we show that this reduction method also allows us to obtain an upper bound for the fidelity of a single qubit transfer on an XY spin network.

  18. Systematic Dimensionality Reduction for Quantum Walks: Optimal Spatial Search and Transport on Non-Regular Graphs

    PubMed Central

    Novo, Leonardo; Chakraborty, Shantanav; Mohseni, Masoud; Neven, Hartmut; Omar, Yasser

    2015-01-01

    Continuous time quantum walks provide an important framework for designing new algorithms and modelling quantum transport and state transfer problems. Often, the graph representing the structure of a problem contains certain symmetries that confine the dynamics to a smaller subspace of the full Hilbert space. In this work, we use invariant subspace methods, that can be computed systematically using the Lanczos algorithm, to obtain the reduced set of states that encompass the dynamics of the problem at hand without the specific knowledge of underlying symmetries. First, we apply this method to obtain new instances of graphs where the spatial quantum search algorithm is optimal: complete graphs with broken links and complete bipartite graphs, in particular, the star graph. These examples show that regularity and high-connectivity are not needed to achieve optimal spatial search. We also show that this method considerably simplifies the calculation of quantum transport efficiencies. Furthermore, we observe improved efficiencies by removing a few links from highly symmetric graphs. Finally, we show that this reduction method also allows us to obtain an upper bound for the fidelity of a single qubit transfer on an XY spin network. PMID:26330082

  19. Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings.

    PubMed

    May, Damon H; Tamura, Kaipo; Noble, William S

    2017-03-13

    In shotgun proteomics analysis, user-specified parameters are critical to database search performance and therefore to the yield of confident peptide-spectrum matches (PSMs). Two of the most important parameters are related to the accuracy of the mass spectrometer. Precursor mass tolerance defines the peptide candidates considered for each spectrum. Fragment mass tolerance or bin size determines how close observed and theoretical fragments must be to be considered a match. For either of these two parameters, too wide a setting yields randomly high-scoring false PSMs, whereas too narrow a setting erroneously excludes true PSMs, in both cases, lowering the yield of peptides detected at a given false discovery rate. We describe a strategy for inferring optimal search parameters by assembling and analyzing pairs of spectra that are likely to have been generated by the same peptide ion to infer precursor and fragment mass error. This strategy does not rely on a database search, making it usable in a wide variety of settings. In our experiments on data from a variety of instruments including Orbitrap and Q-TOF acquisitions, this strategy yields more high-confidence PSMs than using settings based on instrument defaults or determined by experts. Param-Medic is open-source and cross-platform. It is available as a standalone tool ( http://noble.gs.washington.edu/proj/param-medic/ ) and has been integrated into the Crux proteomics toolkit ( http://crux.ms ), providing automatic parameter selection for the Comet and Tide search engines.

  20. Quantum spin ice: a search for gapless quantum spin liquids in pyrochlore magnets.

    PubMed

    Gingras, M J P; McClarty, P A

    2014-05-01

    The spin ice materials, including Ho2Ti2O7 and Dy2Ti2O7, are rare-earth pyrochlore magnets which, at low temperatures, enter a constrained paramagnetic state with an emergent gauge freedom. Spin ices provide one of very few experimentally realized examples of fractionalization because their elementary excitations can be regarded as magnetic monopoles and, over some temperature range, spin ice materials are best described as liquids of these emergent charges. In the presence of quantum fluctuations, one can obtain, in principle, a quantum spin liquid descended from the classical spin ice state characterized by emergent photon-like excitations. Whereas in classical spin ices the excitations are akin to electrostatic charges with a mutual Coulomb interaction, in the quantum spin liquid these charges interact through a dynamic and emergent electromagnetic field. In this review, we describe the latest developments in the study of such a quantum spin ice, focusing on the spin liquid phenomenology and the kinds of materials where such a phase might be found.

  1. GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array.

    PubMed

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

    2014-01-01

    DNA sequences are translated into protein coding sequences and then further assigned to protein families in metagenomic analyses, because of the need for sensitivity. However, huge amounts of sequence data create the problem that even general homology search analyses using BLASTX become difficult in terms of computational cost. We designed a new homology search algorithm that finds seed sequences based on the suffix arrays of a query and a database, and have implemented it as GHOSTX. GHOSTX achieved approximately 131-165 times acceleration over a BLASTX search at similar levels of sensitivity. GHOSTX is distributed under the BSD 2-clause license and is available for download at http://www.bi.cs.titech.ac.jp/ghostx/. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We offer this tool as a potential solution to this problem.

  2. Low template STR typing: effect of replicate number and consensus method on genotyping reliability and DNA database search results.

    PubMed

    Benschop, Corina C G; van der Beek, Cornelis P; Meiland, Hugo C; van Gorp, Ankie G M; Westen, Antoinette A; Sijen, Titia

    2011-08-01

    To analyze DNA samples with very low DNA concentrations, various methods have been developed that sensitize short tandem repeat (STR) typing. Sensitized DNA typing is accompanied by stochastic amplification effects, such as allele drop-outs and drop-ins. Therefore low template (LT) DNA profiles are interpreted with care. One can either try to infer the genotype by a consensus method that uses alleles confirmed in replicate analyses, or one can use a statistical model to evaluate the strength of the evidence in a direct comparison with a known DNA profile. In this study we focused on the first strategy and we show that the procedure by which the consensus profile is assembled will affect genotyping reliability. In order to gain insight in the roles of replicate number and requested level of reproducibility, we generated six independent amplifications of samples of known donors. The LT methods included both increased cycling and enhanced capillary electrophoresis (CE) injection [1]. Consensus profiles were assembled from two to six of the replications using four methods: composite (include all alleles), n-1 (include alleles detected in all but one replicate), n/2 (include alleles detected in at least half of the replicates) and 2× (include alleles detected twice). We compared the consensus DNA profiles with the DNA profile of the known donor, studied the stochastic amplification effects and examined the effect of the consensus procedure on DNA database search results. From all these analyses we conclude that the accuracy of LT DNA typing and the efficiency of database searching improve when the number of replicates is increased and the consensus method is n/2. The most functional number of replicates within this n/2 method is four (although a replicate number of three suffices for samples showing >25% of the alleles in standard STR typing). This approach was also the optimal strategy for the analysis of 2-person mixtures, although modified search strategies may be

  3. Review and Comparison of the Search Effectiveness and User Interface of Three Major Online Chemical Databases

    ERIC Educational Resources Information Center

    Bharti, Neelam; Leonard, Michelle; Singh, Shailendra

    2016-01-01

    Online chemical databases are the largest source of chemical information and, therefore, the main resource for retrieving results from published journals, books, patents, conference abstracts, and other relevant sources. Various commercial, as well as free, chemical databases are available. SciFinder, Reaxys, and Web of Science are three major…

  4. Reach for Reference. Don't Judge a Database by Its Search Screen

    ERIC Educational Resources Information Center

    Safford, Barbara Ripp

    2005-01-01

    In this column, the author provides a description and brief review of the "Children's Literature Comprehensive Database" (CLCD). This subscription database is a 1999 spinoff from Marilyn Courtot's "Children's Literature" website, which began in 1993 and is a free resource of reviews and features about books, authors, and illustrators. The separate…

  5. Closing the loop in cortically-coupled computer vision: a brain-computer interface for searching image databases.

    PubMed

    Pohlmeyer, Eric A; Wang, Jun; Jangraw, David C; Lou, Bin; Chang, Shih-Fu; Sajda, Paul

    2011-06-01

    We describe a closed-loop brain-computer interface that re-ranks an image database by iterating between user generated 'interest' scores and computer vision generated visual similarity measures. The interest scores are based on decoding the electroencephalographic (EEG) correlates of target detection, attentional shifts and self-monitoring processes, which result from the user paying attention to target images interspersed in rapid serial visual presentation (RSVP) sequences. The highest scored images are passed to a semi-supervised computer vision system that reorganizes the image database accordingly, using a graph-based representation that captures visual similarity between images. The system can either query the user for more information, by adaptively resampling the database to create additional RSVP sequences, or it can converge to a 'done' state. The done state includes a final ranking of the image database and also a 'guess' of the user's chosen category of interest. We find that the closed-loop system's re-rankings can substantially expedite database searches for target image categories chosen by the subjects. Furthermore, better reorganizations are achieved than by relying on EEG interest rankings alone, or if the system were simply run in an open loop format without adaptive resampling.

  6. Lead generation using pharmacophore mapping and three-dimensional database searching: application to muscarinic M(3) receptor antagonists.

    PubMed

    Marriott, D P; Dougall, I G; Meghani, P; Liu, Y J; Flower, D R

    1999-08-26

    By using a pharmacophore model, a geometrical representation of the features necessary for molecules to show a particular biological activity, it is possible to search databases containing the 3D structures of molecules and identify novel compounds which may possess this activity. We describe our experiences of establishing a working 3D database system and its use in rational drug design. By using muscarinic M(3) receptor antagonists as an example, we show that it is possible to identify potent novel lead compounds using this approach. Pharmacophore generation based on the structures of known M(3) receptor antagonists, 3D database searching, and medium-throughput screening were used to identify candidate compounds. Three compounds were chosen to define the pharmacophore: a lung-selective M(3) antagonist patented by Pfizer and two Astra compounds which show affinity at the M(3) receptor. From these, a pharmacophore model was generated, using the program DISCO, and this was used subsequently to search a UNITY 3D database of proprietary compounds; 172 compounds were found to fit the pharmacophore. These compounds were then screened, and 1-[2-(2-(diethylamino)ethoxy)phenyl]-2-phenylethanone (pA(2) 6.67) was identified as the best hit, with N-[2-(piperidin-1-ylmethyl)cycohexyl]-2-propoxybenz amide (pA(2) 4. 83) and phenylcarbamic acid 2-(morpholin-4-ylmethyl)cyclohexyl ester (pA(2) 5.54) demonstrating lower activity. As well as its potency, 1-[2-(2-(diethylamino)ethoxy)phenyl]-2-phenylethanone is a simple structure with limited similarity to existing M(3) receptor antagonists.

  7. Materials Design and Discovery with High-Throughput Density Functional Theory: The Open Quantum Materials Database (OQMD)

    NASA Astrophysics Data System (ADS)

    Saal, James E.; Kirklin, Scott; Aykol, Muratahan; Meredig, Bryce; Wolverton, C.

    2013-11-01

    High-throughput density functional theory (HT DFT) is fast becoming a powerful tool for accelerating materials design and discovery by the amassing tens and even hundreds of thousands of DFT calculations in large databases. Complex materials problems can be approached much more efficiently and broadly through the sheer quantity of structures and chemistries available in such databases. Our HT DFT database, the Open Quantum Materials Database (OQMD), contains over 200,000 DFT calculated crystal structures and will be freely available for public use at http://oqmd.org. In this review, we describe the OQMD and its use in five materials problems, spanning a wide range of applications and materials types: (I) Li-air battery combination catalyst/electrodes, (II) Li-ion battery anodes, (III) Li-ion battery cathode coatings reactive with HF, (IV) Mg-alloy long-period stacking ordered (LPSO) strengthening precipitates, and (V) training a machine learning model to predict new stable ternary compounds.

  8. Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.

    PubMed

    Griss, Johannes; Côté, Richard G; Gerner, Christopher; Hermjakob, Henning; Vizcaíno, Juan Antonio

    2011-09-01

    In proteomics, protein identifications are reported and stored using an unstable reference system: protein identifiers. These proprietary identifiers are created individually by every protein database and can change or may even be deleted over time. To estimate the effect of the searched protein sequence database on the long-term storage of proteomics data we analyzed the changes of reported protein identifiers from all public experiments in the Proteomics Identifications (PRIDE) database by November 2010. To map the submitted protein identifier to a currently active entry, two distinct approaches were used. The first approach used the Protein Identifier Cross Referencing (PICR) service at the EBI, which maps protein identifiers based on 100% sequence identity. The second one (called logical mapping algorithm) accessed the source databases and retrieved the current status of the reported identifier. Our analysis showed the differences between the main protein databases (International Protein Index (IPI), UniProt Knowledgebase (UniProtKB), National Center for Biotechnological Information nr database (NCBI nr), and Ensembl) in respect to identifier stability. For example, whereas 20% of submitted IPI entries were deleted after two years, virtually all UniProtKB entries remained either active or replaced. Furthermore, the two mapping algorithms produced markedly different results. For example, the PICR service reported 10% more IPI entries deleted compared with the logical mapping algorithm. We found several cases where experiments contained more than 10% deleted identifiers already at the time of publication. We also assessed the proportion of peptide identifications in these data sets that still fitted the originally identified protein sequences. Finally, we performed the same overall analysis on all records from IPI, Ensembl, and UniProtKB: two releases per year were used, from 2005. This analysis showed for the first time the true effect of changing protein

  9. Boolean Logic: An Aid for Searching Computer Databases in Special Education and Rehabilitation.

    ERIC Educational Resources Information Center

    Summers, Edward G.

    1989-01-01

    The article discusses using Boolean logic as a tool for searching computerized information retrieval systems in special education and rehabilitation technology. It includes discussion of the Boolean search operators AND, OR, and NOT; Venn diagrams; and disambiguating parentheses. Six suggestions are offered for development of good Boolean logic…

  10. The Magnetics Information Consortium (MagIC) Online Database: Uploading, Searching and Visualizing Paleomagnetic and Rock Magnetic Data

    NASA Astrophysics Data System (ADS)

    Koppers, A.; Tauxe, L.; Constable, C.; Pisarevsky, S.; Jackson, M.; Solheid, P.; Banerjee, S.; Johnson, C.; Genevey, A.; Delaney, R.; Baker, P.; Sbarbori, E.

    2005-12-01

    The Magnetics Information Consortium (MagIC) operates an online relational database including both rock and paleomagnetic data. The goal of MagIC is to store all measurements and their derived properties for studies of paleomagnetic directions (inclination, declination) and their intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. These nodes provide basic search capabilities based on location, reference, methods applied, material type and geological age, while allowing the user to drill down from sites all the way to the measurements. At each stage, the data can be saved and, if the available data supports it, the data can be visualized by plotting equal area plots, VGP location maps or typical Zijderveld, hysteresis, FORC, and various magnetization and remanence diagrams. All plots are made in SVG (scalable vector graphics) and thus can be saved and easily read into the user's favorite graphics programs without loss of resolution. User contributions to the MagIC database are critical to achieve a useful research tool. We have developed a standard data and metadata template (version 1.6) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate easy population of these templates within Microsoft Excel. These tools allow for the import/export of text files and they provide advanced functionality to manage/edit the data, and to perform various internal checks to high grade the data and to make them ready for uploading. The uploading is all done online by using the MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm that takes only a few minutes to process a contribution of approximately 5,000 data records. After uploading these standardized MagIC template files will be stored in the

  11. Federated Search Tools in Fusion Centers: Bridging Databases in the Information Sharing Environment

    DTIC Science & Technology

    2012-09-01

    German and Jay Stanley , “Fusion Center Update,” American Civil Liberties Union, July 2008, http://www.aclu.org/files/pdfs/privacy...Intelligence, ed. Jennifer E. Sims and Burton Gerber (Washington DC: Georgetown University Press, 2005), 107. 16 Ibid. 11 through a federated search tool...SurveyMonkey. Last modified June 23, 2012. https://www.surveymonkey.com/s/FederatedSearchToolsinFCs. German, Mike and Jay Stanley . “Fusion Center

  12. Code optimization of the subroutine to remove near identical matches in the sequence database homology search tool PSI-BLAST.

    PubMed

    Aspnäs, Mats; Mattila, Kimmo; Osowski, Kristoffer; Westerholm, Jan

    2010-06-01

    A central task in protein sequence characterization is the use of a sequence database homology search tool to find similar protein sequences in other individuals or species. PSI-BLAST is a widely used module of the BLAST package that calculates a position-specific score matrix from the best matching sequences and performs iterated searches using a method to avoid many similar sequences for the score. For some queries and parameter settings, PSI-BLAST may find many similar high-scoring matches, and therefore up to 80% of the total run time may be spent in this procedure. In this article, we present code optimizations that improve the cache utilization and the overall performance of this procedure. Measurements show that, for queries where the number of similar matches is high, the optimized PSI-BLAST program may be as much as 2.9 times faster than the original program.

  13. Dynamics of the quantum search and quench-induced first-order phase transitions.

    PubMed

    Coulamy, Ivan B; Saguia, Andreia; Sarandy, Marcelo S

    2017-02-01

    We investigate the excitation dynamics at a first-order quantum phase transition (QPT). More specifically, we consider the quench-induced QPT in the quantum search algorithm, which aims at finding out a marked element in an unstructured list. We begin by deriving the exact dynamics of the model, which is shown to obey a Riccati differential equation. Then, we discuss the probabilities of success by adopting either global or local adiabaticity strategies. Moreover, we determine the disturbance of the quantum criticality as a function of the system size. In particular, we show that the critical point exponentially converges to its thermodynamic limit even in a fast evolution regime, which is characterized by both entanglement QPT estimators and the Schmidt gap. The excitation pattern is manifested in terms of quantum domain walls separated by kinks. The kink density is then shown to follow an exponential scaling as a function of the evolution speed, which can be interpreted as a Kibble-Zurek mechanism for first-order QPTs.

  14. Dynamics of the quantum search and quench-induced first-order phase transitions

    NASA Astrophysics Data System (ADS)

    Coulamy, Ivan B.; Saguia, Andreia; Sarandy, Marcelo S.

    2017-02-01

    We investigate the excitation dynamics at a first-order quantum phase transition (QPT). More specifically, we consider the quench-induced QPT in the quantum search algorithm, which aims at finding out a marked element in an unstructured list. We begin by deriving the exact dynamics of the model, which is shown to obey a Riccati differential equation. Then, we discuss the probabilities of success by adopting either global or local adiabaticity strategies. Moreover, we determine the disturbance of the quantum criticality as a function of the system size. In particular, we show that the critical point exponentially converges to its thermodynamic limit even in a fast evolution regime, which is characterized by both entanglement QPT estimators and the Schmidt gap. The excitation pattern is manifested in terms of quantum domain walls separated by kinks. The kink density is then shown to follow an exponential scaling as a function of the evolution speed, which can be interpreted as a Kibble-Zurek mechanism for first-order QPTs.

  15. Searching for quantum gravity with high-energy atmospheric neutrinos and AMANDA-II

    NASA Astrophysics Data System (ADS)

    Kelley, John Lawrence

    2008-06-01

    The AMANDA-II detector, operating since 2000 in the deep ice at the geographic South Pole, has accumulated a large sample of atmospheric muon neutrinos in the 100 GeV to 10 TeV energy range. The zenith angle and energy distribution of these events can be used to search for various phenomenological signatures of quantum gravity in the neutrino sector, such as violation of Lorentz invariance (VLI) or quantum decoherence (QD). Analyzing a set of 5511 candidate neutrino events collected during 1387 days of livetime from 2000 to 2006, we find no evidence for such effects and set upper limits on VLI and QD parameters using a maximum likelihood method. Given the absence of new flavor-changing physics, we use the same methodology to determine the conventional atmospheric muon neutrino flux above 100 GeV.

  16. Searches for Decaying Sterile Neutrinos with the X-Ray Quantum Calorimeter Sounding Rocket

    NASA Astrophysics Data System (ADS)

    Goldfinger, David; XQC Collaboration

    2016-01-01

    Rocket borne X-ray spectrometers can produce high-resolution spectra for wide field-of-view observations. This is useful in searches for dark matter candidates that produce X-ray lines in the Milky Way, such as decaying keV scale sterile neutrinos. In spite of exposure times and effective areas that are significantly smaller than satellite observatories, similar sensitivity to decaying sterile neutrinos can be attained due to the high spectral resolution and large field of view. We present recent results of such a search analyzing the telemetered data from the 2011 flight of the X-Ray Quantum Colorimeter instrument as well as ongoing progress in expanding the data set to include the more complete onboard data over additional flights.

  17. The Magnetics Information Consortium (MagIC) Online Database: Uploading, Searching and Visualizing Paleomagnetic and Rock Magnetic Data

    NASA Astrophysics Data System (ADS)

    Minnett, R.; Koppers, A.; Tauxe, L.; Constable, C.; Pisarevsky, S. A.; Jackson, M.; Solheid, P.; Banerjee, S.; Johnson, C.

    2006-12-01

    The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by both rock and paleomagnetic data. The goal of MagIC is to archive all measurements and the derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual map interface to browse and select locations. The query result set is displayed in a digestible tabular format allowing the user to descend through hierarchical levels such as from locations to sites, samples, specimens, and measurements. At each stage, the result set can be saved and, if supported by the data, can be visualized by plotting global location maps, equal area plots, or typical Zijderveld, hysteresis, and various magnetization and remanence diagrams. User contributions to the MagIC database are critical to achieving a useful research tool. We have developed a standard data and metadata template (Version 2.1) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate population of these templates within Microsoft Excel. These tools allow for the import/export of text files and provide advanced functionality to manage and edit the data, and to perform various internal checks to maintain data integrity and prepare for uploading. The MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm executes the upload and takes only a few minutes to process several thousand data records. The standardized MagIC template files are stored in the digital archives of EarthRef.org where they

  18. Online Searching of Bibliographic Databases: Microcomputer Access to National Information Systems.

    ERIC Educational Resources Information Center

    Coons, Bill

    This paper describes the range and scope of various information databases available for technicians, researchers, and managers employed in forestry and the forest products industry. Availability of information on reports of field and laboratory research, business trends, product prices, and company profiles through national distributors of…

  19. Online/CD-ROM Bibliographic Database Searching in a Small Academic Library.

    ERIC Educational Resources Information Center

    Pitet, Lynn T.

    The purpose of the project described in this paper was to gather information about online/CD-ROM database systems that would be useful in improving the services offered at the University of Findlay, a small private liberal arts college in northwestern Ohio. A survey was sent to 67 libraries serving colleges similar in size which included questions…

  20. Fast 3D molecular superposition and similarity search in databases of flexible molecules

    NASA Astrophysics Data System (ADS)

    Krämer, Andreas; Horn, Hans W.; Rice, Julia E.

    2003-01-01

    We present a new method (fFLASH) for the virtual screening of compound databases that is based on explicit three-dimensional molecular superpositions. fFLASH takes the torsional flexibility of the database molecules fully into account, and can deal with an arbitrary number of conformation-dependent molecular features. The method utilizes a fragmentation-reassembly approach which allows for an efficient sampling of the conformational space. A fast clique-based pattern matching algorithm generates alignments of pairs of adjacent molecular fragments on the rigid query molecule that are subsequently reassembled to complete database molecules. Using conventional molecular features (hydrogen bond donors and acceptors, charges, and hydrophobic groups) we show that fFLASH is able to rapidly produce accurate alignments of medium-sized drug-like molecules. Experiments with a test database containing a diverse set of 1780 drug-like molecules (including all conformers) have shown that average query processing times of the order of 0.1 seconds per molecule can be achieved on a PC.

  1. SCOOP: A Measurement and Database of Student Online Search Behavior and Performance

    ERIC Educational Resources Information Center

    Zhou, Mingming

    2015-01-01

    The ability to access and process massive amounts of online information is required in many learning situations. In order to develop a better understanding of student online search process especially in academic contexts, an online tool (SCOOP) is developed for tracking mouse behavior on the web to build a more extensive account of student web…

  2. A Search for Nontriggered Gamma-Ray Bursts in the BATSE Database

    NASA Technical Reports Server (NTRS)

    Kommers, Jefferson M.; Lewin, Walter H. G.; Kouveliotou, Chryssa; VanParadus, Jan; Pendleton, Geoffrey N.; Meegan, Charles A.; Fishman, Gerald J.

    1997-01-01

    We describe a search of archival data from the Burst and Transient Source Experiment (BATSE). The purpose of the search is to find astronomically interesting transients that did not activate the burst-detection (or "trigger") system on board the spacecraft. Our search is sensitive to events with peak fluxes (on the 1.024 s timescale) that are lower by a factor of approximately 2 than can be detected with the on-board burst trigger. In a search of 345 days of archival data, we detected 91 events in the 50-300 keV range that resemble classical gamma-ray bursts but that did not activate the on-board burst trigger. We also detected 110 low-energy (25-50 keV) events of unknown origin that may include activity from' soft gamma repeater (SGR) 1806-20 and bursts and flares from X-ray binaries. This paper gives the occurrence times, estimated source directions, durations, peak fluxes, and fluences for the 91 gamma-ray burst candidates. The direction and intensity distributions of these bursts imply that the biases inherent in the on-board trigger mechanism have not significantly affected the completeness of the published BATSE gamma-ray burst catalogs.

  3. Information Retrieval Strategies of Millennial Undergraduate Students in Web and Library Database Searches

    ERIC Educational Resources Information Center

    Porter, Brandi

    2009-01-01

    Millennial students make up a large portion of undergraduate students attending colleges and universities, and they have a variety of online resources available to them to complete academically related information searches, primarily Web based and library-based online information retrieval systems. The content, ease of use, and required search…

  4. Exchange, interpretation, and database-search of ion mobility spectra supported by data format JCAMP-DX

    NASA Technical Reports Server (NTRS)

    Baumback, J. I.; Davies, A. N.; Vonirmer, A.; Lampen, P. H.

    1995-01-01

    To assist peak assignment in ion mobility spectrometry it is important to have quality reference data. The reference collection should be stored in a database system which is capable of being searched using spectral or substance information. We propose to build such a database customized for ion mobility spectra. To start off with it is important to quickly reach a critical mass of data in the collection. We wish to obtain as many spectra combined with their IMS parameters as possible. Spectra suppliers will be rewarded for their participation with access to the database. To make the data exchange between users and system administration possible, it is important to define a file format specially made for the requirements of ion mobility spectra. The format should be computer readable and flexible enough for extensive comments to be included. In this document we propose a data exchange format, and we would like you to give comments on it. For the international data exchange it is important, to have a standard data exchange format. We propose to base the definition of this format on the JCAMP-DX protocol, which was developed for the exchange of infrared spectra. This standard made by the Joint Committee on Atomic and Molecular Physical Data is of a flexible design. The aim of this paper is to adopt JCAMP-DX to the special requirements of ion mobility spectra.

  5. Searching the UVSP database and a list of experiments showing mass motions

    NASA Technical Reports Server (NTRS)

    Thompson, William

    1986-01-01

    Since the Solar Maximum Mission (SMM) satellite was launched, a large database has been built up of experiments using the Ultraviolet Spectrometer and Polarimeter (UVSP) instrument. Access to this database can be gained through the SMM Vax 750 computer at Goddard Space Flight Center. One useful way to do this is with a program called USEARCH. This program allows one to make a listing of different types of UVSP experiments. It is evident that this program is useful to those who would wish to make use of UVSP data, but who don't know what data is available. Therefore it was decided to include a short description of how to make use of the USEARCH program. Also described, but not included, is a listing of all UVSP experiments showing mass motions in prominences and filaments. This list was made with the aid of the USEARCH program.

  6. Silicon photonic chips for search on improved-glued-binary-tree based on continuous-time quantum walk

    NASA Astrophysics Data System (ADS)

    Qi, Fan; Ma, Qingyan; Wang, Yufei; Zheng, Wanhua

    2016-11-01

    Search on improved-glued-binary-trees is a representative example of quantum superiority, where exponential acceleration can be achieved using quantum walk with respect to any classical algorithms. Here we analyzed the evolution process of this quantum-walk-based algorithm. Several remarkable features of the process are revealed. Generation of the model by introducing tunable defect strength and double defects is also discussed and the effects of these generalization on evolution process, arrival probability and residual probability are discussed in details. Physical implementation with silicon ridge waveguide array is presented. The design of the array with FEM method are presented and light propagation simulation with FDTD method shows that this kind of structure is feasible for the task. Lastly, preliminary experimental demonstration with classical coherent light simulation are presented. Our results show that silicon photonic chips are suitable for such search problems and opening a route towards large-scale photonic quantum computation.

  7. On-line biomedical databases-the best source for quick search of the scientific information in the biomedicine.

    PubMed

    Masic, Izet; Milinovic, Katarina

    2012-06-01

    Most of medical journals now has it's electronic version, available over public networks. Although there are parallel printed and electronic versions, and one other form need not to be simultaneously published. Electronic version of a journal can be published a few weeks before the printed form and must not has identical content. Electronic form of a journals may have an extension that does not contain a printed form, such as animation, 3D display, etc., or may have available fulltext, mostly in PDF or XML format, or just the contents or a summary. Access to a full text is usually not free and can be achieved only if the institution (library or host) enters into an agreement on access. Many medical journals, however, provide free access for some articles, or after a certain time (after 6 months or a year) to complete content. The search for such journals provide the network archive as High Wire Press, Free Medical Journals.com. It is necessary to allocate PubMed and PubMed Central, the first public digital archives unlimited collect journals of available medical literature, which operates in the system of the National Library of Medicine in Bethesda (USA). There are so called on- line medical journals published only in electronic form. It could be searched over on-line databases. In this paper authors shortly described about 30 data bases and short instructions how to make access and search the published papers in indexed medical journals.

  8. Image Content Engine (ICE): A System for Fast Image Database Searches

    SciTech Connect

    Brase, J M; Paglieroni, D W; Weinert, G F; Grant, C W; Lopez, A S; Nikolaev, S

    2005-03-22

    The Image Content Engine (ICE) is being developed to provide cueing assistance to human image analysts faced with increasingly large and intractable amounts of image data. The ICE architecture includes user configurable feature extraction pipelines which produce intermediate feature vector and match surface files which can then be accessed by interactive relational queries. Application of the feature extraction algorithms to large collections of images may be extremely time consuming and is launched as a batch job on a Linux cluster. The query interface accesses only the intermediate files and returns candidate hits nearly instantaneously. Queries may be posed for individual objects or collections. The query interface prompts the user for feedback, and applies relevance feedback algorithms to revise the feature vector weighting and focus on relevant search results. Examples of feature extraction and both model-based and search-by-example queries are presented.

  9. Crescendo: A Protein Sequence Database Search Engine for Tandem Mass Spectra

    NASA Astrophysics Data System (ADS)

    Wang, Jianqi; Zhang, Yajie; Yu, Yonghao

    2015-07-01

    A search engine that discovers more peptides reliably is essential to the progress of the computational proteomics. We propose two new scoring functions (L- and P-scores), which aim to capture similar characteristics of a peptide-spectrum match (PSM) as Sequest and Comet do. Crescendo, introduced here, is a software program that implements these two scores for peptide identification. We applied Crescendo to test datasets and compared its performance with widely used search engines, including Mascot, Sequest, and Comet. The results indicate that Crescendo identifies a similar or larger number of peptides at various predefined false discovery rates (FDR). Importantly, it also provides a better separation between the true and decoy PSMs, warranting the future development of a companion post-processing filtering algorithm.

  10. Crescendo: A Protein Sequence Database Search Engine for Tandem Mass Spectra.

    PubMed

    Wang, Jianqi; Zhang, Yajie; Yu, Yonghao

    2015-07-01

    A search engine that discovers more peptides reliably is essential to the progress of the computational proteomics. We propose two new scoring functions (L- and P-scores), which aim to capture similar characteristics of a peptide-spectrum match (PSM) as Sequest and Comet do. Crescendo, introduced here, is a software program that implements these two scores for peptide identification. We applied Crescendo to test datasets and compared its performance with widely used search engines, including Mascot, Sequest, and Comet. The results indicate that Crescendo identifies a similar or larger number of peptides at various predefined false discovery rates (FDR). Importantly, it also provides a better separation between the true and decoy PSMs, warranting the future development of a companion post-processing filtering algorithm.

  11. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect

    1997-11-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  12. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). NewSearch

    SciTech Connect

    Not Available

    1994-10-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology. (Contains 250 citations and includes a subject term index and title list.)

  13. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect

    1996-10-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  14. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect

    1995-09-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  15. Chemical and biological warfare: General studies. (Latest citations from the NTIS Bibliographic database). Published Search

    SciTech Connect

    Not Available

    1993-11-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology. (Contains 250 citations and includes a subject term index and title list.)

  16. The Quantum Monte Carlo Database: towards high-accuracy and high-throughput calculation of material properties

    NASA Astrophysics Data System (ADS)

    Schiller, Joshua; Plante, Raymond; Wagner, Lucas; Ertekin, Elif

    Quantum Monte Carlo (QMC) techniques comprise a class of promising methods that offer a path towards higher accuracy for materials property prediction. However, their application in bulk materials has historically been limited to one-at-a-time evaluation of a given material. While these results often provide benchmark-level accuracy for quantities of interest, they do not allow for high-throughput analysis of the data since each calculation is done slightly differently. We present a combined data format and automatic generation platform based on the QWalk code for QMC data: QMCDB. This platform collects QMC results and provenance information automatically and stores the information in a database. We will report on the construction of this database and what lessons can be learned about using QMC for high-throughput applications.

  17. Searching the databases: a quick look at Amazon and two other online catalogues.

    PubMed

    Potts, Hilary

    2003-01-01

    The Amazon Online Catalogue was compared with the Library of Congress Catalogue and the British Library Catalogue, both also available online, by searching on both neutral (Gay, Lesbian, Homosexual) and pejorative (Perversion, Sex Crime) subject terms, and also by searches using Boolean logic in an attempt to identify Lesbian Fiction items and religion-based anti-gay material. Amazon was much more likely to be the first port of call for non-academic enquiries. Although excluding much material necessary for academic research, it carried more information about the individual books and less historical homophobic baggage in its terminology than the great national catalogues. Its back catalogue of second-hand books outnumbered those in print. Current attitudes may partially be gauged by the relative numbers of titles published under each heading--e.g., there may be an inverse relationship between concern about child sex abuse and homophobia, more noticeable in U.S. because of the activities of the religious right.

  18. Heart research advances using database search engines, Human Protein Atlas and the Sydney Heart Bank.

    PubMed

    Li, Amy; Estigoy, Colleen; Raftery, Mark; Cameron, Darryl; Odeberg, Jacob; Pontén, Fredrik; Lal, Sean; Dos Remedios, Cristobal G

    2013-10-01

    This Methodological Review is intended as a guide for research students who may have just discovered a human "novel" cardiac protein, but it may also help hard-pressed reviewers of journal submissions on a "novel" protein reported in an animal model of human heart failure. Whether you are an expert or not, you may know little or nothing about this particular protein of interest. In this review we provide a strategic guide on how to proceed. We ask: How do you discover what has been published (even in an abstract or research report) about this protein? Everyone knows how to undertake literature searches using PubMed and Medline but these are usually encyclopaedic, often producing long lists of papers, most of which are either irrelevant or only vaguely relevant to your query. Relatively few will be aware of more advanced search engines such as Google Scholar and even fewer will know about Quertle. Next, we provide a strategy for discovering if your "novel" protein is expressed in the normal, healthy human heart, and if it is, we show you how to investigate its subcellular location. This can usually be achieved by visiting the website "Human Protein Atlas" without doing a single experiment. Finally, we provide a pathway to discovering if your protein of interest changes its expression level with heart failure/disease or with ageing.

  19. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System.

    PubMed

    Liu, Yu; Hong, Yang; Lin, Chun-Yuan; Hung, Che-Lun

    2015-01-01

    The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively.

  20. Pivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS database searching.

    PubMed

    Yates, John R

    2015-11-01

    Advances in computer technology and software have driven developments in mass spectrometry over the last 50 years. Computers and software have been impactful in three areas: the automation of difficult calculations to aid interpretation, the collection of data and control of instruments, and data interpretation. As the power of computers has grown, so too has the utility and impact on mass spectrometers and their capabilities. This has been particularly evident in the use of tandem mass spectrometry data to search protein and nucleotide sequence databases to identify peptide and protein sequences. This capability has driven the development of many new approaches to study biological systems, including the use of "bottom-up shotgun proteomics" to directly analyze protein mixtures. Graphical Abstract ᅟ.

  1. Pivotal Role of Computers and Software in Mass Spectrometry - SEQUEST and 20 Years of Tandem MS Database Searching

    NASA Astrophysics Data System (ADS)

    Yates, John R.

    2015-11-01

    Advances in computer technology and software have driven developments in mass spectrometry over the last 50 years. Computers and software have been impactful in three areas: the automation of difficult calculations to aid interpretation, the collection of data and control of instruments, and data interpretation. As the power of computers has grown, so too has the utility and impact on mass spectrometers and their capabilities. This has been particularly evident in the use of tandem mass spectrometry data to search protein and nucleotide sequence databases to identify peptide and protein sequences. This capability has driven the development of many new approaches to study biological systems, including the use of "bottom-up shotgun proteomics" to directly analyze protein mixtures.

  2. An ultra-tolerant database search reveals that a myriad of modified peptides contributes to unassigned spectra in shotgun proteomics

    PubMed Central

    Chick, Joel M.; Kolippakkam, Deepak; Nusinow, David P.; Zhai, Bo; Rad, Ramin; Huttlin, Edward L.; Gygi, Steven P.

    2015-01-01

    Fewer than half of all tandem mass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to a peptide with high confidence. Here we determine the identity of unassigned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with modifications of unknown masses up to ±500 Da. In a proteome-wide dataset on HEK293 cells (9,513 proteins and 396,736 peptides), this approach matched an additional 184,000 modified peptides, which were linked to biological and chemical modifications representing 523 distinct mass bins, including phosphorylation, glycosylation, and methylation. We localized all unknown modification masses to specific regions within a peptide. Known modifications were assigned to the correct amino acids with frequencies often >90%. We conclude that at least one third of unassigned spectra arise from peptides with substoichiometric modifications. PMID:26076430

  3. FTP-Server for exchange, interpretation, and database-search of ion mobility spectra, literature, preprints and software

    NASA Technical Reports Server (NTRS)

    Baumbach, J. I.; Vonirmer, A.

    1995-01-01

    To assist current discussion in the field of ion mobility spectrometry, at the Institut fur Spectrochemie und angewandte Spektroskopie, Dortmund, start with 4th of December, 1994 work of an FTP-Server, available for all research groups at univerisities, institutes and research worker in industry. We support the exchange, interpretation, and database-search of ion mobility spectra through data format JCAMP-DS (Joint Committee on Atomic and Molecular Physical Data) as well as literature retrieval, pre-print, notice, and discussion board. We describe in general lines the entrance conditions, local addresses, and main code words. For further details, a monthly news report will be prepared for all common users. Internet email address for subscribing is included in document.

  4. Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

    PubMed Central

    Huang, Liang-Tsung; Wu, Chao-Chin; Lai, Lien-Fu; Li, Yun-Ju

    2015-01-01

    Sequence alignment lies at heart of the bioinformatics. The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units (GPUs). In this paper, we focused on how to improve the mapping, especially for short query sequences, by better usage of shared memory. We performed and evaluated the proposed method on two different platforms (Tesla C1060 and Tesla K20) and compared it with two classic methods in CUDASW++. Further, the performance on different numbers of threads and blocks has been analyzed. The results showed that the proposed method significantly improves Smith-Waterman algorithm on CUDA-enabled GPUs in proper allocation of block and thread numbers. PMID:26339591

  5. Quality Control of Biomedicinal Allergen Products - Highly Complex Isoallergen Composition Challenges Standard MS Database Search and Requires Manual Data Analyses.

    PubMed

    Spiric, Jelena; Engin, Anna M; Karas, Michael; Reuter, Andreas

    2015-01-01

    Allergy against birch pollen is among the most common causes of spring pollinosis in Europe and is diagnosed and treated using extracts from natural sources. Quality control is crucial for safe and effective diagnosis and treatment. However, current methods are very difficult to standardize and do not address individual allergen or isoallergen composition. MS provides information regarding selected proteins or the entire proteome and could overcome the aforementioned limitations. We studied the proteome of birch pollen, focusing on allergens and isoallergens, to clarify which of the 93 published sequence variants of the major allergen, Bet v 1, are expressed as proteins within one source material in parallel. The unexpectedly complex Bet v 1 isoallergen composition required manual data interpretation and a specific design of databases, as current database search engines fail to unambiguously assign spectra to highly homologous, partially identical proteins. We identified 47 non-allergenic proteins and all 5 known birch pollen allergens, and unambiguously proved the existence of 18 Bet v 1 isoallergens and variants by manual data analysis. This highly complex isoallergen composition raises questions whether isoallergens can be ignored or must be included for the quality control of allergen products, and which data analysis strategies are to be applied.

  6. The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching.

    PubMed

    Howe, Douglas G; Bradford, Yvonne M; Eagle, Anne; Fashena, David; Frazer, Ken; Kalita, Patrick; Mani, Prita; Martin, Ryan; Moxon, Sierra Taylor; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruzicka, Leyla; Schaper, Kevin; Shao, Xiang; Singer, Amy; Toro, Sabrina; Van Slyke, Ceri; Westerfield, Monte

    2017-01-04

    The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for zebrafish (Danio rerio) genetic, genomic, phenotypic and developmental data. ZFIN curators provide expert manual curation and integration of comprehensive data involving zebrafish genes, mutants, transgenic constructs and lines, phenotypes, genotypes, gene expressions, morpholinos, TALENs, CRISPRs, antibodies, anatomical structures, models of human disease and publications. We integrate curated, directly submitted, and collaboratively generated data, making these available to zebrafish research community. Among the vertebrate model organisms, zebrafish are superbly suited for rapid generation of sequence-targeted mutant lines, characterization of phenotypes including gene expression patterns, and generation of human disease models. The recent rapid adoption of zebrafish as human disease models is making management of these data particularly important to both the research and clinical communities. Here, we describe recent enhancements to ZFIN including use of the zebrafish experimental conditions ontology, 'Fish' records in the ZFIN database, support for gene expression phenotypes, models of human disease, mutation details at the DNA, RNA and protein levels, and updates to the ZFIN single box search.

  7. The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

    PubMed Central

    Howe, Douglas G.; Bradford, Yvonne M.; Eagle, Anne; Fashena, David; Frazer, Ken; Kalita, Patrick; Mani, Prita; Martin, Ryan; Moxon, Sierra Taylor; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruzicka, Leyla; Schaper, Kevin; Shao, Xiang; Singer, Amy; Toro, Sabrina; Van Slyke, Ceri; Westerfield, Monte

    2017-01-01

    The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for zebrafish (Danio rerio) genetic, genomic, phenotypic and developmental data. ZFIN curators provide expert manual curation and integration of comprehensive data involving zebrafish genes, mutants, transgenic constructs and lines, phenotypes, genotypes, gene expressions, morpholinos, TALENs, CRISPRs, antibodies, anatomical structures, models of human disease and publications. We integrate curated, directly submitted, and collaboratively generated data, making these available to zebrafish research community. Among the vertebrate model organisms, zebrafish are superbly suited for rapid generation of sequence-targeted mutant lines, characterization of phenotypes including gene expression patterns, and generation of human disease models. The recent rapid adoption of zebrafish as human disease models is making management of these data particularly important to both the research and clinical communities. Here, we describe recent enhancements to ZFIN including use of the zebrafish experimental conditions ontology, ‘Fish’ records in the ZFIN database, support for gene expression phenotypes, models of human disease, mutation details at the DNA, RNA and protein levels, and updates to the ZFIN single box search. PMID:27899582

  8. Utility of rapid database searching for quality assurance: 'detective work' in uncovering radiology coding and billing errors

    NASA Astrophysics Data System (ADS)

    Horii, Steven C.; Kim, Woojin; Boonn, William; Iyoob, Christopher; Maston, Keith; Coleman, Beverly G.

    2011-03-01

    When the first quarter of 2010 Department of Radiology statistics were provided to the Section Chiefs, the authors (SH, BC) were alarmed to discover that Ultrasound showed a decrease of 2.5 percent in billed examinations. This seemed to be in direct contradistinction to the experience of the ultrasound faculty members and sonographers. Their experience was that they were far busier than during the same quarter of 2009. The one exception that all acknowledged was the month of February, 2010 when several major winter storms resulted in a much decreased Hospital admission and Emergency Department visit rate. Since these statistics in part help establish priorities for capital budget items, professional and technical staffing levels, and levels of incentive salary, they are taken very seriously. The availability of a desktop, Web-based RIS database search tool developed by two of the authors (WK, WB) and built-in database functions of the ultrasound miniPACS, made it possible for us very rapidly to develop and test hypotheses for why the number of billable examinations was declining in the face of what experience told the authors was an increasing number of examinations being performed. Within a short time, we identified the major cause as errors on the part of the company retained to verify billable Current Procedural Terminology (CPT) codes against ultrasound reports. This information is being used going forward to recover unbilled examinations and take measures to reduce or eliminate the types of coding errors that resulted in the problem.

  9. A Cautionary Tale on the Inclusion of Variable Posttranslational Modifications in Database-Dependent Searches of Mass Spectrometry Data.

    PubMed

    Svozil, J; Baerenfaller, K

    2017-01-01

    Mass spectrometry-based proteomics allows in principle the identification of unknown target proteins of posttranslational modifications and the sites of attachment. Including a variety of posttranslational modifications in database-dependent searches of high-throughput mass spectrometry data holds the promise to gain spectrum assignments to modified peptides, thereby increasing the number of assigned spectra, and to identify potentially interesting modification events. However, these potential benefits come for the price of an increased search space, which can lead to reduced scores, increased score thresholds, and erroneous peptide spectrum matches. We have assessed here the advantages and disadvantages of including the variable posttranslational modifications methionine oxidation, protein N-terminal acetylation, cysteine carbamidomethylation, transformation of N-terminal glutamine to pyroglutamic acid (Gln→pyro-Glu), and deamidation of asparagine and glutamine. Based on calculations of local false discovery rates and comparisons to known features of the respective modifications, we recommend for searches of samples that were not enriched for specific posttranslational modifications to only include methionine oxidation, protein N-terminal acetylation, and peptide N-terminal Gln→pyro-Glu as variable modifications. The principle of the validation strategy adopted here can also be applied for assessing the inclusion of posttranslational modifications for differently prepared samples, or for additional modifications. In addition, we have reassessed the special properties of the ubiquitin footprint, which is the remainder of ubiquitin moieties attached to lysines after tryptic digest. We show here that the ubiquitin footprint often breaks off as neutral loss and that it can be distinguished from dicarbamidomethylation events.

  10. Similarity landscapes: An improved method for scientific visualization of information from protein and DNA database searches

    SciTech Connect

    Dogget, N.; Myers, G.; Wills, C.J.

    1998-12-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have used computer simulations and examination of a variety of databases to answer questions about a wide range of evolutionary questions. The authors have found that there is a clear distinction in the evolution of HIV-1 and HIV-2, with the former and more virulent virus evolving more rapidly at a functional level. The authors have discovered highly non-random patterns in the evolution of HIV-1 that can be attributed to a variety of selective pressures. In the course of examination of microsatellite DNA (short repeat regions) in microorganisms, the authors have found clear differences between prokaryotes and eukaryotes in their distribution, differences that can be tied to different selective pressures. They have developed a new method (topiary pruning) for enhancing the phylogenetic information contained in DNA sequences. Most recently, the authors have discovered effects in complex rainforest ecosystems that indicate strong frequency-dependent interactions between host species and their parasites, leading to the maintenance of ecosystem variability.

  11. Searching for new physics at the frontiers with lattice quantum chromodynamics.

    PubMed

    Van de Water, Ruth S

    2012-07-01

    Numerical lattice-quantum chromodynamics (QCD) simulations, when combined with experimental measurements, allow the determination of fundamental parameters of the particle-physics Standard Model and enable searches for physics beyond-the-Standard Model. We present the current status of lattice-QCD weak matrix element calculations needed to obtain the elements and phase of the Cabibbo-Kobayashi-Maskawa (CKM) matrix and to test the Standard Model in the quark-flavor sector. We then discuss evidence that may hint at the presence of new physics beyond the Standard Model CKM framework. Finally, we discuss two opportunities where we expect lattice QCD to play a pivotal role in searching for, and possibly discovery of, new physics at upcoming high-intensity experiments: rare decays and the muon anomalous magnetic moment. The next several years may witness the discovery of new elementary particles at the Large Hadron Collider (LHC). The interplay between lattice QCD, high-energy experiments at the LHC, and high-intensity experiments will be needed to determine the underlying structure of whatever physics beyond-the-Standard Model is realized in nature.

  12. pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data.

    PubMed

    Chi, Hao; He, Kun; Yang, Bing; Chen, Zhen; Sun, Rui-Xiang; Fan, Sheng-Bo; Zhang, Kun; Liu, Chao; Yuan, Zuo-Fei; Wang, Quan-Hui; Liu, Si-Qi; Dong, Meng-Qiu; He, Si-Min

    2015-07-01

    Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.

  13. Reprint of "pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data".

    PubMed

    Chi, Hao; He, Kun; Yang, Bing; Chen, Zhen; Sun, Rui-Xiang; Fan, Sheng-Bo; Zhang, Kun; Liu, Chao; Yuan, Zuo-Fei; Wang, Quan-Hui; Liu, Si-Qi; Dong, Meng-Qiu; He, Si-Min

    2015-11-03

    Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.This article is part of a Special Issue entitled: Computational Proteomics.

  14. Automatic sorting of toxicological information into the IUCLID (International Uniform Chemical Information Database) endpoint-categories making use of the semantic search engine Go3R.

    PubMed

    Sauer, Ursula G; Wächter, Thomas; Hareng, Lars; Wareing, Britta; Langsch, Angelika; Zschunke, Matthias; Alvers, Michael R; Landsiedel, Robert

    2014-06-01

    The knowledge-based search engine Go3R, www.Go3R.org, has been developed to assist scientists from industry and regulatory authorities in collecting comprehensive toxicological information with a special focus on identifying available alternatives to animal testing. The semantic search paradigm of Go3R makes use of expert knowledge on 3Rs methods and regulatory toxicology, laid down in the ontology, a network of concepts, terms, and synonyms, to recognize the contents of documents. Search results are automatically sorted into a dynamic table of contents presented alongside the list of documents retrieved. This table of contents allows the user to quickly filter the set of documents by topics of interest. Documents containing hazard information are automatically assigned to a user interface following the endpoint-specific IUCLID5 categorization scheme required, e.g. for REACH registration dossiers. For this purpose, complex endpoint-specific search queries were compiled and integrated into the search engine (based upon a gold standard of 310 references that had been assigned manually to the different endpoint categories). Go3R sorts 87% of the references concordantly into the respective IUCLID5 categories. Currently, Go3R searches in the 22 million documents available in the PubMed and TOXNET databases. However, it can be customized to search in other databases including in-house databanks.

  15. Novel lead generation through hypothetical pharmacophore three-dimensional database searching: discovery of isoflavonoids as nonsteroidal inhibitors of rat 5 alpha-reductase.

    PubMed

    Chen, G S; Chang, C S; Kan, W M; Chang, C L; Wang, K C; Chern, J W

    2001-11-08

    A hypothetical pharmacophore of 5 alpha-reductase inhibitors was generated and served as a template in virtual screening. When the pharmacophore was used, eight isoflavone derivatives were characterized as novel potential nonsteroidal inhibitors of rat 5 alpha-reductase. This investigation has demonstrated a practical approach toward the development of lead compounds through a hypothetic pharmacophore via three-dimensional database searching.

  16. Conceptual changes arising from the use of a search interface developed for an elementary science curriculum database

    NASA Astrophysics Data System (ADS)

    Dwyer, William Michael

    1998-12-01

    The purpose of this study was to look for evidence of change in preservice elementary teachers, notions of science teaching after practice using a search interface for a database of elementary science curriculum materials. The Science Helper K--8 CD-ROM uses search criteria that include science content and process theme to provide appropriate science lessons for elementary educators. Training that took place when Science Helper was first disseminated revealed the possibility that notions about teaching science change with use of the resource. This study looked for evidence of conceptual change compatible with notions in recent reform materials, such as the National Science Education Standards. The study design consisted of a pretest-treatment-posttest model. The treatment included a brief training session in the use of Science Helper, followed by practical application, which consisted of finding appropriate lessons to form a science mini-unit. An analysis of covariance (ANCOVA), however, did not find significant differences between pretest and posttest scores for the treatment group. Study participants also wrote brief narratives about their experiences using Science Helper. A pattern analysis of the narratives found that most of the preservice teachers had positive experiences, saying the resource was easy to use and contained many interesting science activities. A closer examination of the comments revealed a subset of participants who expressed an understanding of the importance of criteria searches and the relatedness of the lessons produced. An ANCOVA of the treatment group controlling for pretest did not find significant differences between pretest and posttest scores for the group who expressed such understanding. Science Helper, with its affordances as a teacher resource, can be regarded as a "knowledge system" in a distributed environment. The interactions among people and material resources in a distributed environment results in a distributed

  17. Evidential significance of automotive paint trace evidence using a pattern recognition based infrared library search engine for the Paint Data Query Forensic Database.

    PubMed

    Lavine, Barry K; White, Collin G; Allen, Matthew D; Fasasi, Ayuba; Weakley, Andrew

    2016-10-01

    A prototype library search engine has been further developed to search the infrared spectral libraries of the paint data query database to identify the line and model of a vehicle from the clear coat, surfacer-primer, and e-coat layers of an intact paint chip. For this study, search prefilters were developed from 1181 automotive paint systems spanning 3 manufacturers: General Motors, Chrysler, and Ford. The best match between each unknown and the spectra in the hit list generated by the search prefilters was identified using a cross-correlation library search algorithm that performed both a forward and backward search. In the forward search, spectra were divided into intervals and further subdivided into windows (which corresponds to the time lag for the comparison) within those intervals. The top five hits identified in each search window were compiled; a histogram was computed that summarized the frequency of occurrence for each library sample, with the IR spectra most similar to the unknown flagged. The backward search computed the frequency and occurrence of each line and model without regard to the identity of the individual spectra. Only those lines and models with a frequency of occurrence greater than or equal to 20% were included in the final hit list. If there was agreement between the forward and backward search results, the specific line and model common to both hit lists was always the correct assignment. Samples assigned to the same line and model by both searches are always well represented in the library and correlate well on an individual basis to specific library samples. For these samples, one can have confidence in the accuracy of the match. This was not the case for the results obtained using commercial library search algorithms, as the hit quality index scores for the top twenty hits were always greater than 99%.

  18. On the hypothesis that quantum mechanism manifests classical mechanics: Numerical approach to the correspondence in search of quantum chaos

    SciTech Connect

    Lee, Sang-Bong

    1993-09-01

    Quantum manifestation of classical chaos has been one of the extensively studied subjects for more than a decade. Yet clear understanding of its nature still remains to be an open question partly due to the lack of a canonical definition of quantum chaos. The classical definition seems to be unsuitable in quantum mechanics partly because of the Heisenberg quantum uncertainty. In this regard, quantum chaos is somewhat misleading and needs to be clarified at the very fundamental level of physics. Since it is well known that quantum mechanics is more fundamental than classical mechanics, the quantum description of classically chaotic nature should be attainable in the limit of large quantum numbers. The focus of my research, therefore, lies on the correspondence principle for classically chaotic systems. The chaotic damped driven pendulum is mainly studied numerically using the split operator method that solves the time-dependent Schroedinger equation. For classically dissipative chaotic systems in which (multi)fractal strange attractors often emerge, several quantum dissipative mechanisms are also considered. For instance, Hoover`s and Kubo-Fox-Keizer`s approaches are studied with some computational analyses. But the notion of complex energy with non-Hermiticity is extensively applied. Moreover, the Wigner and Husimi distribution functions are examined with an equivalent classical distribution in phase-space, and dynamical properties of the wave packet in configuration and momentum spaces are also explored. The results indicate that quantum dynamics embraces classical dynamics although the classicalquantum correspondence fails to be observed in the classically chaotic regime. Even in the semi-classical limits, classically chaotic phenomena would eventually be suppressed by the quantum uncertainty.

  19. Image Databases.

    ERIC Educational Resources Information Center

    Pettersson, Rune

    Different kinds of pictorial databases are described with respect to aims, user groups, search possibilities, storage, and distribution. Some specific examples are given for databases used for the following purposes: (1) labor markets for artists; (2) document management; (3) telling a story; (4) preservation (archives and museums); (5) research;…

  20. Pattern Recognition-Assisted Infrared Library Searching of the Paint Data Query Database to Enhance Lead Information from Automotive Paint Trace Evidence.

    PubMed

    Lavine, Barry K; White, Collin G; Allen, Matthew D; Weakley, Andrew

    2017-03-01

    Multilayered automotive paint fragments, which are one of the most complex materials encountered in the forensic science laboratory, provide crucial links in criminal investigations and prosecutions. To determine the origin of these paint fragments, forensic automotive paint examiners have turned to the paint data query (PDQ) database, which allows the forensic examiner to compare the layer sequence and color, texture, and composition of the sample to paint systems of the original equipment manufacturer (OEM). However, modern automotive paints have a thin color coat and this layer on a microscopic fragment is often too thin to obtain accurate chemical and topcoat color information. A search engine has been developed for the infrared (IR) spectral libraries of the PDQ database in an effort to improve discrimination capability and permit quantification of discrimination power for OEM automotive paint comparisons. The similarity of IR spectra of the corresponding layers of various records for original finishes in the PDQ database often results in poor discrimination using commercial library search algorithms. A pattern recognition approach employing pre-filters and a cross-correlation library search algorithm that performs both a forward and backward search has been used to significantly improve the discrimination of IR spectra in the PDQ database and thus improve the accuracy of the search. This improvement permits inter-comparison of OEM automotive paint layer systems using the IR spectra alone. Such information can serve to quantify the discrimination power of the original automotive paint encountered in casework and further efforts to succinctly communicate trace evidence to the courts.

  1. Use of DNA profiles for investigation using a simulated national DNA database: Part II. Statistical and ethical considerations on familial searching.

    PubMed

    Hicks, T; Taroni, F; Curran, J; Buckleton, J; Castella, V; Ribaux, O

    2010-10-01

    Familial searching consists of searching for a full profile left at a crime scene in a National DNA Database (NDNAD). In this paper we are interested in the circumstance where no full match is returned, but a partial match is found between a database member's profile and the crime stain. Because close relatives share more of their DNA than unrelated persons, this partial match may indicate that the crime stain was left by a close relative of the person with whom the partial match was found. This approach has successfully solved important crimes in the UK and the USA. In a previous paper, a model, which takes into account substructure and siblings, was used to simulate a NDNAD. In this paper, we have used this model to test the usefulness of familial searching and offer guidelines for pre-assessment of the cases based on the likelihood ratio. Siblings of "persons" present in the simulated Swiss NDNAD were created. These profiles (N=10,000) were used as traces and were then compared to the whole database (N=100,000). The statistical results obtained show that the technique has great potential confirming the findings of previous studies. However, effectiveness of the technique is only one part of the story. Familial searching has juridical and ethical aspects that should not be ignored. In Switzerland for example, there are no specific guidelines to the legality or otherwise of familial searching. This article both presents statistical results, and addresses criminological and civil liberties aspects to take into account risks and benefits of familial searching.

  2. Matching unknown empirical formulas to chemical structure using LC/MS TOF accurate mass and database searching: example of unknown pesticides on tomato skins.

    PubMed

    Thurman, E Michael; Ferrer, Imma; Fernández-Alba, Amadeo Rodriguez

    2005-03-04

    Traditionally, the screening of unknown pesticides in food has been accomplished by GC/MS methods using conventional library searching routines. However, many of the new polar and thermally labile pesticides and their degradates are more readily and easily analyzed by LC/MS methods and no searchable libraries currently exist (with the exception of some user libraries, which are limited). Therefore, there is a need for LC/MS approaches to detect unknown non-target pesticides in food. This report develops an identification scheme using a combination of LC/MS time-of-flight (accurate mass) and LC/MS ion trap MS (MS/MS) with searching of empirical formulas generated through accurate mass and a ChemIndex database or Merck Index database. The approach is different than conventional library searching of fragment ions. The concept here consists of four parts. First is the initial detection of a possible unknown pesticide in actual market-place vegetable extracts (tomato skins) using accurate mass and generating empirical formulas. Second is searching either the Merck Index database on CD (10,000 compounds) or the ChemIndex (77,000 compounds) for possible structures. Third is MS/MS of the unknown pesticide in the tomato-skin extract followed by fragment ion identification using chemical drawing software and comparison with accurate-mass ion fragments. Fourth is the verification with authentic standards, if available. Three examples of unknown, non-target pesticides are shown using a tomato-skin extract from an actual market place sample. Limitations of the approach are discussed including the use of A + 2 isotope signatures, extended databases, lack of authentic standards, and natural product unknowns in food extracts.

  3. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

    PubMed Central

    2010-01-01

    Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE

  4. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System

    PubMed Central

    Liu, Yu; Hong, Yang; Lin, Chun-Yuan; Hung, Che-Lun

    2015-01-01

    The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively. PMID:26568953

  5. Racial differences in the association between preoperative serum cholesterol and prostate cancer recurrence: results from the SEARCH database

    PubMed Central

    Allott, Emma H.; Howard, Lauren E.; Aronson, William J.; Terris, Martha K.; Kane, Christopher J.; Amling, Christopher L.; Cooperberg, Matthew R.; Freedland, Stephen J.

    2016-01-01

    Background Black men are disproportionately affected by both cardiovascular disease and prostate cancer. Epidemiologic evidence linking dyslipidemia, an established cardiovascular risk factor, and prostate cancer progression is mixed. As existing studies were conducted in predominantly non-black populations, research in black men is lacking. Methods We identified 628 black and 1,020 non-black men who underwent radical prostatectomy and never used statins before surgery in the Shared Equal Access Regional Cancer Hospital (SEARCH) database. Median follow up was 2.9 years. The impact of preoperative hypercholesterolemia on risk of biochemical recurrence was examined using multivariable, race-stratified proportional hazards. In secondary analysis, we examined associations with low-density lipoprotein (LDL), high-density lipoprotein (HDL) and triglycerides, overall and among men with dyslipidemia. Results High cholesterol was associated with increased risk of recurrence in black (HRper10mg/dl 1.06; 95%CI 1.02–1.11) but not non-black men (HRper10mg/dl 0.99; 95%CI 0.95–1.03; p-interaction=0.011). Elevated triglycerides were associated with increased risk in both black and non-black men (HRper10mg/dl 1.02; 95%CI 1.00–1.03 and 1.02; 95%CI 1.00–1.02, respectively; p-interaction=0.458). There were no significant associations between LDL or HDL and recurrence risk in either race. Associations with cholesterol, LDL and triglycerides were similar among men with dyslipidemia, but low HDL was associated with increased risk of recurrence in black, but not non-black men with dyslipidemia (p-interaction=0.047). Conclusion Elevated cholesterol was a risk factor for recurrence in black but not non-black men, whereas high triglycerides were associated with increased risk regardless of race. Impact Significantly contrasting associations by race may provide insight into prostate cancer racial disparities. PMID:26809276

  6. Similarity searching in databases of flexible 3D structures using autocorrelation vectors derived from smoothed bounded distance matrices.

    PubMed

    Rhodes, Nicholas; Clark, David E; Willett, Peter

    2006-01-01

    This paper presents an exploratory study of a novel method for flexible 3-D similarity searching based on autocorrelation vectors and smoothed bounded distance matrices. Although the new approach is unable to outperform an existing 2-D similarity searching in terms of enrichment factors, it is able to retrieve different compounds at a given percentage of the hit-list and so may be a useful adjunct to other similarity searching methods.

  7. Familial searching: a specialist forensic DNA profiling service utilising the National DNA Database to identify unknown offenders via their relatives--the UK experience.

    PubMed

    Maguire, C N; McCallum, L A; Storey, C; Whitaker, J P

    2014-01-01

    The National DNA Database (NDNAD) of England and Wales was established on April 10th 1995. The NDNAD is governed by a variety of legislative instruments that mean that DNA samples can be taken if an individual is arrested and detained in a police station. The biological samples and the DNA profiles derived from them can be used for purposes related to the prevention and detection of crime, the investigation of an offence and for the conduct of a prosecution. Following the South East Asian Tsunami of December 2004, the legislation was amended to allow the use of the NDNAD to assist in the identification of a deceased person or of a body part where death has occurred from natural causes or from a natural disaster. The UK NDNAD now contains the DNA profiles of approximately 6 million individuals representing 9.6% of the UK population. As the science of DNA profiling advanced, the National DNA Database provided a potential resource for increased intelligence beyond the direct matching for which it was originally created. The familial searching service offered to the police by several UK forensic science providers exploits the size and geographic coverage of the NDNAD and the fact that close relatives of an offender may share a significant proportion of that offender's DNA profile and will often reside in close geographic proximity to him or her. Between 2002 and 2011 Forensic Science Service Ltd. (FSS) provided familial search services to support 188 police investigations, 70 of which are still active cases. This technique, which may be used in serious crime cases or in 'cold case' reviews when there are few or no investigative leads, has led to the identification of 41 perpetrators or suspects. In this paper we discuss the processes, utility, and governance of the familial search service in which the NDNAD is searched for close genetic relatives of an offender who has left DNA evidence at a crime scene, but whose DNA profile is not represented within the NDNAD. We

  8. Reduction in database search space by utilization of amino acid composition information from electron transfer dissociation and higher-energy collisional dissociation mass spectra.

    PubMed

    Hansen, Thomas A; Kryuchkov, Fedor; Kjeldsen, Frank

    2012-08-07

    With high-mass accuracy and consecutively obtained electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS), reliable (≥97%) and sensitive fragment ions have been extracted for identification of specific amino acid residues in peptide sequences. The analytical benefit of these specific amino acid composition (AAC) ions is to restrict the database search space and provide identification of peptides with higher confidence and reduced false negative rates. The 6706 uniquely identified peptide sequences determined with a conservative Mascot score of >30 were used to characterize the AAC ions. The loss of amino acid side chains (small neutral losses, SNLs) from the charge reduced peptide radical cations was studied using ETD. Complementary AAC information from HCD spectra was provided by immonium ions. From the ETD/HCD mass spectra, 5162 and 6720 reliable SNLs and immonium ions were successfully extracted, respectively. Automated application of the AAC information during database searching resulted in an average 3.5-fold higher confidence level of peptide identification. In addition, 4% and 28% more peptides were identified above the significance level in a standard and extended search space, respectively.

  9. JICST Factual Database JICST DNA Database

    NASA Astrophysics Data System (ADS)

    Shirokizawa, Yoshiko; Abe, Atsushi

    Japan Information Center of Science and Technology (JICST) has started the on-line service of DNA database in October 1988. This database is composed of EMBL Nucleotide Sequence Library and Genetic Sequence Data Bank. The authors outline the database system, data items and search commands. Examples of retrieval session are presented.

  10. Effect of cleavage enzyme, search algorithm and decoy database on mass spectrometric identification of wheat gluten proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tandem mass spectrometry (MS/MS) is routinely used to identify proteins by comparing peptide spectra to those generated in silico from protein sequence databases. Wheat storage proteins (gliadins and glutenins) are difficult to distinguish by MS/MS as they have few cleavable tryptic sites, often res...

  11. The Opera del Vocabolario Italiano Database: Full-Text Searching Early Italian Vernacular Sources on the Web.

    ERIC Educational Resources Information Center

    DuPont, Christian

    2001-01-01

    Introduces and describes the functions of the Opera del Vocabolario Italiano (OVI) database, a powerful Web-based, full-text, searchable electronic archive that contains early Italian vernacular texts whose composition may be dated prior to 1375. Examples are drawn from scholars in various disciplines who have employed the OVI in support of their…

  12. Visualization Tools and Techniques for Search and Validation of Large Earth Science Spatial-Temporal Metadata Databases

    NASA Astrophysics Data System (ADS)

    Baskin, W. E.; Herbert, A.; Kusterer, J.

    2014-12-01

    Spatial-temporal metadata databases are critical components of interactive data discovery services for ordering Earth Science datasets. The development staff at the Atmospheric Science Data Center (ASDC) works closely with satellite Earth Science mission teams such as CERES, CALIPSO, TES, MOPITT, and CATS to create and maintain metadata databases that are tailored to the data discovery needs of the Earth Science community. This presentation focuses on the visualization tools and techniques used by the ASDC software development team for data discovery and validation/optimization of spatial-temporal objects in large multi-mission spatial-temporal metadata databases. The following topics will be addressed: Optimizing the level of detail of spatial temporal metadata to provide interactive spatial query performance over a multi-year Earth Science mission Generating appropriately scaled sensor footprint gridded (raster) metadata from Level1 and Level2 Satellite and Aircraft time-series data granules Performance comparison of raster vs vector spatial granule footprint mask queries in large metadata database and a description of the visualization tools used to assist with this analysis

  13. Identifying Gel-Separated Proteins Using In-Gel Digestion, Mass Spectrometry, and Database Searching: Consider the Chemistry

    ERIC Educational Resources Information Center

    Albright, Jessica C.; Dassenko, David J.; Mohamed, Essa A.; Beussman, Douglas J.

    2009-01-01

    Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is an important bioanalytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. This is an especially powerful tool when combined with gel separation of proteins and database mining using the mass spectral data. Currently, few hands-on…

  14. Proteome analysis of Sorangium cellulosum employing 2D-HPLC-MS/MS and improved database searching strategies for CID and ETD fragment spectra.

    PubMed

    Leinenbach, Andreas; Hartmer, Ralf; Lubeck, Markus; Kneissl, Benny; Elnakady, Yasser A; Baessmann, Carsten; Müller, Rolf; Huber, Christian G

    2009-09-01

    Shotgun proteome analysis of the myxobacterial model strain for secondary metabolite biosynthesis Sorangium cellulosum was performed employing off-line two-dimensional high-pH reversed-phase HPLC x low-pH ion-pair reversed-phase HPLC and dual tandem mass spectrometry with collision-induced dissociation (CID) and electron transfer dissociation (ETD) as complementary fragmentation techniques. Peptide identification using database searching was optimized for ETD fragment spectra to obtain the maximum number of identifications at equivalent false discovery rates (1.0%) in the evaluation of both fragmentation techniques. In the database search of the CID MS/MS data, the mass tolerance was set to the well-established 0.3 Da window, whereas for ETD data, it was widened to 1.1 Da to account for hydrogen-rearrangement in the radical-intermediate of the peptide precursor ion. To achieve a false discovery rate comparable to the CID results, we increased the significance threshold for peptide identification to 0.001 for the ETD data. The ETD based analysis yielded about 74% of all peptides and about 78% of all proteins compared to the CID-method. In the combined data set, 952 proteins of S. cellulosum were confidently identified by at least two peptides per protein, facilitating the study of the function of regulatory proteins in the social myxobacteria and their role in secondary metabolism.

  15. Local image descriptor-based searching framework of usable similar cases in a radiation treatment planning database for stereotactic body radiotherapy

    NASA Astrophysics Data System (ADS)

    Nonaka, Ayumi; Arimura, Hidetaka; Nakamura, Katsumasa; Shioyama, Yoshiyuki; Soufi, Mazen; Magome, Taiki; Honda, Hiroshi; Hirata, Hideki

    2014-03-01

    Radiation treatment planning (RTP) of the stereotactic body radiotherapy (SBRT) was more complex compared with conventional radiotherapy because of using a number of beam directions. We reported that similar planning cases could be helpful for determination of beam directions for treatment planners, who have less experiences of SBRT. The aim of this study was to develop a framework of searching for usable similar cases to an unplanned case in a RTP database based on a local image descriptor. This proposed framework consists of two steps searching and rearrangement. In the first step, the RTP database was searched for 10 cases most similar to object cases based on the shape similarity of two-dimensional lung region at the isocenter plane. In the second step, the 5 most similar cases were selected by using geometric features related to the location, size and shape of the planning target volume, lung and spinal cord. In the third step, the selected 5 cases were rearranged by use of the Euclidean distance of a local image descriptor, which is a similarity index based on the magnitudes and orientations of image gradients within a region of interest around an isocenter. It was assumed that the local image descriptor represents the information around lung tumors related to treatment planning. The cases, which were selected as cases most similar to test cases by the proposed method, were more resemble in terms of the tumor location than those selected by a conventional method. For evaluation of the proposed method, we applied a similar-cases-based beam arrangement method developed in the previous study to the similar cases selected by the proposed method based on a linear registration. The proposed method has the potential to suggest the superior beam-arrangements from the treatment point of view.

  16. VIEWCACHE: An incremental database access method for autonomous interoperable databases

    NASA Technical Reports Server (NTRS)

    Roussopoulos, Nick; Sellis, Timoleon

    1991-01-01

    The objective is to illustrate the concept of incremental access to distributed databases. An experimental database management system, ADMS, which has been developed at the University of Maryland, in College Park, uses VIEWCACHE, a database access method based on incremental search. VIEWCACHE is a pointer-based access method that provides a uniform interface for accessing distributed databases and catalogues. The compactness of the pointer structures formed during database browsing and the incremental access method allow the user to search and do inter-database cross-referencing with no actual data movement between database sites. Once the search is complete, the set of collected pointers pointing to the desired data are dereferenced.

  17. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  18. Quantum corrections in modern gauge theories of fundamental interactions and the search for new physics

    SciTech Connect

    Zucchini, R.

    1988-01-01

    We show that the analysis of the quantum effects in gauge theories yields several constraints which may be used to test their internal consistency and physical viability. We have studied, in particular, the Higgs sector of the minimal standard model and tested the universality of the weak interactions and the conserved-vector-current hypothesis. Finally, we have analyzed modular invariance in the closed bosonic string.

  19. MapReduce Implementation of a Hybrid Spectral Library-Database Search Method for Large-Scale Peptide Identification

    SciTech Connect

    Kalyanaraman, Anantharaman; Cannon, William R.; Latt, Benjamin K.; Baxter, Douglas J.

    2011-11-01

    A MapReduce-based implementation called MR- MSPolygraph for parallelizing peptide identification from mass spectrometry data is presented. The underlying serial method, MSPolygraph, uses a novel hybrid approach to match an experimental spectrum against a combination of a protein sequence database and a spectral library. Our MapReduce implementation can run on any Hadoop cluster environment. Experimental results demonstrate that, relative to the serial version, MR-MSPolygraph reduces the time to solution from weeks to hours, for processing tens of thousands of experimental spectra. Speedup and other related performance studies are also reported on a 400-core Hadoop cluster using spectral datasets from environmental microbial communities as inputs.

  20. The use of quantum molecular calculations to guide a genetic algorithm: a way to search for new chemistry.

    PubMed

    Durrant, Marcus C

    2007-01-01

    The process of gene-based molecular evolution has been simulated in silico by using massively parallel density functional theory quantum calculations, coupled with a genetic algorithm, to test for fitness with respect to a target chemical reaction in populations of genetically encoded molecules. The goal of this study was the identification of transition-metal complexes capable of mediating a known reaction, namely the cleavage of N(2) to give the metal nitride. Each complex within the search space was uniquely specified by a nanogene consisting of an eight-digit number. Propagation of an individual nanogene into successive generations was determined by the fitness of its phenotypic molecule to perform the target reaction and new generations were created by recombination and mutation of surviving nanogenes. In its simplest implementation, the quantum-directed genetic algorithm (QDGA) quickly located a local minimum on the evolutionary fitness hypersurface, but proved incapable of progressing towards the global minimum. A strategy for progressing beyond local minima consistent with the Darwinian paradigm by the use of environmental variations coupled with mass extinctions was therefore developed. This allowed for the identification of nitriding complexes that are very closely related to known examples from the chemical literature. Examples of mutations that appear to be beneficial at the genetic level but prove to be harmful at the phenotypic level are described. As well as revealing fundamental aspects of molecular evolution, QDGA appears to be a powerful tool for the identification of lead compounds capable of carrying out a target chemical reaction.

  1. Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.

    PubMed

    Naghdi, Mohammad Reza; Smail, Katia; Wang, Joy X; Wade, Fallou; Breaker, Ronald R; Perreault, Jonathan

    2017-03-15

    The discovery of noncoding RNAs (ncRNAs) and their importance for gene regulation led us to develop bioinformatics tools to pursue the discovery of novel ncRNAs. Finding ncRNAs de novo is challenging, first due to the difficulty of retrieving large numbers of sequences for given gene activities, and second due to exponential demands on calculation needed for comparative genomics on a large scale. Recently, several tools for the prediction of conserved RNA secondary structure were developed, but many of them are not designed to uncover new ncRNAs, or are too slow for conducting analyses on a large scale. Here we present various approaches using the database RiboGap as a primary tool for finding known ncRNAs and for uncovering simple sequence motifs with regulatory roles. This database also can be used to easily extract intergenic sequences of eubacteria and archaea to find conserved RNA structures upstream of given genes. We also show how to extend analysis further to choose the best candidate ncRNAs for experimental validation.

  2. The Search for Universal Constants and the Birth of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Robotti, Nadia; Badino, Massimiliano

    The origin of quantum theory and Max Planck's theoretical work are without doubt two of the most frequently quoted episodes in the history of quantum physics, for the obvious reason that they represented the first steps in its formulation. Paradoxically however there are relatively few specific studies of Planck and those differ on a range of questions. In our opinion this is due to the extremely synthetic nature of some of Planck's papers, and especially the "fundamentals" of October and December 1900. Faced with such brevity, a number of historians of science and philosophers have preferred to give a comprehensive analysis of the landmarks in Planck's work, often resorting to a more or less retrospective reconstruction process rather than attempting to build an all-embracing vision of Planck's work as a whole. In this paper we have therefore attempted to rebuild Planck's steps from 1899 to 1900. An analysis of this type shows that Planck's work has a profound internal unity throughout the entire period leading up to the discovery of the "quantum of energy". In our opinion a key to interpreting the mutual relationships between the various parts and stages of the theory in an intelligible manner is provided by Planck's interest in universal constants. This interest was grounded in two factors: 1) universal constants gave the entire theory a precise physical meaning, 2) they could be used to build a universal system of units of measurement. In particular we show that various pairs of constants are a clear feature of Planck's treatment of the blackbody problem throughout the period in question and that for Planck the appearance of these constants in the distribution law represented a fundamental criteria. So much so that it inevitably played a key role in what has been defined as the crucial moment of the entire process - the decision to use a probabilistic definition of entropy.

  3. Comparing the Hematopoetic Syndrome Time Course in the NHP Animal Model to Radiation Accident Cases From the Database Search.

    PubMed

    Graessle, Dieter H; Dörr, Harald; Bennett, Alexander; Shapiro, Alla; Farese, Ann M; MacVittie, Thomas J; Meineke, Viktor

    2015-11-01

    Since controlled clinical studies on drug administration for the acute radiation syndrome are lacking, clinical data of human radiation accident victims as well as experimental animal models are the main sources of information. This leads to the question of how to compare and link clinical observations collected after human radiation accidents with experimental observations in non-human primate (NHP) models. Using the example of granulocyte counts in the peripheral blood following radiation exposure, approaches for adaptation between NHP and patient databases on data comparison and transformation are introduced. As a substitute for studying the effects of administration of granulocyte-colony stimulating factor (G-CSF) in human clinical trials, the method of mathematical modeling is suggested using the example of G-CSF administration to NHP after total body irradiation.

  4. Detection and identification of heme c-modified peptides by histidine affinity chromatography, high-performance liquid chromatography-mass spectrometry, and database searching.

    PubMed

    Merkley, Eric D; Anderson, Brian J; Park, Jea; Belchik, Sara M; Shi, Liang; Monroe, Matthew E; Smith, Richard D; Lipton, Mary S

    2012-12-07

    Multiheme c-type cytochromes (proteins with covalently attached heme c moieties) play important roles in extracellular metal respiration in dissimilatory metal-reducing bacteria. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of c-type cytochromes is hindered by the presence of multiple heme groups, since the heme c modified peptides are typically not observed or, if observed, not identified. Using a recently reported histidine affinity chromatography (HAC) procedure, we enriched heme c tryptic peptides from purified bovine heart cytochrome c, two bacterial decaheme cytochromes, and subjected these samples to LC-MS/MS analysis. Enriched bovine cytochrome c samples yielded 3- to 6-fold more confident peptide-spectrum matches to heme c containing peptides than unenriched digests. In unenriched digests of the decaheme cytochrome MtoA from Sideroxydans lithotrophicus ES-1, heme c peptides for 4 of the 10 expected sites were observed by LC-MS/MS; following HAC fractionation, peptides covering 9 out of 10 sites were obtained. Heme c peptide spiked into E. coli lysates at mass ratios as low as 1×10(-4) was detected with good signal-to-noise after HAC and LC-MS/MS analysis. In addition to HAC, we have developed a proteomics database search strategy that takes into account the unique physicochemical properties of heme c peptides. The results suggest that accounting for the double thioether link between heme c and peptide, and the use of the labile heme fragment as a reporter ion, can improve database searching results. The combination of affinity chromatography and heme-specific informatics yielded increases in the number of peptide-spectrum matches of 20-100-fold for bovine cytochrome c.

  5. Detection and Identification of Heme c-Modified Peptides by Histidine Affinity Chromatography, High-Performance Liquid Chromatography-Mass Spectrometry, and Database Searching

    SciTech Connect

    Merkley, Eric D.; Anderson, Brian J.; Park, Jea H.; Belchik, Sara M.; Shi, Liang; Monroe, Matthew E.; Smith, Richard D.; Lipton, Mary S.

    2012-12-07

    Multiheme c-type cytochromes (proteins with covalently attached heme c moieties) play important roles in extracellular metal respiration in dissimilatory metal-reducing bacteria. Liquid chromatography-tandem mass spectrometry-(LC-MS/MS) characterization of c-type cytochromes is hindered by the presence of multiple heme groups, since the heme c modified peptides are typically not observed, or if observed, not identified. Using a recently reported histidine affinity chromatography (HAC) procedure, we enriched heme c tryptic peptides from purified bovine heart cytochrome c, a bacterial decaheme cytochrome, and subjected these samples to LC-MS/MS analysis. Enriched bovine cytochrome c samples yielded three- to six-fold more confident peptide-spectrum matches to heme-c containing peptides than unenriched digests. In unenriched digests of the decaheme cytochrome MtoA from Sideroxydans lithotrophicus ES-1, heme c peptides for four of the ten expected sites were observed by LC-MS/MS; following HAC fractionation, peptides covering nine out of ten sites were obtained. Heme c peptide spiked into E. coli lysates at mass ratios as low as 10-4 was detected with good signal-to-noise after HAC and LC-MS/MS analysis. In addition to HAC, we have developed a proteomics database search strategy that takes into account the unique physicochemical properties of heme c peptides. The results suggest that accounting for the double thioether link between heme c and peptide, and the use of the labile heme fragment as a reporter ion, can improve database searching results. The combination of affinity chromatography and heme-specific informatics yielded increases in the number of peptide-spectrum matches of 20-100-fold for bovine cytochrome c.

  6. Chemical and biological warfare: Protection, decontamination, and disposal. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect

    1997-11-01

    The bibliography contains citations concerning the means to defend against chemical and biological agents used in military operations, and to eliminate the effects of such agents on personnel, equipment, and grounds. Protection is accomplished through protective clothing and masks, and in buildings and shelters through filtration. Elimination of effects includes decontamination and removal of the agents from clothing, equipment, buildings, grounds, and water, using chemical deactivation, incineration, and controlled disposal of material in injection wells and ocean dumping. Other Published Searches in this series cover chemical warfare detection; defoliants; general studies; biochemistry and therapy; and biology, chemistry, and toxicology associated with chemical warfare agents.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  7. Robots for hazardous duties: Military, space, and nuclear facility applications. (Latest citations from the NTIS bibliographic database). Published Search

    SciTech Connect

    1993-09-01

    The bibliography contains citations concerning the design and application of robots used in place of humans where the environment could be hazardous. Military applications include autonomous land vehicles, robotic howitzers, and battlefield support operations. Space operations include docking, maintenance, mission support, and intra-vehicular and extra-vehicular activities. Nuclear applications include operations within the containment vessel, radioactive waste operations, fueling operations, and plant security. Many of the articles reference control techniques and the use of expert systems in robotic operations. Applications involving industrial manufacturing, walking robots, and robot welding are cited in other published searches in this series. (Contains a minimum of 183 citations and includes a subject term index and title list.)

  8. Quality Control of Biomedicinal Allergen Products – Highly Complex Isoallergen Composition Challenges Standard MS Database Search and Requires Manual Data Analyses

    PubMed Central

    Spiric, Jelena; Engin, Anna M.; Karas, Michael; Reuter, Andreas

    2015-01-01

    Allergy against birch pollen is among the most common causes of spring pollinosis in Europe and is diagnosed and treated using extracts from natural sources. Quality control is crucial for safe and effective diagnosis and treatment. However, current methods are very difficult to standardize and do not address individual allergen or isoallergen composition. MS provides information regarding selected proteins or the entire proteome and could overcome the aforementioned limitations. We studied the proteome of birch pollen, focusing on allergens and isoallergens, to clarify which of the 93 published sequence variants of the major allergen, Bet v 1, are expressed as proteins within one source material in parallel. The unexpectedly complex Bet v 1 isoallergen composition required manual data interpretation and a specific design of databases, as current database search engines fail to unambiguously assign spectra to highly homologous, partially identical proteins. We identified 47 non-allergenic proteins and all 5 known birch pollen allergens, and unambiguously proved the existence of 18 Bet v 1 isoallergens and variants by manual data analysis. This highly complex isoallergen composition raises questions whether isoallergens can be ignored or must be included for the quality control of allergen products, and which data analysis strategies are to be applied. PMID:26561299

  9. Discovery of novel aldose reductase inhibitors using a protein structure-based approach: 3D-database search followed by design and synthesis.

    PubMed

    Iwata, Y; Arisawa, M; Hamada, R; Kita, Y; Mizutani, M Y; Tomioka, N; Itai, A; Miyamoto, S

    2001-05-24

    Aldose reductase (AR) has been implicated in the etiology of diabetic complications. Due to the limited number of currently available drugs for the treatment of diabetic complications, we have carried out structure-based drug design and synthesis in an attempt to find new types of AR inhibitors. With the ADAM&EVE program, a three-dimensional database (ACD3D) was searched using the ligand binding site of the AR crystal structure. Out of 179 compounds selected through this search followed by visual inspection, 36 compounds were purchased and subjected to a biological assay. Ten compounds showed more than 40% inhibition of AR at a 15 microg/mL concentration. In a subsequent lead optimization, a series of analogues of the most active compound were synthesized based on the docking mode derived by ADAM&EVE. Many of these congeners exhibited higher activities compared to the mother compound. Indeed, the most potent, synthesized compound showed an approximately 20-fold increase in inhibitory activity (IC(50) = 0.21 vs 4.3 microM). Furthermore, a hydrophobic subsite was newly inferred, which would be useful for the design of inhibitors with improved affinity for AR.

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

    PubMed

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

    2013-09-01

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

  11. Quantum Navigation and Ranking in Complex Networks

    PubMed Central

    Sánchez-Burillo, Eduardo; Duch, Jordi; Gómez-Gardeñes, Jesús; Zueco, David

    2012-01-01

    Complex networks are formal frameworks capturing the interdependencies between the elements of large systems and databases. This formalism allows to use network navigation methods to rank the importance that each constituent has on the global organization of the system. A key example is Pagerank navigation which is at the core of the most used search engine of the World Wide Web. Inspired in this classical algorithm, we define a quantum navigation method providing a unique ranking of the elements of a network. We analyze the convergence of quantum navigation to the stationary rank of networks and show that quantumness decreases the number of navigation steps before convergence. In addition, we show that quantum navigation allows to solve degeneracies found in classical ranks. By implementing the quantum algorithm in real networks, we confirm these improvements and show that quantum coherence unveils new hierarchical features about the global organization of complex systems. PMID:22930671

  12. Quantum Navigation and Ranking in Complex Networks

    NASA Astrophysics Data System (ADS)

    Sánchez-Burillo, Eduardo; Duch, Jordi; Gómez-Gardeñes, Jesús; Zueco, David

    2012-08-01

    Complex networks are formal frameworks capturing the interdependencies between the elements of large systems and databases. This formalism allows to use network navigation methods to rank the importance that each constituent has on the global organization of the system. A key example is Pagerank navigation which is at the core of the most used search engine of the World Wide Web. Inspired in this classical algorithm, we define a quantum navigation method providing a unique ranking of the elements of a network. We analyze the convergence of quantum navigation to the stationary rank of networks and show that quantumness decreases the number of navigation steps before convergence. In addition, we show that quantum navigation allows to solve degeneracies found in classical ranks. By implementing the quantum algorithm in real networks, we confirm these improvements and show that quantum coherence unveils new hierarchical features about the global organization of complex systems.

  13. Communication: overcoming the root search problem in complex quantum trajectory calculations.

    PubMed

    Zamstein, Noa; Tannor, David J

    2014-01-28

    Three new developments are presented regarding the semiclassical coherent state propagator. First, we present a conceptually different derivation of Huber and Heller's method for identifying complex root trajectories and their equations of motion [D. Huber and E. J. Heller, J. Chem. Phys. 87, 5302 (1987)]. Our method proceeds directly from the time-dependent Schrödinger equation and therefore allows various generalizations of the formalism. Second, we obtain an analytic expression for the semiclassical coherent state propagator. We show that the prefactor can be expressed in a form that requires solving significantly fewer equations of motion than in alternative expressions. Third, the semiclassical coherent state propagator is used to formulate a final value representation of the time-dependent wavefunction that avoids the root search, eliminates problems with caustics and automatically includes interference. We present numerical results for the 1D Morse oscillator showing that the method may become an attractive alternative to existing semiclassical approaches.

  14. Communication: Overcoming the root search problem in complex quantum trajectory calculations

    SciTech Connect

    Zamstein, Noa; Tannor, David J.

    2014-01-28

    Three new developments are presented regarding the semiclassical coherent state propagator. First, we present a conceptually different derivation of Huber and Heller's method for identifying complex root trajectories and their equations of motion [D. Huber and E. J. Heller, J. Chem. Phys. 87, 5302 (1987)]. Our method proceeds directly from the time-dependent Schrödinger equation and therefore allows various generalizations of the formalism. Second, we obtain an analytic expression for the semiclassical coherent state propagator. We show that the prefactor can be expressed in a form that requires solving significantly fewer equations of motion than in alternative expressions. Third, the semiclassical coherent state propagator is used to formulate a final value representation of the time-dependent wavefunction that avoids the root search, eliminates problems with caustics and automatically includes interference. We present numerical results for the 1D Morse oscillator showing that the method may become an attractive alternative to existing semiclassical approaches.

  15. Scopus database: a review.

    PubMed

    Burnham, Judy F

    2006-03-08

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

  16. Rotational population patterns and searches for the nuclear SQUID (Superconducting Quantum Interference Device)

    SciTech Connect

    Canto, L.F.; Donangelo, R.J.; Farhan, A.R.; Guidry, M.W.; Rasmussen, J.O.; Ring, P.; Stoyer, M.A. . Inst. de Fisica; Kuwait Univ. . Dept. of Physics; Tennessee Univ., Knoxville, TN . Dept. of Physics; Lawrence Berkeley Lab., CA; Technische Univ. Muenchen, Garching . Physikdepartment; Lawrence Berkeley Lab., CA )

    1989-11-01

    This paper presents new theoretical results for rotational population patterns in the nuclear SQUID effect. (The term nuclear SQUID is in analogy to the solid-state Superconducting Quantum Interference Devices.) The SQUID effect is an interesting new twist to an old quest to understand Coriolis anti-pairing (CAP) effects in nuclear rotational bands. Two-neutron transfer reaction cross sections among high-spin states have long been touted as more specific CAP probes than other nuclear properties. Heavy projectiles like Sn or Pb generally are recommended to pump the deformed nucleus to as high spin as possible for transfer. The interference and sign reversal of 2n transfer amplitudes at high spin, as predicted in the early SQUID work imposes the difficult requirement of Coulomb pumping to near back-bending spins at closest approach. For Pb on rare earths we find a dramatic departure from sudden-approximation, so that the population depression occurs as low as final spin 10h. 14 refs., 8 figs.

  17. Realization of a quantum gate using gravitational search algorithm by perturbing three-dimensional harmonic oscillator with an electromagnetic field

    NASA Astrophysics Data System (ADS)

    Sharma, Navneet; Rawat, Tarun Kumar; Parthasarathy, Harish; Gautam, Kumar

    2016-06-01

    The aim of this paper is to design a current source obtained as a representation of p information symbols \\{I_k\\} so that the electromagnetic (EM) field generated interacts with a quantum atomic system producing after a fixed duration T a unitary gate U( T) that is as close as possible to a given unitary gate U_g. The design procedure involves calculating the EM field produced by \\{I_k\\} and hence the perturbing Hamiltonian produced by \\{I_k\\} finally resulting in the evolution operator produced by \\{I_k\\} up to cubic order based on the Dyson series expansion. The gate error energy is thus obtained as a cubic polynomial in \\{I_k\\} which is minimized using gravitational search algorithm. The signal to noise ratio (SNR) in the designed gate is higher as compared to that using quadratic Dyson series expansion. The SNR is calculated as the ratio of the Frobenius norm square of the desired gate to that of the desired gate error.

  18. 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.

  19. Web Search Engines: Search Syntax and Features.

    ERIC Educational Resources Information Center

    Ojala, Marydee

    2002-01-01

    Presents a chart that explains the search syntax, features, and commands used by the 12 most widely used general Web search engines. Discusses Web standardization, expanded types of content searched, size of databases, and search engines that include both simple and advanced versions. (LRW)

  20. Basics of Online Searching.

    ERIC Educational Resources Information Center

    Meadow, Charles T.; Cochrane, Pauline (Atherton)

    Intended to teach the principles of interactive bibliographic searching to those with little or no prior experience, this textbook explains the basic elements of online information retrieval and compares the major database search systems. Its chapters address (1) relevant definitions and vocabulary; (2) the conceptual facets of database searching,…

  1. Searching Sociological Abstracts.

    ERIC Educational Resources Information Center

    Kerbel, Sandra Sandor

    1981-01-01

    Describes the scope, content, and retrieval characteristics of Sociological Abstracts, an online database of literature in the social sciences. Sample searches are displayed, and the strengths and weaknesses of the database are summarized. (FM)

  2. Atomic Spectra Database (ASD)

    National Institute of Standards and Technology Data Gateway

    SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

  3. A Quantum Origin of Life?

    NASA Astrophysics Data System (ADS)

    Davies, Paul C. W.

    The following sections are included: * Chemistry and Information * Q-life * The Problem of Decoherence * Life as the "Solution" of a Quantum Search Algorithm * Quantum Choreography * Acknowledgements * References

  4. JICST Factual Database

    NASA Astrophysics Data System (ADS)

    Suzuki, Kazuaki; Shimura, Kazuki; Monma, Yoshio; Sakamoto, Masao; Morishita, Hiroshi; Kanazawa, Kenji

    The Japan Information Center of Science and Technology (JICST) has started the on-line service of JICST/NRIM Materials Strength Database for Engineering Steels and Alloys (JICST ME) in this March (1990). This database has been developed under the joint research between JICST and the National Research Institute for Metals (NRIM). It provides material strength data (creep, fatigue, etc.) of engineering steels and alloys. It is able to search and display on-line, and to analyze the searched data statistically and plot the result on graphic display. The database system and the data in JICST ME are described.

  5. Mathematical Notation in Bibliographic Databases.

    ERIC Educational Resources Information Center

    Pasterczyk, Catherine E.

    1990-01-01

    Discusses ways in which using mathematical symbols to search online bibliographic databases in scientific and technical areas can improve search results. The representations used for Greek letters, relations, binary operators, arrows, and miscellaneous special symbols in the MathSci, Inspec, Compendex, and Chemical Abstracts databases are…

  6. Exact diagonalization study of ν = 1 / 3 + 1 / 3 bilayer quantum Hall in search of Fibonnacci anyons

    NASA Astrophysics Data System (ADS)

    Kim, Eun-Ah; Vaezi, Abolhassan; Lee, Kyungmin

    2015-03-01

    Non-abelian states with Fibonnacci anyons that can support universal topological quantum computation have been elusive. Recently it has been proposed that a remarkably simple setting of Abelian quantum Hall bilayer could support an exotic state with Fibonnacci anyons (Vaezi and Barkeshli, arXiv:1403.3383). Here we explore ν = 1 / 3 + 1 / 3 bilayer quantum Hall system considering different possibilities for interaction between bilayers using exact diagonalization. We find a sizable region in phase space potentially exhibiting topological degeneracy expected of Fibonnacci anyon states. This work has been supported by NSF CAREER with Grant Number DMR-0955822.

  7. Criteria for Comparing Children's Web Search Tools.

    ERIC Educational Resources Information Center

    Kuntz, Jerry

    1999-01-01

    Presents criteria for evaluating and comparing Web search tools designed for children. Highlights include database size; accountability; categorization; search access methods; help files; spell check; URL searching; links to alternative search services; advertising; privacy policy; and layout and design. (LRW)

  8. Quantum algorithms: an overview

    NASA Astrophysics Data System (ADS)

    Montanaro, Ashley

    2016-01-01

    Quantum computers are designed to outperform standard computers by running quantum algorithms. Areas in which quantum algorithms can be applied include cryptography, search and optimisation, simulation of quantum systems and solving large systems of linear equations. Here we briefly survey some known quantum algorithms, with an emphasis on a broad overview of their applications rather than their technical details. We include a discussion of recent developments and near-term applications of quantum algorithms.

  9. Quantum decision tree classifier

    NASA Astrophysics Data System (ADS)

    Lu, Songfeng; Braunstein, Samuel L.

    2013-11-01

    We study the quantum version of a decision tree classifier to fill the gap between quantum computation and machine learning. The quantum entropy impurity criterion which is used to determine which node should be split is presented in the paper. By using the quantum fidelity measure between two quantum states, we cluster the training data into subclasses so that the quantum decision tree can manipulate quantum states. We also propose algorithms constructing the quantum decision tree and searching for a target class over the tree for a new quantum object.

  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. JICST Factual DatabaseJICST Chemical Substance Safety Regulation Database

    NASA Astrophysics Data System (ADS)

    Abe, Atsushi; Sohma, Tohru

    JICST Chemical Substance Safety Regulation Database is based on the Database of Safety Laws for Chemical Compounds constructed by Japan Chemical Industry Ecology-Toxicology & Information Center (JETOC) sponsored by the Sience and Technology Agency in 1987. JICST has modified JETOC database system, added data and started the online service through JOlS-F (JICST Online Information Service-Factual database) in January 1990. JICST database comprises eighty-three laws and fourteen hundred compounds. The authors outline the database, data items, files and search commands. An example of online session is presented.

  12. Quantum annealing search of Ising spin glass ground state(s) with tunable transverse and longitudinal fields

    NASA Astrophysics Data System (ADS)

    Rajak, A.; Chakrabarti, B. K.

    2014-09-01

    Here we first discuss briefly the quantum annealing technique. We then study the quantum annealing of Sherrington-Kirkpatrick spin glass model with the tuning of both transverse and longitudinal fields. Both the fields are time-dependent and vanish adiabatically at the same time, starting from high values. We solve, for rather small systems, the time-dependent Schrodinger equation of the total Hamiltonian by employing a numerical technique. At the end of annealing we obtain the final state having high overlap with the exact ground state(s) of classical spin glass system (obtained independently).

  13. Chemical Kinetics Database

    National Institute of Standards and Technology Data Gateway

    SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

  14. Diatomic Spectral Database

    National Institute of Standards and Technology Data Gateway

    SRD 114 Diatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 121 diatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty, and reference are given for each transition reported.

  15. Hydrocarbon Spectral Database

    National Institute of Standards and Technology Data Gateway

    SRD 115 Hydrocarbon Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 91 hydrocarbon molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

  16. Triatomic Spectral Database

    National Institute of Standards and Technology Data Gateway

    SRD 117 Triatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 55 triatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

  17. Specialist Bibliographic Databases.

    PubMed

    Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A; Trukhachev, Vladimir I; Kostyukova, Elena I; Gerasimov, Alexey N; Kitas, George D

    2016-05-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls.

  18. Specialist Bibliographic Databases

    PubMed Central

    2016-01-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

  19. Online Petroleum Industry Bibliographic Databases: A Review.

    ERIC Educational Resources Information Center

    Anderson, Margaret B.

    This paper discusses the present status of the bibliographic database industry, reviews the development of online databases of interest to the petroleum industry, and considers future developments in online searching and their effect on libraries and information centers. Three groups of databases are described: (1) databases developed by the…

  20. Measuring peptide mass spectrum correlation using the quantum Grover algorithm.

    PubMed

    Choo, Keng Wah

    2007-03-01

    We investigated the use of the quantum Grover algorithm in the mass-spectrometry-based protein identification process. The approach coded the mass spectra on a quantum register and uses the Grover search algorithm for searching multiple solutions to find matches from a database. Measurement of the fidelity between the input and final states was used to quantify the similarity between the experimental and theoretical spectra. The optimal number of iteration is proven to be pi/4sqrt[N/k] , where k refers to the number of marked states. We found that one iteration is sufficient for the search if we let more that 62% of the N states be marked states. By measuring the fidelity after only one iteration of Grover search, we discovered that it resembles that of the correlation-based measurement used in the existing protein identification software. We concluded that the quantum Grover algorithm can be adapted for a correlation-based mass spectra database search, provided that decoherence can be kept to a minimum.

  1. Evaluation of Online Databases and Their Uses in Collection Evaluation.

    ERIC Educational Resources Information Center

    Rice, Barbara A.

    1985-01-01

    Addresses importance of online databases as part of library reference collection and focuses on bibliographic databases (ready reference, print versus online migration, bibliographic utilities); selection/evaluation of online databases (vendor selection, individual databases); full-text databases; numeric databases; end-user searching; and use of…

  2. Content-addressable holographic databases

    NASA Astrophysics Data System (ADS)

    Grawert, Felix; Kobras, Sebastian; Burr, Geoffrey W.; Coufal, Hans J.; Hanssen, Holger; Riedel, Marc; Jefferson, C. Michael; Jurich, Mark C.

    2000-11-01

    Holographic data storage allows the simultaneous search of an entire database by performing multiple optical correlations between stored data pages and a search argument. We have recently developed fuzzy encoding techniques for this fast parallel search and demonstrated a holographic data storage system that searches digital data records with high fidelity. This content-addressable retrieval is based on the ability to take the two-dimensional inner product between the search page and each stored data page. We show that this ability is lost when the correlator is defocussed to avoid material oversaturation, but can be regained by the combination of a random phase mask and beam confinement through total internal reflection. Finally, we propose an architecture in which spatially multiplexed holograms are distributed along the path of the search beam, allowing parallel search of large databases.

  3. Evaluation of Federated Searching Options for the School Library

    ERIC Educational Resources Information Center

    Abercrombie, Sarah E.

    2008-01-01

    Three hosted federated search tools, Follett One Search, Gale PowerSearch Plus, and WebFeat Express, were configured and implemented in a school library. Databases from five vendors and the OPAC were systematically searched. Federated search results were compared with each other and to the results of the same searches in the database's native…

  4. Reliable but Timesaving: In Search of an Efficient Quantum-chemical Method for the Description of Functional Fullerenes.

    PubMed

    Reis, H; Rasulev, B; Papadopoulos, M G; Leszczynski, J

    2015-01-01

    Fullerene and its derivatives are currently one of the most intensively investigated species in the area of nanomedicine and nanochemistry. Various unique properties of fullerenes are responsible for their wide range applications in industry, biology and medicine. A large pool of functionalized C60 and C70 fullerenes is investigated theoretically at different levels of quantum-mechanical theory. The semiempirial PM6 method, density functional theory with the B3LYP functional, and correlated ab initio MP2 method are employed to compute the optimized structures, and an array of properties for the considered species. In addition to the calculations for isolated molecules, the results of solution calculations are also reported at the DFT level, using the polarizable continuum model (PCM). Ionization potentials (IPs) and electron affinities (EAs) are computed by means of Koopmans' theorem as well as with the more accurate but computationally expensive ΔSCF method. Both procedures yield comparable values, while comparison of IPs and EAs computed with different quantum-mechanical methods shows surprisingly large differences. Harmonic vibrational frequencies are computed at the PM6 and B3LYP levels of theory and compared with each other. A possible application of the frequencies as 3D descriptors in the EVA (EigenVAlues) method is shown. All the computed data are made available, and may be used to replace experimental data in routine applications where large amounts of data are required, e.g. in structure-activity relationship studies of the toxicity of fullerene derivatives.

  5. Advanced Web Searching: Tricks of the Trade.

    ERIC Educational Resources Information Center

    Zorn, Peggy; And Others

    1996-01-01

    Discusses World Wide Web searching techniques for information professionals, and describes and evaluates four search systems that provide advanced search features and that search a comprehensive and authoritative database of Internet sites. Sample searches are explained and professional searching on the Web is discussed. (LRW)

  6. The ERIC Search: A Programmed Text.

    ERIC Educational Resources Information Center

    Szymanski, Cynthia; Arnold, Joann

    This text is intended as a guide for searching ERIC using the SilverPlatter CD-ROM database. The text describes the content and function of the ERIC database and demonstrates fundamental search techniques by following an example of a successful ERIC computer search. The search begins with the choice of a topic, the formulation of a search…

  7. A search for pre-main sequence stars in the high-latitude molecular clouds. II - A survey of the Einstein database

    NASA Technical Reports Server (NTRS)

    Caillault, Jean-Pierre; Magnani, Loris

    1990-01-01

    The preliminary results are reported of a survey of every EINSTEIN image which overlaps any high-latitude molecular cloud in a search for X-ray emitting pre-main sequence stars. This survey, together with complementary KPNO and IRAS data, will allow the determination of how prevalent low mass star formation is in these clouds in general and, particularly, in the translucent molecular clouds.

  8. Standardization of Keyword Search Mode

    ERIC Educational Resources Information Center

    Su, Di

    2010-01-01

    In spite of its popularity, keyword search mode has not been standardized. Though information professionals are quick to adapt to various presentations of keyword search mode, novice end-users may find keyword search confusing. This article compares keyword search mode in some major reference databases and calls for standardization. (Contains 3…

  9. WWW Search Tools in Reference Services.

    ERIC Educational Resources Information Center

    Kimmel, Stacey

    1997-01-01

    Provides an introduction to World Wide Web search tools for reference services. Discusses characteristics of search services and types of tools available, including search engines/robot-generated databases, directories, metasearch engines, and review/rating sites. (AEF)

  10. In search of quantum-limited contact resistance: understanding the intrinsic and extrinsic effects on the graphene-metal interface

    NASA Astrophysics Data System (ADS)

    Nath, Anindya; Currie, Marc; Boyd, Anthony K.; Wheeler, Virginia D.; Koehler, Andrew D.; Tadjer, Marko J.; Robinson, Zachary R.; Sridhara, Karthik; Hernandez, Sandra C.; Wollmershauser, James A.; Robinson, Jeremy T.; Myers-Ward, Rachael L.; Rao, Mulpuri V.; Gaskill, D. Kurt

    2016-06-01

    Owing to its two-dimensional structure, graphene is extremely sensitive to surface contamination. Conventional processing techniques inevitably modify graphene’s intrinsic properties by introducing adsorbents and/or defects which limit device performance and understanding the intrinsic properties of graphene. Here we demonstrate femtosecond laser direct patterning of graphene microstructures, without the aid of resists or other chemicals, that enables us to study both intrinsic and extrinsic effects on the graphene-metal interface. The pulsed femtosecond laser was configured to ablate epitaxial graphene (EG) on a sub-micrometer scale and form a precisely defined region without damaging the surrounding material or substrate. The ablated area was sufficient to electrically isolate transfer length measurement structures and Hall devices for subsequent transport measurements. Using pristine and systematically contaminated surfaces, we found that Ni does not form bonds to EG synthesized on SiC in contrast to the well-known C-Ni bond formation for graphene synthesized on metals; known as end-contacting. Without end-contacting, the contact resistance (R C) of Ni to pristine and resist-contaminated EG are one and two orders of magnitude larger, respectively, than the intrinsic quantum limited contact resistance. The range of reported R C values is explained using carrier transmission probability, as exemplified by the Landauer-Büttiker model, which is dependent on the presence or absence of end-contacts and dopant/work-function mediated conduction. The model predicts the need for both end-contacts and a clean graphene-metal interface as necessary conditions to approach quantum limited contact resistance.

  11. Biofuel Database

    National Institute of Standards and Technology Data Gateway

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  12. Search for quantum black hole production in high-invariant-mass lepton+jet final states using pp collisions at √s=8  TeV and the ATLAS detector.

    PubMed

    Aad, G; Abajyan, T; Abbott, B; Abdallah, J; Abdel Khalek, S; Abdinov, O; Aben, R; Abi, B; Abolins, M; Abouzeid, O S; Abramowicz, H; Abreu, H; Abulaiti, Y; Acharya, B S; Adamczyk, L; Adams, D L; Addy, T N; Adelman, J; Adomeit, S; Adye, T; Aefsky, S; Agatonovic-Jovin, T; Aguilar-Saavedra, J A; Agustoni, M; Ahlen, S P; Ahmad, A; Ahmadov, F; Aielli, G; Akesson, T P A; Akimoto, G; Akimov, A V; Alam, M A; Albert, J; Albrand, S; Alconada Verzini, M J; Aleksa, M; Aleksandrov, I N; Alexa, C; Alexander, G; Alexandre, G; Alexopoulos, T; Alhroob, M; Alimonti, G; Alio, L; Alison, J; Allbrooke, B M M; Allison, L J; Allport, P P; Allwood-Spiers, S E; Almond, J; Aloisio, A; Alon, R; Alonso, A; Alonso, F; Altheimer, A; Alvarez Gonzalez, B; Alviggi, M G; Amako, K; Amaral Coutinho, Y; Amelung, C; Ammosov, V V; Amor Dos Santos, S P; Amorim, A; Amoroso, S; Amram, N; Amundsen, G; Anastopoulos, C; Ancu, L S; Andari, N; Andeen, T; Anders, C F; Anders, G; Anderson, K J; Andreazza, A; Andrei, V; Anduaga, X S; Angelidakis, S; Anger, P; Angerami, A; Anghinolfi, F; Anisenkov, A V; Anjos, N; Annovi, A; Antonaki, A; Antonelli, M; Antonov, A; Antos, J; Anulli, F; Aoki, M; Aperio Bella, L; Apolle, R; Arabidze, G; Aracena, I; Arai, Y; Arce, A T H; Arguin, J-F; Argyropoulos, S; Arik, E; Arik, M; Armbruster, A J; Arnaez, O; Arnal, V; Arslan, O; Artamonov, A; Artoni, G; Asai, S; Asbah, N; Ask, S; Asman, B; Asquith, L; Assamagan, K; Astalos, R; Astbury, A; Atkinson, M; Atlay, N B; Auerbach, B; Auge, E; Augsten, K; Aurousseau, M; Avolio, G; Azuelos, G; Azuma, Y; Baak, M A; Bacci, C; Bach, A M; Bachacou, H; Bachas, K; Backes, M; Backhaus, M; Backus Mayes, J; Badescu, E; Bagiacchi, P; Bagnaia, P; Bai, Y; Bailey, D C; Bain, T; Baines, J T; Baker, O K; Baker, S; Balek, P; Balli, F; Banas, E; Banerjee, Sw; Banfi, D; Bangert, A; Bansal, V; Bansil, H S; Barak, L; Baranov, S P; Barber, T; Barberio, E L; Barberis, D; Barbero, M; Barillari, T; Barisonzi, M; Barklow, T; Barlow, N; Barnett, B M; Barnett, R M; Baroncelli, A; Barone, G; Barr, A J; Barreiro, F; Barreiro Guimarães da Costa, J; Bartoldus, R; Barton, A E; Bartos, P; Bartsch, V; Bassalat, A; Basye, A; Bates, R L; Batkova, L; Batley, J R; Battistin, M; Bauer, F; Bawa, H S; Beau, T; Beauchemin, P H; Beccherle, R; Bechtle, P; Beck, H P; Becker, K; Becker, S; Beckingham, M; Beddall, A J; Beddall, A; Bedikian, S; Bednyakov, V A; Bee, C P; Beemster, L J; Beermann, T A; Begel, M; Behr, K; Belanger-Champagne, C; Bell, P J; Bell, W H; Bella, G; Bellagamba, L; Bellerive, A; Bellomo, M; Belloni, A; Beloborodova, O L; Belotskiy, K; Beltramello, O; Benary, O; Benchekroun, D; Bendtz, K; Benekos, N; Benhammou, Y; Benhar Noccioli, E; Benitez Garcia, J A; Benjamin, D P; Bensinger, J R; Benslama, K; Bentvelsen, S; Berge, D; Bergeaas Kuutmann, E; Berger, N; Berghaus, F; Berglund, E; Beringer, J; Bernard, C; Bernat, P; Bernius, C; Bernlochner, F U; Berry, T; Berta, P; Bertella, C; Bertolucci, F; Besana, M I; Besjes, G J; Bessidskaia, O; Besson, N; Bethke, S; Bhimji, W; Bianchi, R M; Bianchini, L; Bianco, M; Biebel, O; Bieniek, S P; Bierwagen, K; Biesiada, J; Biglietti, M; Bilbao De Mendizabal, J; Bilokon, H; Bindi, M; Binet, S; Bingul, A; Bini, C; Bittner, B; Black, C W; Black, J E; Black, K M; Blackburn, D; Blair, R E; Blanchard, J-B; Blazek, T; Bloch, I; Blocker, C; Blum, W; Blumenschein, U; Bobbink, G J; Bobrovnikov, V S; Bocchetta, S S; Bocci, A; Boddy, C R; Boehler, M; Boek, J; Boek, T T; Bogaerts, J A; Bogdanchikov, A G; Bogouch, A; Bohm, C; Bohm, J; Boisvert, V; Bold, T; Boldea, V; Boldyrev, A S; Bolnet, N M; Bomben, M; Bona, M; Boonekamp, M; Borisov, A; Borissov, G; Borri, M; Borroni, S; Bortfeldt, J; Bortolotto, V; Bos, K; Boscherini, D; Bosman, M; Boterenbrood, H; Bouchami, J; Boudreau, J; Bouhova-Thacker, E V; Boumediene, D; Bourdarios, C; Bousson, N; Boutouil, S; Boveia, A; Boyd, J; Boyko, I R; Bozovic-Jelisavcic, I; Bracinik, J; Branchini, P; Brandt, A; Brandt, G; Brandt, O; Bratzler, U; Brau, B; Brau, J E; Braun, H M; Brazzale, S F; Brelier, B; Brendlinger, K; Brennan, A J; Brenner, R; Bressler, S; Bristow, K; Bristow, T M; Britton, D; Brochu, F M; Brock, I; Brock, R; Bromberg, C; Bronner, J; Brooijmans, G; Brooks, T; Brooks, W K; Brosamer, J; Brost, E; Brown, G; Brown, J; Bruckman de Renstrom, P A; Bruncko, D; Bruneliere, R; Brunet, S; Bruni, A; Bruni, G; Bruschi, M; Bryngemark, L; Buanes, T; Buat, Q; Bucci, F; Buchholz, P; Buckingham, R M; Buckley, A G; Buda, S I; Budagov, I A; Budick, B; Buehrer, F; Bugge, L; Bugge, M K; Bulekov, O; Bundock, A C; Bunse, M; Burckhart, H; Burdin, S; Burghgrave, B; Burke, S; Burmeister, I; Busato, E; Büscher, V; Bussey, P; Buszello, C P; Butler, B; Butler, J M; Butt, A I; Buttar, C M; Butterworth, J M; Buttinger, W; Buzatu, A; Byszewski, M; Cabrera Urbán, S; Caforio, D; Cakir, O; Calafiura, P; Calderini, G; Calfayan, P; Calkins, R; Caloba, L P; Caloi, R; Calvet, D; Calvet, S; Camacho Toro, R; Camarri, P; Cameron, D; Caminada, L M; Caminal Armadans, R; Campana, S; Campanelli, M; Campoverde, A; Canale, V; Canelli, F; Canepa, A; Cantero, J; Cantrill, R; Cao, T; Capeans Garrido, M D M; Caprini, I; Caprini, M; Capua, M; Caputo, R; Cardarelli, R; Carli, T; Carlino, G; Carminati, L; Caron, S; Carquin, E; Carrillo-Montoya, G D; Carter, A A; Carter, J R; Carvalho, J; Casadei, D; Casado, M P; Castaneda-Miranda, E; Castelli, A; Castillo Gimenez, V; Castro, N F; Catastini, P; Catinaccio, A; Catmore, J R; Cattai, A; Cattani, G; Caughron, S; Cavaliere, V; Cavalli, D; Cavalli-Sforza, M; Cavasinni, V; Ceradini, F; Cerio, B; Cerny, K; Cerqueira, A S; Cerri, A; Cerrito, L; Cerutti, F; Cerv, M; Cervelli, A; Cetin, S A; Chafaq, A; Chakraborty, D; Chalupkova, I; Chan, K; Chang, P; Chapleau, B; Chapman, J D; Charfeddine, D; Charlton, D G; Chavda, V; Chavez Barajas, C A; Cheatham, S; Chekanov, S; Chekulaev, S V; Chelkov, G A; Chelstowska, M A; Chen, C; Chen, H; Chen, K; Chen, L; Chen, S; Chen, X; Chen, Y; Cheng, H C; Cheng, Y; Cheplakov, A; Cherkaoui El Moursli, R; Chernyatin, V; Cheu, E; Chevalier, L; Chiarella, V; Chiefari, G; Childers, J T; Chilingarov, A; Chiodini, G; Chisholm, A S; Chislett, R T; Chitan, A; Chizhov, M V; Chouridou, S; Chow, B K B; Christidi, I A; Chromek-Burckhart, D; Chu, M L; Chudoba, J; Ciapetti, G; Ciftci, A K; Ciftci, R; Cinca, D; Cindro, V; Ciocio, A; Cirkovic, P; Citron, Z H; Citterio, M; Ciubancan, M; Clark, A; Clark, P J; Clarke, R N; Cleland, W; Clemens, J C; Clement, B; Clement, C; Coadou, Y; Cobal, M; Coccaro, A; Cochran, J; Coffey, L; Cogan, J G; Coggeshall, J; Cole, B; Cole, S; Colijn, A P; Collins-Tooth, C; Collot, J; Colombo, T; Colon, G; Compostella, G; Conde Muiño, P; Coniavitis, E; Conidi, M C; Connelly, I A; Consonni, S M; Consorti, V; Constantinescu, S; Conta, C; Conti, G; Conventi, F; Cooke, M; Cooper, B D; Cooper-Sarkar, A M; Cooper-Smith, N J; Copic, K; Cornelissen, T; Corradi, M; Corriveau, F; Corso-Radu, A; Cortes-Gonzalez, A; Cortiana, G; Costa, G; Costa, M J; Costa Batalha Pedro, R; Costanzo, D; Côté, D; Cottin, G; Cowan, G; Cox, B E; Cranmer, K; Cree, G; Crépé-Renaudin, S; Crescioli, F; Crispin Ortuzar, M; Cristinziani, M; Crosetti, G; Cuciuc, C-M; Cuenca Almenar, C; Cuhadar Donszelmann, T; Cummings, J; Curatolo, M; Cuthbert, C; Czirr, H; Czodrowski, P; Czyczula, Z; D'Auria, S; D'Onofrio, M; D'Orazio, A; Da Cunha Sargedas De Sousa, M J; Da Via, C; Dabrowski, W; Dafinca, A; Dai, T; Dallaire, F; Dallapiccola, C; Dam, M; Daniells, A C; Dano Hoffmann, M; Dao, V; Darbo, G; Darlea, G L; Darmora, S; Dassoulas, J A; Davey, W; David, C; Davidek, T; Davies, E; Davies, M; Davignon, O; Davison, A R; Davygora, Y; Dawe, E; Dawson, I; Daya-Ishmukhametova, R K; De, K; de Asmundis, R; De Castro, S; De Cecco, S; de Graat, J; De Groot, N; de Jong, P; De La Taille, C; De la Torre, H; De Lorenzi, F; De Nooij, L; De Pedis, D; De Salvo, A; De Sanctis, U; De Santo, A; De Vivie De Regie, J B; De Zorzi, G; Dearnaley, W J; Debbe, R; Debenedetti, C; Dechenaux, B; Dedovich, D V; Degenhardt, J; Deigaard, I; Del Peso, J; Del Prete, T; Delemontex, T; Deliot, F; Deliyergiyev, M; Dell'acqua, A; Dell'asta, L; Della Pietra, M; Della Volpe, D; Delmastro, M; Delsart, P A; Deluca, C; Demers, S; Demichev, M; Demilly, A; Demirkoz, B; Denisov, S P; Derendarz, D; Derkaoui, J E; Derue, F; Dervan, P; Desch, K; Deviveiros, P O; Dewhurst, A; Dhaliwal, S; Di Ciaccio, A; Di Ciaccio, L; Di Donato, C; Di Girolamo, A; Di Girolamo, B; Di Mattia, A; Di Micco, B; Di Nardo, R; Di Simone, A; Di Sipio, R; Di Valentino, D; Diaz, M A; Diehl, E B; Dietrich, J; Dietzsch, T A; Diglio, S; Dimitrievska, A; Dindar Yagci, K; Dingfelder, J; Dionisi, C; Dita, P; Dita, S; Dittus, F; Djama, F; Djobava, T; do Vale, M A B; Do Valle Wemans, A; Doan, T K O; Dobos, D; Dobson, E; Doglioni, C; Doherty, T; Dohmae, T; Dolejsi, J; Dolezal, Z; Dolgoshein, B A; Donadelli, M; Donati, S; Dondero, P; Donini, J; Dopke, J; Doria, A; Dos Anjos, A; Dotti, A; Dova, M T; Doyle, A T; Dris, M; Dubbert, J; Dube, S; Dubreuil, E; Duchovni, E; Duckeck, G; Ducu, O A; Duda, D; Dudarev, A; Dudziak, F; Duflot, L; Duguid, L; Dührssen, M; Dunford, M; Duran Yildiz, H; Düren, M; Dwuznik, M; Ebke, J; Edson, W; Edwards, C A; Edwards, N C; Ehrenfeld, W; Eifert, T; Eigen, G; Einsweiler, K; Ekelof, T; El Kacimi, M; Ellert, M; Elles, S; Ellinghaus, F; Ellis, K; Ellis, N; Elmsheuser, J; Elsing, M; Emeliyanov, D; Enari, Y; Endner, O C; Endo, M; Engelmann, R; Erdmann, J; Ereditato, A; Eriksson, D; Ernis, G; Ernst, J; Ernst, M; Ernwein, J; Errede, D; Errede, S; Ertel, E; Escalier, M; Esch, H; Escobar, C; Espinal Curull, X; Esposito, B; Etienne, F; Etienvre, A I; Etzion, E; Evangelakou, D; Evans, H; Fabbri, L; Facini, G; Fakhrutdinov, R M; Falciano, S; Fang, Y; Fanti, M; Farbin, A; Farilla, A; Farooque, T; Farrell, S; Farrington, S M; Farthouat, P; Fassi, F; Fassnacht, P; Fassouliotis, D; Fatholahzadeh, B; Favareto, A; Fayard, L; Federic, P; Fedin, O L; Fedorko, W; Fehling-Kaschek, M; Feigl, S; Feligioni, L; Feng, C; Feng, E J; Feng, H; Fenyuk, A B; Fernandez Perez, S; Fernando, W; Ferrag, S; Ferrando, J; Ferrara, V; Ferrari, A; Ferrari, P; Ferrari, R; Ferreira de Lima, D E; Ferrer, A; Ferrere, D; Ferretti, C; Ferretto Parodi, A; Fiascaris, M; Fiedler, F; Filipčič, A; Filipuzzi, M; Filthaut, F; Fincke-Keeler, M; Finelli, K D; Fiolhais, M C N; Fiorini, L; Firan, A; Fischer, J; Fisher, M J; Fitzgerald, E A; Flechl, M; Fleck, I; Fleischmann, P; Fleischmann, S; Fletcher, G T; Fletcher, G; Flick, T; Floderus, A; Flores Castillo, L R; Florez Bustos, A C; Flowerdew, M J; Formica, A; Forti, A; Fortin, D; Fournier, D; Fox, H; Francavilla, P; Franchini, M; Franchino, S; Francis, D; Franklin, M; Franz, S; Fraternali, M; Fratina, S; French, S T; Friedrich, C; Friedrich, F; Froidevaux, D; Frost, J A; Fukunaga, C; Fullana Torregrosa, E; Fulsom, B G; Fuster, J; Gabaldon, C; Gabizon, O; Gabrielli, A; Gabrielli, A; Gadatsch, S; Gadfort, T; Gadomski, S; Gagliardi, G; Gagnon, P; Galea, C; Galhardo, B; Gallas, E J; Gallo, V; Gallop, B J; Gallus, P; Galster, G; Gan, K K; Gandrajula, R P; Gao, J; Gao, Y S; Garay Walls, F M; Garberson, F; García, C; García Navarro, J E; Garcia-Sciveres, M; Gardner, R W; Garelli, N; Garonne, V; Gatti, C; Gaudio, G; Gaur, B; Gauthier, L; Gauzzi, P; Gavrilenko, I L; Gay, C; Gaycken, G; Gazis, E N; Ge, P; Gecse, Z; Gee, C N P; Geerts, D A A; Geich-Gimbel, Ch; Gellerstedt, K; Gemme, C; Gemmell, A; Genest, M H; Gentile, S; George, M; George, S; Gerbaudo, D; Gershon, A; Ghazlane, H; Ghodbane, N; Giacobbe, B; Giagu, S; Giangiobbe, V; Giannetti, P; Gianotti, F; Gibbard, B; Gibson, S M; Gilchriese, M; Gillam, T P S; Gillberg, D; Gillman, A R; Gingrich, D M; Giokaris, N; Giordani, M P; Giordano, R; Giorgi, F M; Giovannini, P; Giraud, P F; Giugni, D; Giuliani, C; Giunta, M; Gjelsten, B K; Gkialas, I; Gladilin, L K; Glasman, C; Glatzer, J; Glazov, A; Glonti, G L; Goblirsch-Kolb, M; Goddard, J R; Godfrey, J; Godlewski, J; Goeringer, C; Goldfarb, S; Golling, T; Golubkov, D; Gomes, A; Gomez Fajardo, L S; Gonçalo, R; Goncalves Pinto Firmino Da Costa, J; Gonella, L; González de la Hoz, S; Gonzalez Parra, G; Gonzalez Silva, M L; Gonzalez-Sevilla, S; Goossens, L; Gorbounov, P A; Gordon, H A; Gorelov, I; Gorfine, G; Gorini, B; Gorini, E; Gorišek, A; Gornicki, E; Goshaw, A T; Gössling, C; Gostkin, M I; Gouighri, M; Goujdami, D; Goulette, M P; Goussiou, A G; Goy, C; Gozpinar, S; Grabas, H M X; Graber, L; Grabowska-Bold, I; Grafström, P; Grahn, K-J; Gramling, J; Gramstad, E; Grancagnolo, F; Grancagnolo, S; Grassi, V; Gratchev, V; Gray, H M; Gray, J A; Graziani, E; Grebenyuk, O G; Greenwood, Z D; Gregersen, K; Gregor, I M; Grenier, P; Griffiths, J; Grigalashvili, N; Grillo, A A; Grimm, K; Grinstein, S; Gris, Ph; Grishkevich, Y V; Grivaz, J-F; Grohs, J P; Grohsjean, A; Gross, E; Grosse-Knetter, J; Grossi, G C; Groth-Jensen, J; Grout, Z J; Grybel, K; Guan, L; Guescini, F; Guest, D; Gueta, O; Guicheney, C; Guido, E; Guillemin, T; Guindon, S; Gul, U; Gumpert, C; Gunther, J; Guo, J; Gupta, S; Gutierrez, P; Gutierrez Ortiz, N G; Gutschow, C; Guttman, N; Guyot, C; Gwenlan, C; Gwilliam, C B; Haas, A; Haber, C; Hadavand, H K; Haefner, P; Hageboeck, S; Hajduk, Z; Hakobyan, H; Haleem, M; Hall, D; Halladjian, G; Hamacher, K; Hamal, P; Hamano, K; Hamer, M; Hamilton, A; Hamilton, S; Han, L; Hanagaki, K; Hanawa, K; Hance, M; Hanke, P; Hansen, J R; Hansen, J B; Hansen, J D; Hansen, P H; Hansson, P; Hara, K; Hard, A S; Harenberg, T; Harkusha, S; Harper, D; Harrington, R D; Harris, O M; Harrison, P F; Hartjes, F; Harvey, A; Hasegawa, S; Hasegawa, Y; Hassani, S; Haug, S; Hauschild, M; Hauser, R; Havranek, M; Hawkes, C M; Hawkings, R J; Hawkins, A D; Hayashi, T; Hayden, D; Hays, C P; Hayward, H S; Haywood, S J; Head, S J; Heck, T; Hedberg, V; Heelan, L; Heim, S; Heim, T; Heinemann, B; Heinrich, L; Heisterkamp, S; Hejbal, J; Helary, L; Heller, C; Heller, M; Hellman, S; Hellmich, D; Helsens, C; Henderson, J; Henderson, R C W; Hengler, C; Henrichs, A; Henriques Correia, A M; Henrot-Versille, S; Hensel, C; Herbert, G H; Hernández Jiménez, Y; Herrberg-Schubert, R; Herten, G; Hertenberger, R; Hervas, L; Hesketh, G G; Hessey, N P; Hickling, R; Higón-Rodriguez, E; Hill, J C; Hiller, K H; Hillert, S; Hillier, S J; Hinchliffe, I; Hines, E; Hirose, M; Hirschbuehl, D; Hobbs, J; Hod, N; Hodgkinson, M C; Hodgson, P; Hoecker, A; Hoeferkamp, M R; Hoffman, J; Hoffmann, D; Hofmann, J I; Hohlfeld, M; Holmes, T R; Hong, T M; Hooft van Huysduynen, L; Hostachy, J-Y; Hou, S; Hoummada, A; Howard, J; Howarth, J; Hrabovsky, M; Hristova, I; Hrivnac, J; Hryn'ova, T; Hsu, P J; Hsu, S-C; Hu, D; Hu, X; Huang, Y; Hubacek, Z; Hubaut, F; Huegging, F; Huettmann, A; Huffman, T B; Hughes, E W; Hughes, G; Huhtinen, M; Hülsing, T A; Hurwitz, M; Huseynov, N; Huston, J; Huth, J; Iacobucci, G; Iakovidis, G; Ibragimov, I; Iconomidou-Fayard, L; Idarraga, J; Ideal, E; Iengo, P; Igonkina, O; Iizawa, T; Ikegami, Y; Ikematsu, K; Ikeno, M; Iliadis, D; Ilic, N; Inamaru, Y; Ince, T; Ioannou, P; Iodice, M; Iordanidou, K; Ippolito, V; Irles Quiles, A; Isaksson, C; Ishino, M; Ishitsuka, M; Ishmukhametov, R; Issever, C; Istin, S; Iturbe Ponce, J M; Ivashin, A V; Iwanski, W; Iwasaki, H; Izen, J M; Izzo, V; Jackson, B; Jackson, J N; Jackson, M; Jackson, P; Jaekel, M R; Jain, V; Jakobs, K; Jakobsen, S; Jakoubek, T; Jakubek, J; Jamin, D O; Jana, D K; Jansen, E; Jansen, H; Janssen, J; Janus, M; Jarlskog, G; Jeanty, L; Jeng, G-Y; Jen-La Plante, I; Jennens, D; Jenni, P; Jentzsch, J; Jeske, C; Jézéquel, S; Jha, M K; Ji, H; Ji, W; Jia, J; Jiang, Y; Jimenez Belenguer, M; Jin, S; Jinaru, A; Jinnouchi, O; Joergensen, M D; Joffe, D; Johansson, K E; Johansson, P; Johns, K A; Jon-And, K; Jones, G; Jones, R W L; Jones, T J; Jorge, P M; Joshi, K D; Jovicevic, J; Ju, X; Jung, C A; Jungst, R M; Jussel, P; Juste Rozas, A; Kaci, M; Kaczmarska, A; Kado, M; Kagan, H; Kagan, M; Kajomovitz, E; Kama, S; Kanaya, N; Kaneda, M; Kaneti, S; Kanno, T; Kantserov, V A; Kanzaki, J; Kaplan, B; Kapliy, A; Kar, D; Karakostas, K; Karastathis, N; Karnevskiy, M; Karpov, S N; Karthik, K; Kartvelishvili, V; Karyukhin, A N; Kashif, L; Kasieczka, G; Kass, R D; Kastanas, A; Kataoka, Y; Katre, A; Katzy, J; Kaushik, V; Kawagoe, K; Kawamoto, T; Kawamura, G; Kazama, S; Kazanin, V F; Kazarinov, M Y; Keeler, R; Keener, P T; Kehoe, R; Keil, M; Keller, J S; Keoshkerian, H; Kepka, O; Kerševan, B P; Kersten, S; Kessoku, K; Keung, J; Khalil-Zada, F; Khandanyan, H; Khanov, A; Kharchenko, D; Khodinov, A; Khomich, A; Khoo, T J; Khoriauli, G; Khoroshilov, A; Khovanskiy, V; Khramov, E; Khubua, J; Kim, H; Kim, S H; Kimura, N; Kind, O; King, B T; King, M; King, R S B; King, S B; Kirk, J; Kiryunin, A E; Kishimoto, T; Kisielewska, D; Kitamura, T; Kittelmann, T; Kiuchi, K; Kladiva, E; Klein, M; Klein, U; Kleinknecht, K; Klimek, P; Klimentov, A; Klingenberg, R; Klinger, J A; Klinkby, E B; Klioutchnikova, T; Klok, P F; Kluge, E-E; Kluit, P; Kluth, S; Kneringer, E; Knoops, E B F G; Knue, A; Kobayashi, T; Kobel, M; Kocian, M; Kodys, P; Koenig, S; Koevesarki, P; Koffas, T; Koffeman, E; Kogan, L A; Kohlmann, S; Kohout, Z; Kohriki, T; Koi, T; Kolanoski, H; Koletsou, I; Koll, J; Komar, A A; Komori, Y; Kondo, T; Köneke, K; König, A C; Kono, T; Konoplich, R; Konstantinidis, N; Kopeliansky, R; Koperny, S; Köpke, L; Kopp, A K; Korcyl, K; Kordas, K; Korn, A; Korol, A A; Korolkov, I; Korolkova, E V; Korotkov, V A; Kortner, O; Kortner, S; Kostyukhin, V V; Kotov, S; Kotov, V M; Kotwal, A; Kourkoumelis, C; Kouskoura, V; Koutsman, A; Kowalewski, R; Kowalski, T Z; Kozanecki, W; Kozhin, A S; Kral, V; Kramarenko, V A; Kramberger, G; Krasnopevtsev, D; Krasny, M W; Krasznahorkay, A; Kraus, J K; Kravchenko, A; Kreiss, S; Kretzschmar, J; Kreutzfeldt, K; Krieger, N; Krieger, P; Kroeninger, K; Kroha, H; Kroll, J; Kroseberg, J; Krstic, J; Kruchonak, U; Krüger, H; Kruker, T; Krumnack, N; Krumshteyn, Z V; Kruse, A; Kruse, M C; Kruskal, M; Kubota, T; Kuday, S; Kuehn, S; Kugel, A; Kuhl, T; Kukhtin, V; Kulchitsky, Y; Kuleshov, S; Kuna, M; Kunkle, J; Kupco, A; Kurashige, H; Kurochkin, Y A; Kurumida, R; Kus, V; Kuwertz, E S; Kuze, M; Kvita, J; La Rosa, A; La Rotonda, L; Labarga, L; Lablak, S; Lacasta, C; Lacava, F; Lacey, J; Lacker, H; Lacour, D; Lacuesta, V R; Ladygin, E; Lafaye, R; Laforge, B; Lagouri, T; Lai, S; Laier, H; Laisne, E; Lambourne, L; Lampen, C L; Lampl, W; Lançon, E; Landgraf, U; Landon, M P J; Lang, V S; Lange, C; Lankford, A J; Lanni, F; Lantzsch, K; Lanza, A; Laplace, S; Lapoire, C; Laporte, J F; Lari, T; Larner, A; Lassnig, M; Laurelli, P; Lavorini, V; Lavrijsen, W; Laycock, P; Le, B T; Le Dortz, O; Le Guirriec, E; Le Menedeu, E; Lecompte, T; Ledroit-Guillon, F; Lee, C A; Lee, H; Lee, J S H; Lee, S C; Lee, L; Lefebvre, G; Lefebvre, M; Legger, F; Leggett, C; Lehan, A; Lehmacher, M; Lehmann Miotto, G; Lei, X; Leister, A G; Leite, M A L; Leitner, R; Lellouch, D; Lemmer, B; Leney, K J C; Lenz, T; Lenzen, G; Lenzi, B; Leone, R; Leonhardt, K; Leontsinis, S; Leroy, C; Lester, C G; Lester, C M; Levêque, J; Levin, D; Levinson, L J; Lewis, A; Lewis, G H; Leyko, A M; Leyton, M; Li, B; Li, B; Li, H; Li, H L; Li, S; Li, X; Liang, Z; Liao, H; Liberti, B; Lichard, P; Lie, K; Liebal, J; Liebig, W; Limbach, C; Limosani, A; Limper, M; Lin, S C; Linde, F; Lindquist, B E; Linnemann, J T; Lipeles, E; Lipniacka, A; Lisovyi, M; Liss, T M; Lissauer, D; Lister, A; Litke, A M; Liu, B; Liu, D; Liu, J B; Liu, K; Liu, L; Liu, M; Liu, M; Liu, Y; Livan, M; Livermore, S S A; Lleres, A; Llorente Merino, J; Lloyd, S L; Lo Sterzo, F; Lobodzinska, E; Loch, P; Lockman, W S; Loddenkoetter, T; Loebinger, F K; Loevschall-Jensen, A E; Loginov, A; Loh, C W; Lohse, T; Lohwasser, K; Lokajicek, M; Lombardo, V P; Long, J D; Long, R E; Lopes, L; Lopez Mateos, D; Lopez Paredes, B; Lorenz, J; Lorenzo Martinez, N; Losada, M; Loscutoff, P; Losty, M J; Lou, X; Lounis, A; Love, J; Love, P A; Lowe, A J; Lu, F; Lubatti, H J; Luci, C; Lucotte, A; Ludwig, D; Ludwig, I; Luehring, F; Lukas, W; Luminari, L; Lundberg, J; Lundberg, O; Lund-Jensen, B; Lungwitz, M; Lynn, D; Lysak, R; Lytken, E; Ma, H; Ma, L L; Maccarrone, G; Macchiolo, A; Maček, B; Machado Miguens, J; Macina, D; Mackeprang, R; Madar, R; Maddocks, H J; Mader, W F; Madsen, A; Maeno, M; Maeno, T; Magnoni, L; Magradze, E; Mahboubi, K; Mahlstedt, J; Mahmoud, S; Mahout, G; Maiani, C; Maidantchik, C; Maio, A; Majewski, S; Makida, Y; Makovec, N; Mal, P; Malaescu, B; Malecki, Pa; Maleev, V P; Malek, F; Mallik, U; Malon, D; Malone, C; Maltezos, S; Malyshev, V M; Malyukov, S; Mamuzic, J; Mandelli, B; Mandelli, L; Mandić, I; Mandrysch, R; Maneira, J; Manfredini, A; Manhaes de Andrade Filho, L; Manjarres Ramos, J A; Mann, A; Manning, P M; Manousakis-Katsikakis, A; Mansoulie, B; Mantifel, R; Mapelli, L; March, L; Marchand, J F; Marchese, F; Marchiori, G; Marcisovsky, M; Marino, C P; Marques, C N; Marroquim, F; Marshall, Z; Marti, L F; Marti-Garcia, S; Martin, B; Martin, B; Martin, J P; Martin, T A; Martin, V J; Martin Dit Latour, B; Martinez, H; Martinez, M; Martin-Haugh, S; Martyniuk, A C; Marx, M; Marzano, F; Marzin, A; Masetti, L; Mashimo, T; Mashinistov, R; Masik, J; Maslennikov, A L; Massa, I; Massol, N; Mastrandrea, P; Mastroberardino, A; Masubuchi, T; Matsunaga, H; Matsushita, T; Mättig, P; Mättig, S; Mattmann, J; Mattravers, C; Maurer, J; Maxfield, S J; Maximov, D A; Mazini, R; Mazzaferro, L; Mc Goldrick, G; Mc Kee, S P; McCarn, A; McCarthy, R L; McCarthy, T G; McCubbin, N A; McFarlane, K W; McFayden, J A; McHedlidze, G; McLaughlan, T; McMahon, S J; McPherson, R A; Meade, A; Mechnich, J; Mechtel, M; Medinnis, M; Meehan, S; Meera-Lebbai, R; Mehlhase, S; Mehta, A; Meier, K; Meineck, C; Meirose, B; Melachrinos, C; Mellado Garcia, B R; Meloni, F; Mendoza Navas, L; Mengarelli, A; Menke, S; Meoni, E; Mercurio, K M; Mergelmeyer, S; Meric, N; Mermod, P; Merola, L; Meroni, C; Merritt, F S; Merritt, H; Messina, A; Metcalfe, J; Mete, A S; Meyer, C; Meyer, C; Meyer, J-P; Meyer, J; Meyer, J; Middleton, R P; Migas, S; Mijović, L; Mikenberg, G; Mikestikova, M; Mikuž, M; Miller, D W; Mills, C; Milov, A; Milstead, D A; Milstein, D; Minaenko, A A; Miñano Moya, M; Minashvili, I A; Mincer, A I; Mindur, B; Mineev, M; Ming, Y; Mir, L M; Mirabelli, G; Mitani, T; Mitrevski, J; Mitsou, V A; Mitsui, S; Miucci, A; Miyagawa, P S; Mjörnmark, J U; Moa, T; Moeller, V; Mohapatra, S; Mohr, W; Molander, S; Moles-Valls, R; Mönig, K; Monini, C; Monk, J; Monnier, E; Montejo Berlingen, J; Monticelli, F; Monzani, S; Moore, R W; Mora Herrera, C; Moraes, A; Morange, N; Morel, J; Moreno, D; Moreno Llácer, M; Morettini, P; Morgenstern, M; Morii, M; Moritz, S; Morley, A K; Mornacchi, G; Morris, J D; Morvaj, L; Moser, H G; Mosidze, M; Moss, J; Mount, R; Mountricha, E; Mouraviev, S V; Moyse, E J W; Muanza, S G; Mudd, R D; Mueller, F; Mueller, J; Mueller, K; Mueller, T; Mueller, T; Muenstermann, D; Munwes, Y; Murillo Quijada, J A; Murray, W J; Mussche, I; Musto, E; Myagkov, A G; Myska, M; Nackenhorst, O; Nadal, J; Nagai, K; Nagai, R; Nagai, Y; Nagano, K; Nagarkar, A; Nagasaka, Y; Nagel, M; Nairz, A M; Nakahama, Y; Nakamura, K; Nakamura, T; Nakano, I; Namasivayam, H; Nanava, G; Napier, A; Narayan, R; Nash, M; Nattermann, T; Naumann, T; Navarro, G; Nayyar, R; Neal, H A; Nechaeva, P Yu; Neep, T J; Negri, A; Negri, G; Negrini, M; Nektarijevic, S; Nelson, A; Nelson, T K; Nemecek, S; Nemethy, P; Nepomuceno, A A; Nessi, M; Neubauer, M S; Neumann, M; Neusiedl, A; Neves, R M; Nevski, P; Newcomer, F M; Newman, P R; Nguyen, D H; Nguyen Thi Hong, V; Nickerson, R B; Nicolaidou, R; Nicquevert, B; Nielsen, J; Nikiforou, N; Nikiforov, A; Nikolaenko, V; Nikolic-Audit, I; Nikolics, K; Nikolopoulos, K; Nilsson, P; Ninomiya, Y; Nisati, A; Nisius, R; Nobe, T; Nodulman, L; Nomachi, M; Nomidis, I; Norberg, S; Nordberg, M; Novakova, J; Nozaki, M; Nozka, L; Ntekas, K; Nuncio-Quiroz, A-E; Nunes Hanninger, G; Nunnemann, T; Nurse, E; Nuti, F; O'Brien, B J; O'grady, F; O'Neil, D C; O'Shea, V; Oakham, F G; Oberlack, H; Ocariz, J; Ochi, A; Ochoa, M I; Oda, S; Odaka, S; Ogren, H; Oh, A; Oh, S H; Ohm, C C; Ohshima, T; Okamura, W; Okawa, H; Okumura, Y; Okuyama, T; Olariu, A; Olchevski, A G; Olivares Pino, S A; Oliveira Damazio, D; Oliver Garcia, E; Olivito, D; Olszewski, A; Olszowska, J; Onofre, A; Onyisi, P U E; Oram, C J; Oreglia, M J; Oren, Y; Orestano, D; Orlando, N; Oropeza Barrera, C; Orr, R S; Osculati, B; Ospanov, R; Otero Y Garzon, G; Otono, H; Ouchrif, M; Ouellette, E A; Ould-Saada, F; Ouraou, A; Oussoren, K P; Ouyang, Q; Ovcharova, A; Owen, M; Owen, S; Ozcan, V E; Ozturk, N; Pachal, K; Pacheco Pages, A; Padilla Aranda, C; Pagan Griso, S; Paganis, E; Pahl, C; Paige, F; Pais, P; Pajchel, K; Palacino, G; Palestini, S; Pallin, D; Palma, A; Palmer, J D; Pan, Y B; Panagiotopoulou, E; Panduro Vazquez, J G; Pani, P; Panikashvili, N; Panitkin, S; Pantea, D; Papadopoulou, Th D; Papageorgiou, K; Paramonov, A; Paredes Hernandez, D; Parker, M A; Parodi, F; Parsons, J A; Parzefall, U; Pasqualucci, E; Passaggio, S; Passeri, A; Pastore, F; Pastore, Fr; Pásztor, G; Pataraia, S; Patel, N D; Pater, J R; Patricelli, S; Pauly, T; Pearce, J; Pedersen, M; Pedraza Lopez, S; Peleganchuk, S V; Pelikan, D; Peng, H; Penning, B; Penwell, J; Perepelitsa, D V; Perez Codina, E; Pérez García-Estañ, M T; Perez Reale, V; Perini, L; Pernegger, H; Perrino, R; Peschke, R; Peshekhonov, V D; Peters, K; Peters, R F Y; Petersen, B A; Petersen, J; Petersen, T C; Petit, E; Petridis, A; Petridou, C; Petrolo, E; Petrucci, F; Petteni, M; Pezoa, R; Phillips, P W; Piacquadio, G; Pianori, E; Picazio, A; Piccaro, E; Piccinini, M; Piec, S M; Piegaia, R; Pignotti, D T; Pilcher, J E; Pilkington, A D; Pina, J; Pinamonti, M; Pinder, A; Pinfold, J L; Pingel, A; Pinto, B; Pizio, C; Pleier, M-A; Pleskot, V; Plotnikova, E; Plucinski, P; Poddar, S; Podlyski, F; Poettgen, R; Poggioli, L; Pohl, D; Pohl, M; Polesello, G; Policicchio, A; Polifka, R; Polini, A; Pollard, C S; Polychronakos, V; Pomeroy, D; Pommès, K; Pontecorvo, L; Pope, B G; Popeneciu, G A; Popovic, D S; Poppleton, A; Portell Bueso, X; Pospelov, G E; Pospisil, S; Potamianos, K; Potrap, I N; Potter, C J; Potter, C T; Poulard, G; Poveda, J; Pozdnyakov, V; Prabhu, R; Pralavorio, P; Pranko, A; Prasad, S; Pravahan, R; Prell, S; Price, D; Price, J; Price, L E; Prieur, D; Primavera, M; Proissl, M; Prokofiev, K; Prokoshin, F; Protopapadaki, E; Protopopescu, S; Proudfoot, J; Prudent, X; Przybycien, M; Przysiezniak, H; Psoroulas, S; Ptacek, E; Pueschel, E; Puldon, D; Purohit, M; Puzo, P; Pylypchenko, Y; Qian, J; Quadt, A; Quarrie, D R; Quayle, W B; Quilty, D; Radeka, V; Radescu, V; Radhakrishnan, S K; Radloff, P; Ragusa, F; Rahal, G; Rajagopalan, S; Rammensee, M; Rammes, M; Randle-Conde, A S; Rangel-Smith, C; Rao, K; Rauscher, F; Rave, T C; Ravenscroft, T; Raymond, M; Read, A L; Rebuzzi, D M; Redelbach, A; Redlinger, G; Reece, R; Reeves, K; Rehnisch, L; Reinsch, A; Reisin, H; Relich, M; Rembser, C; Ren, Z L; Renaud, A; Rescigno, M; Resconi, S; Resende, B; Reznicek, P; Rezvani, R; Richter, R; Ridel, M; Rieck, P; Rijssenbeek, M; Rimoldi, A; Rinaldi, L; Ritsch, E; Riu, I; Rizatdinova, F; Rizvi, E; Robertson, S H; Robichaud-Veronneau, A; Robinson, D; Robinson, J E M; Robson, A; Rocha de Lima, J G; Roda, C; Roda Dos Santos, D; Rodrigues, L; Roe, S; Røhne, O; Rolli, S; Romaniouk, A; Romano, M; Romeo, G; Romero Adam, E; Rompotis, N; Roos, L; Ros, E; Rosati, S; Rosbach, K; Rose, A; Rose, M; Rosendahl, P L; Rosenthal, O; Rossetti, V; Rossi, E; Rossi, L P; Rosten, R; Rotaru, M; Roth, I; Rothberg, J; Rousseau, D; Royon, C R; Rozanov, A; Rozen, Y; Ruan, X; Rubbo, F; Rubinskiy, I; Rud, V I; Rudolph, C; Rudolph, M S; Rühr, F; Ruiz-Martinez, A; Rurikova, Z; Rusakovich, N A; Ruschke, A; Rutherfoord, J P; Ruthmann, N; Ruzicka, P; Ryabov, Y F; Rybar, M; Rybkin, G; Ryder, N C; Saavedra, A F; Sacerdoti, S; Saddique, A; Sadeh, I; Sadrozinski, H F-W; Sadykov, R; Safai Tehrani, F; Sakamoto, H; Sakurai, Y; Salamanna, G; Salamon, A; Saleem, M; Salek, D; Sales De Bruin, P H; Salihagic, D; Salnikov, A; Salt, J; Salvachua Ferrando, B M; Salvatore, D; Salvatore, F; Salvucci, A; Salzburger, A; Sampsonidis, D; Sanchez, A; Sánchez, J; Sanchez Martinez, V; Sandaker, H; Sander, H G; Sanders, M P; Sandhoff, M; Sandoval, T; Sandoval, C; Sandstroem, R; Sankey, D P C; Sansoni, A; Santoni, C; Santonico, R; Santos, H; Santoyo Castillo, I; Sapp, K; Sapronov, A; Saraiva, J G; Sarkisyan-Grinbaum, E; Sarrazin, B; Sartisohn, G; Sasaki, O; Sasaki, Y; Satsounkevitch, I; Sauvage, G; Sauvan, E; Sauvan, J B; Savard, P; Savu, D O; Sawyer, C; Sawyer, L; Saxon, D H; Saxon, J; Sbarra, C; Sbrizzi, A; Scanlon, T; Scannicchio, D A; Scarcella, M; Schaarschmidt, J; Schacht, P; Schaefer, D; Schaelicke, A; Schaepe, S; Schaetzel, S; Schäfer, U; Schaffer, A C; Schaile, D; Schamberger, R D; Scharf, V; Schegelsky, V A; Scheirich, D; Schernau, M; Scherzer, M I; Schiavi, C; Schieck, J; Schillo, C; Schioppa, M; Schlenker, S; Schmidt, E; Schmieden, K; Schmitt, C; Schmitt, C; Schmitt, S; Schneider, B; Schnellbach, Y J; Schnoor, U; Schoeffel, L; Schoening, A; Schoenrock, B D; Schorlemmer, A L S; Schott, M; Schouten, D; Schovancova, J; Schram, M; Schramm, S; Schreyer, M; Schroeder, C; Schroer, N; Schuh, N; Schultens, M J; Schultz-Coulon, H-C; Schulz, H; Schumacher, M; Schumm, B A; Schune, Ph; Schwartzman, A; Schwegler, Ph; Schwemling, Ph; Schwienhorst, R; Schwindling, J; Schwindt, T; Schwoerer, M; Sciacca, F G; Scifo, E; Sciolla, G; Scott, W G; Scuri, F; Scutti, F; Searcy, J; Sedov, G; Sedykh, E; Seidel, S C; Seiden, A; Seifert, F; Seixas, J M; Sekhniaidze, G; Sekula, S J; Selbach, K E; Seliverstov, D M; Sellers, G; Seman, M; Semprini-Cesari, N; Serfon, C; Serin, L; Serkin, L; Serre, T; Seuster, R; Severini, H; Sforza, F; Sfyrla, A; Shabalina, E; Shamim, M; Shan, L Y; Shank, J T; Shao, Q T; Shapiro, M; Shatalov, P B; Shaw, K; Sherwood, P; Shimizu, S; Shimmin, C O; Shimojima, M; Shin, T; Shiyakova, M; Shmeleva, A; Shochet, M J; Short, D; Shrestha, S; Shulga, E; Shupe, M A; Shushkevich, S; Sicho, P; Sidorov, D; Sidoti, A; Siegert, F; Sijacki, Dj; Silbert, O; Silva, J; Silver, Y; Silverstein, D; Silverstein, S B; Simak, V; Simard, O; Simic, Lj; Simion, S; Simioni, E; Simmons, B; Simoniello, R; Simonyan, M; Sinervo, P; Sinev, N B; Sipica, V; Siragusa, G; Sircar, A; Sisakyan, A N; Sivoklokov, S Yu; Sjölin, J; Sjursen, T B; Skinnari, L A; Skottowe, H P; Skovpen, K Yu; Skubic, P; Slater, M; Slavicek, T; Sliwa, K; Smakhtin, V; Smart, B H; Smestad, L; Smirnov, S Yu; Smirnov, Y; Smirnova, L N; Smirnova, O; Smith, K M; Smizanska, M; Smolek, K; Snesarev, A A; Snidero, G; Snow, J; Snyder, S; Sobie, R; Socher, F; Sodomka, J; Soffer, A; Soh, D A; Solans, C A; Solar, M; Solc, J; Soldatov, E Yu; Soldevila, U; Solfaroli Camillocci, E; Solodkov, A A; Solovyanov, O V; Solovyev, V; Soni, N; Sood, A; Sopko, V; Sopko, B; Sosebee, M; Soualah, R; Soueid, P; Soukharev, A M; South, D; Spagnolo, S; Spanò, F; Spearman, W R; Spighi, R; Spigo, G; Spousta, M; Spreitzer, T; Spurlock, B; St Denis, R D; Stahlman, J; Stamen, R; Stanecka, E; Stanek, R W; Stanescu, C; Stanescu-Bellu, M; Stanitzki, M M; Stapnes, S; Starchenko, E A; Stark, J; Staroba, P; Starovoitov, P; Staszewski, R; Stavina, P; Steele, G; Steinbach, P; Steinberg, P; Stekl, I; Stelzer, B; Stelzer, H J; Stelzer-Chilton, O; Stenzel, H; Stern, S; Stewart, G A; Stillings, J A; Stockton, M C; Stoebe, M; Stoerig, K; Stoicea, G; Stonjek, S; Stradling, A R; Straessner, A; Strandberg, J; Strandberg, S; Strandlie, A; Strauss, E; Strauss, M; Strizenec, P; Ströhmer, R; Strom, D M; Stroynowski, R; Stucci, S A; Stugu, B; Stumer, I; Stupak, J; Styles, N A; Su, D; Su, J; Subramania, Hs; Subramaniam, R; Succurro, A; Sugaya, Y; Suhr, C; Suk, M; Sulin, V V; Sultansoy, S; Sumida, T; Sun, X; Sundermann, J E; Suruliz, K; Susinno, G; Sutton, M R; Suzuki, Y; Svatos, M; Swedish, S; Swiatlowski, M; Sykora, I; Sykora, T; Ta, D; Tackmann, K; Taenzer, J; Taffard, A; Tafirout, R; Taiblum, N; Takahashi, Y; Takai, H; Takashima, R; Takeda, H; Takeshita, T; Takubo, Y; Talby, M; Talyshev, A A; Tam, J Y C; Tamsett, M C; Tan, K G; Tanaka, J; Tanaka, R; Tanaka, S; Tanaka, S; Tanasijczuk, A J; Tani, K; Tannoury, N; Tapprogge, S; Tarem, S; Tarrade, F; Tartarelli, G F; Tas, P; Tasevsky, M; Tashiro, T; Tassi, E; Tavares Delgado, A; Tayalati, Y; Taylor, C; Taylor, F E; Taylor, G N; Taylor, W; Teischinger, F A; Teixeira Dias Castanheira, M; Teixeira-Dias, P; Temming, K K; Ten Kate, H; Teng, P K; Terada, S; Terashi, K; Terron, J; Terzo, S; Testa, M; Teuscher, R J; Therhaag, J; Theveneaux-Pelzer, T; Thoma, S; Thomas, J P; Thomas-Wilsker, J; Thompson, E N; Thompson, P D; Thompson, P D; Thompson, A S; Thomsen, L A; Thomson, E; Thomson, M; Thong, W M; Thun, R P; Tian, F; Tibbetts, M J; Tic, T; Tikhomirov, V O; Tikhonov, Yu A; Timoshenko, S; Tiouchichine, E; Tipton, P; Tisserant, S; Todorov, T; Todorova-Nova, S; Toggerson, B; Tojo, J; Tokár, S; Tokushuku, K; Tollefson, K; Tomlinson, L; Tomoto, M; Tompkins, L; Toms, K; Topilin, N D; Torrence, E; Torres, H; Torró Pastor, E; Toth, J; Touchard, F; Tovey, D R; Tran, H L; Trefzger, T; Tremblet, L; Tricoli, A; Trigger, I M; Trincaz-Duvoid, S; Tripiana, M F; Triplett, N; Trischuk, W; Trocmé, B; Troncon, C; Trottier-McDonald, M; Trovatelli, M; True, P; Trzebinski, M; Trzupek, A; Tsarouchas, C; Tseng, J C-L; Tsiareshka, P V; Tsionou, D; Tsipolitis, G; Tsirintanis, N; Tsiskaridze, S; Tsiskaridze, V; Tskhadadze, E G; Tsukerman, I I; Tsulaia, V; Tsung, J-W; Tsuno, S; Tsybychev, D; Tua, A; Tudorache, A; Tudorache, V; Tuna, A N; Tupputi, S A; Turchikhin, S; Turecek, D; Turk Cakir, I; Turra, R; Tuts, P M; Tykhonov, A; Tylmad, M; Tyndel, M; Uchida, K; Ueda, I; Ueno, R; Ughetto, M; Ugland, M; Uhlenbrock, M; Ukegawa, F; Unal, G; Undrus, A; Unel, G; Ungaro, F C; Unno, Y; Urbaniec, D; Urquijo, P; Usai, G; Usanova, A; Vacavant, L; Vacek, V; Vachon, B; Valencic, N; Valentinetti, S; Valero, A; Valery, L; Valkar, S; Valladolid Gallego, E; Vallecorsa, S; Valls Ferrer, J A; Van Berg, R; Van Der Deijl, P C; van der Geer, R; van der Graaf, H; Van Der Leeuw, R; van der Ster, D; van Eldik, N; van Gemmeren, P; Van Nieuwkoop, J; van Vulpen, I; van Woerden, M C; Vanadia, M; Vandelli, W; Vaniachine, A; Vankov, P; Vannucci, F; Vardanyan, G; Vari, R; Varnes, E W; Varol, T; Varouchas, D; Vartapetian, A; Varvell, K E; Vassilakopoulos, V I; Vazeille, F; Vazquez Schroeder, T; Veatch, J; Veloso, F; Veneziano, S; Ventura, A; Ventura, D; Venturi, M; Venturi, N; Venturini, A; Vercesi, V; Verducci, M; Verkerke, W; Vermeulen, J C; Vest, A; Vetterli, M C; Viazlo, O; Vichou, I; Vickey, T; Vickey Boeriu, O E; Viehhauser, G H A; Viel, S; Vigne, R; Villa, M; Villaplana Perez, M; Vilucchi, E; Vincter, M G; Vinogradov, V B; Virzi, J; Vitells, O; Vivarelli, I; Vives Vaque, F; Vlachos, S; Vladoiu, D; Vlasak, M; Vogel, A; Vokac, P; Volpi, G; Volpi, M; von der Schmitt, H; von Radziewski, H; von Toerne, E; Vorobel, V; Vos, M; Voss, R; Vossebeld, J H; Vranjes, N; Vranjes Milosavljevic, M; Vrba, V; Vreeswijk, M; Vu Anh, T; Vuillermet, R; Vukotic, I; Vykydal, Z; Wagner, W; Wagner, P; Wahrmund, S; Wakabayashi, J; Walder, J; Walker, R; Walkowiak, W; Wall, R; Waller, P; Walsh, B; Wang, C; Wang, C; Wang, H; Wang, H; Wang, J; Wang, J; Wang, K; Wang, R; Wang, S M; Wang, T; Wang, X; Warburton, A; Ward, C P; Wardrope, D R; Warsinsky, M; Washbrook, A; Wasicki, C; Watanabe, I; Watkins, P M; Watson, A T; Watson, I J; Watson, M F; Watts, G; Watts, S; Waugh, A T; Waugh, B M; Webb, S; Weber, M S; Weber, S W; Webster, J S; Weidberg, A R; Weigell, P; Weingarten, J; Weiser, C; Weits, H; Wells, P S; Wenaus, T; Wendland, D; Weng, Z; Wengler, T; Wenig, S; Wermes, N; Werner, M; Werner, P; Wessels, M; Wetter, J; Whalen, K; White, A; White, M J; White, R; White, S; Whiteson, D; Whittington, D; Wicke, D; Wickens, F J; Wiedenmann, W; Wielers, M; Wienemann, P; Wiglesworth, C; Wiik-Fuchs, L A M; Wijeratne, P A; Wildauer, A; Wildt, M A; Wilkens, H G; Will, J Z; Williams, H H; Williams, S; Willocq, S; Wilson, J A; Wilson, A; Wingerter-Seez, I; Winkelmann, S; Winklmeier, F; Wittgen, M; Wittig, T; Wittkowski, J; Wollstadt, S J; Wolter, M W; Wolters, H; Wosiek, B K; Wotschack, J; Woudstra, M J; Wozniak, K W; Wraight, K; Wright, M; Wu, S L; Wu, X; Wu, Y; Wulf, E; Wyatt, T R; Wynne, B M; Xella, S; Xiao, M; Xu, D; Xu, L; Yabsley, B; Yacoob, S; Yamada, M; Yamaguchi, H; Yamaguchi, Y; Yamamoto, A; Yamamoto, K; Yamamoto, S; Yamamura, T; Yamanaka, T; Yamauchi, K; Yamazaki, Y; Yan, Z; Yang, H; Yang, H; Yang, U K; Yang, Y; Yanush, S; Yao, L; Yasu, Y; Yatsenko, E; Yau Wong, K H; Ye, J; Ye, S; Yen, A L; Yildirim, E; Yilmaz, M; Yoosoofmiya, R; Yorita, K; Yoshida, R; Yoshihara, K; Young, C; Young, C J S; Youssef, S; Yu, D R; Yu, J; Yu, J M; Yu, J; Yuan, L; Yurkewicz, A; Zabinski, B; Zaidan, R; Zaitsev, A M; Zaman, A; Zambito, S; Zanello, L; Zanzi, D; Zaytsev, A; Zeitnitz, C; Zeman, M; Zemla, A; Zengel, K; Zenin, O; Zeniš, T; Zerwas, D; Zevi Della Porta, G; Zhang, D; Zhang, H; Zhang, J; Zhang, L; Zhang, X; Zhang, Z; Zhao, Z; Zhemchugov, A; Zhong, J; Zhou, B; Zhou, L; Zhou, N; Zhu, C G; Zhu, H; Zhu, J; Zhu, Y; Zhuang, X; Zibell, A; Zieminska, D; Zimin, N I; Zimmermann, C; Zimmermann, R; Zimmermann, S; Zimmermann, S; Zinonos, Z; Ziolkowski, M; Zitoun, R; Zivković, L; Zobernig, G; Zoccoli, A; Zur Nedden, M; Zurzolo, G; Zutshi, V; Zwalinski, L

    2014-03-07

    This Letter presents a search for quantum black-hole production using 20.3 fb-1 of data collected with the ATLAS detector in pp collisions at the LHC at √s = 8 TeV. The quantum black holes are assumed to decay into a final state characterized by a lepton (electron or muon) and a jet. In either channel, no event with a lepton-jet invariant mass of 3.5 TeV or more is observed, consistent with the expected background. Limits are set on the product of cross sections and branching fractions for the lepton+jet final states of quantum black holes produced in a search region for invariant masses above 1 TeV. The combined 95% confidence level upper limit on this product for quantum black holes with threshold mass above 3.5 TeV is 0.18 fb. This limit constrains the threshold quantum black-hole mass to be above 5.3 TeV in the model considered.

  13. Hawaii bibliographic database

    NASA Astrophysics Data System (ADS)

    Wright, Thomas L.; Takahashi, Taeko Jane

    The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and s or (if no ) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

  14. Hawaii bibliographic database

    USGS Publications Warehouse

    Wright, T.L.; Takahashi, T.J.

    1998-01-01

    The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and abstracts or (if no abstract) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

  15. Database Administrator

    ERIC Educational Resources Information Center

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  16. IDPredictor: predict database links in biomedical database.

    PubMed

    Mehlhorn, Hendrik; Lange, Matthias; Scholz, Uwe; Schreiber, Falk

    2012-06-26

    Knowledge found in biomedical databases, in particular in Web information systems, is a major bioinformatics resource. In general, this biological knowledge is worldwide represented in a network of databases. These data is spread among thousands of databases, which overlap in content, but differ substantially with respect to content detail, interface, formats and data structure. To support a functional annotation of lab data, such as protein sequences, metabolites or DNA sequences as well as a semi-automated data exploration in information retrieval environments, an integrated view to databases is essential. Search engines have the potential of assisting in data retrieval from these structured sources, but fall short of providing a comprehensive knowledge except out of the interlinked databases. A prerequisite of supporting the concept of an integrated data view is to acquire insights into cross-references among database entities. This issue is being hampered by the fact, that only a fraction of all possible cross-references are explicitely tagged in the particular biomedical informations systems. In this work, we investigate to what extend an automated construction of an integrated data network is possible. We propose a method that predicts and extracts cross-references from multiple life science databases and possible referenced data targets. We study the retrieval quality of our method and report on first, promising results. The method is implemented as the tool IDPredictor, which is published under the DOI 10.5447/IPK/2012/4 and is freely available using the URL: http://dx.doi.org/10.5447/IPK/2012/4.

  17. A search for pre-main-sequence stars in high-latitude molecular clouds. 3: A survey of the Einstein database

    NASA Technical Reports Server (NTRS)

    Caillault, Jean-Pierre; Magnani, Loris; Fryer, Chris

    1995-01-01

    In order to discern whether the high-latitude molecular clouds are regions of ongoing star formation, we have used X-ray emission as a tracer of youthful stars. The entire Einstein database yields 18 images which overlap 10 of the clouds mapped partially or completely in the CO (1-0) transition, providing a total of approximately 6 deg squared of overlap. Five previously unidentified X-ray sources were detected: one has an optical counterpart which is a pre-main-sequence (PMS) star, and two have normal main-sequence stellar counterparts, while the other two are probably extragalactic sources. The PMS star is located in a high Galactic latitude Lynds dark cloud, so this result is not too suprising. The translucent clouds, though, have yet to reveal any evidence of star formation.

  18. Database Selection in the Life Sciences.

    ERIC Educational Resources Information Center

    Snow, Bonnie

    1985-01-01

    Focuses on indexing refinements in major life science databases--those specializing in biological/biomedical literature coverage--which influence cross-life searching decisions. Tables included highlight database descriptions, comparisons in coverage, ease of access (indexing of secondary concepts or search modifiers), chemical substance indexing…

  19. Online Database Coverage of Forensic Medicine.

    ERIC Educational Resources Information Center

    Snow, Bonnie; Ifshin, Steven L.

    1984-01-01

    Online seaches of sample topics in the area of forensic medicine were conducted in the following life science databases: Biosis Previews, Excerpta Medica, Medline, Scisearch, and Chemical Abstracts Search. Search outputs analyzed according to criteria of recall, uniqueness, overlap, and utility reveal the need for a cross-database approach to…

  20. The Giardia genome project database.

    PubMed

    McArthur, A G; Morrison, H G; Nixon, J E; Passamaneck, N Q; Kim, U; Hinkle, G; Crocker, M K; Holder, M E; Farr, R; Reich, C I; Olsen, G E; Aley, S B; Adam, R D; Gillin, F D; Sogin, M L

    2000-08-15

    The Giardia genome project database provides an online resource for Giardia lamblia (WB strain, clone C6) genome sequence information. The database includes edited single-pass reads, the results of BLASTX searches, and details of progress towards sequencing the entire 12 million-bp Giardia genome. Pre-sorted BLASTX results can be retrieved based on keyword searches and BLAST searches of the high throughput Giardia data can be initiated from the web site or through NCBI. Descriptions of the genomic DNA libraries, project protocols and summary statistics are also available. Although the Giardia genome project is ongoing, new sequences are made available on a bi-monthly basis to ensure that researchers have access to information that may assist them in the search for genes and their biological function. The current URL of the Giardia genome project database is www.mbl.edu/Giardia.

  1. Using Quick Search.

    ERIC Educational Resources Information Center

    Maxfield, Sandy, Ed.; Kabus, Karl, Ed.

    This document is a guide to the use of Quick Search, a library service that provides access to more than 100 databases which contain references to journal articles and other research materials through two commercial systems--BRS After/Dark and DIALOG's Knowledge Index. The guide is divided into five sections: (1) Using Quick Search; (2) The…

  2. Full-Text Databases in Medicine.

    ERIC Educational Resources Information Center

    Sievert, MaryEllen C.; And Others

    1995-01-01

    Describes types of full-text databases in medicine; discusses features for searching full-text journal databases available through online vendors; reviews research on full-text databases in medicine; and describes the MEDLINE/Full-Text Research Project at the University of Missouri (Columbia) which investigated precision, recall, and relevancy.…

  3. Adjacency and Proximity Searching in the Science Citation Index and Google

    DTIC Science & Technology

    2005-01-01

    major database search engines , including commercial S&T database search engines (e.g., Science Citation Index (SCI), Engineering Compendex (EC...PubMed, OVID), Federal agency award database search engines (e.g., NSF, NIH, DOE, EPA, as accessed in Federal R&D Project Summaries), Web search Engines (e.g...searching. Some database search engines allow strict constrained co- occurrence searching as a user option (e.g., OVID, EC), while others do not (e.g., SCI

  4. The comprehensive peptaibiotics database.

    PubMed

    Stoppacher, Norbert; Neumann, Nora K N; Burgstaller, Lukas; Zeilinger, Susanne; Degenkolb, Thomas; Brückner, Hans; Schuhmacher, Rainer

    2013-05-01

    Peptaibiotics are nonribosomally biosynthesized peptides, which - according to definition - contain the marker amino acid α-aminoisobutyric acid (Aib) and possess antibiotic properties. Being known since 1958, a constantly increasing number of peptaibiotics have been described and investigated with a particular emphasis on hypocrealean fungi. Starting from the existing online 'Peptaibol Database', first published in 1997, an exhaustive literature survey of all known peptaibiotics was carried out and resulted in a list of 1043 peptaibiotics. The gathered information was compiled and used to create the new 'The Comprehensive Peptaibiotics Database', which is presented here. The database was devised as a software tool based on Microsoft (MS) Access. It is freely available from the internet at http://peptaibiotics-database.boku.ac.at and can easily be installed and operated on any computer offering a Windows XP/7 environment. It provides useful information on characteristic properties of the peptaibiotics included such as peptide category, group name of the microheterogeneous mixture to which the peptide belongs, amino acid sequence, sequence length, producing fungus, peptide subfamily, molecular formula, and monoisotopic mass. All these characteristics can be used and combined for automated search within the database, which makes The Comprehensive Peptaibiotics Database a versatile tool for the retrieval of valuable information about peptaibiotics. Sequence data have been considered as to December 14, 2012.

  5. MS-ONLINE Mass Spectral Database

    NASA Astrophysics Data System (ADS)

    Tokizane, Soichi; Nagaoka, Nobuaki

    A mass spectral database, MS-ONLINE, is described which is produced by FIZ Chemie, in Federal Republic of Germany and offered online through the INKADATA system. The data source of this database is WILEY/NBS MASS SPECTRAL DATA BASE and it includes 80,680 spectra. Spectral data can be retrieved from a substance search (by assigning molecular weight, molecular formula or name), a specific peak search, or a similarity search of peak patterns called SISCOM search. Further more, the system has functions supporting the component identification of mixtures and the identification from an isotopic abundance. The algorism of the SISCOM search is explained in detail.

  6. Maize databases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter is a succinct overview of maize data held in the species-specific database MaizeGDB (the Maize Genomics and Genetics Database), and selected multi-species data repositories, such as Gramene/Ensembl Plants, Phytozome, UniProt and the National Center for Biotechnology Information (NCBI), ...

  7. Search for lepton flavour violating decays of heavy resonances and quantum black holes to an mathrm {e}μ pair in proton-proton collisions at √{s}=8 {TeV}

    NASA Astrophysics Data System (ADS)

    Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Knünz, V.; König, A.; Krammer, M.; Krätschmer, I.; Liko, D.; Matsushita, T.; Mikulec, I.; Rabady, D.; Rad, N.; Rahbaran, B.; Rohringer, H.; Schieck, J.; Schöfbeck, R.; Strauss, J.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Cornelis, T.; de Wolf, E. A.; Janssen, X.; Knutsson, A.; Lauwers, J.; Luyckx, S.; van de Klundert, M.; van Haevermaet, H.; van Mechelen, P.; van Remortel, N.; van Spilbeeck, A.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; Daci, N.; de Bruyn, I.; Deroover, K.; Heracleous, N.; Keaveney, J.; Lowette, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; van Doninck, W.; van Mulders, P.; van Onsem, G. P.; van Parijs, I.; Barria, P.; Brun, H.; Caillol, C.; Clerbaux, B.; de Lentdecker, G.; Fang, W.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Léonard, A.; Maerschalk, T.; Marinov, A.; Perniè, L.; Randle-Conde, A.; Seva, T.; Vander Velde, C.; Vanlaer, P.; Yonamine, R.; Zenoni, F.; Zhang, F.; Beernaert, K.; Benucci, L.; Cimmino, A.; Crucy, S.; Dobur, D.; Fagot, A.; Garcia, G.; Gul, M.; McCartin, J.; Ocampo Rios, A. A.; Poyraz, D.; Ryckbosch, D.; Salva, S.; Sigamani, M.; Tytgat, M.; van Driessche, W.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; Ceard, L.; Delaere, C.; Favart, D.; Forthomme, L.; Giammanco, A.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Mertens, A.; Musich, M.; Nuttens, C.; Perrini, L.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Beliy, N.; Hammad, G. H.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Hamer, M.; Hensel, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; da Costa, E. M.; de Jesus Damiao, D.; de Oliveira Martins, C.; Fonseca de Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Matos Figueiredo, D.; Mora Herrera, C.; Mundim, L.; Nogima, H.; Prado da Silva, W. L.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; de Souza Santos, A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Moon, C. S.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Cheng, T.; Du, R.; Jiang, C. H.; Leggat, D.; Plestina, R.; Romeo, F.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Zhang, H.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Micanovic, S.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Bodlak, M.; Finger, M.; Finger, M.; Assran, Y.; Elgammal, S.; Ellithi Kamel, A.; Mahmoud, M. A.; Calpas, B.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Peltola, T.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Machet, M.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Zghiche, A.; Abdulsalam, A.; Antropov, I.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Chapon, E.; Charlot, C.; Davignon, O.; Filipovic, N.; Granier de Cassagnac, R.; Jo, M.; Lisniak, S.; Mastrolorenzo, L.; Miné, P.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Pigard, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Strebler, T.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Buttignol, M.; Chabert, E. C.; Chanon, N.; Collard, C.; Conte, E.; Coubez, X.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Merlin, J. A.; Skovpen, K.; van Hove, P.; Gadrat, S.

    2016-06-01

    A search for narrow resonances decaying to an electron and a muon is presented. The mathrm {e} {μ } mass spectrum is also investigated for non-resonant contributions from the production of quantum black holes (QBHs). The analysis is performed using data corresponding to an integrated luminosity of 19.7 {fb}^ {-1} collected in proton-proton collisions at a centre-of-mass energy of 8 {TeV} with the CMS detector at the LHC. With no evidence for physics beyond the standard model in the invariant mass spectrum of selected mathrm {e}μ pairs, upper limits are set at 95 % confidence level on the product of cross section and branching fraction for signals arising in theories with charged lepton flavour violation. In the search for narrow resonances, the resonant production of a mathrm {τ } sneutrino in R-parity violating supersymmetry is considered. The mathrm {τ } sneutrino is excluded for masses below 1.28 {TeV} for couplings λ _{132}=λ _{231}=λ '_{311}=0.01, and below 2.30 {TeV} for λ _{132}=λ _{231}=0.07 and λ '_{311}=0.11. These are the most stringent limits to date from direct searches at high-energy colliders. In addition, the resonance searches are interpreted in terms of a model with heavy partners of the {Z} boson and the photon. In a framework of TeV-scale quantum gravity based on a renormalization of Newton's constant, the search for non-resonant contributions to the mathrm {e} {μ } mass spectrum excludes QBH production below a threshold mass M_{th} of 1.99 {TeV}. In models that invoke extra dimensions, the bounds range from 2.36 {TeV} for one extra dimension to 3.63 {TeV} for six extra dimensions. This is the first search for QBHs decaying into the mathrm {e} {μ } final state.

  8. Working with Data: Discovering Knowledge through Mining and Analysis; Systematic Knowledge Management and Knowledge Discovery; Text Mining; Methodological Approach in Discovering User Search Patterns through Web Log Analysis; Knowledge Discovery in Databases Using Formal Concept Analysis; Knowledge Discovery with a Little Perspective.

    ERIC Educational Resources Information Center

    Qin, Jian; Jurisica, Igor; Liddy, Elizabeth D.; Jansen, Bernard J; Spink, Amanda; Priss, Uta; Norton, Melanie J.

    2000-01-01

    These six articles discuss knowledge discovery in databases (KDD). Topics include data mining; knowledge management systems; applications of knowledge discovery; text and Web mining; text mining and information retrieval; user search patterns through Web log analysis; concept analysis; data collection; and data structure inconsistency. (LRW)

  9. Hierarchies of Indices for Text Searching.

    ERIC Educational Resources Information Center

    Baeza-Yates, Ricardo; And Others

    1996-01-01

    Discusses indexes for text databases and presents an efficient implementation of an index for text searching called PAT array, or suffix array, where the database is stored on secondary storage devices such as magnetic or optical disks. Additional hierarchical index structures and searching algorithms are proposed that improve searching time, and…

  10. The Weaknesses of Full-Text Searching

    ERIC Educational Resources Information Center

    Beall, Jeffrey

    2008-01-01

    This paper provides a theoretical critique of the deficiencies of full-text searching in academic library databases. Because full-text searching relies on matching words in a search query with words in online resources, it is an inefficient method of finding information in a database. This matching fails to retrieve synonyms, and it also retrieves…

  11. Zero Result Searches. . . How to Minimize Them.

    ERIC Educational Resources Information Center

    Atkinson, Steve

    1986-01-01

    Based on manual observation of 187 zero result online searches at a university library, this article addresses three types of problems that can produce such search results: multiple database searching, topic negotiation, and database availability. A summary of conceptual and practical recommendations for searchers are provided. (6 references) (EJS)

  12. Course 10: Basic Concepts in Quantum Computation

    NASA Astrophysics Data System (ADS)

    Ekert, A.; Hayden, P. M.; Inamori, H.

    Contents 1 Qubits, gates and networks 2 Quantum arithmetic and function evaluations 3 Algorithms and their complexity 4 From interferometers to computers 5 The first quantum algorithms 6 Quantum search 7 Optimal phase estimation 8 Periodicity and quantum factoring 9 Cryptography 10 Conditional quantum dynamics 11 Decoherence and recoherence 12 Concluding remarks

  13. Quantum Particles From Quantum Information

    NASA Astrophysics Data System (ADS)

    Görnitz, T.; Schomäcker, U.

    2012-08-01

    Many problems in modern physics demonstrate that for a fundamental entity a more general conception than quantum particles or quantum fields are necessary. These concepts cannot explain the phenomena of dark energy or the mind-body-interaction. Instead of any kind of "small elementary building bricks", the Protyposis, an abstract and absolute quantum information, free of special denotation and open for some purport, gives the solution in the search for a fundamental substance. However, as long as at least relativistic particles are not constructed from the Protyposis, such an idea would remain in the range of natural philosophy. Therefore, the construction of relativistic particles without and with rest mass from quantum information is shown.

  14. (Meta)Search like Google

    ERIC Educational Resources Information Center

    Rochkind, Jonathan

    2007-01-01

    The ability to search and receive results in more than one database through a single interface--or metasearch--is something many users want. Google Scholar--the search engine of specifically scholarly content--and library metasearch products like Ex Libris's MetaLib, Serials Solution's Central Search, WebFeat, and products based on MuseGlobal used…

  15. Search Engines for Tomorrow's Scholars

    ERIC Educational Resources Information Center

    Fagan, Jody Condit

    2011-01-01

    Today's scholars face an outstanding array of choices when choosing search tools: Google Scholar, discipline-specific abstracts and index databases, library discovery tools, and more recently, Microsoft's re-launch of their academic search tool, now dubbed Microsoft Academic Search. What are these tools' strengths for the emerging needs of…

  16. Demystifying the Search Button

    PubMed Central

    McKeever, Liam; Nguyen, Van; Peterson, Sarah J.; Gomez-Perez, Sandra

    2015-01-01

    A thorough review of the literature is the basis of all research and evidence-based practice. A gold-standard efficient and exhaustive search strategy is needed to ensure all relevant citations have been captured and that the search performed is reproducible. The PubMed database comprises both the MEDLINE and non-MEDLINE databases. MEDLINE-based search strategies are robust but capture only 89% of the total available citations in PubMed. The remaining 11% include the most recent and possibly relevant citations but are only searchable through less efficient techniques. An effective search strategy must employ both the MEDLINE and the non-MEDLINE portion of PubMed to ensure all studies have been identified. The robust MEDLINE search strategies are used for the MEDLINE portion of the search. Usage of the less robust strategies is then efficiently confined to search only the remaining 11% of PubMed citations that have not been indexed for MEDLINE. The current article offers step-by-step instructions for building such a search exploring methods for the discovery of medical subject heading (MeSH) terms to search MEDLINE, text-based methods for exploring the non-MEDLINE database, information on the limitations of convenience algorithms such as the “related citations feature,” the strengths and pitfalls associated with commonly used filters, the proper usage of Boolean operators to organize a master search strategy, and instructions for automating that search through “MyNCBI” to receive search query updates by email as new citations become available. PMID:26129895

  17. NASA Records Database

    NASA Technical Reports Server (NTRS)

    Callac, Christopher; Lunsford, Michelle

    2005-01-01

    The NASA Records Database, comprising a Web-based application program and a database, is used to administer an archive of paper records at Stennis Space Center. The system begins with an electronic form, into which a user enters information about records that the user is sending to the archive. The form is smart : it provides instructions for entering information correctly and prompts the user to enter all required information. Once complete, the form is digitally signed and submitted to the database. The system determines which storage locations are not in use, assigns the user s boxes of records to some of them, and enters these assignments in the database. Thereafter, the software tracks the boxes and can be used to locate them. By use of search capabilities of the software, specific records can be sought by box storage locations, accession numbers, record dates, submitting organizations, or details of the records themselves. Boxes can be marked with such statuses as checked out, lost, transferred, and destroyed. The system can generate reports showing boxes awaiting destruction or transfer. When boxes are transferred to the National Archives and Records Administration (NARA), the system can automatically fill out NARA records-transfer forms. Currently, several other NASA Centers are considering deploying the NASA Records Database to help automate their records archives.

  18. Citation Searching: Search Smarter & Find More

    ERIC Educational Resources Information Center

    Hammond, Chelsea C.; Brown, Stephanie Willen

    2008-01-01

    The staff at University of Connecticut are participating in Elsevier's Student Ambassador Program (SAmP) in which graduate students train their peers on "citation searching" research using Scopus and Web of Science, two tremendous citation databases. They are in the fourth semester of these training programs, and they are wildly successful: They…

  19. MetaBase—the wiki-database of biological databases

    PubMed Central

    Bolser, Dan M.; Chibon, Pierre-Yves; Palopoli, Nicolas; Gong, Sungsam; Jacob, Daniel; Angel, Victoria Dominguez Del; Swan, Dan; Bassi, Sebastian; González, Virginia; Suravajhala, Prashanth; Hwang, Seungwoo; Romano, Paolo; Edwards, Rob; Bishop, Bryan; Eargle, John; Shtatland, Timur; Provart, Nicholas J.; Clements, Dave; Renfro, Daniel P.; Bhak, Daeui; Bhak, Jong

    2012-01-01

    Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project. PMID:22139927

  20. USGS Dam Removal Science Database

    USGS Publications Warehouse

    Bellmore, J. Ryan; Vittum, Katherine; Duda, Jeff J.; Greene, Samantha L.

    2015-01-01

    This database is the result of an extensive literature search aimed at identifying documents relevant to the emerging field of dam removal science. In total the database contains 179 citations that contain empirical monitoring information associated with 130 different dam removals across the United States and abroad. Data includes publications through 2014 and supplemented with the U.S. Army Corps of Engineers National Inventory of Dams database, U.S. Geological Survey National Water Information System and aerial photos to estimate locations when coordinates were not provided. Publications were located using the Web of Science, Google Scholar, and Clearinghouse for Dam Removal Information.

  1. Experiment Databases

    NASA Astrophysics Data System (ADS)

    Vanschoren, Joaquin; Blockeel, Hendrik

    Next to running machine learning algorithms based on inductive queries, much can be learned by immediately querying the combined results of many prior studies. Indeed, all around the globe, thousands of machine learning experiments are being executed on a daily basis, generating a constant stream of empirical information on machine learning techniques. While the information contained in these experiments might have many uses beyond their original intent, results are typically described very concisely in papers and discarded afterwards. If we properly store and organize these results in central databases, they can be immediately reused for further analysis, thus boosting future research. In this chapter, we propose the use of experiment databases: databases designed to collect all the necessary details of these experiments, and to intelligently organize them in online repositories to enable fast and thorough analysis of a myriad of collected results. They constitute an additional, queriable source of empirical meta-data based on principled descriptions of algorithm executions, without reimplementing the algorithms in an inductive database. As such, they engender a very dynamic, collaborative approach to experimentation, in which experiments can be freely shared, linked together, and immediately reused by researchers all over the world. They can be set up for personal use, to share results within a lab or to create open, community-wide repositories. Here, we provide a high-level overview of their design, and use an existing experiment database to answer various interesting research questions about machine learning algorithms and to verify a number of recent studies.

  2. Semantics for Biological Data Resource: Cell Image Database

    National Institute of Standards and Technology Data Gateway

    SRD 165 NIST Semantics for Biological Data Resource: Cell Image Database (Web, free access)   This Database is a prototype to test concepts for semantic searching of cell image data based on experimental details.

  3. Aggregated Interdisciplinary Databases and the Needs of Undergraduate Researchers

    ERIC Educational Resources Information Center

    Fister, Barbara; Gilbert, Julie; Fry, Amy Ray

    2008-01-01

    After seeing growing frustration among inexperienced undergraduate researchers searching a popular aggregated interdisciplinary database, the authors questioned whether the leading interdisciplinary databases are serving undergraduates' needs. As a preliminary exploration of this question, the authors queried vendors, analyzed their marketing…

  4. Solubility Database

    National Institute of Standards and Technology Data Gateway

    SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

  5. Search Moves Made by Novice End Users.

    ERIC Educational Resources Information Center

    Wildemuth, Barbara M.; And Others

    1992-01-01

    Describes a study at the University of North Carolina at Chapel Hill that analyzed the transaction logs of medical students' searches of a factual database to determine the overall frequency of search moves, the interaction between the problem statement and students' search strategies, the search moves selected, and the tactics used by students.…

  6. Quantum Gravitational Spectroscopy

    SciTech Connect

    Nesvizhevsky, Valery V.; Antoniadis, Ignatios; Baessler, Stefan; Pignol, Guillaume

    2015-01-01

    We report that one of the main goals for improving the accuracy of quantum gravitational spectroscopy with neutrons is searches for extra short-range fundamental forces. We discuss also any progress in all competing nonneutron methods as well as constraints at other characteristic distances. Among major methodical developments related to the phenomenon of gravitational quantum states are the detailed theoretical analysis and the planning experiments on observation of gravitational quantum states of antihydrogen atoms.

  7. Artificial Intelligence Databases: A Survey and Comparison.

    ERIC Educational Resources Information Center

    Stern, David

    1990-01-01

    Identifies and describes online databases containing references to materials on artificial intelligence, robotics, and expert systems, and compares them in terms of scope and usage. Recommendations for conducting online searches on artificial intelligence and related fields are offered. (CLB)

  8. Expert searching in public health

    PubMed Central

    Alpi, Kristine M.

    2005-01-01

    Objective: The article explores the characteristics of public health information needs and the resources available to address those needs that distinguish it as an area of searching requiring particular expertise. Methods: Public health searching activities from reference questions and literature search requests at a large, urban health department library were reviewed to identify the challenges in finding relevant public health information. Results: The terminology of the information request frequently differed from the vocabularies available in the databases. Searches required the use of multiple databases and/or Web resources with diverse interfaces. Issues of the scope and features of the databases relevant to the search questions were considered. Conclusion: Expert searching in public health differs from other types of expert searching in the subject breadth and technical demands of the databases to be searched, the fluidity and lack of standardization of the vocabulary, and the relative scarcity of high-quality investigations at the appropriate level of geographic specificity. Health sciences librarians require a broad exposure to databases, gray literature, and public health terminology to perform as expert searchers in public health. PMID:15685281

  9. Search for lepton flavour violating decays of heavy resonances and quantum black holes to an eμ pair in proton-proton collisions at √s = 8 TeV

    SciTech Connect

    Khachatryan, Vardan

    2016-06-10

    A search for narrow resonances decaying to an electron and a muon is presented. The $\\mathrm {e}$ ${\\mu }$ mass spectrum is also investigated for non-resonant contributions from the production of quantum black holes (QBHs). The analysis is performed using data corresponding to an integrated luminosity of 19.7 $~\\text {fb}^\\text {-1}$ collected in proton-proton collisions at a centre-of-mass energy of 8 $~\\text {TeV}$ with the CMS detector at the LHC. With no evidence for physics beyond the standard model in the invariant mass spectrum of selected $\\mathrm {e}\\mu $ pairs, upper limits are set at 95  $\\%$ confidence level on the product of cross section and branching fraction for signals arising in theories with charged lepton flavour violation. In the search for narrow resonances, the resonant production of a $\\mathrm {\\tau }$ sneutrino in R-parity violating supersymmetry is considered. The $\\mathrm {\\tau }$ sneutrino is excluded for masses below 1.28 $~\\text {TeV}$ for couplings $\\lambda _{132}=\\lambda _{231}=\\lambda '_{311}=0.01$ , and below 2.30 $~\\text {TeV}$ for $\\lambda _{132}=\\lambda _{231}=0.07$ and $\\lambda '_{311}=0.11$ . These are the most stringent limits to date from direct searches at high-energy colliders. In addition, the resonance searches are interpreted in terms of a model with heavy partners of the ${\\mathrm {Z}} $ boson and the photon. In a framework of TeV-scale quantum gravity based on a renormalization of Newton’s constant, the search for non-resonant contributions to the $\\mathrm {e}$ ${\\mu }$ mass spectrum excludes QBH production below a threshold mass $M_{\\mathrm {th}}$ of 1.99 $~\\text {TeV}$ . In models that invoke extra dimensions, the bounds range from 2.36 $~\\text {TeV}$ for one extra dimension to 3.63 $~\\text {TeV}$ for six extra dimensions. Furthermore, this is the first search for QBHs decaying into the $\\mathrm {e}$ ${\\mu }$ final state.

  10. Search for lepton flavour violating decays of heavy resonances and quantum black holes to an eμ pair in proton-proton collisions at √s = 8 TeV

    DOE PAGES

    Khachatryan, Vardan

    2016-06-10

    A search for narrow resonances decaying to an electron and a muon is presented. Themore » $$\\mathrm {e}$$ $${\\mu }$$ mass spectrum is also investigated for non-resonant contributions from the production of quantum black holes (QBHs). The analysis is performed using data corresponding to an integrated luminosity of 19.7 $$~\\text {fb}^\\text {-1}$$ collected in proton-proton collisions at a centre-of-mass energy of 8 $$~\\text {TeV}$$ with the CMS detector at the LHC. With no evidence for physics beyond the standard model in the invariant mass spectrum of selected $$\\mathrm {e}\\mu $$ pairs, upper limits are set at 95  $$\\%$$ confidence level on the product of cross section and branching fraction for signals arising in theories with charged lepton flavour violation. In the search for narrow resonances, the resonant production of a $$\\mathrm {\\tau }$$ sneutrino in R-parity violating supersymmetry is considered. The $$\\mathrm {\\tau }$$ sneutrino is excluded for masses below 1.28 $$~\\text {TeV}$$ for couplings $$\\lambda _{132}=\\lambda _{231}=\\lambda '_{311}=0.01$$ , and below 2.30 $$~\\text {TeV}$$ for $$\\lambda _{132}=\\lambda _{231}=0.07$$ and $$\\lambda '_{311}=0.11$$ . These are the most stringent limits to date from direct searches at high-energy colliders. In addition, the resonance searches are interpreted in terms of a model with heavy partners of the $${\\mathrm {Z}} $$ boson and the photon. In a framework of TeV-scale quantum gravity based on a renormalization of Newton’s constant, the search for non-resonant contributions to the $$\\mathrm {e}$$ $${\\mu }$$ mass spectrum excludes QBH production below a threshold mass $$M_{\\mathrm {th}}$$ of 1.99 $$~\\text {TeV}$$ . In models that invoke extra dimensions, the bounds range from 2.36 $$~\\text {TeV}$$ for one extra dimension to 3.63 $$~\\text {TeV}$$ for six extra dimensions. Furthermore, this is the first search for QBHs decaying into the $$\\mathrm {e}$$ $${\\mu }$$ final state.« less

  11. Are we safe? NLM's household products database.

    PubMed

    Bronson Fitzpatrick, Roberta

    2004-01-01

    This column features an overview of the Division of Specialized Information Services, National Library of Medicine Household Products Database. Basic searching techniques are presented, as well as a brief overview of the data contained in this file. The Household Products Database contains information on chemical ingredients in various products used in U.S. homes.

  12. Six Online Periodical Databases: A Librarian's View.

    ERIC Educational Resources Information Center

    Willems, Harry

    1999-01-01

    Compares the following World Wide Web-based periodical databases, focusing on their usefulness in K-12 school libraries: EBSCO, Electric Library, Facts on File, SIRS, Wilson, and UMI. Search interfaces, display options, help screens, printing, home access, copyright restrictions, database administration, and making a decision are discussed. A…

  13. Web Database Development: Implications for Academic Publishing.

    ERIC Educational Resources Information Center

    Fernekes, Bob

    This paper discusses the preliminary planning, design, and development of a pilot project to create an Internet accessible database and search tool for locating and distributing company data and scholarly work. Team members established four project objectives: (1) to develop a Web accessible database and decision tool that creates Web pages on the…

  14. Developing an Inhouse Database from Online Sources.

    ERIC Educational Resources Information Center

    Smith-Cohen, Deborah

    1993-01-01

    Describes the development of an in-house bibliographic database by the U.S. Army Corp of Engineers Cold Regions Research and Engineering Laboratory on arctic wetlands research. Topics discussed include planning; identifying relevant search terms and commercial online databases; downloading citations; criteria for software selection; management…

  15. Electronic Reference Library: Silverplatter's Database Networking Solution.

    ERIC Educational Resources Information Center

    Millea, Megan

    Silverplatter's Electronic Reference Library (ERL) provides wide area network access to its databases using TCP/IP communications and client-server architecture. ERL has two main components: The ERL clients (retrieval interface) and the ERL server (search engines). ERL clients provide patrons with seamless access to multiple databases on multiple…

  16. RLIN Special Databases: Serving the Humanist.

    ERIC Educational Resources Information Center

    Muratori, Fred

    1990-01-01

    Describes online databases available through the Research Libraries Information Network (RLIN) that focus on research in the humanities. A survey of five databases (AVERY, ESTC, RIPD, SCIPIO, and AMC) is presented that includes contents, search capabilities, and record formats; and future plans are discussed. (12 references) (LRW)

  17. Quantum Walk Schemes for Universal Quantum Computation

    NASA Astrophysics Data System (ADS)

    Underwood, Michael S.

    Random walks are a powerful tool for the efficient implementation of algorithms in classical computation. Their quantum-mechanical analogues, called quantum walks, hold similar promise. Quantum walks provide a model of quantum computation that has recently been shown to be equivalent in power to the standard circuit model. As in the classical case, quantum walks take place on graphs and can undergo discrete or continuous evolution, though quantum evolution is unitary and therefore deterministic until a measurement is made. This thesis considers the usefulness of continuous-time quantum walks to quantum computation from the perspectives of both their fundamental power under various formulations, and their applicability in practical experiments. In one extant scheme, logical gates are effected by scattering processes. The results of an exhaustive search for single-qubit operations in this model are presented. It is shown that the number of distinct operations increases exponentially with the number of vertices in the scattering graph. A catalogue of all graphs on up to nine vertices that implement single-qubit unitaries at a specific set of momenta is included in an appendix. I develop a novel scheme for universal quantum computation called the discontinuous quantum walk, in which a continuous-time quantum walker takes discrete steps of evolution via perfect quantum state transfer through small 'widget' graphs. The discontinuous quantum-walk scheme requires an exponentially sized graph, as do prior discrete and continuous schemes. To eliminate the inefficient vertex resource requirement, a computation scheme based on multiple discontinuous walkers is presented. In this model, n interacting walkers inhabiting a graph with 2n vertices can implement an arbitrary quantum computation on an input of length n, an exponential savings over previous universal quantum walk schemes. This is the first quantum walk scheme that allows for the application of quantum error correction

  18. A database/knowledge structure for a robotics vision system

    NASA Technical Reports Server (NTRS)

    Dearholt, D. W.; Gonzales, N. N.

    1987-01-01

    Desirable properties of robotics vision database systems are given, and structures which possess properties appropriate for some aspects of such database systems are examined. Included in the structures discussed is a family of networks in which link membership is determined by measures of proximity between pairs of the entities stored in the database. This type of network is shown to have properties which guarantee that the search for a matching feature vector is monotonic. That is, the database can be searched with no backtracking, if there is a feature vector in the database which matches the feature vector of the external entity which is to be identified. The construction of the database is discussed, and the search procedure is presented. A section on the support provided by the database for description of the decision-making processes and the search path is also included.

  19. Spectroscopic data for an astronomy database

    NASA Technical Reports Server (NTRS)

    Parkinson, W. H.; Smith, Peter L.

    1995-01-01

    Very few of the atomic and molecular data used in analyses of astronomical spectra are currently available in World Wide Web (WWW) databases that are searchable with hypertext browsers. We have begun to rectify this situation by making extensive atomic data files available with simple search procedures. We have also established links to other on-line atomic and molecular databases. All can be accessed from our database homepage with URL: http:// cfa-www.harvard.edu/ amp/ data/ amdata.html.

  20. Searches Conducted for Engineers.

    ERIC Educational Resources Information Center

    Lorenz, Patricia

    This paper reports an industrial information specialist's experience in performing online searches for engineers and surveys the databases used. Engineers seeking assistance fall into three categories: (1) those who recognize the value of online retrieval; (2) referrals by colleagues; and (3) those who do not seek help. As more successful searches…

  1. Needle Federated Search Engine

    SciTech Connect

    2009-12-01

    The Idaho National Laboratory (INL) has combined a number of technologies, tools, and resources to accomplish a new means of federating search results. The resulting product is a search engine called Needle, an open-source-based tool that the INL uses internally for researching across a wide variety of information repositories. Needle has a flexible search interface that allows end users to point at any available data source. A user can select multiple sources such as commercial databases (Web of Science, Engineering Index), external resources (WorldCat, Google Scholar), and internal corporate resources (email, document management system, library collections) in a single interface with one search query. In the future, INL hopes to offer this open-source engine to the public. This session will outline the development processes for making Needle™s search interface and simplifying the federation of internal and external data sources.

  2. A Search Engine Features Comparison.

    ERIC Educational Resources Information Center

    Vorndran, Gerald

    Until recently, the World Wide Web (WWW) public access search engines have not included many of the advanced commands, options, and features commonly available with the for-profit online database user interfaces, such as DIALOG. This study evaluates the features and characteristics common to both types of search interfaces, examines the Web search…

  3. Literature searches on Ayurveda: An update

    PubMed Central

    Aggithaya, Madhur G.; Narahari, Saravu R.

    2015-01-01

    Introduction: The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. Aims: To update on Ayurveda literature search and strategy to retrieve maximum publications. Methods: Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Results: Five among 46 databases are now relevant – AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. “The Researches in Ayurveda” and “Ayurvedic Research Database” (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. Conclusion: AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five

  4. Variable stars in the MACHO Collaboration database

    SciTech Connect

    Cook, K.H.; Alcock, C.; Allsman, R.A.

    1995-02-01

    The MACHO Collaboration`s search for baryonic dark matter via its gravitational microlensing signature has generated a massive database of time ordered photometry of millions Of stars in the LMC and the bulge of the Milky Way. The search`s experimental design and capabilities are reviewed and the dark matter results are briefly noted. Preliminary analysis of the {approximately} 39,000 variable stars discovered in the LMC database is presented and examples of periodic variables are shown. A class of aperiodically variable Be stars is described which is the closest background to microlensing which has been found. Plans for future work on variable stars using the MACHO data are described.

  5. Atomic Databases

    NASA Astrophysics Data System (ADS)

    Mendoza, Claudio

    2000-10-01

    Atomic and molecular data are required in a variety of fields ranging from the traditional astronomy, atmospherics and fusion research to fast growing technologies such as lasers, lighting, low-temperature plasmas, plasma assisted etching and radiotherapy. In this context, there are some research groups, both theoretical and experimental, scattered round the world that attend to most of this data demand, but the implementation of atomic databases has grown independently out of sheer necessity. In some cases the latter has been associated with the data production process or with data centers involved in data collection and evaluation; but sometimes it has been the result of individual initiatives that have been quite successful. In any case, the development and maintenance of atomic databases call for a number of skills and an entrepreneurial spirit that are not usually associated with most physics researchers. In the present report we present some of the highlights in this area in the past five years and discuss what we think are some of the main issues that have to be addressed.

  6. Experimental fault tolerant universal quantum gates with solid-state spins under ambient conditions

    NASA Astrophysics Data System (ADS)

    Rong, Xing

    Quantum computation provides great speedup over classical counterpart for certain problems, such as quantum simulations, prime factoring and database searching. One of the challenges for realizing quantum computation is to execute precise control of the quantum system in the presence of noise. Recently, high fidelity control of spin-qubits has been achieved in several quantum systems. However, control of the spin-qubits with the accuracy required by the fault tolerant quantum computation under ambient conditions remains exclusive. Here we demonstrate a universal set of logic gates in nitrogen-vacancy centers with an average single-qubit gate fidelity of 0.99995 and two qubit gate fidelity of 0.992. These high control fidelities have been achieved in the C naturally abundant diamonds at room temperature via composite pulses and optimal control method. This experimental implementation of quantum gates with fault tolerant control fidelity sets an important step towards the fault-tolerant quantum computation under ambient conditions. National Key Basic Research Program of China (Grant No. 2013CB921800).

  7. On Building a Search Interface Discovery System

    NASA Astrophysics Data System (ADS)

    Shestakov, Denis

    A huge portion of the Web known as the deep Web is accessible via search interfaces to myriads of databases on the Web. While relatively good approaches for querying the contents of web databases have been recently proposed, one cannot fully utilize them having most search interfaces unlocated. Thus, the automatic recognition of search interfaces to online databases is crucial for any application accessing the deep Web. This paper describes the architecture of the I-Crawler, a system for finding and classifying search interfaces. The I-Crawler is intentionally designed to be used in the deep web characterization surveys and for constructing directories of deep web resources.

  8. Subject Retrieval from Full-Text Databases in the Humanities

    ERIC Educational Resources Information Center

    East, John W.

    2007-01-01

    This paper examines the problems involved in subject retrieval from full-text databases of secondary materials in the humanities. Ten such databases were studied and their search functionality evaluated, focusing on factors such as Boolean operators, document surrogates, limiting by subject area, proximity operators, phrase searching, wildcards,…

  9. Databases for Computer Science and Electronics: COMPENDEX, ELCOM, and INSPEC.

    ERIC Educational Resources Information Center

    Marsden, Tom; Laub, Barbara

    1981-01-01

    Describes the selection policies, subject access, search aids, indexing, coverage, and currency of three online databases in the fields of electronics and computer science: COMPENDEX, ELCOM, and INSPEC. Sample searches are displayed for each database. A bibliography cites five references. (FM)

  10. Robot-Generated Databases on the World Wide Web.

    ERIC Educational Resources Information Center

    Kimmel, Stacey

    1996-01-01

    Provides an overview of robots that retrieve World Wide Web documents and index data and then store it in a database. Nine robot-generated databases are described, including record content, services, search features, and sample search results; and sidebars discuss the controversy about Web robots and other resource discovery tools. (LRW)

  11. Superconducting quantum circuits at the surface code threshold for fault tolerance.

    PubMed

    Barends, R; Kelly, J; Megrant, A; Veitia, A; Sank, D; Jeffrey, E; White, T C; Mutus, J; Fowler, A G; Campbell, B; Chen, Y; Chen, Z; Chiaro, B; Dunsworth, A; Neill, C; O'Malley, P; Roushan, P; Vainsencher, A; Wenner, J; Korotkov, A N; Cleland, A N; Martinis, John M

    2014-04-24

    A quantum computer can solve hard problems, such as prime factoring, database searching and quantum simulation, at the cost of needing to protect fragile quantum states from error. Quantum error correction provides this protection by distributing a logical state among many physical quantum bits (qubits) by means of quantum entanglement. Superconductivity is a useful phenomenon in this regard, because it allows the construction of large quantum circuits and is compatible with microfabrication. For superconducting qubits, the surface code approach to quantum computing is a natural choice for error correction, because it uses only nearest-neighbour coupling and rapidly cycled entangling gates. The gate fidelity requirements are modest: the per-step fidelity threshold is only about 99 per cent. Here we demonstrate a universal set of logic gates in a superconducting multi-qubit processor, achieving an average single-qubit gate fidelity of 99.92 per cent and a two-qubit gate fidelity of up to 99.4 per cent. This places Josephson quantum computing at the fault-tolerance threshold for surface code error correction. Our quantum processor is a first step towards the surface code, using five qubits arranged in a linear array with nearest-neighbour coupling. As a further demonstration, we construct a five-qubit Greenberger-Horne-Zeilinger state using the complete circuit and full set of gates. The results demonstrate that Josephson quantum computing is a high-fidelity technology, with a clear path to scaling up to large-scale, fault-tolerant quantum circuits.

  12. Overview of selected molecular biological databases

    SciTech Connect

    Rayl, K.D.; Gaasterland, T.

    1994-11-01

    This paper presents an overview of the purpose, content, and design of a subset of the currently available biological databases, with an emphasis on protein databases. Databases included in this summary are 3D-ALI, Berlin RNA databank, Blocks, DSSP, EMBL Nucleotide Database, EMP, ENZYME, FSSP, GDB, GenBank, HSSP, LiMB, PDB, PIR, PKCDD, ProSite, and SWISS-PROT. The goal is to provide a starting point for researchers who wish to take advantage of the myriad available databases. Rather than providing a complete explanation of each database, we present its content and form by explaining the details of typical entries. Pointers to more complete ``user guides`` are included, along with general information on where to search for a new database.

  13. Quantum rendering

    NASA Astrophysics Data System (ADS)

    Lanzagorta, Marco O.; Gomez, Richard B.; Uhlmann, Jeffrey K.

    2003-08-01

    In recent years, computer graphics has emerged as a critical component of the scientific and engineering process, and it is recognized as an important computer science research area. Computer graphics are extensively used for a variety of aerospace and defense training systems and by Hollywood's special effects companies. All these applications require the computer graphics systems to produce high quality renderings of extremely large data sets in short periods of time. Much research has been done in "classical computing" toward the development of efficient methods and techniques to reduce the rendering time required for large datasets. Quantum Computing's unique algorithmic features offer the possibility of speeding up some of the known rendering algorithms currently used in computer graphics. In this paper we discuss possible implementations of quantum rendering algorithms. In particular, we concentrate on the implementation of Grover's quantum search algorithm for Z-buffering, ray-tracing, radiosity, and scene management techniques. We also compare the theoretical performance between the classical and quantum versions of the algorithms.

  14. Stackfile Database

    NASA Technical Reports Server (NTRS)

    deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

    2013-01-01

    This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

  15. Integrating Variances into an Analytical Database

    NASA Technical Reports Server (NTRS)

    Sanchez, Carlos

    2010-01-01

    For this project, I enrolled in numerous SATERN courses that taught the basics of database programming. These include: Basic Access 2007 Forms, Introduction to Database Systems, Overview of Database Design, and others. My main job was to create an analytical database that can handle many stored forms and make it easy to interpret and organize. Additionally, I helped improve an existing database and populate it with information. These databases were designed to be used with data from Safety Variances and DCR forms. The research consisted of analyzing the database and comparing the data to find out which entries were repeated the most. If an entry happened to be repeated several times in the database, that would mean that the rule or requirement targeted by that variance has been bypassed many times already and so the requirement may not really be needed, but rather should be changed to allow the variance's conditions permanently. This project did not only restrict itself to the design and development of the database system, but also worked on exporting the data from the database to a different format (e.g. Excel or Word) so it could be analyzed in a simpler fashion. Thanks to the change in format, the data was organized in a spreadsheet that made it possible to sort the data by categories or types and helped speed up searches. Once my work with the database was done, the records of variances could be arranged so that they were displayed in numerical order, or one could search for a specific document targeted by the variances and restrict the search to only include variances that modified a specific requirement. A great part that contributed to my learning was SATERN, NASA's resource for education. Thanks to the SATERN online courses I took over the summer, I was able to learn many new things about computers and databases and also go more in depth into topics I already knew about.

  16. Policy implications for familial searching.

    PubMed

    Kim, Joyce; Mammo, Danny; Siegel, Marni B; Katsanis, Sara H

    2011-11-01

    In the United States, several states have made policy decisions regarding whether and how to use familial searching of the Combined DNA Index System (CODIS) database in criminal investigations. Familial searching pushes DNA typing beyond merely identifying individuals to detecting genetic relatedness, an application previously reserved for missing persons identifications and custody battles. The intentional search of CODIS for partial matches to an item of evidence offers law enforcement agencies a powerful tool for developing investigative leads, apprehending criminals, revitalizing cold cases and exonerating wrongfully convicted individuals. As familial searching involves a range of logistical, social, ethical and legal considerations, states are now grappling with policy options for implementing familial searching to balance crime fighting with its potential impact on society. When developing policies for familial searching, legislators should take into account the impact of familial searching on select populations and the need to minimize personal intrusion on relatives of individuals in the DNA database. This review describes the approaches used to narrow a suspect pool from a partial match search of CODIS and summarizes the economic, ethical, logistical and political challenges of implementing familial searching. We examine particular US state policies and the policy options adopted to address these issues. The aim of this review is to provide objective background information on the controversial approach of familial searching to inform policy decisions in this area. Herein we highlight key policy options and recommendations regarding effective utilization of familial searching that minimize harm to and afford maximum protection of US citizens.

  17. Policy implications for familial searching

    PubMed Central

    2011-01-01

    In the United States, several states have made policy decisions regarding whether and how to use familial searching of the Combined DNA Index System (CODIS) database in criminal investigations. Familial searching pushes DNA typing beyond merely identifying individuals to detecting genetic relatedness, an application previously reserved for missing persons identifications and custody battles. The intentional search of CODIS for partial matches to an item of evidence offers law enforcement agencies a powerful tool for developing investigative leads, apprehending criminals, revitalizing cold cases and exonerating wrongfully convicted individuals. As familial searching involves a range of logistical, social, ethical and legal considerations, states are now grappling with policy options for implementing familial searching to balance crime fighting with its potential impact on society. When developing policies for familial searching, legislators should take into account the impact of familial searching on select populations and the need to minimize personal intrusion on relatives of individuals in the DNA database. This review describes the approaches used to narrow a suspect pool from a partial match search of CODIS and summarizes the economic, ethical, logistical and political challenges of implementing familial searching. We examine particular US state policies and the policy options adopted to address these issues. The aim of this review is to provide objective background information on the controversial approach of familial searching to inform policy decisions in this area. Herein we highlight key policy options and recommendations regarding effective utilization of familial searching that minimize harm to and afford maximum protection of US citizens. PMID:22040348

  18. Using the TIGR gene index databases for biological discovery.

    PubMed

    Lee, Yuandan; Quackenbush, John

    2003-11-01

    The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

  19. Medical literature search dot com.

    PubMed

    Jain, Vivek; Raut, Deepak K

    2011-01-01

    The Internet provides a quick access to a plethora of the medical literature, in the form of journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualized, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Commercial web resources (Medscape, MedConnect, MedicineNet) add to the list of resource databases providing some of their content for open access. Several web-libraries (Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. Availability of specific dermatology-related websites (DermIs, DermNet, and Genamics Jornalseek) is useful addition to the ever growing list of web-based resources. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature and levels of detail available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine.

  20. DEPOT database: Reference manual and user's guide

    SciTech Connect

    Clancey, P.; Logg, C.

    1991-03-01

    DEPOT has been developed to provide tracking for the Stanford Linear Collider (SLC) control system equipment. For each piece of equipment entered into the database, complete location, service, maintenance, modification, certification, and radiation exposure histories can be maintained. To facilitate data entry accuracy, efficiency, and consistency, barcoding technology has been used extensively. DEPOT has been an important tool in improving the reliability of the microsystems controlling SLC. This document describes the components of the DEPOT database, the elements in the database records, and the use of the supporting programs for entering data, searching the database, and producing reports from the information.

  1. Search Cloud

    MedlinePlus

    ... this page: https://medlineplus.gov/cloud.html Search Cloud To use the sharing features on this page, ... chest pa and lateral Share the MedlinePlus search cloud with your users by embedding our search cloud ...

  2. Database Management Systems: New Homes for Migrating Bibliographic Records.

    ERIC Educational Resources Information Center

    Brooks, Terrence A.; Bierbaum, Esther G.

    1987-01-01

    Assesses bibliographic databases as part of visionary text systems such as hypertext and scholars' workstations. Downloading is discussed in terms of the capability to search records and to maintain unique bibliographic descriptions, and relational database management systems, file managers, and text databases are reviewed as possible hosts for…

  3. The Cystic Fibrosis Database: Content and Research Opportunities.

    ERIC Educational Resources Information Center

    Shaw, William M., Jr.; And Others

    1991-01-01

    Describes the files contained in the Cystic Fibrosis (CF) database and discusses educational and research opportunities using this database. Topics discussed include queries, evaluating the relevance of items retrieved, and use of the database in an online searching course in the School of Information and Library Science at the University of North…

  4. A survey of scholarly literature databases for clinical laboratory science.

    PubMed

    O'Malley, Donna L

    2008-01-01

    This article reviews the use of journal literature databases including CINAHL, EMBASE, and Web of Science; summarizing databases including Cochrane Database of Systematic Reviews, online textbooks, and clinical decision-support tools; and the Internet search engines Google and Google Scholar. The series closes with a practical example employing a cross-section of the knowledge and skills gained from all three articles.

  5. A Longitudinal Study of Database-Assisted Problem Solving.

    ERIC Educational Resources Information Center

    Wildemuth, Barbara M.; Friedman, Charles P.; Keyes, John; Downs, Stephen M.

    2000-01-01

    Examines the effects of database assistance on clinical problem solving across three cohorts of medical students and two database interfaces. Discusses the relationship between personal domain knowledge and problem solving, personal domain knowledge and database searching, and comparisons of different interface styles in information retrieval…

  6. The Majorana Parts Tracking Database

    SciTech Connect

    Abgrall, N.

    2015-01-16

    The Majorana Demonstrator is an ultra-low background physics experiment searching for the neutrinoless double beta decay of 76Ge. The Majorana Parts Tracking Database is used to record the history of components used in the construction of the Demonstrator. The tracking implementation takes a novel approach based on the schema-free database technology CouchDB. Transportation, storage, and processes undergone by parts such as machining or cleaning are linked to part records. Tracking parts provides a great logistics benefit and an important quality assurance reference during construction. In addition, the location history of parts provides an estimate of their exposure to cosmic radiation. In summary, a web application for data entry and a radiation exposure calculator have been developed as tools for achieving the extreme radio-purity required for this rare decay search.

  7. The Majorana Parts Tracking Database

    DOE PAGES

    Abgrall, N.

    2015-01-16

    The Majorana Demonstrator is an ultra-low background physics experiment searching for the neutrinoless double beta decay of 76Ge. The Majorana Parts Tracking Database is used to record the history of components used in the construction of the Demonstrator. The tracking implementation takes a novel approach based on the schema-free database technology CouchDB. Transportation, storage, and processes undergone by parts such as machining or cleaning are linked to part records. Tracking parts provides a great logistics benefit and an important quality assurance reference during construction. In addition, the location history of parts provides an estimate of their exposure to cosmic radiation.more » In summary, a web application for data entry and a radiation exposure calculator have been developed as tools for achieving the extreme radio-purity required for this rare decay search.« less

  8. Robust Quantum Private Queries

    NASA Astrophysics Data System (ADS)

    Wang, Tian-Yin; Wang, Shu-Yu; Ma, Jian-Feng

    2016-07-01

    We propose a new quantum private query protocol with the technique of decoherence-free states, which is a theoretical study of how decoherence-free states can be used for the protection of quantum information in such a protocol. This protocol can solve the noise problem that will make the user obtain a wrong answer and hence give rise to a bad influence on the reputation of the database provider. Furthermore, this protocol is also flexible, loss-resistant and easily generalized to a large database similar to the previous works.

  9. Multitasking Information Seeking and Searching Processes.

    ERIC Educational Resources Information Center

    Spink, Amanda; Ozmutlu, H. Cenk; Ozmutlu, Seda

    2002-01-01

    Presents findings from four studies of the prevalence of multitasking information seeking and searching by Web (via the Excite search engine), information retrieval system (mediated online database searching), and academic library users. Highlights include human information coordinating behavior (HICB); and implications for models of information…

  10. Precision and Recall in Title Keyword Searches.

    ERIC Educational Resources Information Center

    McJunkin, Monica Cahill

    This study examines precision and recall for title and keyword searches performed in the "FirstSearch" WorldCat database when keywords are used with and without adjacency of terms specified. A random sample of 68 titles in economics were searched in the OCLC (Online Computer Library Center) Online Union Catalog in order to obtain their…

  11. Searching Chemical Abstracts Online in Undergraduate Chemistry.

    ERIC Educational Resources Information Center

    Krumpolc, Miroslav; And Others

    1987-01-01

    Discusses the advantages of conducting online computer searches of "Chemical Abstracts." Introduces the logical sequences involved in searching an online database. Explains Boolean logic, proximity operators, truncation, searchable fields, and command language, as they relate to the use of online searches in undergraduate chemistry…

  12. The new international GLE database

    NASA Astrophysics Data System (ADS)

    Duldig, M. L.; Watts, D. J.

    2001-08-01

    The Australian Antarctic Division has agreed to host the international GLE database. Access to the database is via a world-wide-web interface and initially covers all GLEs since the start of the 22nd solar cycle. Access restriction for recent events is controlled by password protection and these data are available only to those groups contributing data to the database. The restrictions to data will be automatically removed for events older than 2 years, in accordance with the data exchange provisions of the Antarctic Treaty. Use of the data requires acknowledgment of the database as the source of the data and acknowledgment of the specific groups that provided the data used. Furthermore, some groups that provide data to the database have specific acknowledgment requirements or wording. A new submission format has been developed that will allow easier exchange of data, although the old format will be acceptable for some time. Data download options include direct web based download and email. Data may also be viewed as listings or plots with web browsers. Search options have also been incorporated. Development of the database will be ongoing with extension to viewing and delivery options, addition of earlier data and the development of mirror sites. It is expected that two mirror sites, one in North America and one in Europe, will be developed to enable fast access for the whole cosmic ray community.

  13. Rice Glycosyltransferase (GT) Phylogenomic Database

    DOE Data Explorer

    Ronald, Pamela

    The Ronald Laboratory staff at the University of California-Davis has a primary research focus on the genes of the rice plant. They study the role that genetics plays in the way rice plants respond to their environment. They created the Rice GT Database in order to integrate functional genomic information for putative rice Glycosyltransferases (GTs). This database contains information on nearly 800 putative rice GTs (gene models) identified by sequence similarity searches based on the Carbohydrate Active enZymes (CAZy) database. The Rice GT Database provides a platform to display user-selected functional genomic data on a phylogenetic tree. This includes sequence information, mutant line information, expression data, etc. An interactive chromosomal map shows the position of all rice GTs, and links to rice annotation databases are included. The format is intended to "facilitate the comparison of closely related GTs within different families, as well as perform global comparisons between sets of related families." [From http://ricephylogenomics.ucdavis.edu/cellwalls/gt/genInfo.shtml] See also the primary paper discussing this work: Peijian Cao, Laura E. Bartley, Ki-Hong Jung and Pamela C. Ronalda. Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases. Molecular Plant, 2008, 1(5): 858-877.

  14. Quantum probability ranking principle for ligand-based virtual screening.

    PubMed

    Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

    2017-04-01

    Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP). The QPRP ranking criteria would make an attempt to draw an analogy between the physical experiment and molecular structure ranking process for 2D fingerprints in ligand based virtual screening (LBVS). The development of QPRP criteria in LBVS has employed the concepts of quantum at three different levels, firstly at representation level, this model makes an effort to develop a new framework of molecular representation by connecting the molecular compounds with mathematical quantum space. Secondly, estimate the similarity between chemical libraries and references based on quantum-based similarity searching method. Finally, rank the molecules using QPRP approach. Simulated virtual screening experiments with MDL drug data report (MDDR) data sets showed that QPRP outperformed the classical ranking principle (PRP) for molecular chemical compounds.

  15. Recursive linear optical networks for realizing quantum algorithms

    NASA Astrophysics Data System (ADS)

    Tabia, Gelo Noel

    Linear optics has played a leading role in the development of practical quantum technologies. In recent years, advances in integrated quantum photonics have significantly improved the functionality and scalability of linear optical devices. In this talk, I present recursive schemes for implementing quantum Fourier transforms and inversion about the mean in Grover's algorithm with photonic integrated circuits. By recursive, I mean that two copies of a d-dimensional unitary operation is used to build the corresponding unitary operation on 2 d modes. The linear optical networks operate on path-encoded qudits and realize d-dimensional unitary operations using O (d2) elements. To demonstrate that the recursive circuits are viable in practice, I conducted simulations of proof-of-principle experiments using a fabrication model of realistic errors in silicon-based photonic integrated devices. The results indicate high-fidelity performance in the circuits for 2-qubit and 3-qubit quantum Fourier transforms, and for quantum search on 4-item and 8-item databases. This work was funded by institutional research grant IUT2-1 from the Estonian Research Council and by the European Union through the European Regional Development Fund.

  16. Quantum probability ranking principle for ligand-based virtual screening

    NASA Astrophysics Data System (ADS)

    Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

    2017-02-01

    Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP). The QPRP ranking criteria would make an attempt to draw an analogy between the physical experiment and molecular structure ranking process for 2D fingerprints in ligand based virtual screening (LBVS). The development of QPRP criteria in LBVS has employed the concepts of quantum at three different levels, firstly at representation level, this model makes an effort to develop a new framework of molecular representation by connecting the molecular compounds with mathematical quantum space. Secondly, estimate the similarity between chemical libraries and references based on quantum-based similarity searching method. Finally, rank the molecules using QPRP approach. Simulated virtual screening experiments with MDL drug data report (MDDR) data sets showed that QPRP outperformed the classical ranking principle (PRP) for molecular chemical compounds.

  17. Pre-Service Teachers' Use of Library Databases: Some Insights

    ERIC Educational Resources Information Center

    Lamb, Janeen; Howard, Sarah; Easey, Michael

    2014-01-01

    The aim of this study is to investigate if providing mathematics education pre-service teachers with animated library tutorials on library and database searches changes their searching practices. This study involved the completion of a survey by 138 students and seven individual interviews before and after library search demonstration videos were…

  18. Talent Searches.

    ERIC Educational Resources Information Center

    Silverman, Linda Kreger, Ed.

    1994-01-01

    Talent searches are discussed in this journal theme issue, with two feature articles and several recurring columns. "Talent Search: A Driving Force in Gifted Education," by Paula Olszewski-Kubilius, defines what a talent search is, how the Talent Search was developed by Dr. Julian Stanley at Johns Hopkins University in Maryland, the…

  19. Irreconcilable difference between quantum walks and adiabatic quantum computing

    NASA Astrophysics Data System (ADS)

    Wong, Thomas G.; Meyer, David A.

    2016-06-01

    Continuous-time quantum walks and adiabatic quantum evolution are two general techniques for quantum computing, both of which are described by Hamiltonians that govern their evolutions by Schrödinger's equation. In the former, the Hamiltonian is fixed, while in the latter, the Hamiltonian varies with time. As a result, their formulations of Grover's algorithm evolve differently through Hilbert space. We show that this difference is fundamental; they cannot be made to evolve along each other's path without introducing structure more powerful than the standard oracle for unstructured search. For an adiabatic quantum evolution to evolve like the quantum walk search algorithm, it must interpolate between three fixed Hamiltonians, one of which is complex and introduces structure that is stronger than the oracle for unstructured search. Conversely, for a quantum walk to evolve along the path of the adiabatic search algorithm, it must be a chiral quantum walk on a weighted, directed star graph with structure that is also stronger than the oracle for unstructured search. Thus, the two techniques, although similar in being described by Hamiltonians that govern their evolution, compute by fundamentally irreconcilable means.

  20. Non-Abelian quantum order in spin-orbit-coupled semiconductors: Search for topological Majorana particles in solid-state systems

    NASA Astrophysics Data System (ADS)

    Sau, Jay D.; Tewari, Sumanta; Lutchyn, Roman M.; Stanescu, Tudor D.; Das Sarma, S.

    2010-12-01

    We show that an ordinary semiconducting thin film with spin-orbit coupling can, under appropriate circumstances, be in a quantum topologically ordered state supporting exotic Majorana excitations which follow non-Abelian statistics. The key to the quantum topological order is the coexistence of spin-orbit coupling with proximity-induced s -wave superconductivity and an externally induced Zeeman coupling of the spins. For the Zeeman coupling below a critical value, the system is a nontopological (proximity-induced) s -wave superconductor. However, for a range of Zeeman coupling above the critical value, the lowest energy excited state inside a vortex is a zero-energy Majorana fermion state. The system, thus, has entered into a non-Abelian s -wave superconducting state via a topological quantum phase transition (TQPT) tuned by the Zeeman coupling. In the topological phase, since the time-reversal symmetry is explicitly broken by the Zeeman term in the Hamiltonian, the edge of the film constitutes a chiral Majorana wire. Just like the s -wave superconductivity, the Zeeman coupling can also be proximity induced in the film by an adjacent magnetic insulator. We show this by an explicit model tight-binding calculation for both types of proximity effects in the heterostructure geometry. Here we show that the same TQPT can be accessed by varying the interface transparency between the film and the superconductor. For the transparency below (above) a critical value, the system is a topological (regular) s -wave superconductor. In the one-dimensional version of the same structure and for the Zeeman coupling above the critical value, there are localized Majorana zero-energy modes at the two ends of a semiconducting quantum nanowire. In this case, the Zeeman coupling can be induced more easily by an external magnetic field parallel to the wire, obviating the need for a magnetic insulator. We show that, despite the fact that the superconducting pair potential in the nanowire is

  1. Summary Report for the SINBAD Search Tool Project

    SciTech Connect

    Cunha Da Silva, Alice

    2012-06-01

    The Shielding Integral Benchmark Archive Database (SINBAD) Search Tool has been developed to serve as an interface with the SINBAD database to facilitate a simple and quick means of searching for information related to experimental benchmark problems. The Search Tool is written in Java and provides a better and efficient way to retrieve information from the SINBAD database. Searches can be performed quickly and easily. With regard to improvements, users are no longer required to know the name of the benchmarks to search the database. Instead, a search can be performed by specifying the experimental facility, constituents of the experimental benchmark, etc. In summary, a new powerful database search tool has been developed for SINBAD.

  2. Searching for resonances in the reaction Cl+CH4-->HCl+CH3: quantum versus quasiclassical dynamics and comparison with experiments.

    PubMed

    Martínez, Rodrigo; González, Miguel; Defazio, Paolo; Petrongolo, Carlo

    2007-09-14

    A quantum-mechanical (QM) and quasiclassical trajectory (QCT) study was performed on the title reaction, using a pseudotriatomic ab initio based surface. Probabilities and integral cross sections present some clear peaks versus the collision energy E(col), which we assign to Feshbach resonances of the transition state, where the light H atom oscillates between the heavy Cl and CH(3) groups. For ground-state reactants, reactivity is essentially of quantum origin (QCT observables and oscillations are smaller, or much smaller, than QM ones), and the calculated integral cross section and product distributions are in reasonable agreement with the experiment. The reaction occurs through an abstraction mechanism, following both a direct and an indirect mechanism. The quasiclassical trajectory calculations show the participation of a short-lived collision complex in the microscopic reaction mechanism. Finally, QCT differential cross sections of Cl+CH(4)-->HCl (nu(')=0 and 1)+CH(3) oscillate versus E(col), whereas experimentally this only occurs for HCl (nu(')=1). This theoretical result and other oscillating properties found here could, however, be related to the existence of a Feshbach resonance for the production of HCl (nu(')=1), as suggested by experimentalists.

  3. Extending a geocoding database by Web information extraction

    NASA Astrophysics Data System (ADS)

    Wu, Yunchao; Niu, Zheng

    2008-10-01

    Local Search has recently attracted much attention. And the popular architecture of Local Search is map-and-hyperlinks, which links geo-referenced Web content to a map interface. This architecture shows that a good Local Search not only depends on search engine techniques, but also on a perfect geocoding database. The process of building and updating a geocoding database is laborious and time consuming so that it is usually difficult to keep up with the change of the real world. However, the Web provides a rich resource of location related information, which would be a supplementary information source for geocoding. Therefore, this paper introduces how to extract geographic information from Web documents to extend a geocoding database. Our approach involves two major steps. First, geographic named entities are identified and extracted from Web content. Then, named entities are geocoded and put into storage. By this way, we can extend a geocoding database to provide better local Web search services.

  4. Database of Novel and Emerging Adsorbent Materials

    National Institute of Standards and Technology Data Gateway

    SRD 205 NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials (Web, free access)   The NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials is a free, web-based catalog of adsorbent materials and measured adsorption properties of numerous materials obtained from article entries from the scientific literature. Search fields for the database include adsorbent material, adsorbate gas, experimental conditions (pressure, temperature), and bibliographic information (author, title, journal), and results from queries are provided as a list of articles matching the search parameters. The database also contains adsorption isotherms digitized from the cataloged articles, which can be compared visually online in the web application or exported for offline analysis.

  5. Distributed Search and Pattern Matching

    NASA Astrophysics Data System (ADS)

    Ahmed, Reaz; Boutaba, Raouf

    Peer-to-peer (P2P) technology has triggered a wide range of distributed applications including file-sharing, distributed XML databases, distributed computing, server-less web publishing and networked resource/service sharing. Despite of the diversity in application, these systems share common requirements for searching due to transitory nodes population and content volatility. In such dynamic environment, users do not have the exact information about available resources. Queries are based on partial information. This mandates the search mechanism to be emphflexible. On the other hand, the search mechanism is required to be bandwidth emphefficient to support large networks. Variety of search techniques have been proposed to provide satisfactory solution to the conflicting requirements of search efficiency and flexibility. This chapter highlights the search requirements in large scale distributed systems and the ability of the existing distributed search techniques in satisfying these requirements. Representative search techniques from three application domains, namely, P2P content sharing, service discovery and distributed XML databases, are considered. An abstract problem formulation called Distributed Pattern Matching (DPM) is presented as well. The DPM framework can be used as a common ground for addressing the search problem in these three application domains.

  6. Undergraduate Use of CD-ROM Databases: Observations of Human-Computer Interaction and Relevance Judgments.

    ERIC Educational Resources Information Center

    Shaw, Debora

    1996-01-01

    Describes a study that observed undergraduates as they searched bibliographic databases on a CD-ROM local area network. Topics include related research, information needs, evolution of search topics, database selection, search strategies, relevance judgments, CD-ROM interfaces, and library instruction. (Author/LRW)

  7. REDIdb: the RNA editing database.

    PubMed

    Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

    2007-01-01

    The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

  8. The Never-Ending Quest: Search Engine Relevance.

    ERIC Educational Resources Information Center

    Notess, Greg R.

    2000-01-01

    Discusses relevance in search engines for the World Wide Web. Highlights include types of searches submitted; database scope; how organizations position their Web sites; link analysis; spelling errors; offering alternatives to queries; and the single-answer approach. (LRW)

  9. Quantum entanglement and coherence in molecular magnets

    NASA Astrophysics Data System (ADS)

    Shiddiq, Muhandis

    Quantum computers are predicted to outperform classical computers in certain tasks, such as factoring large numbers and searching databases. The construction of a computer whose operation is based on the principles of quantum mechanics appears extremely challenging. Solid state approaches offer the potential to answer this challenge by tailor-making novel nanomaterials for quantum information processing (QIP). Molecular magnets, which are materials whose energy levels and magnetic quantum states are well defined at the molecular level, have been identified as a class of material with properties that make them attractive for quantum computing purpose. In this dissertation, I explore the possibilities and challenges for molecular magnets to be used in quantum computing architecture. The properties of molecular magnets that are critical for applications in quantum computing, i.e., quantum entanglement and coherence, are comprehensively investigated to probe the feasibility of molecular magnets to be used as quantum bits (qubits). Interactions of qubits with photons are at the core of QIP. Photons can be used to detect and manipulate qubits, after which information can then be transferred over long distances. As a potential candidate for qubits, the interactions between Fe8 single-molecule magnets (SMMs) and cavity photons were studied. An earlier report described that a cavity mode splitting was observed in a spectrum of a cavity filled with a single-crystal of Fe8 SMMs. This splitting was interpreted as a vacuum Rabi splitting (VRS), which is a signature of an entanglement between a large number of SMMs and a cavity photon. However, find that large absorption and dispersion of the magnetic susceptibility are the reasons for this splitting. This finding highlights the fact that an observation of a peak splitting in a cavity transmission spectrum neither represents an unambiguous indication of quantum coherence in a large number of spins, nor a signature of

  10. The North Carolina State University Libraries Search Experience: Usability Testing Tabbed Search Interfaces for Academic Libraries

    ERIC Educational Resources Information Center

    Teague-Rector, Susan; Ballard, Angela; Pauley, Susan K.

    2011-01-01

    Creating a learnable, effective, and user-friendly library Web site hinges on providing easy access to search. Designing a search interface for academic libraries can be particularly challenging given the complexity and range of searchable library collections, such as bibliographic databases, electronic journals, and article search silos. Library…

  11. Adding to the Students' Toolbox: Using Directories, Search Engines, and the Hidden Web in Search Processes.

    ERIC Educational Resources Information Center

    Mardis, Marcia A.

    2002-01-01

    Discussion of searching for information on the Web focuses on resources that are not always found by traditional Web searches. Describes sources on the hidden Web, including full-text databases, clearinghouses, digital libraries, and learning objects; explains how search engines operate; and suggests that traditional print sources are still…

  12. Disability search tips and resources.

    PubMed

    Schaefer, Nancy

    2015-01-01

    Demographic projections for people living in the United States indicate a growing need for information on disabilities. This article discusses a limited number of concepts in disability, along with relevant thesaurus terms and suggested search techniques in four databases: PubMed, CINAHL, REHABDATA, and the Center for International Rehabilitation Research Information and Exchange's (CIRRIE) Database of International Research. The article closes with annotations of potentially useful websites that focus on concerns of persons with disabilities, their caregivers, and researchers in disability.

  13. A Survey in Indexing and Searching XML Documents.

    ERIC Educational Resources Information Center

    Luk, Robert W. P.; Leong, H. V.; Dillon, Tharam S.; Chan, Alvin T. S.; Croft, W. Bruce; Allan, James

    2002-01-01

    Discussion of XML focuses on indexing techniques for XML documents, grouping them into flat-file, semistructured, and structured indexing paradigms. Highlights include searching techniques, including full text search and multistage search; search result presentations; database and information retrieval system integration; XML query languages; and…

  14. A Detailed Analysis of End-User Search Behaviors.

    ERIC Educational Resources Information Center

    Wildemuth, Barbara M.; And Others

    1991-01-01

    Discussion of search strategy formulation focuses on a study at the University of North Carolina at Chapel Hill that analyzed how medical students developed and revised search strategies for microbiology database searches. Implications for future research on search behavior, for system interface design, and for end user training are suggested. (16…

  15. Generalized Geometric Quantum Speed Limits

    NASA Astrophysics Data System (ADS)

    Pires, Diego Paiva; Cianciaruso, Marco; Céleri, Lucas C.; Adesso, Gerardo; Soares-Pinto, Diogo O.

    2016-04-01

    The attempt to gain a theoretical understanding of the concept of time in quantum mechanics has triggered significant progress towards the search for faster and more efficient quantum technologies. One of such advances consists in the interpretation of the time-energy uncertainty relations as lower bounds for the minimal evolution time between two distinguishable states of a quantum system, also known as quantum speed limits. We investigate how the nonuniqueness of a bona fide measure of distinguishability defined on the quantum-state space affects the quantum speed limits and can be exploited in order to derive improved bounds. Specifically, we establish an infinite family of quantum speed limits valid for unitary and nonunitary evolutions, based on an elegant information geometric formalism. Our work unifies and generalizes existing results on quantum speed limits and provides instances of novel bounds that are tighter than any established one based on the conventional quantum Fisher information. We illustrate our findings with relevant examples, demonstrating the importance of choosing different information metrics for open system dynamics, as well as clarifying the roles of classical populations versus quantum coherences, in the determination and saturation of the speed limits. Our results can find applications in the optimization and control of quantum technologies such as quantum computation and metrology, and might provide new insights in fundamental investigations of quantum thermodynamics.

  16. Confidential Searches.

    ERIC Educational Resources Information Center

    Kenney, Linda Chion

    2003-01-01

    Will the stealth superintendent hunt in Cincinnati become tomorrow's standard approach? Search consultants and superintendents offer their views on how far confidentiality should go. Also includes a search firm's process for shielding identities and a confidentiality pledge. (MLF)

  17. IDBD: infectious disease biomarker database.

    PubMed

    Yang, In Seok; Ryu, Chunsun; Cho, Ki Joon; Kim, Jin Kwang; Ong, Swee Hoe; Mitchell, Wayne P; Kim, Bong Su; Oh, Hee-Bok; Kim, Kyung Hyun

    2008-01-01

    Biomarkers enable early diagnosis, guide molecularly targeted therapy and monitor the activity and therapeutic responses across a variety of diseases. Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling. Moreover, no solution is yet available that efficiently retrieves and processes biomarker information pertaining to infectious diseases. Infectious Disease Biomarker Database (IDBD) is one of the first efforts to build an easily accessible and comprehensive literature-derived database covering known infectious disease biomarkers. IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online. It allows users to link infectious diseases or pathogens to protein, gene or carbohydrate biomarkers through the use of search tools. It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers. Currently, IDBD integrates 611 biomarkers for 66 infectious diseases and 70 pathogens. It is publicly accessible at http://biomarker.cdc.go.kr and http://biomarker.korea.ac.kr.

  18. Potential Energy Surface Database of Group II Dimer

    National Institute of Standards and Technology Data Gateway

    SRD 143 NIST Potential Energy Surface Database of Group II Dimer (Web, free access)   This database provides critical atomic and molecular data needed in order to evaluate the feasibility of using laser cooled and trapped Group II atomic species (Mg, Ca, Sr, and Ba) for ultra-precise optical clocks or quantum information processing devices.

  19. Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data.

    PubMed

    Kumar, Dhirendra; Yadav, Amit Kumar; Dash, Debasis

    2017-01-01

    Database searching is the preferred method for protein identification from digital spectra of mass to charge ratios (m/z) detected for protein samples through mass spectrometers. The search database is one of the major influencing factors in discovering proteins present in the sample and thus in deriving biological conclusions. In most cases the choice of search database is arbitrary. Here we describe common search databases used in proteomic studies and their impact on final list of identified proteins. We also elaborate upon factors like composition and size of the search database that can influence the protein identification process. In conclusion, we suggest that choice of the database depends on the type of inferences to be derived from proteomics data. However, making additional efforts to build a compact and concise database for a targeted question should generally be rewarding in achieving confident protein identifications.

  20. US Department of Energy Chernobyl Database

    SciTech Connect

    Kennedy, R.A.; Mahaffey, J.A.; Smith, S.K.; Carr, F. Jr.

    1992-05-01

    The Chernobyl Database project is developing and maintaining an information to provide researchers with data and resource materials relating to the Chernobyl nuclear accident of April 1986. The system is the official United States repository for Chernobyl data. The system includes a collection of Chernobyl-related documents, a database of bibliographic references, and a collection of radiological measurements records. In addition, projects have been developed to make the resources more accessible and easy to use. These products include a personal-computer-based bibliographic search system (ChernoLit{trademark}), two printed bibliographies, and a personal- computer-based radiological measurements database system (ChernoDat).

  1. Suspicionless Searches.

    ERIC Educational Resources Information Center

    Zirkel, Perry A.

    2000-01-01

    In a federal case involving a vice-principal's pat-down search of middle-school students in a cafeteria (for a missing pizza knife), the court upheld the search, saying it was relatively unintrusive and met "TLO's" reasonable-suspicion standards. Principals need reasonable justification for searching a group. (Contains 18 references.)…

  2. Partition search

    SciTech Connect

    Ginsberg, M.L.

    1996-12-31

    We introduce a new form of game search called partition search that incorporates dependency analysis, allowing substantial reductions in the portion of the tree that needs to be expanded. Both theoretical results and experimental data are presented. For the game of bridge, partition search provides approximately as much of an improvement over existing methods as {alpha}-{beta} pruning provides over minimax.

  3. Team X Spacecraft Instrument Database Consolidation

    NASA Technical Reports Server (NTRS)

    Wallenstein, Kelly A.

    2005-01-01

    In the past decade, many changes have been made to Team X's process of designing each spacecraft, with the purpose of making the overall procedure more efficient over time. One such improvement is the use of information databases from previous missions, designs, and research. By referring to these databases, members of the design team can locate relevant instrument data and significantly reduce the total time they spend on each design. The files in these databases were stored in several different formats with various levels of accuracy. During the past 2 months, efforts have been made in an attempt to combine and organize these files. The main focus was in the Instruments department, where spacecraft subsystems are designed based on mission measurement requirements. A common database was developed for all instrument parameters using Microsoft Excel to minimize the time and confusion experienced when searching through files stored in several different formats and locations. By making this collection of information more organized, the files within them have become more easily searchable. Additionally, the new Excel database offers the option of importing its contents into a more efficient database management system in the future. This potential for expansion enables the database to grow and acquire more search features as needed.

  4. A Brief Index for Proximity Searching

    NASA Astrophysics Data System (ADS)

    Téllez, Eric Sadit; Chávez, Edgar; Camarena-Ibarrola, Antonio

    Many pattern recognition tasks can be modeled as proximity searching. Here the common task is to quickly find all the elements close to a given query without sequentially scanning a very large database.

  5. VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

    NASA Technical Reports Server (NTRS)

    Roussopoulos, N.; Sellis, Timos

    1992-01-01

    One of biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental database access method, VIEWCACHE, provides such an interface for accessing distributed data sets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image data sets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate distributed database search.

  6. YMDB: the Yeast Metabolome Database

    PubMed Central

    Jewison, Timothy; Knox, Craig; Neveu, Vanessa; Djoumbou, Yannick; Guo, An Chi; Lee, Jacqueline; Liu, Philip; Mandal, Rupasri; Krishnamurthy, Ram; Sinelnikov, Igor; Wilson, Michael; Wishart, David S.

    2012-01-01

    The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated ‘metabolomic’ database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of S. cervesiae's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers, but also to yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry. PMID:22064855

  7. Reflective Database Access Control

    ERIC Educational Resources Information Center

    Olson, Lars E.

    2009-01-01

    "Reflective Database Access Control" (RDBAC) is a model in which a database privilege is expressed as a database query itself, rather than as a static privilege contained in an access control list. RDBAC aids the management of database access controls by improving the expressiveness of policies. However, such policies introduce new interactions…

  8. Databases: Beyond the Basics.

    ERIC Educational Resources Information Center

    Whittaker, Robert

    This presented paper offers an elementary description of database characteristics and then provides a survey of databases that may be useful to the teacher and researcher in Slavic and East European languages and literatures. The survey focuses on commercial databases that are available, usable, and needed. Individual databases discussed include:…

  9. National Geochronological Database

    USGS Publications Warehouse

    Revised by Sloan, Jan; Henry, Christopher D.; Hopkins, Melanie; Ludington, Steve; Original database by Zartman, Robert E.; Bush, Charles A.; Abston, Carl

    2003-01-01

    The National Geochronological Data Base (NGDB) was established by the United States Geological Survey (USGS) to collect and organize published isotopic (also known as radiometric) ages of rocks in the United States. The NGDB (originally known as the Radioactive Age Data Base, RADB) was started in 1974. A committee appointed by the Director of the USGS was given the mission to investigate the feasibility of compiling the published radiometric ages for the United States into a computerized data bank for ready access by the user community. A successful pilot program, which was conducted in 1975 and 1976 for the State of Wyoming, led to a decision to proceed with the compilation of the entire United States. For each dated rock sample reported in published literature, a record containing information on sample location, rock description, analytical data, age, interpretation, and literature citation was constructed and included in the NGDB. The NGDB was originally constructed and maintained on a mainframe computer, and later converted to a Helix Express relational database maintained on an Apple Macintosh desktop computer. The NGDB and a program to search the data files were published and distributed on Compact Disc-Read Only Memory (CD-ROM) in standard ISO 9660 format as USGS Digital Data Series DDS-14 (Zartman and others, 1995). As of May 1994, the NGDB consisted of more than 18,000 records containing over 30,000 individual ages, which is believed to represent approximately one-half the number of ages published for the United States through 1991. Because the organizational unit responsible for maintaining the database was abolished in 1996, and because we wanted to provide the data in more usable formats, we have reformatted the data, checked and edited the information in some records, and provided this online version of the NGDB. This report describes the changes made to the data and formats, and provides instructions for the use of the database in geographic

  10. A Scalable Database Infrastructure

    NASA Astrophysics Data System (ADS)

    Arko, R. A.; Chayes, D. N.

    2001-12-01

    The rapidly increasing volume and complexity of MG&G data, and the growing demand from funding agencies and the user community that it be easily accessible, demand that we improve our approach to data management in order to reach a broader user-base and operate more efficient and effectively. We have chosen an approach based on industry-standard relational database management systems (RDBMS) that use community-wide data specifications, where there is a clear and well-documented external interface that allows use of general purpose as well as customized clients. Rapid prototypes assembled with this approach show significant advantages over the traditional, custom-built data management systems that often use "in-house" legacy file formats, data specifications, and access tools. We have developed an effective database prototype based a public domain RDBMS (PostgreSQL) and metadata standard (FGDC), and used it as a template for several ongoing MG&G database management projects - including ADGRAV (Antarctic Digital Gravity Synthesis), MARGINS, the Community Review system of the Digital Library for Earth Science Education, multibeam swath bathymetry metadata, and the R/V Maurice Ewing onboard acquisition system. By using standard formats and specifications, and working from a common prototype, we are able to reuse code and deploy rapidly. Rather than spend time on low-level details such as storage and indexing (which are built into the RDBMS), we can focus on high-level details such as documentation and quality control. In addition, because many commercial off-the-shelf (COTS) and public domain data browsers and visualization tools have built-in RDBMS support, we can focus on backend development and leave the choice of a frontend client(s) up to the end user. While our prototype is running under an open source RDBMS on a single processor host, the choice of standard components allows this implementation to scale to commercial RDBMS products and multiprocessor servers as

  11. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.

    PubMed

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-09-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.

  12. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

    PubMed Central

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-01-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  13. Human Mitochondrial Protein Database

    National Institute of Standards and Technology Data Gateway

    SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

  14. The New NRL Crystallographic Database

    NASA Astrophysics Data System (ADS)

    Mehl, Michael; Curtarolo, Stefano; Hicks, David; Toher, Cormac; Levy, Ohad; Hart, Gus

    For many years the Naval Research Laboratory maintained an online graphical database of crystal structures for a wide variety of materials. This database has now been redesigned, updated and integrated with the AFLOW framework for high throughput computational materials discovery (http://materials.duke.edu/aflow.html). For each structure we provide an image showing the atomic positions; the primitive vectors of the lattice and the basis vectors of every atom in the unit cell; the space group and Wyckoff positions; Pearson symbols; common names; and Strukturbericht designations, where available. References for each structure are provided, as well as a Crystallographic Information File (CIF). The database currently includes almost 300 entries and will be continuously updated and expanded. It enables easy search of the various structures based on their underlying symmetries, either by Bravais lattice, Pearson symbol, Strukturbericht designation or commonly used prototypes. The talk will describe the features of the database, and highlight its utility for high throughput computational materials design. Work at NRL is funded by a Contract with the Duke University Department of Mechanical Engineering.

  15. CADDIS Volume 5. Causal Databases: Interactive Conceptual Diagrams (ICDs)

    EPA Pesticide Factsheets

    In Interactive Conceptual Diagram (ICD) section of CADDIS allows users to create conceptual model diagrams, search a literature-based evidence database, and then attach that evidence to their diagrams.

  16. Advantages for the use of standardized phenotyping in databases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic sequence data is becoming prevalent in databases; however, associated phenotypic data is much more expensive and difficult to obtain. Standardized ontologies for trait classification provide a mechanism by which searches can be efficiently performed. Through standardization efforts, result...

  17. Joanna Briggs Institute: an evidence-based practice database.

    PubMed

    Vardell, Emily; Malloy, Michele

    2013-01-01

    The Joanna Briggs Institute Evidence-Based Practice Database offers systematic reviews, practice recommendations, and consumer information designed to support evidence-based practice. A sample search was conducted within the Ovid platform to demonstrate functionality and available tools.

  18. New Approaches to Quantum Computing using Nuclear Magnetic Resonance Spectroscopy

    SciTech Connect

    Colvin, M; Krishnan, V V

    2003-02-07

    The power of a quantum computer (QC) relies on the fundamental concept of the superposition in quantum mechanics and thus allowing an inherent large-scale parallelization of computation. In a QC, binary information embodied in a quantum system, such as spin degrees of freedom of a spin-1/2 particle forms the qubits (quantum mechanical bits), over which appropriate logical gates perform the computation. In classical computers, the basic unit of information is the bit, which can take a value of either 0 or 1. Bits are connected together by logic gates to form logic circuits to implement complex logical operations. The expansion of modern computers has been driven by the developments of faster, smaller and cheaper logic gates. As the size of the logic gates become smaller toward the level of atomic dimensions, the performance of such a system is no longer considered classical but is rather governed by quantum mechanics. Quantum computers offer the potentially superior prospect of solving computational problems that are intractable to classical computers such as efficient database searches and cryptography. A variety of algorithms have been developed recently, most notably Shor's algorithm for factorizing long numbers into prime factors in polynomial time and Grover's quantum search algorithm. The algorithms that were of only theoretical interest as recently, until several methods were proposed to build an experimental QC. These methods include, trapped ions, cavity-QED, coupled quantum dots, Josephson junctions, spin resonance transistors, linear optics and nuclear magnetic resonance. Nuclear magnetic resonance (NMR) is uniquely capable of constructing small QCs and several algorithms have been implemented successfully. NMR-QC differs from other implementations in one important way that it is not a single QC, but a statistical ensemble of them. Thus, quantum computing based on NMR is considered as ensemble quantum computing. In NMR quantum computing, the spins with

  19. Choosing the Right Database Management Program.

    ERIC Educational Resources Information Center

    Vockell, Edward L.; Kopenec, Donald

    1989-01-01

    Provides a comparison of four database management programs commonly used in schools: AppleWorks, the DOS 3.3 and ProDOS versions of PFS, and MECC's Data Handler. Topics discussed include information storage, spelling checkers, editing functions, search strategies, graphs, printout formats, library applications, and HyperCard. (LRW)

  20. Invisible Authorship: Women's Names, Databases, and Technology.

    ERIC Educational Resources Information Center

    Tescione, Susan M.

    Bibliographic databases act as search tools to locate relevant literature and information, but they also disseminate information about the works indexed in the records. Articles and authors that cannot be found cannot be cited, and the ability to disseminate data for that particular work is diminished. This study found no significant differences…

  1. Public Opinion Poll Question Databases: An Evaluation

    ERIC Educational Resources Information Center

    Woods, Stephen

    2007-01-01

    This paper evaluates five polling resource: iPOLL, Polling the Nations, Gallup Brain, Public Opinion Poll Question Database, and Polls and Surveys. Content was evaluated on disclosure standards from major polling organizations, scope on a model for public opinion polls, and presentation on a flow chart discussing search limitations and usability.

  2. Comparison Shopping of Tax Research Databases.

    ERIC Educational Resources Information Center

    Scanlan, Jean M.

    1990-01-01

    Examines and compares online sources for primary and secondary federal and state tax information. The criteria used to evaluate the four systems (CCH ACCESS, LEXIS, PHINet, and WESTLAW) include the contents of each database, search features, hardware requirements, software, pricing, availability of CD-ROM, online billing, and network…

  3. The RECONS 25 Parsec Database

    NASA Astrophysics Data System (ADS)

    Henry, Todd J.; Jao, Wei-Chun; Pewett, Tiffany; Riedel, Adric R.; Silverstein, Michele L.; Slatten, Kenneth J.; Winters, Jennifer G.; Recons Team

    2015-01-01

    The REsearch Consortium On Nearby Stars (RECONS, www.recons.org) Team has been mapping the solar neighborhood since 1994. Nearby stars provide the fundamental framework upon which all of stellar astronomy is based, both for individual stars and stellar populations. The nearest stars are also the primary targets for extrasolar planet searches, and will undoubtedly play key roles in understanding the prevalence and structure of solar systems, and ultimately, in our search for life elsewhere.We have built the RECONS 25 Parsec Database to encourage and enable exploration of the Sun's nearest neighbors. The Database, slated for public release in 2015, contains 3088 stars, brown dwarfs, andexoplanets in 2184 systems as of October 1, 2014. All of these systems have accurate trigonometric parallaxes in the refereed literature placing them closer than 25.0 parsecs, i.e., parallaxes greater than 40 mas with errors less than 10 mas. Carefully vetted astrometric, photometric, and spectroscopic data are incorporated intothe Database from reliable sources, including significant original data collected by members of the RECONS Team.Current exploration of the solar neighborhood by RECONS, enabled by the Database, focuses on the ubiquitous red dwarfs, including: assessing the stellar companion population of ~1200 red dwarfs (Winters), investigating the astrophysical causes that spread red dwarfs of similar temperatures by a factor of 16 in luminosity (Pewett), and canvassing ~3000 red dwarfs for excess emission due to unseen companions and dust (Silverstein). In addition, a decade long astrometric survey of ~500 red dwarfs in the southern sky has begun, in an effort to understand the stellar, brown dwarf, and planetary companion populations for the stars that make up at least 75% of all stars in the Universe.This effort has been supported by the NSF through grants AST-0908402, AST-1109445, and AST-1412026, and via observations made possible by the SMARTS Consortium.

  4. E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

    PubMed Central

    Boutselakis, H.; Dimitropoulos, D.; Fillon, J.; Golovin, A.; Henrick, K.; Hussain, A.; Ionides, J.; John, M.; Keller, P. A.; Krissinel, E.; McNeil, P.; Naim, A.; Newman, R.; Oldfield, T.; Pineda, J.; Rachedi, A.; Copeland, J.; Sitnov, A.; Sobhany, S.; Suarez-Uruena, A.; Swaminathan, J.; Tagari, M.; Tate, J.; Tromm, S.; Velankar, S.; Vranken, W.

    2003-01-01

    The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool. PMID:12520052

  5. The Majorana Parts Tracking Database

    SciTech Connect

    Abgrall, N.; Aguayo, E.; Avignone, F. T.; Barabash, A. S.; Bertrand, F. E.; Brudanin, V.; Busch, M.; Byram, D.; Caldwell, A. S.; Chan, Y-D.; Christofferson, C. D.; Combs, D. C.; Cuesta, C.; Detwiler, J. A.; Doe, P. J.; Efremenko, Yu.; Egorov, V.; Ejiri, H.; Elliott, S. R.; Esterline, J.; Fast, J. E.; Finnerty, P.; Fraenkle, F. M.; Galindo-Uribarri, A.; Giovanetti, G. K.; Goett, J.; Green, M. P.; Gruszko, J.; Guiseppe, V. E.; Gusev, K.; Hallin, A. L.; Hazama, R.; Hegai, A.; Henning, R.; Hoppe, E. W.; Howard, S.; Howe, M. A.; Keeter, K. J.; Kidd, M. F.; Kochetov, O.; Konovalov, S. I.; Kouzes, R. T.; LaFerriere, B. D.; Leon, J. Diaz; Leviner, L. E.; Loach, J. C.; MacMullin, J.; Martin, R. D.; Meijer, S. J.; Mertens, S.; Miller, M. L.; Mizouni, L.; Nomachi, M.; Orrell, J. L.; O׳Shaughnessy, C.; Overman, N. R.; Petersburg, R.; Phillips, D. G.; Poon, A. W. P.; Pushkin, K.; Radford, D. C.; Rager, J.; Rielage, K.; Robertson, R. G. H.; Romero-Romero, E.; Ronquest, M. C.; Shanks, B.; Shima, T.; Shirchenko, M.; Snavely, K. J.; Snyder, N.; Soin, A.; Suriano, A. M.; Tedeschi, D.; Thompson, J.; Timkin, V.; Tornow, W.; Trimble, J. E.; Varner, R. L.; Vasilyev, S.; Vetter, K.; Vorren, K.; White, B. R.; Wilkerson, J. F.; Wiseman, C.; Xu, W.; Yakushev, E.; Young, A. R.; Yu, C. -H.; Yumatov, V.; Zhitnikov, I.

    2015-04-01

    The MAJORANA DEMONSTRATOR is an ultra-low background physics experiment searching for the neutrinoless double beta decay of 76Ge. The MAJORANA Parts Tracking Database is used to record the history of components used in the construction of the DEMONSTRATOR. Transportation, storage, and processes undergone by parts such as machining or cleaning are linked to part records. Tracking parts provides a great logistics benefit and an important quality assurance reference during construction. In addition, the location history of parts provides an estimate of their exposure to cosmic radiation. A web application for data entry and a radiation exposure calculator have been developed as tools for achieving the extreme radiopurity required for this rare decay search.

  6. Public chemical compound databases.

    PubMed

    Williams, Anthony J

    2008-05-01

    The internet has rapidly become the first port of call for all information searches. The increasing array of chemistry-related resources that are now available provides chemists with a direct path to the information that was previously accessed via library services and was limited by commercial and costly resources. The diversity of the information that can be accessed online is expanding at a dramatic rate, and the support for publicly available resources offers significant opportunities in terms of the benefits to science and society. While the data online do not generally meet the quality standards of manually curated sources, there are efforts underway to gather scientists together and 'crowdsource' an improvement in the quality of the available data. This review discusses the types of public compound databases that are available online and provides a series of examples. Focus is also given to the benefits and disruptions associated with the increased availability of such data and the integration of technologies to data mine this information.

  7. Assessment of bibliographic databases performance in information retrieval for occupational and environmental toxicology

    PubMed Central

    Gehanno, J. F.; Paris, C.; Thirion, B.; Caillard, J. F.

    1998-01-01

    OBJECTIVE: To determine the efficiency of the major bibliographic databases by assessing the percentage of references among the total literature available that can be retrieved from each database. We also evaluated the best database combinations to carry out an exhaustive search. METHODS: BIOSIS, EMBASE, MEDLINE, NIOSH-TIC, and TOXLINE were searched on two topics: allergy to latex and asbestos and mesothelioma, in the title, abstract, or keywords (textwords). This search was performed for the years 1994 and 1995. All the records were classified by journal and author's name and were verified for each record whether or not it was indexed in each database. Statistical analysis was performed with chi 2 test. RESULTS: 777 articles in 510 issues were found. The efficiency of each database (percentage of articles recovered) and of combinations varied between 11% and 63% for one database and between 42% and 86% for a combination of two databases. The reasons why these differences exist between databases, and within a database, between two different subjects or two different years are reported. CONCLUSION: Firstly, it is not advisable to assert that a bibliography is complete when only one database is searched. Secondly, the efficiency of the databases may be quite different. Finally, it is suggested that the best way to be as exhaustive as possible is to search two or more databases-for example, in EMBASE and TOXLINE, or to a lesser extent EMBASE and MEDLINE. This seems to be the best compromise solution between time consumed for searching and efficiency.   PMID:9849544

  8. The peptaibiotics database--a comprehensive online resource.

    PubMed

    Neumann, Nora K N; Stoppacher, Norbert; Zeilinger, Susanne; Degenkolb, Thomas; Brückner, Hans; Schuhmacher, Rainer

    2015-05-01

    In this work, we present the 'Peptaibiotics Database' (PDB), a comprehensive online resource, which intends to cover all Aib-containing non-ribosomal fungal peptides currently described in scientific literature. This database shall extend and update the recently published 'Comprehensive Peptaibiotics Database' and currently consists of 1,297 peptaibiotic sequences. In a literature survey, a total of 235 peptaibiotic sequences published between January 2013 and June 2014 have been compiled, and added to the list of 1,062 peptides in the recently published 'Comprehensive Peptaibiotics Database'. The presented database is intended as a public resource freely accessible to the scientific community at peptaibiotics-database.boku.ac.at. The search options of the previously published repository and the presentation of sequence motif searches have been extended significantly. All of the available search options can be combined to create complex database queries. As a public repository, the presented database enables the easy upload of new peptaibiotic sequences or the correction of existing informations. In addition, an administrative interface for maintenance of the content of the database has been implemented, and the design of the database can be easily extended to store additional information to accommodate future needs of the 'peptaibiomics community'.

  9. Willow: a uniform search interface.

    PubMed Central

    Ketchell, D S; Freedman, M M; Jordan, W E; Lightfoot, E M; Heyano, S; Libbey, P A

    1996-01-01

    The objective of the Willow Project is to develop a uniform search interface that allows a diverse community of users to retrieve information from heterogeneous network-based information resources. Willow separates the user interface from the database management or information retrieval system. It provides a graphic user interface to a variety of information resources residing on diverse hosts, and using different search engines and idiomatic query languages through networked-based client-server and Transmission Control Protocol/Internet Protocol (TCP/IP) protocols. It is based on a "database driver'' model, which allows new database hosts to be added without altering Willow itself. Willow employs a multimedia extension mechanism to launch external viewers to handle data in almost any form. Drivers are currently available for a local BRS/SEARCH system and the Z39.50 protocol. Students, faculty, clinicians, and researchers at the University of Washington are currently offered 30 local and remote databases via Willow. They conduct more than 250,000 sessions a month in libraries, medical centers and clinics, laboratories, and offices, and from home. The Massachusetts Institute of Technology is implementing Willow as its uniform search interface to Z39.50 hosts. PMID:8750388

  10. Topical Search: AIDS and Youth.

    ERIC Educational Resources Information Center

    Department of Justice, Washington, DC. National Inst. of Justice.

    This topical search includes 30 of the most representative citations on the subject of Acquired Immune Deficiency Syndrome (AIDS) and youth selected from the National Institute of Justice/NCJRS (National Criminal Justice Reference Service) database. Topics covered in this package include education programs for in-school youth, policies and…

  11. Optimal strategies for literature search

    PubMed Central

    Siva, Siddharth

    2009-01-01

    With the large number of urological journals now indexed in online search engines, just reading a few journals will not keep urologists up to date on the latest developments. This paper proposes search strategies to quicken the search and retrieval of the required literature, so that the best evidence may be used to guide practice. This survey of optimal strategies begins with framing the inquiry so the search engine returns results within an accurate scope. The researcher must also isolate the type of evidence appropriate for the scenario and determine its validity. Finally, regardless of the extent of their institution's subscriptions, researchers should be able to attain the complete document. Besides search strategies, this article extensively reviews sources of information valuable to urologists, including databases and web links. PMID:19672359

  12. The TIGR Plant Transcript Assemblies database.

    PubMed

    Childs, Kevin L; Hamilton, John P; Zhu, Wei; Ly, Eugene; Cheung, Foo; Wu, Hank; Rabinowicz, Pablo D; Town, Chris D; Buell, C Robin; Chan, Agnes P

    2007-01-01

    The TIGR Plant Transcript Assemblies (TA) database (http://plantta.tigr.org) uses expressed sequences collected from the NCBI GenBank Nucleotide database for the construction of transcript assemblies. The sequences collected include expressed sequence tags (ESTs) and full-length and partial cDNAs, but exclude computationally predicted gene sequences. The TA database includes all plant species for which more than 1000 EST or cDNA sequences are publicly available. The EST and cDNA sequences are first clustered based on an all-versus-all pairwise sequence comparison, followed by the generation of consensus sequences (TAs) from individual clusters. The clustering and assembly procedures use the TGICL tool, Megablast and the CAP3 assembler. The UniProt Reference Clusters (UniRef100) protein database is used as the reference database for the functional annotation of the assemblies. The transcription orientation of each TA is determined based on the orientation of the alignment with the best protein hit. The TA sequences and annotation are available via web interfaces and FTP downloads. Assemblies can be retrieved by a text-based keyword search or a sequence-based BLAST search. The current version of the TA database is Release 2 (July 17, 2006) and includes a total of 215 plant species.

  13. Enhancing the diversity of a corporate database using chemical database clustering and analysis

    NASA Astrophysics Data System (ADS)

    Shemetulskis, Norah E.; Dunbar, James B., Jr.; Dunbar, Bonnie W.; Moreland, David W.; Humblet, Christine

    1995-10-01

    The contribution that the Chemical Abstracts structural database (CAST-3D) and the Maybridge database (MAY) would make to diversifying the structural information and property space spanned by our corporate database (CBI) is assessed. A subset of the CAST-3D database has been selected to augment the structural diversity of various electronic databases used in computer-assisted drug design projects. The analysis of the MAY database directly offers the potential to expand the CBI compound library, but also provides a source for structural diversity in a format suitable for computer-assisted database searching and molecular design. The analysis performed is twofold. First, a nonhierarchical clustering technique available in the Daylight clustering package is applied to evaluate the structural differences between databases. The comparison is then extended to analyze various structure-derived property spaces calculated from molecular descriptors such as the logarithm of the octanol-water partition coefficient (CLOGP), the molar refractivity (CMR) and the electronic dipole moment (CDM). The diversity contribution of each database to these property spaces is quantified in relation to our corporate database.

  14. IPD--the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Waller, Matthew J; Stoehr, Peter; Marsh, Steven G E

    2005-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute.

  15. Searching Lexis and Westlaw: Part III.

    ERIC Educational Resources Information Center

    Franklin, Carl

    1986-01-01

    This last installment in a three-part series covers several important areas in the searching of legal information: online (group) training and customer service, documentation (search manuals and other aids), account representatives, microcomputer software, and pricing. Advantages and drawbacks of both the LEXIS and WESTLAW databases are noted.…

  16. Developing a Systematic Patent Search Training Program

    ERIC Educational Resources Information Center

    Zhang, Li

    2009-01-01

    This study aims to develop a systematic patent training program using patent analysis and citation analysis techniques applied to patents held by the University of Saskatchewan. The results indicate that the target audience will be researchers in life sciences, and aggregated patent database searching and advanced search techniques should be…

  17. An Improved Forensic Science Information Search.

    PubMed

    Teitelbaum, J

    2015-01-01

    Although thousands of search engines and databases are available online, finding answers to specific forensic science questions can be a challenge even to experienced Internet users. Because there is no central repository for forensic science information, and because of the sheer number of disciplines under the forensic science umbrella, forensic scientists are often unable to locate material that is relevant to their needs. The author contends that using six publicly accessible search engines and databases can produce high-quality search results. The six resources are Google, PubMed, Google Scholar, Google Books, WorldCat, and the National Criminal Justice Reference Service. Carefully selected keywords and keyword combinations, designating a keyword phrase so that the search engine will search on the phrase and not individual keywords, and prompting search engines to retrieve PDF files are among the techniques discussed.

  18. Online-Expert: An Expert System for Online Database Selection.

    ERIC Educational Resources Information Center

    Zahir, Sajjad; Chang, Chew Lik

    1992-01-01

    Describes the design and development of a prototype expert system called ONLINE-EXPERT that helps users select online databases and vendors that meet users' needs. Search strategies are discussed; knowledge acquisition and knowledge bases are described; and the Analytic Hierarchy Process (AHP), a decision analysis technique that ranks databases,…

  19. Accessing the BIOSIS Previews Database in Clinical Psychology.

    ERIC Educational Resources Information Center

    Piotrowski, Chris; Perdue, Bob

    The efficacy of using the BIOSIS Previews database as an online information retrieval tool in clinical psychology was investigated in a study conducted at the University of West Florida. Recognizing the importance of multi-database searching strategies when seeking comprehensive results, this study compared the citation output of this…

  20. Enhancing NTIS Database Access at a Multi-Campus University.

    ERIC Educational Resources Information Center

    Conkling, Thomas W.; Jordan, Kelly

    1997-01-01

    The Pennsylvania State University Libraries and the National Technical Information Service (NTIS) collaborated to bring the entire NTIS bibliographic database online on the University-wide information system and make it available for searching at all 21 Pennsylvania State campuses. This article also reviews the level of database and technical…