Continuous-time quantum search on balanced trees

NASA Astrophysics Data System (ADS)

Philipp, Pascal; Tarrataca, Luís; Boettcher, Stefan

2016-03-01

We examine the effect of network heterogeneity on the performance of quantum search algorithms. To this end, we study quantum search on a tree for the oracle Hamiltonian formulation employed by continuous-time quantum walks. We use analytical and numerical arguments to show that the exponent of the asymptotic running time ˜Nβ changes uniformly from β =0.5 to β =1 as the searched-for site is moved from the root of the tree towards the leaves. These results imply that the time complexity of the quantum search algorithm on a balanced tree is closely correlated with certain path-based centrality measures of the searched-for site.

Data Structures in Natural Computing: Databases as Weak or Strong Anticipatory Systems

NASA Astrophysics Data System (ADS)

Rossiter, B. N.; Heather, M. A.

2004-08-01

Information systems anticipate the real world. Classical databases store, organise and search collections of data of that real world but only as weak anticipatory information systems. This is because of the reductionism and normalisation needed to map the structuralism of natural data on to idealised machines with von Neumann architectures consisting of fixed instructions. Category theory developed as a formalism to explore the theoretical concept of naturality shows that methods like sketches arising from graph theory as only non-natural models of naturality cannot capture real-world structures for strong anticipatory information systems. Databases need a schema of the natural world. Natural computing databases need the schema itself to be also natural. Natural computing methods including neural computers, evolutionary automata, molecular and nanocomputing and quantum computation have the potential to be strong. At present they are mainly at the stage of weak anticipatory systems.

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.

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.

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

2017-04-01

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.

Connectivity is a Poor Indicator of Fast Quantum Search

NASA Astrophysics Data System (ADS)

Meyer, David A.; Wong, Thomas G.

2015-03-01

A randomly walking quantum particle evolving by Schrödinger's equation searches on d -dimensional cubic lattices in O (√{N }) time when d ≥5 , and with progressively slower runtime as d decreases. This suggests that graph connectivity (including vertex, edge, algebraic, and normalized algebraic connectivities) is an indicator of fast quantum search, a belief supported by fast quantum search on complete graphs, strongly regular graphs, and hypercubes, all of which are highly connected. In this Letter, we show this intuition to be false by giving two examples of graphs for which the opposite holds true: one with low connectivity but fast search, and one with high connectivity but slow search. The second example is a novel two-stage quantum walk algorithm in which the walking rate must be adjusted to yield high search probability.

Sensors and detectors based on superconducting devices. (Latest citations from the Compendex database). Published Search

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

Not Available

1993-02-01

The bibliography contains citations concerning gradiometers, magnetometers, and infrared detectors which use superconductors to improve sensitivity. Applications include biomagnetic measurements for medical studies, gravity wave experiments, geomagnetism and ocean bottom magnetic exploration, galvanometers and voltmeters, and bolometers and radiometers. Some articles refer to design considerations for cooling systems for the sensors and detectors, and fabrication techniques for SQUIDS (superconducting quantum interference devices.) (Contains 250 citations and includes a subject term index and title list.)

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

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.

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.

Adiabatic quantum computation along quasienergies

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

Tanaka, Atushi; Nemoto, Kae; National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda ku, Tokyo 101-8430

2010-02-15

The parametric deformations of quasienergies and eigenvectors of unitary operators are applied to the design of quantum adiabatic algorithms. The conventional, standard adiabatic quantum computation proceeds along eigenenergies of parameter-dependent Hamiltonians. By contrast, discrete adiabatic computation utilizes adiabatic passage along the quasienergies of parameter-dependent unitary operators. For example, such computation can be realized by a concatenation of parameterized quantum circuits, with an adiabatic though inevitably discrete change of the parameter. A design principle of adiabatic passage along quasienergy was recently proposed: Cheon's quasienergy and eigenspace anholonomies on unitary operators is available to realize anholonomic adiabatic algorithms [A. Tanaka and M.more » Miyamoto, Phys. Rev. Lett. 98, 160407 (2007)], which compose a nontrivial family of discrete adiabatic algorithms. It is straightforward to port a standard adiabatic algorithm to an anholonomic adiabatic one, except an introduction of a parameter |v>, which is available to adjust the gaps of the quasienergies to control the running time steps. In Grover's database search problem, the costs to prepare |v> for the qualitatively different (i.e., power or exponential) running time steps are shown to be qualitatively different.« less

Generalized Jaynes-Cummings model as a quantum search algorithm

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

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.

Quantum Computation

NASA Astrophysics Data System (ADS)

Aharonov, Dorit

In the last few years, theoretical study of quantum systems serving as computational devices has achieved tremendous progress. We now have strong theoretical evidence that quantum computers, if built, might be used as a dramatically powerful computational tool, capable of performing tasks which seem intractable for classical computers. This review is about to tell the story of theoretical quantum computation. I l out the developing topic of experimental realizations of the model, and neglected other closely related topics which are quantum information and quantum communication. As a result of narrowing the scope of this paper, I hope it has gained the benefit of being an almost self contained introduction to the exciting field of quantum computation. The review begins with background on theoretical computer science, Turing machines and Boolean circuits. In light of these models, I define quantum computers, and discuss the issue of universal quantum gates. Quantum algorithms, including Shor's factorization algorithm and Grover's algorithm for searching databases, are explained. I will devote much attention to understanding what the origins of the quantum computational power are, and what the limits of this power are. Finally, I describe the recent theoretical results which show that quantum computers maintain their complexity power even in the presence of noise, inaccuracies and finite precision. This question cannot be separated from that of quantum complexity because any realistic model will inevitably be subjected to such inaccuracies. I tried to put all results in their context, asking what the implications to other issues in computer science and physics are. In the end of this review, I make these connections explicit by discussing the possible implications of quantum computation on fundamental physical questions such as the transition from quantum to classical physics.

Dynamic Grover search: applications in recommendation systems and optimization problems

NASA Astrophysics Data System (ADS)

Chakrabarty, Indranil; Khan, Shahzor; Singh, Vanshdeep

2017-06-01

In the recent years, we have seen that Grover search algorithm (Proceedings, 28th annual ACM symposium on the theory of computing, pp. 212-219, 1996) by using quantum parallelism has revolutionized the field of solving huge class of NP problems in comparisons to classical systems. In this work, we explore the idea of extending Grover search algorithm to approximate algorithms. Here we try to analyze the applicability of Grover search to process an unstructured database with a dynamic selection function in contrast to the static selection function used in the original work (Grover in Proceedings, 28th annual ACM symposium on the theory of computing, pp. 212-219, 1996). We show that this alteration facilitates us to extend the application of Grover search to the field of randomized search algorithms. Further, we use the dynamic Grover search algorithm to define the goals for a recommendation system based on which we propose a recommendation algorithm which uses binomial similarity distribution space giving us a quadratic speedup over traditional classical unstructured recommendation systems. Finally, we see how dynamic Grover search can be used to tackle a wide range of optimization problems where we improve complexity over existing optimization algorithms.

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.

Test-state approach to the quantum search problem

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

Sehrawat, Arun; Nguyen, Le Huy; Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117597

2011-05-15

The search for 'a quantum needle in a quantum haystack' is a metaphor for the problem of finding out which one of a permissible set of unitary mappings - the oracles - is implemented by a given black box. Grover's algorithm solves this problem with quadratic speedup as compared with the analogous search for 'a classical needle in a classical haystack'. Since the outcome of Grover's algorithm is probabilistic - it gives the correct answer with high probability, not with certainty - the answer requires verification. For this purpose we introduce specific test states, one for each oracle. These testmore » states can also be used to realize 'a classical search for the quantum needle' which is deterministic - it always gives a definite answer after a finite number of steps - and 3.41 times as fast as the purely classical search. Since the test-state search and Grover's algorithm look for the same quantum needle, the average number of oracle queries of the test-state search is the classical benchmark for Grover's algorithm.« less

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

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

Discriminating Drug-Like Compounds by Partition Trees with Quantum Similarity Indices and Graph Invariants.

PubMed

Julián-Ortiz, Jesus V de; Gozalbes, Rafael; Besalú, Emili

2016-01-01

The search for new drug candidates in databases is of paramount importance in pharmaceutical chemistry. The selection of molecular subsets is greatly optimized and much more promising when potential drug-like molecules are detected a priori. In this work, about one hundred thousand molecules are ranked following a new methodology: a drug/non-drug classifier constructed by a consensual set of classification trees. The classification trees arise from the stochastic generation of training sets, which in turn are used to estimate probability factors of test molecules to be drug-like compounds. Molecules were represented by Topological Quantum Similarity Indices and their Graph Theoretical counterparts. The contribution of the present paper consists of presenting an effective ranking method able to improve the probability of finding drug-like substances by using these types of molecular descriptors.

Implementation of Quantum Private Queries Using Nuclear Magnetic Resonance

NASA Astrophysics Data System (ADS)

Wang, Chuan; Hao, Liang; Zhao, Lian-Jie

2011-08-01

We present a modified protocol for the realization of a quantum private query process on a classical database. Using one-qubit query and CNOT operation, the query process can be realized in a two-mode database. In the query process, the data privacy is preserved as the sender would not reveal any information about the database besides her query information, and the database provider cannot retain any information about the query. We implement the quantum private query protocol in a nuclear magnetic resonance system. The density matrix of the memory registers are constructed.

In silico strategies for the selection of chelating compounds with potential application in metal-promoted neurodegenerative diseases

NASA Astrophysics Data System (ADS)

Rodríguez-Rodríguez, Cristina; Rimola, Albert; Alí-Torres, Jorge; Sodupe, Mariona; González-Duarte, Pilar

2011-01-01

The development of new strategies to find commercial molecules with promising biochemical features is a main target in the field of biomedicine chemistry. In this work we present an in silico-based protocol that allows identifying commercial compounds with suitable metal coordinating and pharmacokinetic properties to act as metal-ion chelators in metal-promoted neurodegenerative diseases (MpND). Selection of the chelating ligands is done by combining quantum chemical calculations with the search of commercial compounds on different databases via virtual screening. Starting from different designed molecular frameworks, which mainly constitute the binding site, the virtual screening on databases facilitates the identification of different commercial molecules that enclose such scaffolds and, by imposing a set of chemical and pharmacokinetic filters, obey some drug-like requirements mandatory to deal with MpND. The quantum mechanical calculations are useful to gauge the chelating properties of the selected candidate molecules by determining the structure of metal complexes and evaluating their stability constants. With the proposed strategy, commercial compounds containing N and S donor atoms in the binding sites and capable to cross the BBB have been identified and their chelating properties analyzed.

Faster search by lackadaisical quantum walk

NASA Astrophysics Data System (ADS)

Wong, Thomas G.

2018-03-01

In the typical model, a discrete-time coined quantum walk searching the 2D grid for a marked vertex achieves a success probability of O(1/log N) in O(√{N log N}) steps, which with amplitude amplification yields an overall runtime of O(√{N} log N). We show that making the quantum walk lackadaisical or lazy by adding a self-loop of weight 4 / N to each vertex speeds up the search, causing the success probability to reach a constant near 1 in O(√{N log N}) steps, thus yielding an O(√{log N}) improvement over the typical, loopless algorithm. This improved runtime matches the best known quantum algorithms for this search problem. Our results are based on numerical simulations since the algorithm is not an instance of the abstract search algorithm.

The ``Missing Compounds'' affair in functionality-driven material discovery

NASA Astrophysics Data System (ADS)

Zunger, Alex

2014-03-01

In the paradigm of ``data-driven discovery,'' underlying one of the leading streams of the Material Genome Initiative (MGI), one attempts to compute high-throughput style as many of the properties of as many of the N (about 10**5- 10**6) compounds listed in databases of previously known compounds. One then inspects the ensuing Big Data, searching for useful trends. The alternative and complimentary paradigm of ``functionality-directed search and optimization'' used here, searches instead for the n much smaller than N configurations and compositions that have the desired value of the target functionality. Examples include the use of genetic and other search methods that optimize the structure or identity of atoms on lattice sites, using atomistic electronic structure (such as first-principles) approaches in search of a given electronic property. This addresses a few of the bottlenecks that have faced the alternative, data-driven/high throughput/Big Data philosophy: (i) When the configuration space is theoretically of infinite size, building a complete data base as in data-driven discovery is impossible, yet searching for the optimum functionality, is still a well-posed problem. (ii) The configuration space that we explore might include artificially grown, kinetically stabilized systems (such as 2D layer stacks; superlattices; colloidal nanostructures; Fullerenes) that are not listed in compound databases (used by data-driven approaches), (iii) a large fraction of chemically plausible compounds have not been experimentally synthesized, so in the data-driven approach these are often skipped. In our approach we search explicitly for such ``Missing Compounds''. It is likely that many interesting material properties will be found in cases (i)-(iii) that elude high throughput searches based on databases encapsulating existing knowledge. I will illustrate (a) Functionality-driven discovery of topological insulators and valley-split quantum-computer semiconductors, as well as (b) Use of ``first principles thermodynamics'' to discern which of the previously ``missing compounds'' should, in fact exist and in which structure. Synthesis efforts by Poeppelmeier group at NU realized 20 never-before-made half-Heusler compounds out of the 20 predicted ones, in our predicted space groups. This type of theory-led experimental search of designed materials with target functionalities may shorten the current process of discovery of interesting functional materials. Supported by DOE ,Office of Science, Energy Frontier Research Center for Inverse Design

Spatial Search by Quantum Walk is Optimal for Almost all Graphs.

PubMed

Chakraborty, Shantanav; Novo, Leonardo; Ambainis, Andris; Omar, Yasser

2016-03-11

The problem of finding a marked node in a graph can be solved by the spatial search algorithm based on continuous-time quantum walks (CTQW). However, this algorithm is known to run in optimal time only for a handful of graphs. In this work, we prove that for Erdös-Renyi random graphs, i.e., graphs of n vertices where each edge exists with probability p, search by CTQW is almost surely optimal as long as p≥log^{3/2}(n)/n. Consequently, we show that quantum spatial search is in fact optimal for almost all graphs, meaning that the fraction of graphs of n vertices for which this optimality holds tends to one in the asymptotic limit. We obtain this result by proving that search is optimal on graphs where the ratio between the second largest and the largest eigenvalue is bounded by a constant smaller than 1. Finally, we show that we can extend our results on search to establish high fidelity quantum communication between two arbitrary nodes of a random network of interacting qubits, namely, to perform quantum state transfer, as well as entanglement generation. Our work shows that quantum information tasks typically designed for structured systems retain performance in very disordered structures.

Literature searches on Ayurveda: An update.

PubMed

Aggithaya, Madhur G; Narahari, Saravu R

2015-01-01

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. To update on Ayurveda literature search and strategy to retrieve maximum publications. 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. 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. AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches.

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

Solving search problems by strongly simulating quantum circuits

PubMed Central

Johnson, T. H.; Biamonte, J. D.; Clark, S. R.; Jaksch, D.

2013-01-01

Simulating quantum circuits using classical computers lets us analyse the inner workings of quantum algorithms. The most complete type of simulation, strong simulation, is believed to be generally inefficient. Nevertheless, several efficient strong simulation techniques are known for restricted families of quantum circuits and we develop an additional technique in this article. Further, we show that strong simulation algorithms perform another fundamental task: solving search problems. Efficient strong simulation techniques allow solutions to a class of search problems to be counted and found efficiently. This enhances the utility of strong simulation methods, known or yet to be discovered, and extends the class of search problems known to be efficiently simulable. Relating strong simulation to search problems also bounds the computational power of efficiently strongly simulable circuits; if they could solve all problems in P this would imply that all problems in NP and #P could be solved in polynomial time. PMID:23390585

Limits on efficient computation in the physical world

NASA Astrophysics Data System (ADS)

Aaronson, Scott Joel

More than a speculative technology, quantum computing seems to challenge our most basic intuitions about how the physical world should behave. In this thesis I show that, while some intuitions from classical computer science must be jettisoned in the light of modern physics, many others emerge nearly unscathed; and I use powerful tools from computational complexity theory to help determine which are which. In the first part of the thesis, I attack the common belief that quantum computing resembles classical exponential parallelism, by showing that quantum computers would face serious limitations on a wider range of problems than was previously known. In particular, any quantum algorithm that solves the collision problem---that of deciding whether a sequence of n integers is one-to-one or two-to-one---must query the sequence O (n1/5) times. This resolves a question that was open for years; previously no lower bound better than constant was known. A corollary is that there is no "black-box" quantum algorithm to break cryptographic hash functions or solve the Graph Isomorphism problem in polynomial time. I also show that relative to an oracle, quantum computers could not solve NP-complete problems in polynomial time, even with the help of nonuniform "quantum advice states"; and that any quantum algorithm needs O (2n/4/n) queries to find a local minimum of a black-box function on the n-dimensional hypercube. Surprisingly, the latter result also leads to new classical lower bounds for the local search problem. Finally, I give new lower bounds on quantum one-way communication complexity, and on the quantum query complexity of total Boolean functions and recursive Fourier sampling. The second part of the thesis studies the relationship of the quantum computing model to physical reality. I first examine the arguments of Leonid Levin, Stephen Wolfram, and others who believe quantum computing to be fundamentally impossible. I find their arguments unconvincing without a "Sure/Shor separator"---a criterion that separates the already-verified quantum states from those that appear in Shor's factoring algorithm. I argue that such a separator should be based on a complexity classification of quantum states, and go on to create such a classification. Next I ask what happens to the quantum computing model if we take into account that the speed of light is finite---and in particular, whether Grover's algorithm still yields a quadratic speedup for searching a database. Refuting a claim by Benioff, I show that the surprising answer is yes. Finally, I analyze hypothetical models of computation that go even beyond quantum computing. I show that many such models would be as powerful as the complexity class PP, and use this fact to give a simple, quantum computing based proof that PP is closed under intersection. On the other hand, I also present one model---wherein we could sample the entire history of a hidden variable---that appears to be more powerful than standard quantum computing, but only slightly so.

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

Solution to the satisfiability problem using a complete Grover search with trapped ions

NASA Astrophysics Data System (ADS)

Yang, Wan-Li; Wei, Hua; Zhou, Fei; Chang, Weng-Long; Feng, Mang

2009-07-01

The main idea in the original Grover search (1997 Phys. Rev. Lett. 79 325) is to single out a target state containing the solution to a search problem by amplifying the amplitude of the state, following the Oracle's job, i.e., a black box giving us information about the target state. We design quantum circuits to accomplish a complete Grover search involving both the Oracle's job and the amplification of the target state, which are employed to solve satisfiability (SAT) problems. We explore how to carry out the quantum circuits with currently available ion-trap quantum computing technology.

Comet: an open-source MS/MS sequence database search tool.

PubMed

Eng, Jimmy K; Jahan, Tahmina A; Hoopmann, Michael R

2013-01-01

Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

An approach in building a chemical compound search engine in oracle database.

PubMed

Wang, H; Volarath, P; Harrison, R

2005-01-01

A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

Dissipative environment may improve the quantum annealing performances of the ferromagnetic p -spin model

NASA Astrophysics Data System (ADS)

Passarelli, G.; De Filippis, G.; Cataudella, V.; Lucignano, P.

2018-02-01

We investigate the quantum annealing of the ferromagnetic p -spin model in a dissipative environment (p =5 and p =7 ). This model, in the large-p limit, codifies Grover's algorithm for searching in an unsorted database [L. K. Grover, Proceedings of the 28th Annual ACM Symposium on Theory of Computing (ACM, New York, 1996), pp. 212-219]. The dissipative environment is described by a phonon bath in thermal equilibrium at finite temperature. The dynamics is studied in the framework of a Lindblad master equation for the reduced density matrix describing only the spins. Exploiting the symmetries of our model Hamiltonian, we can describe many spins and extrapolate expected trends for large N and p . While at weak system-bath coupling the dissipative environment has detrimental effects on the annealing results, we show that in the intermediate-coupling regime, the phonon bath seems to speed up the annealing at low temperatures. This improvement in the performance is likely not due to thermal fluctuation but rather arises from a correlated spin-bath state and persists even at zero temperature. This result may pave the way to a new scenario in which, by appropriately engineering the system-bath coupling, one may optimize quantum annealing performances below either the purely quantum or the classical limit.

The Impact of Online Bibliographic Databases on Teaching and Research in Political Science.

ERIC Educational Resources Information Center

Reichel, Mary

The availability of online bibliographic databases greatly facilitates literature searching in political science. The advantages to searching databases online include combination of concepts, comprehensiveness, multiple database searching, free-text searching, currency, current awareness services, document delivery service, and convenience.…

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 carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches. PMID:27313409

A Quantum Private Query Protocol for Enhancing both User and Database Privacy

NASA Astrophysics Data System (ADS)

Zhou, Yi-Hua; Bai, Xue-Wei; Li, Lei-Lei; Shi, Wei-Min; Yang, Yu-Guang

2018-01-01

In order to protect the privacy of query user and database, some QKD-based quantum private query (QPQ) protocols were proposed. Unfortunately some of them cannot resist internal attack from database perfectly; some others can ensure better user privacy but require a reduction of database privacy. In this paper, a novel two-way QPQ protocol is proposed to ensure the privacy of both sides of communication. In our protocol, user makes initial quantum states and derives the key bit by comparing initial quantum state and outcome state returned from database by ctrl or shift mode instead of announcing two non-orthogonal qubits as others which may leak part secret information. In this way, not only the privacy of database be ensured but also user privacy is strengthened. Furthermore, our protocol can also realize the security of loss-tolerance, cheat-sensitive, and resisting JM attack etc. Supported by National Natural Science Foundation of China under Grant Nos. U1636106, 61572053, 61472048, 61602019, 61502016; Beijing Natural Science Foundation under Grant Nos. 4152038, 4162005; Basic Research Fund of Beijing University of Technology (No. X4007999201501); The Scientific Research Common Program of Beijing Municipal Commission of Education under Grant No. KM201510005016

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…

Analysis of human serum phosphopeptidome by a focused database searching strategy.

PubMed

Zhu, Jun; Wang, Fangjun; Cheng, Kai; Song, Chunxia; Qin, Hongqiang; Hu, Lianghai; Figeys, Daniel; Ye, Mingliang; Zou, Hanfa

2013-01-14

As human serum is an important source for early diagnosis of many serious diseases, analysis of serum proteome and peptidome has been extensively performed. However, the serum phosphopeptidome was less explored probably because the effective method for database searching is lacking. Conventional database searching strategy always uses the whole proteome database, which is very time-consuming for phosphopeptidome search due to the huge searching space resulted from the high redundancy of the database and the setting of dynamic modifications during searching. In this work, a focused database searching strategy using an in-house collected human serum pro-peptidome target/decoy database (HuSPep) was established. It was found that the searching time was significantly decreased without compromising the identification sensitivity. By combining size-selective Ti (IV)-MCM-41 enrichment, RP-RP off-line separation, and complementary CID and ETD fragmentation with the new searching strategy, 143 unique endogenous phosphopeptides and 133 phosphorylation sites (109 novel sites) were identified from human serum with high reliability. Copyright © 2012 Elsevier B.V. All rights reserved.

Comment on "flexible protocol for quantum private query based on B92 protocol"

NASA Astrophysics Data System (ADS)

Chang, Yan; Zhang, Shi-Bin; Zhu, Jing-Min

2017-03-01

In a recent paper (Quantum Inf Process 13:805-813, 2014), a flexible quantum private query (QPQ) protocol based on B92 protocol is presented. Here we point out that the B92-based QPQ protocol is insecure in database security when the channel has loss, that is, the user (Alice) will know more records in Bob's database compared with she has bought.

Experimental quantum private queries with linear optics

NASA Astrophysics Data System (ADS)

de Martini, Francesco; Giovannetti, Vittorio; Lloyd, Seth; Maccone, Lorenzo; Nagali, Eleonora; Sansoni, Linda; Sciarrino, Fabio

2009-07-01

The quantum private query is a quantum cryptographic protocol to recover information from a database, preserving both user and data privacy: the user can test whether someone has retained information on which query was asked and the database provider can test the amount of information released. Here we discuss a variant of the quantum private query algorithm that admits a simple linear optical implementation: it employs the photon’s momentum (or time slot) as address qubits and its polarization as bus qubit. A proof-of-principle experimental realization is implemented.

Finding paths in tree graphs with a quantum walk

NASA Astrophysics Data System (ADS)

Koch, Daniel; Hillery, Mark

2018-01-01

We analyze the potential for different types of searches using the formalism of scattering random walks on quantum computers. Given a particular type of graph consisting of nodes and connections, a "tree maze," we would like to find a selected final node as quickly as possible, faster than any classical search algorithm. We show that this can be done using a quantum random walk, both through numerical calculations as well as by using the eigenvectors and eigenvalues of the quantum system.

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification.

PubMed

Li, Honglan; Joh, Yoon Sung; Kim, Hyunwoo; Paek, Eunok; Lee, Sang-Won; Hwang, Kyu-Baek

2016-12-22

Proteogenomics is a promising approach for various tasks ranging from gene annotation to cancer research. Databases for proteogenomic searches are often constructed by adding peptide sequences inferred from genomic or transcriptomic evidence to reference protein sequences. Such inflation of databases has potential of identifying novel peptides. However, it also raises concerns on sensitive and reliable peptide identification. Spurious peptides included in target databases may result in underestimated false discovery rate (FDR). On the other hand, inflation of decoy databases could decrease the sensitivity of peptide identification due to the increased number of high-scoring random hits. Although several studies have addressed these issues, widely applicable guidelines for sensitive and reliable proteogenomic search have hardly been available. To systematically evaluate the effect of database inflation in proteogenomic searches, we constructed a variety of real and simulated proteogenomic databases for yeast and human tandem mass spectrometry (MS/MS) data, respectively. Against these databases, we tested two popular database search tools with various approaches to search result validation: the target-decoy search strategy (with and without a refined scoring-metric) and a mixture model-based method. The effect of separate filtering of known and novel peptides was also examined. The results from real and simulated proteogenomic searches confirmed that separate filtering increases the sensitivity and reliability in proteogenomic search. However, no one method consistently identified the largest (or the smallest) number of novel peptides from real proteogenomic searches. We propose to use a set of search result validation methods with separate filtering, for sensitive and reliable identification of peptides in proteogenomic search.

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.

Quantum search algorithms on a regular lattice

NASA Astrophysics Data System (ADS)

Hein, Birgit; Tanner, Gregor

2010-07-01

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.

Efficient Online Optimized Quantum Control for Adiabatic Quantum Computation

NASA Astrophysics Data System (ADS)

Quiroz, Gregory

Adiabatic quantum computation (AQC) relies on controlled adiabatic evolution to implement a quantum algorithm. While control evolution can take many forms, properly designed time-optimal control has been shown to be particularly advantageous for AQC. Grover's search algorithm is one such example where analytically-derived time-optimal control leads to improved scaling of the minimum energy gap between the ground state and first excited state and thus, the well-known quadratic quantum speedup. Analytical extensions beyond Grover's search algorithm present a daunting task that requires potentially intractable calculations of energy gaps and a significant degree of model certainty. Here, an in situ quantum control protocol is developed for AQC. The approach is shown to yield controls that approach the analytically-derived time-optimal controls for Grover's search algorithm. In addition, the protocol's convergence rate as a function of iteration number is shown to be essentially independent of system size. Thus, the approach is potentially scalable to many-qubit systems.

EasyKSORD: A Platform of Keyword Search Over Relational Databases

NASA Astrophysics Data System (ADS)

Peng, Zhaohui; Li, Jing; Wang, Shan

Keyword Search Over Relational Databases (KSORD) enables casual users to use keyword queries (a set of keywords) to search relational databases just like searching the Web, without any knowledge of the database schema or any need of writing SQL queries. Based on our previous work, we design and implement a novel KSORD platform named EasyKSORD for users and system administrators to use and manage different KSORD systems in a novel and simple manner. EasyKSORD supports advanced queries, efficient data-graph-based search engines, multiform result presentations, and system logging and analysis. Through EasyKSORD, users can search relational databases easily and read search results conveniently, and system administrators can easily monitor and analyze the operations of KSORD and manage KSORD systems much better.

Using SQL Databases for Sequence Similarity Searching and Analysis.

PubMed

Pearson, William R; Mackey, Aaron J

2017-09-13

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

Quantum Associative Neural Network with Nonlinear Search Algorithm

NASA Astrophysics Data System (ADS)

Zhou, Rigui; Wang, Huian; Wu, Qian; Shi, Yang

2012-03-01

Based on analysis on properties of quantum linear superposition, to overcome the complexity of existing quantum associative memory which was proposed by Ventura, a new storage method for multiply patterns is proposed in this paper by constructing the quantum array with the binary decision diagrams. Also, the adoption of the nonlinear search algorithm increases the pattern recalling speed of this model which has multiply patterns to O( {log2}^{2^{n -t}} ) = O( n - t ) time complexity, where n is the number of quantum bit and t is the quantum information of the t quantum bit. Results of case analysis show that the associative neural network model proposed in this paper based on quantum learning is much better and optimized than other researchers' counterparts both in terms of avoiding the additional qubits or extraordinary initial operators, storing pattern and improving the recalling speed.

Faster quantum walk search on a weighted graph

NASA Astrophysics Data System (ADS)

Wong, Thomas G.

2015-09-01

A randomly walking quantum particle evolving by Schrödinger's equation searches for a unique marked vertex on the "simplex of complete graphs" in time Θ (N3 /4) . We give a weighted version of this graph that preserves vertex transitivity, and we show that the time to search on it can be reduced to nearly Θ (√{N }) . To prove this, we introduce two extensions to degenerate perturbation theory: an adjustment that distinguishes the weights of the edges and a method to determine how precisely the jumping rate of the quantum walk must be chosen.

Practical quantum private query with better performance in resisting joint-measurement attack

NASA Astrophysics Data System (ADS)

Wei, Chun-Yan; Wang, Tian-Yin; Gao, Fei

2016-04-01

As a kind of practical protocol, quantum-key-distribution (QKD)-based quantum private queries (QPQs) have drawn lots of attention. However, joint-measurement (JM) attack poses a noticeable threat to the database security in such protocols. That is, by JM attack a malicious user can illegally elicit many more items from the database than the average amount an honest one can obtain. Taking Jacobi et al.'s protocol as an example, by JM attack a malicious user can obtain as many as 500 bits, instead of the expected 2.44 bits, from a 104-bit database in one query. It is a noticeable security flaw in theory, and would also arise in application with the development of quantum memories. To solve this problem, we propose a QPQ protocol based on a two-way QKD scheme, which behaves much better in resisting JM attack. Concretely, the user Alice cannot get more database items by conducting JM attack on the qubits because she has to send them back to Bob (the database holder) before knowing which of them should be jointly measured. Furthermore, JM attack by both Alice and Bob would be detected with certain probability, which is quite different from previous protocols. Moreover, our protocol retains the good characters of QKD-based QPQs, e.g., it is loss tolerant and robust against quantum memory attack.

Native Health Research Database

MedlinePlus

... Indian Health Board) Welcome to the Native Health Database. Please enter your search terms. Basic Search Advanced ... To learn more about searching the Native Health Database, click here. Tutorial Video The NHD has made ...

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.

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;…

Quantum Computer Science

NASA Astrophysics Data System (ADS)

Mermin, N. David

2007-08-01

Preface; 1. Cbits and Qbits; 2. General features and some simple examples; 3. Breaking RSA encryption with a quantum computer; 4. Searching with a quantum computer; 5. Quantum error correction; 6. Protocols that use just a few Qbits; Appendices; Index.

HOWDY: an integrated database system for human genome research

PubMed Central

Hirakawa, Mika

2002-01-01

HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. HOWDY consists of an Internet accessible user interface that allows thorough searching of the human genomic databases using the gene symbols and their aliases. It also permits flexible editing of the sequence data. The database can be searched using simple words and the search can be restricted to a specific cytogenetic location. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query. HOWDY provides a convenient search environment of human genomic data for scientists unsure which database is most appropriate for their search. PMID:11752279

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.

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.

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.

What is lost when searching only one literature database for articles relevant to injury prevention and safety promotion?

PubMed

Lawrence, D W

2008-12-01

To assess what is lost if only one literature database is searched for articles relevant to injury prevention and safety promotion (IPSP) topics. Serial textword (keyword, free-text) searches using multiple synonym terms for five key IPSP topics (bicycle-related brain injuries, ethanol-impaired driving, house fires, road rage, and suicidal behaviors among adolescents) were conducted in four of the bibliographic databases that are most used by IPSP professionals: EMBASE, MEDLINE, PsycINFO, and Web of Science. Through a systematic procedure, an inventory of articles on each topic in each database was conducted to identify the total unduplicated count of all articles on each topic, the number of articles unique to each database, and the articles available if only one database is searched. No single database included all of the relevant articles on any topic, and the database with the broadest coverage differed by topic. A search of only one literature database will return 16.7-81.5% (median 43.4%) of the available articles on any of five key IPSP topics. Each database contributed unique articles to the total bibliography for each topic. A literature search performed in only one database will, on average, lead to a loss of more than half of the available literature on a topic.

Quantum Search and Beyond

DTIC Science & Technology

2008-07-02

an N-atom system. II. Calculation of the eigenstates Terry Rudolph, Itay Yavin and Helen Freedhoff, quant-ph/0206067 Phys. Rev. A. 69, 013815 (2004...Calculation of the eigenstates Terry Rudolph, Itay Yavin and Helen Freedhoff, quant-ph/0206067 Phys. Rev. A. 69, 013815 (2004). 13. Quantum searching a

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.

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…

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

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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.

Content based information retrieval in forensic image databases.

PubMed

Geradts, Zeno; Bijhold, Jurrien

2002-03-01

This paper gives an overview of the various available image databases and ways of searching these databases on image contents. The developments in research groups of searching in image databases is evaluated and compared with the forensic databases that exist. Forensic image databases of fingerprints, faces, shoeprints, handwriting, cartridge cases, drugs tablets, and tool marks are described. The developments in these fields appear to be valuable for forensic databases, especially that of the framework in MPEG-7, where the searching in image databases is standardized. In the future, the combination of the databases (also DNA-databases) and possibilities to combine these can result in stronger forensic evidence.

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

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

Jakobi, Markus; Humboldt-Universitaet zu Berlin, D-10117 Berlin; Simon, Christoph

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 inmore » 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.« less

Optimal Quantum Spatial Search on Random Temporal Networks

NASA Astrophysics Data System (ADS)

Chakraborty, Shantanav; Novo, Leonardo; Di Giorgio, Serena; Omar, Yasser

2017-12-01

To investigate the performance of quantum information tasks on networks whose topology changes in time, we study the spatial search algorithm by continuous time quantum walk to find a marked node on a random temporal network. We consider a network of n nodes constituted by a time-ordered sequence of Erdös-Rényi random graphs G (n ,p ), where p is the probability that any two given nodes are connected: After every time interval τ , a new graph G (n ,p ) replaces the previous one. We prove analytically that, for any given p , there is always a range of values of τ for which the running time of the algorithm is optimal, i.e., O (√{n }), even when search on the individual static graphs constituting the temporal network is suboptimal. On the other hand, there are regimes of τ where the algorithm is suboptimal even when each of the underlying static graphs are sufficiently connected to perform optimal search on them. From this first study of quantum spatial search on a time-dependent network, it emerges that the nontrivial interplay between temporality and connectivity is key to the algorithmic performance. Moreover, our work can be extended to establish high-fidelity qubit transfer between any two nodes of the network. Overall, our findings show that one can exploit temporality to achieve optimal quantum information tasks on dynamical random networks.

Towards communication-efficient quantum oblivious key distribution

NASA Astrophysics Data System (ADS)

Panduranga Rao, M. V.; Jakobi, M.

2013-01-01

Symmetrically private information retrieval, a fundamental problem in the field of secure multiparty computation, is defined as follows: A database D of N bits held by Bob is queried by a user Alice who is interested in the bit Db in such a way that (1) Alice learns Db and only Db and (2) Bob does not learn anything about Alice's choice b. While solutions to this problem in the classical domain rely largely on unproven computational complexity theoretic assumptions, it is also known that perfect solutions that guarantee both database and user privacy are impossible in the quantum domain. Jakobi [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.83.022301 83, 022301 (2011)] proposed a protocol for oblivious transfer using well-known quantum key device (QKD) techniques to establish an oblivious key to solve this problem. Their solution provided a good degree of database and user privacy (using physical principles like the impossibility of perfectly distinguishing nonorthogonal quantum states and the impossibility of superluminal communication) while being loss-resistant and implementable with commercial QKD devices (due to the use of the Scarani-Acin-Ribordy-Gisin 2004 protocol). However, their quantum oblivious key distribution (QOKD) protocol requires a communication complexity of O(NlogN). Since modern databases can be extremely large, it is important to reduce this communication as much as possible. In this paper, we first suggest a modification of their protocol wherein the number of qubits that need to be exchanged is reduced to O(N). A subsequent generalization reduces the quantum communication complexity even further in such a way that only a few hundred qubits are needed to be transferred even for very large databases.

Searching for religion and mental health studies required health, social science, and grey literature databases.

PubMed

Wright, Judy M; Cottrell, David J; Mir, Ghazala

2014-07-01

To determine the optimal databases to search for studies of faith-sensitive interventions for treating depression. We examined 23 health, social science, religious, and grey literature databases searched for an evidence synthesis. Databases were prioritized by yield of (1) search results, (2) potentially relevant references identified during screening, (3) included references contained in the synthesis, and (4) included references that were available in the database. We assessed the impact of databases beyond MEDLINE, EMBASE, and PsycINFO by their ability to supply studies identifying new themes and issues. We identified pragmatic workload factors that influence database selection. PsycINFO was the best performing database within all priority lists. ArabPsyNet, CINAHL, Dissertations and Theses, EMBASE, Global Health, Health Management Information Consortium, MEDLINE, PsycINFO, and Sociological Abstracts were essential for our searches to retrieve the included references. Citation tracking activities and the personal library of one of the research teams made significant contributions of unique, relevant references. Religion studies databases (Am Theo Lib Assoc, FRANCIS) did not provide unique, relevant references. Literature searches for reviews and evidence syntheses of religion and health studies should include social science, grey literature, non-Western databases, personal libraries, and citation tracking activities. Copyright © 2014 Elsevier Inc. All rights reserved.

Single-hidden-layer feed-forward quantum neural network based on Grover learning.

PubMed

Liu, Cheng-Yi; Chen, Chein; Chang, Ching-Ter; Shih, Lun-Min

2013-09-01

In this paper, a novel single-hidden-layer feed-forward quantum neural network model is proposed based on some concepts and principles in the quantum theory. By combining the quantum mechanism with the feed-forward neural network, we defined quantum hidden neurons and connected quantum weights, and used them as the fundamental information processing unit in a single-hidden-layer feed-forward neural network. The quantum neurons make a wide range of nonlinear functions serve as the activation functions in the hidden layer of the network, and the Grover searching algorithm outstands the optimal parameter setting iteratively and thus makes very efficient neural network learning possible. The quantum neuron and weights, along with a Grover searching algorithm based learning, result in a novel and efficient neural network characteristic of reduced network, high efficient training and prospect application in future. Some simulations are taken to investigate the performance of the proposed quantum network and the result show that it can achieve accurate learning. Copyright © 2013 Elsevier Ltd. All rights reserved.

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 shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework. PMID:24325762

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

PubMed

Kiener, Joos

2013-12-11

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. 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. By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

QKD-based quantum private query without a failure probability

NASA Astrophysics Data System (ADS)

Liu, Bin; Gao, Fei; Huang, Wei; Wen, QiaoYan

2015-10-01

In this paper, we present a quantum-key-distribution (QKD)-based quantum private query (QPQ) protocol utilizing single-photon signal of multiple optical pulses. It maintains the advantages of the QKD-based QPQ, i.e., easy to implement and loss tolerant. In addition, different from the situations in the previous QKD-based QPQ protocols, in our protocol, the number of the items an honest user will obtain is always one and the failure probability is always zero. This characteristic not only improves the stability (in the sense that, ignoring the noise and the attack, the protocol would always succeed), but also benefits the privacy of the database (since the database will no more reveal additional secrets to the honest users). Furthermore, for the user's privacy, the proposed protocol is cheat sensitive, and for security of the database, we obtain an upper bound for the leaked information of the database in theory.

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

Lees, R. M.; Xu, Li-Hong; Appadoo, D. R. T.

New astronomical facilities such as HIFI on the Herschel Space Observatory, the SOFIA airborne IR telescope and the ALMA sub-mm telescope array will yield spectra from interstellar and protostellar sources with vastly increased sensitivity and frequency coverage. This creates the need for major enhancements to laboratory databases for the more prominent interstellar 'weed' species in order to model and account for their lines in observed spectra in the search for new and more exotic interstellar molecular 'flowers'. With its large-amplitude internal torsional motion, methanol has particularly rich spectra throughout the FIR and IR regions and, being very widely distributed throughoutmore » the galaxy, is perhaps the most notorious interstellar weed. Thus, we have recorded new spectra for a variety of methanol isotopic species on the high-resolution FTIR spectrometer on the CLS FIR beamline. The aim is to extend quantum number coverage of the data, improve our understanding of the energy level structure, and provide the astronomical community with better databases and models of the spectral patterns with greater predictive power for a range of astrophysical conditions.« less

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

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

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

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

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

Large-scale feature searches of collections of medical imagery

NASA Astrophysics Data System (ADS)

Hedgcock, Marcus W.; Karshat, Walter B.; Levitt, Tod S.; Vosky, D. N.

1993-09-01

Large scale feature searches of accumulated collections of medical imagery are required for multiple purposes, including clinical studies, administrative planning, epidemiology, teaching, quality improvement, and research. To perform a feature search of large collections of medical imagery, one can either search text descriptors of the imagery in the collection (usually the interpretation), or (if the imagery is in digital format) the imagery itself. At our institution, text interpretations of medical imagery are all available in our VA Hospital Information System. These are downloaded daily into an off-line computer. The text descriptors of most medical imagery are usually formatted as free text, and so require a user friendly database search tool to make searches quick and easy for any user to design and execute. We are tailoring such a database search tool (Liveview), developed by one of the authors (Karshat). To further facilitate search construction, we are constructing (from our accumulated interpretation data) a dictionary of medical and radiological terms and synonyms. If the imagery database is digital, the imagery which the search discovers is easily retrieved from the computer archive. We describe our database search user interface, with examples, and compare the efficacy of computer assisted imagery searches from a clinical text database with manual searches. Our initial work on direct feature searches of digital medical imagery is outlined.

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments.

PubMed

Linder, Suzanne K; Kamath, Geetanjali R; Pratt, Gregory F; Saraykar, Smita S; Volk, Robert J

2015-04-01

To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a health care decision-making instrument commonly used in clinical settings. We searched the literature using two methods: (1) keyword searching using variations of "Control Preferences Scale" and (2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, and Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Keyword searches in bibliographic databases yielded high average precision (90%) but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45-54%), but precision ranged from 35% to 75% with Scopus being the most precise. Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time, and resources should dictate the combination of which methods and databases are used. Copyright © 2015 Elsevier Inc. All rights reserved.

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments

PubMed Central

Linder, Suzanne K.; Kamath, Geetanjali R.; Pratt, Gregory F.; Saraykar, Smita S.; Volk, Robert J.

2015-01-01

Objective To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a healthcare decision-making instrument commonly used in clinical settings. Study Design & Setting We searched the literature using two methods: 1) keyword searching using variations of “control preferences scale” and 2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Results Keyword searches in bibliographic databases yielded high average precision (90%), but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45–54%), but precision ranged from 35–75% with Scopus being the most precise. Conclusion Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time and resources should dictate the combination of which methods and databases are used. PMID:25554521

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.

Nontrivial Quantum Effects in Biology: A Skeptical Physicists' View

NASA Astrophysics Data System (ADS)

Wiseman, Howard; Eisert, Jens

The following sections are included: * Introduction * A Quantum Life Principle * A quantum chemistry principle? * The anthropic principle * Quantum Computing in the Brain * Nature did everything first? * Decoherence as the make or break issue * Quantum error correction * Uselessness of quantum algorithms for organisms * Quantum Computing in Genetics * Quantum search * Teleological aspects and the fast-track to life * Quantum Consciousness * Computability and free will * Time scales * Quantum Free Will * Predictability and free will * Determinism and free will * Acknowledgements * References

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…

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

Online Patent Searching: The Realities.

ERIC Educational Resources Information Center

Kaback, Stuart M.

1983-01-01

Considers patent subject searching capabilities of major online databases, noting patent claims, "deep-indexed" files, test searches, retrieval of related references, multi-database searching, improvements needed in indexing of chemical structures, full text searching, improvements needed in handling numerical data, and augmenting a…

Using "Reader's Guide to Periodical Literature" on CD-Rom To Teach Database Searching to High School Students.

ERIC Educational Resources Information Center

Kern, Joanne F.

The lack of opportunity for high school sophomores to learn database searching was addressed by the implementation of a computerized magazine article search program. "Reader's Guide to Periodical Literature" on CD-ROM was used to train students in database searching during the time they were assigned to the library to do research papers…

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

PubMed

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

2010-04-29

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

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.

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

PubMed

Mackey, Aaron J; Pearson, William R

2004-10-01

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

DNA profiles, computer searches, and the Fourth Amendment.

PubMed

Kimel, Catherine W

2013-01-01

Pursuant to federal statutes and to laws in all fifty states, the United States government has assembled a database containing the DNA profiles of over eleven million citizens. Without judicial authorization, the government searches each of these profiles one-hundred thousand times every day, seeking to link database subjects to crimes they are not suspected of committing. Yet, courts and scholars that have addressed DNA databasing have focused their attention almost exclusively on the constitutionality of the government's seizure of the biological samples from which the profiles are generated. This Note fills a gap in the scholarship by examining the Fourth Amendment problems that arise when the government searches its vast DNA database. This Note argues that each attempt to match two DNA profiles constitutes a Fourth Amendment search because each attempted match infringes upon database subjects' expectations of privacy in their biological relationships and physical movements. The Note further argues that database searches are unreasonable as they are currently conducted, and it suggests an adaptation of computer-search procedures to remedy the constitutional deficiency.

Mixing times in quantum walks on two-dimensional grids

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

Marquezino, F. L.; Portugal, R.; Abal, G.

2010-10-15

Mixing properties of discrete-time quantum walks on two-dimensional grids with toruslike boundary conditions are analyzed, focusing on their connection to the complexity of the corresponding abstract search algorithm. In particular, an exact expression for the stationary distribution of the coherent walk over odd-sided lattices is obtained after solving the eigenproblem for the evolution operator for this particular graph. The limiting distribution and mixing time of a quantum walk with a coin operator modified as in the abstract search algorithm are obtained numerically. On the basis of these results, the relation between the mixing time of the modified walk and themore » running time of the corresponding abstract search algorithm is discussed.« less

Mixing times in quantum walks on two-dimensional grids

NASA Astrophysics Data System (ADS)

Marquezino, F. L.; Portugal, R.; Abal, G.

2010-10-01

Mixing properties of discrete-time quantum walks on two-dimensional grids with toruslike boundary conditions are analyzed, focusing on their connection to the complexity of the corresponding abstract search algorithm. In particular, an exact expression for the stationary distribution of the coherent walk over odd-sided lattices is obtained after solving the eigenproblem for the evolution operator for this particular graph. The limiting distribution and mixing time of a quantum walk with a coin operator modified as in the abstract search algorithm are obtained numerically. On the basis of these results, the relation between the mixing time of the modified walk and the running time of the corresponding abstract search algorithm is discussed.

Chapter 51: How to Build a Simple Cone Search Service Using a Local Database

NASA Astrophysics Data System (ADS)

Kent, B. R.; Greene, G. R.

The cone search service protocol will be examined from the server side in this chapter. A simple cone search service will be setup and configured locally using MySQL. Data will be read into a table, and the Java JDBC will be used to connect to the database. Readers will understand the VO cone search specification and how to use it to query a database on their local systems and return an XML/VOTable file based on an input of RA/DEC coordinates and a search radius. The cone search in this example will be deployed as a Java servlet. The resulting cone search can be tested with a verification service. This basic setup can be used with other languages and relational databases.

muBLASTP: database-indexed protein sequence search on multicore CPUs.

PubMed

Zhang, Jing; Misra, Sanchit; Wang, Hao; Feng, Wu-Chun

2016-11-04

The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e.g., MegaBLAST. Due to different challenges and characteristics between query indexing and database indexing, the existing techniques for query-indexed search cannot be used into database indexed search. muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hits returned to NCBI BLAST. On Intel Haswell multicore CPUs, for a single query, the single-threaded muBLASTP achieves up to a 4.41-fold speedup for alignment stages, and up to a 1.75-fold end-to-end speedup over single-threaded NCBI BLAST. For a batch of queries, the multithreaded muBLASTP achieves up to a 5.7-fold speedups for alignment stages, and up to a 4.56-fold end-to-end speedup over multithreaded NCBI BLAST. With a newly designed index structure for protein database and associated optimizations in BLASTP algorithm, we re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory footprint for the database index.

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.

Alternative Databases for Anthropology Searching.

ERIC Educational Resources Information Center

Brody, Fern; Lambert, Maureen

1984-01-01

Examines online search results of sample questions in several databases covering linguistics, cultural anthropology, and physical anthropology in order to determine if and where any overlap in results might occur, and which files have greatest number of relevant hits. Search results by database are given for each subject area. (EJS)

When is a search not a search? A comparison of searching the AMED complementary health database via EBSCOhost, OVID and DIALOG.

PubMed

Younger, Paula; Boddy, Kate

2009-06-01

The researchers involved in this study work at Exeter Health library and at the Complementary Medicine Unit, Peninsula School of Medicine and Dentistry (PCMD). Within this collaborative environment it is possible to access the electronic resources of three institutions. This includes access to AMED and other databases using different interfaces. The aim of this study was to investigate whether searching different interfaces to the AMED allied health and complementary medicine database produced the same results when using identical search terms. The following Internet-based AMED interfaces were searched: DIALOG DataStar; EBSCOhost and OVID SP_UI01.00.02. Search results from all three databases were saved in an endnote database to facilitate analysis. A checklist was also compiled comparing interface features. In our initial search, DIALOG returned 29 hits, OVID 14 and Ebsco 8. If we assume that DIALOG returned 100% of potential hits, OVID initially returned only 48% of hits and EBSCOhost only 28%. In our search, a researcher using the Ebsco interface to carry out a simple search on AMED would miss over 70% of possible search hits. Subsequent EBSCOhost searches on different subjects failed to find between 21 and 86% of the hits retrieved using the same keywords via DIALOG DataStar. In two cases, the simple EBSCOhost search failed to find any of the results found via DIALOG DataStar. Depending on the interface, the number of hits retrieved from the same database with the same simple search can vary dramatically. Some simple searches fail to retrieve a substantial percentage of citations. This may result in an uninformed literature review, research funding application or treatment intervention. In addition to ensuring that keywords, spelling and medical subject headings (MeSH) accurately reflect the nature of the search, database users should include wildcards and truncation and adapt their search strategy substantially to retrieve the maximum number of appropriate citations possible. Librarians should be aware of these differences when making purchasing decisions, carrying out literature searches and planning user education.

VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1993-01-01

One of the biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental data base access method, VIEWCACHE, provides such an interface for accessing distributed datasets 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 datasets, 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 database search.

Basis for a neuronal version of Grover's quantum algorithm

PubMed Central

Clark, Kevin B.

2014-01-01

Grover's quantum (search) algorithm exploits principles of quantum information theory and computation to surpass the strong Church–Turing limit governing classical computers. The algorithm initializes a search field into superposed N (eigen)states to later execute nonclassical “subroutines” involving unitary phase shifts of measured states and to produce root-rate or quadratic gain in the algorithmic time (O(N1/2)) needed to find some “target” solution m. Akin to this fast technological search algorithm, single eukaryotic cells, such as differentiated neurons, perform natural quadratic speed-up in the search for appropriate store-operated Ca2+ response regulation of, among other processes, protein and lipid biosynthesis, cell energetics, stress responses, cell fate and death, synaptic plasticity, and immunoprotection. Such speed-up in cellular decision making results from spatiotemporal dynamics of networked intracellular Ca2+-induced Ca2+ release and the search (or signaling) velocity of Ca2+ wave propagation. As chemical processes, such as the duration of Ca2+ mobilization, become rate-limiting over interstore distances, Ca2+ waves quadratically decrease interstore-travel time from slow saltatory to fast continuous gradients proportional to the square-root of the classical Ca2+ diffusion coefficient, D1/2, matching the computing efficiency of Grover's quantum algorithm. In this Hypothesis and Theory article, I elaborate on these traits using a fire-diffuse-fire model of store-operated cytosolic Ca2+ signaling valid for glutamatergic neurons. Salient model features corresponding to Grover's quantum algorithm are parameterized to meet requirements for the Oracle Hadamard transform and Grover's iteration. A neuronal version of Grover's quantum algorithm figures to benefit signal coincidence detection and integration, bidirectional synaptic plasticity, and other vital cell functions by rapidly selecting, ordering, and/or counting optional response regulation choices. PMID:24860419

Database Searching by Managers.

ERIC Educational Resources Information Center

Arnold, Stephen E.

Managers and executives need the easy and quick access to business and management information that online databases can provide, but many have difficulty articulating their search needs to an intermediary. One possible solution would be to encourage managers and their immediate support staff members to search textual databases directly as they now…

Constructing Effective Search Strategies for Electronic Searching.

ERIC Educational Resources Information Center

Flanagan, Lynn; Parente, Sharon Campbell

Electronic databases have grown tremendously in both number and popularity since their development during the 1960s. Access to electronic databases in academic libraries was originally offered primarily through mediated search services by trained librarians; however, the advent of CD-ROM and end-user interfaces for online databases has shifted the…

Subject searching of monographs online in the medical literature.

PubMed

Brahmi, F A

1988-01-01

Searching by subject for monographic information online in the medical literature is a challenging task. The NLM database of choice is CATLINE. Other NLM databases of interest are BIOTHICSLINE, CANCERLIT, HEALTH, POPLINE, and TOXLINE. Ten BRS databases are also discussed. Of these, Books in Print, Bookinfo, and OCLC are explored further. The databases are compared as to number of total records and number and percentage of monographs. Three topics were searched on CROSS to compare hits on BBIP, BOOK, and OCLC. The same searches were run on CATLINE. The parameters of time coverage and language were equalized and the resulting citations were compared and analyzed for duplication and uniqueness. With the input of CATLINE tapes into OCLC, OCLC has become the database of choice for searching by subject for medical monographs.

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Search Fermilab Plant Database

Science.gov Websites

Select the characteristics of the plant you want to find below and click the Search button. To see Plants to see all the prairie plants in the database. Click Search All Plants at Fermilab to search for reflects observations at Fermilab. If you need a more sophisticated search, try the Advanced Search. Search

Speculation on quantum mechanics and the operation of life giving catalysts.

PubMed

Haydon, Nathan; McGlynn, Shawn E; Robus, Olin

2011-02-01

The origin of life necessitated the formation of catalytic functionalities in order to realize a number of those capable of supporting reactions that led to the proliferation of biologically accessible molecules and the formation of a proto-metabolic network. Here, the discussion of the significance of quantum behavior on biological systems is extended from recent hypotheses exploring brain function and DNA mutation to include origins of life considerations in light of the concept of quantum decoherence and the transition from the quantum to the classical. Current understandings of quantum systems indicate that in the context of catalysis, substrate-catalyst interaction may be considered as a quantum measurement problem. Exploration of catalytic functionality necessary for life's emergence may have been accommodated by quantum searches within metal sulfide compartments, where catalyst and substrate wave function interaction may allow for quantum based searches of catalytic phase space. Considering the degree of entanglement experienced by catalytic and non catalytic outcomes of superimposed states, quantum contributions are postulated to have played an important role in the operation of efficient catalysts that would provide for the kinetic basis for the emergence of life.

Reducing process delays for real-time earthquake parameter estimation - An application of KD tree to large databases for Earthquake Early Warning

NASA Astrophysics Data System (ADS)

Yin, Lucy; Andrews, Jennifer; Heaton, Thomas

2018-05-01

Earthquake parameter estimations using nearest neighbor searching among a large database of observations can lead to reliable prediction results. However, in the real-time application of Earthquake Early Warning (EEW) systems, the accurate prediction using a large database is penalized by a significant delay in the processing time. We propose to use a multidimensional binary search tree (KD tree) data structure to organize large seismic databases to reduce the processing time in nearest neighbor search for predictions. We evaluated the performance of KD tree on the Gutenberg Algorithm, a database-searching algorithm for EEW. We constructed an offline test to predict peak ground motions using a database with feature sets of waveform filter-bank characteristics, and compare the results with the observed seismic parameters. We concluded that large database provides more accurate predictions of the ground motion information, such as peak ground acceleration, velocity, and displacement (PGA, PGV, PGD), than source parameters, such as hypocenter distance. Application of the KD tree search to organize the database reduced the average searching process by 85% time cost of the exhaustive method, allowing the method to be feasible for real-time implementation. The algorithm is straightforward and the results will reduce the overall time of warning delivery for EEW.

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.

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.

Experimental implementation of local adiabatic evolution algorithms by an NMR quantum information processor.

PubMed

Mitra, Avik; Ghosh, Arindam; Das, Ranabir; Patel, Apoorva; Kumar, Anil

2005-12-01

Quantum adiabatic algorithm is a method of solving computational problems by evolving the ground state of a slowly varying Hamiltonian. The technique uses evolution of the ground state of a slowly varying Hamiltonian to reach the required output state. In some cases, such as the adiabatic versions of Grover's search algorithm and Deutsch-Jozsa algorithm, applying the global adiabatic evolution yields a complexity similar to their classical algorithms. However, using the local adiabatic evolution, the algorithms given by J. Roland and N.J. Cerf for Grover's search [J. Roland, N.J. Cerf, Quantum search by local adiabatic evolution, Phys. Rev. A 65 (2002) 042308] and by Saurya Das, Randy Kobes, and Gabor Kunstatter for the Deutsch-Jozsa algorithm [S. Das, R. Kobes, G. Kunstatter, Adiabatic quantum computation and Deutsh's algorithm, Phys. Rev. A 65 (2002) 062301], yield a complexity of order N (where N=2(n) and n is the number of qubits). In this paper, we report the experimental implementation of these local adiabatic evolution algorithms on a 2-qubit quantum information processor, by Nuclear Magnetic Resonance.

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…

In search of the emotional face: anger versus happiness superiority in visual search.

PubMed

Savage, Ruth A; Lipp, Ottmar V; Craig, Belinda M; Becker, Stefanie I; Horstmann, Gernot

2013-08-01

Previous research has provided inconsistent results regarding visual search for emotional faces, yielding evidence for either anger superiority (i.e., more efficient search for angry faces) or happiness superiority effects (i.e., more efficient search for happy faces), suggesting that these results do not reflect on emotional expression, but on emotion (un-)related low-level perceptual features. The present study investigated possible factors mediating anger/happiness superiority effects; specifically search strategy (fixed vs. variable target search; Experiment 1), stimulus choice (Nimstim database vs. Ekman & Friesen database; Experiments 1 and 2), and emotional intensity (Experiment 3 and 3a). Angry faces were found faster than happy faces regardless of search strategy using faces from the Nimstim database (Experiment 1). By contrast, a happiness superiority effect was evident in Experiment 2 when using faces from the Ekman and Friesen database. Experiment 3 employed angry, happy, and exuberant expressions (Nimstim database) and yielded anger and happiness superiority effects, respectively, highlighting the importance of the choice of stimulus materials. Ratings of the stimulus materials collected in Experiment 3a indicate that differences in perceived emotional intensity, pleasantness, or arousal do not account for differences in search efficiency. Across three studies, the current investigation indicates that prior reports of anger or happiness superiority effects in visual search are likely to reflect on low-level visual features associated with the stimulus materials used, rather than on emotion. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Genetic Testing Registry

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Database Search Strategies & Tips. Reprints from the Best of "ONLINE" [and]"DATABASE."

ERIC Educational Resources Information Center

Online, Inc., Weston, CT.

Reprints of 17 articles presenting strategies and tips for searching databases online appear in this collection, which is one in a series of volumes of reprints from "ONLINE" and "DATABASE" magazines. Edited for information professionals who use electronically distributed databases, these articles address such topics as: (1)…

Equivalence of Szegedy's and coined quantum walks

NASA Astrophysics Data System (ADS)

Wong, Thomas G.

2017-09-01

Szegedy's quantum walk is a quantization of a classical random walk or Markov chain, where the walk occurs on the edges of the bipartite double cover of the original graph. To search, one can simply quantize a Markov chain with absorbing vertices. Recently, Santos proposed two alternative search algorithms that instead utilize the sign-flip oracle in Grover's algorithm rather than absorbing vertices. In this paper, we show that these two algorithms are exactly equivalent to two algorithms involving coined quantum walks, which are walks on the vertices of the original graph with an internal degree of freedom. The first scheme is equivalent to a coined quantum walk with one walk step per query of Grover's oracle, and the second is equivalent to a coined quantum walk with two walk steps per query of Grover's oracle. These equivalences lie outside the previously known equivalence of Szegedy's quantum walk with absorbing vertices and the coined quantum walk with the negative identity operator as the coin for marked vertices, whose precise relationships we also investigate.

Assigning statistical significance to proteotypic peptides via database searches

PubMed Central

Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

2011-01-01

Querying MS/MS spectra against a database containing only proteotypic peptides reduces data analysis time due to reduction of database size. Despite the speed advantage, this search strategy is challenged by issues of statistical significance and coverage. The former requires separating systematically significant identifications from less confident identifications, while the latter arises when the underlying peptide is not present, due to single amino acid polymorphisms (SAPs) or post-translational modifications (PTMs), in the proteotypic peptide libraries searched. To address both issues simultaneously, we have extended RAId’s knowledge database to include proteotypic information, utilized RAId’s statistical strategy to assign statistical significance to proteotypic peptides, and modified RAId’s programs to allow for consideration of proteotypic information during database searches. The extended database alleviates the coverage problem since all annotated modifications, even those occurred within proteotypic peptides, may be considered. Taking into account the likelihoods of observation, the statistical strategy of RAId provides accurate E-value assignments regardless whether a candidate peptide is proteotypic or not. The advantage of including proteotypic information is evidenced by its superior retrieval performance when compared to regular database searches. PMID:21055489

National Center for Biotechnology Information

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Information sources for obesity prevention policy research: a review of systematic reviews.

PubMed

Hanneke, Rosie; Young, Sabrina K

2017-08-08

Systematic identification of evidence in health policy can be time-consuming and challenging. This study examines three questions pertaining to systematic reviews on obesity prevention policy, in order to identify the most efficient search methods: (1) What percentage of the primary studies selected for inclusion in the reviews originated in scholarly as opposed to gray literature? (2) How much of the primary scholarly literature in this topic area is indexed in PubMed/MEDLINE? (3) Which databases index the greatest number of primary studies not indexed in PubMed, and are these databases searched consistently across systematic reviews? We identified systematic reviews on obesity prevention policy and explored their search methods and citations. We determined the percentage of scholarly vs. gray literature cited, the most frequently cited journals, and whether each primary study was indexed in PubMed. We searched 21 databases for all primary study articles not indexed in PubMed to determine which database(s) indexed the highest number of these relevant articles. In total, 21 systematic reviews were identified. Ten of the 21 systematic reviews reported searching gray literature, and 12 reviews ultimately included gray literature in their analyses. Scholarly articles accounted for 577 of the 649 total primary study papers. Of these, 495 (76%) were indexed in PubMed. Google Scholar retrieved the highest number of the remaining 82 non-PubMed scholarly articles, followed by Scopus and EconLit. The Journal of the American Dietetic Association was the most-cited journal. Researchers can maximize search efficiency by searching a small yet targeted selection of both scholarly and gray literature resources. A highly sensitive search of PubMed and those databases that index the greatest number of relevant articles not indexed in PubMed, namely multidisciplinary and economics databases, could save considerable time and effort. When combined with a gray literature search and additional search methods, including cited reference searching and consulting with experts, this approach could help maintain broad retrieval of relevant studies while improving search efficiency. Findings also have implications for designing specialized databases for public health research.

Transterm—extended search facilities and improved integration with other databases

PubMed Central

Jacobs, Grant H.; Stockwell, Peter A.; Tate, Warren P.; Brown, Chris M.

2006-01-01

Transterm has now been publicly available for >10 years. Major changes have been made since its last description in this database issue in 2002. The current database provides data for key regions of mRNA sequences, a curated database of mRNA motifs and tools to allow users to investigate their own motifs or mRNA sequences. The key mRNA regions database is derived computationally from Genbank. It contains 3′ and 5′ flanking regions, the initiation and termination signal context and coding sequence for annotated CDS features from Genbank and RefSeq. The database is non-redundant, enabling summary files and statistics to be prepared for each species. Advances include providing extended search facilities, the database may now be searched by BLAST in addition to regular expressions (patterns) allowing users to search for motifs such as known miRNA sequences, and the inclusion of RefSeq data. The database contains >40 motifs or structural patterns important for translational control. In this release, patterns from UTRsite and Rfam are also incorporated with cross-referencing. Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at . PMID:16381889

National Rehabilitation Information Center

MedlinePlus

... search the NARIC website or one of our databases Select a database or search for a webpage A NARIC webpage ... Projects conducting research and/or development (NIDILRR Program Database). Organizations, agencies, and online resources that support people ...

Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)*

PubMed Central

Renard, Bernhard Y.; Xu, Buote; Kirchner, Marc; Zickmann, Franziska; Winter, Dominic; Korten, Simone; Brattig, Norbert W.; Tzur, Amit; Hamprecht, Fred A.; Steen, Hanno

2012-01-01

Currently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. Although sequencing capacities continue to grow, many organisms remain without reliable, fully annotated reference genomes required for proteomic analyses. Standard database search algorithms fail to identify peptides that are not exactly contained in a protein database. De novo searches are generally hindered by their restricted reliability, and current error-tolerant search strategies are limited by global, heuristic tradeoffs between database and spectral information. We propose a Bayesian information criterion-driven error-tolerant peptide search (BICEPS) and offer an open source implementation based on this statistical criterion to automatically balance the information of each single spectrum and the database, while limiting the run time. We show that BICEPS performs as well as current database search algorithms when such algorithms are applied to sequenced organisms, whereas BICEPS only uses a remotely related organism database. For instance, we use a chicken instead of a human database corresponding to an evolutionary distance of more than 300 million years (International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716). We demonstrate the successful application to cross-species proteomics with a 33% increase in the number of identified proteins for a filarial nematode sample of Litomosoides sigmodontis. PMID:22493179

LigandBox: A database for 3D structures of chemical compounds

PubMed Central

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

LigandBox: A database for 3D structures of chemical compounds.

PubMed

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

The MAO NASU Plate Archive Database. Current Status and Perspectives

NASA Astrophysics Data System (ADS)

Pakuliak, L. K.; Sergeeva, T. P.

2006-04-01

The preliminary online version of the database of the MAO NASU plate archive is constructed on the basis of the relational database management system MySQL and permits an easy supplement of database with new collections of astronegatives, provides a high flexibility in constructing SQL-queries for data search optimization, PHP Basic Authorization protected access to administrative interface and wide range of search parameters. The current status of the database will be reported and the brief description of the search engine and means of the database integrity support will be given. Methods and means of the data verification and tasks for the further development will be discussed.

Adaptation of Decoy Fusion Strategy for Existing Multi-Stage Search Workflows

NASA Astrophysics Data System (ADS)

Ivanov, Mark V.; Levitsky, Lev I.; Gorshkov, Mikhail V.

2016-09-01

A number of proteomic database search engines implement multi-stage strategies aiming at increasing the sensitivity of proteome analysis. These approaches often employ a subset of the original database for the secondary stage of analysis. However, if target-decoy approach (TDA) is used for false discovery rate (FDR) estimation, the multi-stage strategies may violate the underlying assumption of TDA that false matches are distributed uniformly across the target and decoy databases. This violation occurs if the numbers of target and decoy proteins selected for the second search are not equal. Here, we propose a method of decoy database generation based on the previously reported decoy fusion strategy. This method allows unbiased TDA-based FDR estimation in multi-stage searches and can be easily integrated into existing workflows utilizing popular search engines and post-search algorithms.

Searching for evidence or approval? A commentary on database search in systematic reviews and alternative information retrieval methodologies.

PubMed

Delaney, Aogán; Tamás, Peter A

2018-03-01

Despite recognition that database search alone is inadequate even within the health sciences, it appears that reviewers in fields that have adopted systematic review are choosing to rely primarily, or only, on database search for information retrieval. This commentary reminds readers of factors that call into question the appropriateness of default reliance on database searches particularly as systematic review is adapted for use in new and lower consensus fields. It then discusses alternative methods for information retrieval that require development, formalisation, and evaluation. Our goals are to encourage reviewers to reflect critically and transparently on their choice of information retrieval methods and to encourage investment in research on alternatives. Copyright © 2017 John Wiley & Sons, Ltd.

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.

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.

MICA: desktop software for comprehensive searching of DNA databases

PubMed Central

Stokes, William A; Glick, Benjamin S

2006-01-01

Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software. PMID:17018144

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

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.

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

Searching for controlled trials of complementary and alternative medicine: a comparison of 15 databases.

PubMed

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.

End User Information Searching on the Internet: How Do Users Search and What Do They Search For? (SIG USE)

ERIC Educational Resources Information Center

Saracevic, Tefko

2000-01-01

Summarizes a presentation that discussed findings and implications of research projects using an Internet search service and Internet-accessible vendor databases, representing the two sides of public database searching: query formulation and resource utilization. Presenters included: Tefko Saracevic, Amanda Spink, Dietmar Wolfram and Hong Xie.…

Assessment of Metabolome Annotation Quality: A Method for Evaluating the False Discovery Rate of Elemental Composition Searches

PubMed Central

Matsuda, Fumio; Shinbo, Yoko; Oikawa, Akira; Hirai, Masami Yokota; Fiehn, Oliver; Kanaya, Shigehiko; Saito, Kazuki

2009-01-01

Background In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits derived from errors in mass analyses will be included in the results of elemental composition searches. To assess the quality of peak annotation information, a novel methodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databases most reliable for searching are discussed. Methodology/Principal Findings The FDR can be determined from one measured value (i.e., the hit rate for search queries) and four parameters determined by Monte Carlo simulation. The results indicate that relatively high FDR values (30–50%) were obtained when searching time-of-flight (TOF)/MS data using the KNApSAcK and KEGG databases. In addition, searches against large all-in-one databases (e.g., PubChem) always produced unacceptable results (FDR >70%). The estimated FDRs suggest that the quality of search results can be improved not only by performing more accurate mass analysis but also by modifying the properties of the compound database. A theoretical analysis indicates that FDR could be improved by using compound database with smaller but higher completeness entries. Conclusions/Significance High accuracy mass analysis, such as Fourier transform (FT)-MS, is needed for reliable annotation (FDR <10%). In addition, a small, customized compound database is preferable for high-quality annotation of metabolome data. PMID:19847304

NREL: Renewable Resource Data Center - Biomass Resource Publications

Science.gov Websites

Marginal Lands in APEC Economies NREL Publications Database For a comprehensive list of other NREL biomass resource publications, explore NREL's Publications Database. When searching the database, search on "

An assessment of the efficacy of searching in biomedical databases beyond MEDLINE in identifying studies for a systematic review on ward closures as an infection control intervention to control outbreaks.

PubMed

Kwon, Yoojin; Powelson, Susan E; Wong, Holly; Ghali, William A; Conly, John M

2014-11-11

The purpose of our study is to determine the value and efficacy of searching biomedical databases beyond MEDLINE for systematic reviews. We analyzed the results from a systematic review conducted by the authors and others on ward closure as an infection control practice. Ovid MEDLINE including In-Process & Other Non-Indexed Citations, Ovid Embase, CINAHL Plus, LILACS, and IndMED were systematically searched for articles of any study type discussing ward closure, as were bibliographies of selected articles and recent infection control conference abstracts. Search results were tracked, recorded, and analyzed using a relative recall method. The sensitivity of searching in each database was calculated. Two thousand ninety-five unique citations were identified and screened for inclusion in the systematic review: 2,060 from database searching and 35 from hand searching and other sources. Ninety-seven citations were included in the final review. MEDLINE and Embase searches each retrieved 80 of the 97 articles included, only 4 articles from each database were unique. The CINAHL search retrieved 35 included articles, and 4 were unique. The IndMED and LILACS searches did not retrieve any included articles, although 75 of the included articles were indexed in LILACS. The true value of using regional databases, particularly LILACS, may lie with the ability to search in the language spoken in the region. Eight articles were found only through hand searching. Identifying studies for a systematic review where the research is observational is complex. The value each individual study contributes to the review cannot be accurately measured. Consequently, we could not determine the value of results found from searching beyond MEDLINE, Embase, and CINAHL with accuracy. However, hand searching for serendipitous retrieval remains an important aspect due to indexing and keyword challenges inherent in this literature.

Should we search Chinese biomedical databases when performing systematic reviews?

PubMed

Cohen, Jérémie F; Korevaar, Daniël A; Wang, Junfeng; Spijker, René; Bossuyt, Patrick M

2015-03-06

Chinese biomedical databases contain a large number of publications available to systematic reviewers, but it is unclear whether they are used for synthesizing the available evidence. We report a case of two systematic reviews on the accuracy of anti-cyclic citrullinated peptide for diagnosing rheumatoid arthritis. In one of these, the authors did not search Chinese databases; in the other, they did. We additionally assessed the extent to which Cochrane reviewers have searched Chinese databases in a systematic overview of the Cochrane Library (inception to 2014). The two diagnostic reviews included a total of 269 unique studies, but only 4 studies were included in both reviews. The first review included five studies published in the Chinese language (out of 151) while the second included 114 (out of 118). The summary accuracy estimates from the two reviews were comparable. Only 243 of the published 8,680 Cochrane reviews (less than 3%) searched one or more of the five major Chinese databases. These Chinese databases index about 2,500 journals, of which less than 6% are also indexed in MEDLINE. All 243 Cochrane reviews evaluated an intervention, 179 (74%) had at least one author with a Chinese affiliation; 118 (49%) addressed a topic in complementary or alternative medicine. Although searching Chinese databases may lead to the identification of a large amount of additional clinical evidence, Cochrane reviewers have rarely included them in their search strategy. We encourage future initiatives to evaluate more systematically the relevance of searching Chinese databases, as well as collaborative efforts to allow better incorporation of Chinese resources in systematic reviews.

NBIC: Search Ballast Report Database

Science.gov Websites

Smithsonian Environmental Research Center Logo US Coast Guard Logo Submit BW Report | Search NBIC Database developed an online database that can be queried through our website. Data are accessible for all coastal Lakes, have been incorporated into the NBIC database as of August 2004. Information on data availability

Ocean Drilling Program: Science Operator Search Engine

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main -USIO site, plus IODP, ODP, and DSDP Publications, together or separately. ODP | Search | Database

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.

An Online Resource for Flight Test Safety Planning

NASA Technical Reports Server (NTRS)

Lewis, Greg

2007-01-01

A viewgraph presentation describing an online database for flight test safety techniques is shown. The topics include: 1) Goal; 2) Test Hazard Analyses; 3) Online Database Background; 4) Data Gathering; 5) NTPS Role; 6) Organizations; 7) Hazard Titles; 8) FAR Paragraphs; 9) Maneuver Name; 10) Identified Hazard; 11) Matured Hazard Titles; 12) Loss of Control Causes; 13) Mitigations; 14) Database Now Open to the Public; 15) FAR Reference Search; 16) Record Field Search; 17) Keyword Search; and 18) Results of FAR Reference Search.

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…

Conducting a Web Search.

ERIC Educational Resources Information Center

Miller-Whitehead, Marie

Keyword and text string searches of online library catalogs often provide different results according to library and database used and depending upon how books and journals are indexed. For this reason, online databases such as ERIC often provide tutorials and recommendations for searching their site, such as how to use Boolean search strategies.…

Citation searching: a systematic review case study of multiple risk behaviour interventions

PubMed Central

2014-01-01

Background The value of citation searches as part of the systematic review process is currently unknown. While the major guides to conducting systematic reviews state that citation searching should be carried out in addition to searching bibliographic databases there are still few studies in the literature that support this view. Rather than using a predefined search strategy to retrieve studies, citation searching uses known relevant papers to identify further papers. Methods We describe a case study about the effectiveness of using the citation sources Google Scholar, Scopus, Web of Science and OVIDSP MEDLINE to identify records for inclusion in a systematic review. We used the 40 included studies identified by traditional database searches from one systematic review of interventions for multiple risk behaviours. We searched for each of the included studies in the four citation sources to retrieve the details of all papers that have cited these studies. We carried out two analyses; the first was to examine the overlap between the four citation sources to identify which citation tool was the most useful; the second was to investigate whether the citation searches identified any relevant records in addition to those retrieved by the original database searches. Results The highest number of citations was retrieved from Google Scholar (1680), followed by Scopus (1173), then Web of Science (1095) and lastly OVIDSP (213). To retrieve all the records identified by the citation tracking searching all four resources was required. Google Scholar identified the highest number of unique citations. The citation tracking identified 9 studies that met the review’s inclusion criteria. Eight of these had already been identified by the traditional databases searches and identified in the screening process while the ninth was not available in any of the databases when the original searches were carried out. It would, however, have been identified by two of the database search strategies if searches had been carried out later. Conclusions Based on the results from this investigation, citation searching as a supplementary search method for systematic reviews may not be the best use of valuable time and resources. It would be useful to verify these findings in other reviews. PMID:24893958

BEAUTY-X: enhanced BLAST searches for DNA queries.

PubMed

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

1998-01-01

BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced version of the BLAST database search tool that facilitates identification of the functions of matched sequences. Three recent improvements to the BEAUTY program described here make the enhanced output (1) available for DNA queries, (2) available for searches of any protein database, and (3) more up-to-date, with periodic updates of the domain information. BEAUTY searches of the NCBI and EMBL non-redundant protein sequence databases are available from the BCM Search Launcher Web pages (http://gc.bcm.tmc. edu:8088/search-launcher/launcher.html). BEAUTY Post-Processing of submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html (kworley,culpep)@bcm.tmc.edu

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

A comparative study of six European databases of medically oriented Web resources.

PubMed

Abad García, Francisca; González Teruel, Aurora; Bayo Calduch, Patricia; de Ramón Frias, Rosa; Castillo Blasco, Lourdes

2005-10-01

The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

PubMed

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

2017-09-13

Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines. © 2017 Wiley Periodicals, Inc.

Privacy-preserving search for chemical compound databases.

PubMed

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

2015-01-01

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

Privacy-preserving search for chemical compound databases

PubMed Central

2015-01-01

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

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

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

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

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, themore » 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.« less

Proposed Test of Relative Phase as Hidden Variable in Quantum Mechanics

DTIC Science & Technology

2012-01-01

implicitly due to its ubiquity in quantum theory , but searches for dependence of measurement outcome on other parameters have been lacking. For a two -state...implemen- tation for the specific case of an atomic two -state system with laser-induced fluores- cence for measurement. Keywords Quantum measurement...Measurement postulate · Born rule 1 Introduction 1.1 Problems with Quantum Measurement Quantum theory prescribes probabilities for outcomes of measurements

[Profile of a systematic search. Search areas, databases and reports].

PubMed

Korsbek, Lisa; Bendix, Ane Friis; Kidholm, Kristian

2006-04-03

Systematic literature search is a fundamental in evidence-based medicine. But systematic literature search is not yet a very well used way of retrieving evidence-based information. This article profiles a systematic literature search for evidence-based literature. It goes through the most central databases and gives an example of how to document the literature search. The article also sums up the literature search in all reviews in Ugeskrift for Laeger in the year 2004.

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

PubMed

Jagtap, Pratik; Goslinga, Jill; Kooren, Joel A; McGowan, Thomas; Wroblewski, Matthew S; Seymour, Sean L; Griffin, Timothy J

2013-04-01

Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the number of high confidence peptide sequence matches in each case, as compared to the conventional one-step method. The two-step method captured almost all of the same peptides matched by the one-step method, with a majority of the additional matches being false negatives from the one-step method. Furthermore, the two-step method improved results regardless of the database search program used. Our results show that our two-step method maximizes the peptide matching sensitivity for applications requiring large databases, especially valuable for proteogenomics and metaproteomics studies. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

University Faculty Use of Computerized Databases: An Assessment of Needs and Resources.

ERIC Educational Resources Information Center

Borgman, Christine L.; And Others

1985-01-01

Results of survey indicate that: academic faculty are unaware of range of databases available; few recognize need for databases in research; most delegate searching to librarian or assistant, rather than perform searching themselves; and 39 database guides identified tended to be descriptive rather than evaluative. A comparison of the guides is…

Sagace: A web-based search engine for biomedical databases in Japan

PubMed Central

2012-01-01

Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816

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

PubMed

Rijnbeek, Mark; Steinbeck, Christoph

2009-10-22

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

Mass spectrometry-based protein identification by integrating de novo sequencing with database searching.

PubMed

Wang, Penghao; Wilson, Susan R

2013-01-01

Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integrative approach has been developed. The integrative approach firstly infers partial peptide sequences, known as tags, directly from tandem spectra through de novo sequencing, and then puts these sequences into a database search to see if a close peptide match can be found. However the current implementation of this integrative approach has several limitations. Firstly, simplistic de novo sequencing is applied and only very short sequence tags are used. Secondly, most integrative methods apply an algorithm similar to BLAST to search for exact sequence matches and do not accommodate sequence errors well. Thirdly, by applying these methods the integrated de novo sequencing makes a limited contribution to the scoring model which is still largely based on database searching. We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching. Evaluated on large real datasets, our method outperforms popular identification methods.

LMSD: LIPID MAPS structure database

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Brown, Alex; Dennis, Edward A.; Glass, Christopher K.; Merrill, Alfred H.; Murphy, Robert C.; Raetz, Christian R. H.; Russell, David W.; Subramaniam, Shankar

2007-01-01

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available at PMID:17098933

Loss-tolerant measurement-device-independent quantum private queries.

PubMed

Zhao, Liang-Yuan; Yin, Zhen-Qiang; Chen, Wei; Qian, Yong-Jun; Zhang, Chun-Mei; Guo, Guang-Can; Han, Zheng-Fu

2017-01-04

Quantum private queries (QPQ) is an important cryptography protocol aiming to protect both the user's and database's privacy when the database is queried privately. Recently, a variety of practical QPQ protocols based on quantum key distribution (QKD) have been proposed. However, for QKD-based QPQ the user's imperfect detectors can be subjected to some detector- side-channel attacks launched by the dishonest owner of the database. Here, we present a simple example that shows how the detector-blinding attack can damage the security of QKD-based QPQ completely. To remove all the known and unknown detector side channels, we propose a solution of measurement-device-independent QPQ (MDI-QPQ) with single- photon sources. The security of the proposed protocol has been analyzed under some typical attacks. Moreover, we prove that its security is completely loss independent. The results show that practical QPQ will remain the same degree of privacy as before even with seriously uncharacterized detectors.

High Resolution FIR and IR Spectroscopy of Methanol Isotopologues

NASA Astrophysics Data System (ADS)

Lees, R. M.; Xu, Li-Hong; Appadoo, D. R. T.; Billinghurst, B.

2010-02-01

New astronomical facilities such as HIFI on the Herschel Space Observatory, the SOFIA airborne IR telescope and the ALMA sub-mm telescope array will yield spectra from interstellar and protostellar sources with vastly increased sensitivity and frequency coverage. This creates the need for major enhancements to laboratory databases for the more prominent interstellar "weed" species in order to model and account for their lines in observed spectra in the search for new and more exotic interstellar molecular "flowers." With its large-amplitude internal torsional motion, methanol has particularly rich spectra throughout the FIR and IR regions and, being very widely distributed throughout the galaxy, is perhaps the most notorious interstellar weed. Thus, we have recorded new spectra for a variety of methanol isotopic species on the high-resolution FTIR spectrometer on the CLS FIR beamline. The aim is to extend quantum number coverage of the data, improve our understanding of the energy level structure, and provide the astronomical community with better databases and models of the spectral patterns with greater predictive power for a range of astrophysical conditions.

Term Relevance Feedback and Mediated Database Searching: Implications for Information Retrieval Practice and Systems Design.

ERIC Educational Resources Information Center

Spink, Amanda

1995-01-01

This study uses the human approach to examine the sources and effectiveness of search terms selected during 40 mediated interactive database searches and focuses on determining the retrieval effectiveness of search terms identified by users and intermediaries from retrieved items during term relevance feedback. (Author/JKP)

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…

Literature searching for clinical and cost-effectiveness studies used in health technology assessment reports carried out for the National Institute for Clinical Excellence appraisal system.

PubMed

Royle, P; Waugh, N

2003-01-01

To contribute to making searching for Technology Assessment Reports (TARs) more cost-effective by suggesting an optimum literature retrieval strategy. A sample of 20 recent TARs. All sources used to search for clinical and cost-effectiveness studies were recorded. In addition, all studies that were included in the clinical and cost-effectiveness sections of the TARs were identified, and their characteristics recorded, including author, journal, year, study design, study size and quality score. Each was also classified by publication type, and then checked to see whether it was indexed in the following databases: MEDLINE, EMBASE, and then either the Cochrane Controlled Trials Register (CCTR) for clinical effectiveness studies or the NHS Economic Evaluation Database (NHS EED) for the cost-effectiveness studies. Any study not found in at least one of these databases was checked to see whether it was indexed in the Science Citation Index (SCI) and BIOSIS, and the American Society of Clinical Oncology (ASCO) Online if a cancer review. Any studies still not found were checked to see whether they were in a number of additional databases. The median number of sources searched per TAR was 20, and the range was from 13 to 33 sources. Six sources (CCTR, DARE, EMBASE, MEDLINE, NHS EED and sponsor/industry submissions to National Institute for Clinical Excellence) were used in all reviews. After searching the MEDLINE, EMBASE and NHS EED databases, 87.3% of the clinical effectiveness studies and 94.8% of the cost-effectiveness studies were found, rising to 98.2% when SCI, BIOSIS and ASCO Online and 97.9% when SCI and ASCO Online, respectively, were added. The median number of sources searched for the 14 TARs that included an economic model was 9.0 per TAR. A sensitive search filter for identifying non-randomised controlled trials (RCT), constructed for MEDLINE and using the search terms from the bibliographic records in the included studies, retrieved only 85% of the known sample. Therefore, it is recommended that when searching for non-RCT studies a search is done for the intervention alone, and records are then scanned manually for those that look relevant. Searching additional databases beyond the Cochrane Library (which includes CCTR, NHS EED and the HTA database), MEDLINE, EMBASE and SCI, plus BIOSIS limited to meeting abstracts only, was seldom found to be effective in retrieving additional studies for inclusion in the clinical and cost-effectiveness sections of TARs (apart from reviews of cancer therapies, where a search of the ASCO database is recommended). A more selective approach to database searching would suffice in most cases and would save resources, thereby making the TAR process more efficient. However, searching non-database sources (including submissions from manufacturers, recent meeting abstracts, contact with experts and checking reference lists) does appear to be a productive way of identifying further studies.

Evidence-based librarianship: searching for the needed EBL evidence.

PubMed

Eldredge, J D

2000-01-01

This paper discusses the challenges of finding evidence needed to implement Evidence-Based Librarianship (EBL). Focusing first on database coverage for three health sciences librarianship journals, the article examines the information contents of different databases. Strategies are needed to search for relevant evidence in the library literature via these databases, and the problems associated with searching the grey literature of librarianship. Database coverage, plausible search strategies, and the grey literature of library science all pose challenges to finding the needed research evidence for practicing EBL. Health sciences librarians need to ensure that systems are designed that can track and provide access to needed research evidence to support Evidence-Based Librarianship (EBL).

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.

System, method and apparatus for conducting a keyterm search

NASA Technical Reports Server (NTRS)

McGreevy, Michael W. (Inventor)

2004-01-01

A keyterm search is a method of searching a database for subsets of the database that are relevant to an input query. First, a number of relational models of subsets of a database are provided. A query is then input. The query can include one or more keyterms. Next, a gleaning model of the query is created. The gleaning model of the query is then compared to each one of the relational models of subsets of the database. The identifiers of the relevant subsets are then output.

System, method and apparatus for conducting a phrase search

NASA Technical Reports Server (NTRS)

McGreevy, Michael W. (Inventor)

2004-01-01

A phrase search is a method of searching a database for subsets of the database that are relevant to an input query. First, a number of relational models of subsets of a database are provided. A query is then input. The query can include one or more sequences of terms. Next, a relational model of the query is created. The relational model of the query is then compared to each one of the relational models of subsets of the database. The identifiers of the relevant subsets are then output.

Discord as a quantum resource for bi-partite communication

NASA Astrophysics Data System (ADS)

Chrzanowski, Helen M.; Gu, Mile; Assad, Syed M.; Symul, Thomas; Modi, Kavan; Ralph, Timothy C.; Vedral, Vlatko; Lam, Ping Koy

2014-12-01

Coherent interactions that generate negligible entanglement can still exhibit unique quantum behaviour. This observation has motivated a search beyond entanglement for a complete description of all quantum correlations. Quantum discord is a promising candidate. Here, we experimentally demonstrate that under certain measurement constraints, discord between bipartite systems can be consumed to encode information that can only be accessed by coherent quantum interactions. The inability to access this information by any other means allows us to use discord to directly quantify this `quantum advantage'.

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.

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…

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

NASA Astrophysics Data System (ADS)

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

2001-07-01

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

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

PubMed

Su, Xiaoquan; Xu, Jian; Ning, Kang

2012-10-01

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

The Boolean Is Dead, Long Live the Boolean! Natural Language versus Boolean Searching in Introductory Undergraduate Instruction

ERIC Educational Resources Information Center

Lowe, M. Sara; Maxson, Bronwen K.; Stone, Sean M.; Miller, Willie; Snajdr, Eric; Hanna, Kathleen

2018-01-01

Boolean logic can be a difficult concept for first-year, introductory students to grasp. This paper compares the results of Boolean and natural language searching across several databases with searches created from student research questions. Performance differences between databases varied. Overall, natural search language is at least as good as…

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

PubMed

Lemkin, P F; Chipperfield, M; Merril, C; Zullo, S

1996-03-01

We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

A comprehensive and scalable database search system for metaproteomics.

PubMed

Chatterjee, Sandip; Stupp, Gregory S; Park, Sung Kyu Robin; Ducom, Jean-Christophe; Yates, John R; Su, Andrew I; Wolan, Dennis W

2016-08-16

Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations. Our approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed "Blazmass") to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples. The combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomic search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

Network meta-analyses could be improved by searching more sources and by involving a librarian.

PubMed

Li, Lun; Tian, Jinhui; Tian, Hongliang; Moher, David; Liang, Fuxiang; Jiang, Tongxiao; Yao, Liang; Yang, Kehu

2014-09-01

Network meta-analyses (NMAs) aim to rank the benefits (or harms) of interventions, based on all available randomized controlled trials. Thus, the identification of relevant data is critical. We assessed the conduct of the literature searches in NMAs. Published NMAs were retrieved by searching electronic bibliographic databases and other sources. Two independent reviewers selected studies and five trained reviewers abstracted data regarding literature searches, in duplicate. Search method details were examined using descriptive statistics. Two hundred forty-nine NMAs were included. Eight used previous systematic reviews to identify primary studies without further searching, and five did not report any literature searches. In the 236 studies that used electronic databases to identify primary studies, the median number of databases was 3 (interquartile range: 3-5). MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were the most commonly used databases. The most common supplemental search methods included reference lists of included studies (48%), reference lists of previous systematic reviews (40%), and clinical trial registries (32%). None of these supplemental methods was conducted in more than 50% of the NMAs. Literature searches in NMAs could be improved by searching more sources, and by involving a librarian or information specialist. Copyright © 2014 Elsevier Inc. All rights reserved.

Teaching Data Base Search Strategies.

ERIC Educational Resources Information Center

Hannah, Larry

1987-01-01

Discusses database searching as a method for developing thinking skills, and describes an activity suitable for fifth grade through high school using a president's and vice president's database. Teaching methods are presented, including student team activities, and worksheets designed for the AppleWorks database are included. (LRW)

Optimizing literature search in systematic reviews - are MEDLINE, EMBASE and CENTRAL enough for identifying effect studies within the area of musculoskeletal disorders?

PubMed

Aagaard, Thomas; Lund, Hans; Juhl, Carsten

2016-11-22

When conducting systematic reviews, it is essential to perform a comprehensive literature search to identify all published studies relevant to the specific research question. The Cochrane Collaborations Methodological Expectations of Cochrane Intervention Reviews (MECIR) guidelines state that searching MEDLINE, EMBASE and CENTRAL should be considered mandatory. The aim of this study was to evaluate the MECIR recommendations to use MEDLINE, EMBASE and CENTRAL combined, and examine the yield of using these to find randomized controlled trials (RCTs) within the area of musculoskeletal disorders. Data sources were systematic reviews published by the Cochrane Musculoskeletal Review Group, including at least five RCTs, reporting a search history, searching MEDLINE, EMBASE, CENTRAL, and adding reference- and hand-searching. Additional databases were deemed eligible if they indexed RCTs, were in English and used in more than three of the systematic reviews. Relative recall was calculated as the number of studies identified by the literature search divided by the number of eligible studies i.e. included studies in the individual systematic reviews. Finally, cumulative median recall was calculated for MEDLINE, EMBASE and CENTRAL combined followed by the databases yielding additional studies. Deemed eligible was twenty-three systematic reviews and the databases included other than MEDLINE, EMBASE and CENTRAL was AMED, CINAHL, HealthSTAR, MANTIS, OT-Seeker, PEDro, PsychINFO, SCOPUS, SportDISCUS and Web of Science. Cumulative median recall for combined searching in MEDLINE, EMBASE and CENTRAL was 88.9% and increased to 90.9% when adding 10 additional databases. Searching MEDLINE, EMBASE and CENTRAL was not sufficient for identifying all effect studies on musculoskeletal disorders, but additional ten databases did only increase the median recall by 2%. It is possible that searching databases is not sufficient to identify all relevant references, and that reviewers must rely upon additional sources in their literature search. However further research is needed.

A Web-based Tool for SDSS and 2MASS Database Searches

NASA Astrophysics Data System (ADS)

Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

Ophthalmology and vision science research: part 5: surfing or sieving--using literature databases wisely.

PubMed

Sherwin, Trevor; Gilhotra, Amardeep K

2006-02-01

Literature databases are an ever-expanding resource available to the field of medical sciences. Understanding how to use such databases efficiently is critical for those involved in research. However, for the uninitiated, getting started is a major hurdle to overcome and for the occasional user, the finer points of database searching remain an unacquired skill. In the fifth and final article in this series aimed at those embarking on ophthalmology and vision science research, we look at how the beginning researcher can start to use literature databases and, by using a stepwise approach, how they can optimize their use. This instructional paper gives a hypothetical example of a researcher writing a review article and how he or she acquires the necessary scientific literature for the article. A prototype search of the Medline database is used to illustrate how even a novice might swiftly acquire the skills required for a medium-level search. It provides examples and key tips that can increase the proficiency of the occasional user. Pitfalls of database searching are discussed, as are the limitations of which the user should be aware.

Evaluation of DNA mixtures from database search.

PubMed

Chung, Yuk-Ka; Hu, Yue-Qing; Fung, Wing K

2010-03-01

With the aim of bridging the gap between DNA mixture analysis and DNA database search, a novel approach is proposed to evaluate the forensic evidence of DNA mixtures when the suspect is identified by the search of a database of DNA profiles. General formulae are developed for the calculation of the likelihood ratio for a two-person mixture under general situations including multiple matches and imperfect evidence. The influence of the prior probabilities on the weight of evidence under the scenario of multiple matches is demonstrated by a numerical example based on Hong Kong data. Our approach is shown to be capable of presenting the forensic evidence of DNA mixtures in a comprehensive way when the suspect is identified through database search.

Faster sequence homology searches by clustering subsequences.

PubMed

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

2015-04-15

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

Search Filter Precision Can Be Improved By NOTing Out Irrelevant Content

PubMed Central

Wilczynski, Nancy L.; McKibbon, K. Ann; Haynes, R. Brian

2011-01-01

Background: Most methodologic search filters developed for use in large electronic databases such as MEDLINE have low precision. One method that has been proposed but not tested for improving precision is NOTing out irrelevant content. Objective: To determine if search filter precision can be improved by NOTing out the text words and index terms assigned to those articles that are retrieved but are off-target. Design: Analytic survey. Methods: NOTing out unique terms in off-target articles and testing search filter performance in the Clinical Hedges Database. Main Outcome Measures: Sensitivity, specificity, precision and number needed to read (NNR). Results: For all purpose categories (diagnosis, prognosis and etiology) except treatment and for all databases (MEDLINE, EMBASE, CINAHL and PsycINFO), constructing search filters that NOTed out irrelevant content resulted in substantive improvements in NNR (over four-fold for some purpose categories and databases). Conclusion: Search filter precision can be improved by NOTing out irrelevant content. PMID:22195215

Underwater sonar image detection: A combination of non-local spatial information and quantum-inspired shuffled frog leaping algorithm.

PubMed

Wang, Xingmei; Liu, Shu; Liu, Zhipeng

2017-01-01

This paper proposes a combination of non-local spatial information and quantum-inspired shuffled frog leaping algorithm to detect underwater objects in sonar images. Specifically, for the first time, the problem of inappropriate filtering degree parameter which commonly occurs in non-local spatial information and seriously affects the denoising performance in sonar images, was solved with the method utilizing a novel filtering degree parameter. Then, a quantum-inspired shuffled frog leaping algorithm based on new search mechanism (QSFLA-NSM) is proposed to precisely and quickly detect sonar images. Each frog individual is directly encoded by real numbers, which can greatly simplify the evolution process of the quantum-inspired shuffled frog leaping algorithm (QSFLA). Meanwhile, a fitness function combining intra-class difference with inter-class difference is adopted to evaluate frog positions more accurately. On this basis, recurring to an analysis of the quantum-behaved particle swarm optimization (QPSO) and the shuffled frog leaping algorithm (SFLA), a new search mechanism is developed to improve the searching ability and detection accuracy. At the same time, the time complexity is further reduced. Finally, the results of comparative experiments using the original sonar images, the UCI data sets and the benchmark functions demonstrate the effectiveness and adaptability of the proposed method.

Underwater sonar image detection: A combination of non-local spatial information and quantum-inspired shuffled frog leaping algorithm

PubMed Central

Liu, Zhipeng

2017-01-01

This paper proposes a combination of non-local spatial information and quantum-inspired shuffled frog leaping algorithm to detect underwater objects in sonar images. Specifically, for the first time, the problem of inappropriate filtering degree parameter which commonly occurs in non-local spatial information and seriously affects the denoising performance in sonar images, was solved with the method utilizing a novel filtering degree parameter. Then, a quantum-inspired shuffled frog leaping algorithm based on new search mechanism (QSFLA-NSM) is proposed to precisely and quickly detect sonar images. Each frog individual is directly encoded by real numbers, which can greatly simplify the evolution process of the quantum-inspired shuffled frog leaping algorithm (QSFLA). Meanwhile, a fitness function combining intra-class difference with inter-class difference is adopted to evaluate frog positions more accurately. On this basis, recurring to an analysis of the quantum-behaved particle swarm optimization (QPSO) and the shuffled frog leaping algorithm (SFLA), a new search mechanism is developed to improve the searching ability and detection accuracy. At the same time, the time complexity is further reduced. Finally, the results of comparative experiments using the original sonar images, the UCI data sets and the benchmark functions demonstrate the effectiveness and adaptability of the proposed method. PMID:28542266

System for Performing Single Query Searches of Heterogeneous and Dispersed Databases

NASA Technical Reports Server (NTRS)

Maluf, David A. (Inventor); Okimura, Takeshi (Inventor); Gurram, Mohana M. (Inventor); Tran, Vu Hoang (Inventor); Knight, Christopher D. (Inventor); Trinh, Anh Ngoc (Inventor)

2017-01-01

The present invention is a distributed computer system of heterogeneous databases joined in an information grid and configured with an Application Programming Interface hardware which includes a search engine component for performing user-structured queries on multiple heterogeneous databases in real time. This invention reduces overhead associated with the impedance mismatch that commonly occurs in heterogeneous database queries.

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:…

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

PubMed

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

2007-09-01

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

Archive of mass spectral data files on recordable CD-ROMs and creation and maintenance of a searchable computerized database.

PubMed

Amick, G D

1999-01-01

A database containing names of mass spectral data files generated in a forensic toxicology laboratory and two Microsoft Visual Basic programs to maintain and search this database is described. The data files (approximately 0.5 KB/each) were collected from six mass spectrometers during routine casework. Data files were archived on 650 MB (74 min) recordable CD-ROMs. Each recordable CD-ROM was given a unique name, and its list of data file names was placed into the database. The present manuscript describes the use of search and maintenance programs for searching and routine upkeep of the database and creation of CD-ROMs for archiving of data files.

Description of 'REQUEST-KYUSHYU' for KYUKEICHO regional data base

NASA Astrophysics Data System (ADS)

Takimoto, Shin'ichi

Kyushu Economic Research Association (a foundational juridical person) initiated the regional database services, ' REQUEST-Kyushu ' recently. It is the full scale databases compiled based on the information and know-hows which the Association has accumulated over forty years. It covers the regional information database for journal and newspaper articles, and statistical information database for economic statistics. As to the former database it is searched on a personal computer and then a search result (original text) is sent through a facsimile. As to the latter, it is also searched on a personal computer where the data is processed, edited or downloaded. This paper describes characteristics, content and the system outline of 'REQUEST-Kyushu'.

OrChem - An open source chemistry search engine for Oracle®

PubMed Central

2009-01-01

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

Transitionless driving on adiabatic search algorithm

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

Oh, Sangchul, E-mail: soh@qf.org.qa; Kais, Sabre, E-mail: kais@purdue.edu; Department of Chemistry, Department of Physics and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907

We study quantum dynamics of the adiabatic search algorithm with the equivalent two-level system. Its adiabatic and non-adiabatic evolution is studied and visualized as trajectories of Bloch vectors on a Bloch sphere. We find the change in the non-adiabatic transition probability from exponential decay for the short running time to inverse-square decay in asymptotic running time. The scaling of the critical running time is expressed in terms of the Lambert W function. We derive the transitionless driving Hamiltonian for the adiabatic search algorithm, which makes a quantum state follow the adiabatic path. We demonstrate that a uniform transitionless driving Hamiltonian,more » approximate to the exact time-dependent driving Hamiltonian, can alter the non-adiabatic transition probability from the inverse square decay to the inverse fourth power decay with the running time. This may open up a new but simple way of speeding up adiabatic quantum dynamics.« less

The Human Transcript Database: A Catalogue of Full Length cDNA Inserts

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

Bouckk John; Michael McLeod; Kim Worley

1999-09-10

The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search resultsmore » to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.« less

The CIS Database: Occupational Health and Safety Information Online.

ERIC Educational Resources Information Center

Siegel, Herbert; Scurr, Erica

1985-01-01

Describes document acquisition, selection, indexing, and abstracting and discusses online searching of the CIS database, an online system produced by the International Occupational Safety and Health Information Centre. This database comprehensively covers information in the field of occupational health and safety. Sample searches and search…

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

DTIC Science & Technology

2012-09-01

considerable variation in how fusion centers plan for, gather requirements, select and acquire federated search tools to bridge disparate databases...centers, when considering integrating federated search tools; by evaluating the importance of the planning, requirements gathering, selection and...acquisition processes for integrating federated search tools; by acknowledging the challenges faced by some fusion centers during these integration processes

Search for resonances and quantum black holes using dijet mass spectra in proton-proton collisions at $$\\sqrt{s} =$$ 8 TeV

DOE PAGES

Khachatryan, Vardan

2015-03-12

Our search for resonances and quantum black holes is performed using the dijet mass spectra measured in proton-proton collisions at √s=8 TeV with the CMS detector at the LHC. The data set corresponds to an integrated luminosity of 19.7 fb -1. In a search for narrow resonances that couple to quark-quark, quark-gluon, or gluon-gluon pairs, model-independent upper limits, at 95% confidence level, are obtained on the production cross section of resonances, with masses above 1.2 TeV. When interpreted in the context of specific models the limits exclude string resonances with masses below 5.0 TeV; excited quarks below 3.5 TeV; scalarmore » diquarks below 4.7 TeV; W' bosons below 1.9 TeV or between 2.0 and 2.2 TeV; Z' bosons below 1.7 TeV; and Randall-Sundrum gravitons below 1.6 TeV. A separate search is conducted for narrow resonances that decay to final states including b quarks. Furthermore, the first exclusion limit is set for excited b quarks, with a lower mass limit between 1.2 and 1.6 TeV depending on their decay properties. Searches are also carried out for wide resonances, assuming for the first time width-to-mass ratios up to 30%, and for quantum black holes with a range of model parameters. The wide resonance search excludes axigluons and colorons with mass below 3.6 TeV, and color-octet scalars with mass below 2.5 TeV. Lower bounds between 5.0 and 6.3 TeV are set on the masses of quantum black holes.« less

How to locate and appraise qualitative research in complementary and alternative medicine

PubMed Central

2013-01-01

Background The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Methods Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. Results 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. Conclusions This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies. PMID:23731997

How to locate and appraise qualitative research in complementary and alternative medicine.

PubMed

Franzel, Brigitte; Schwiegershausen, Martina; Heusser, Peter; Berger, Bettina

2013-06-03

The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies.

Biomedical Requirements for High Productivity Computing Systems

DTIC Science & Technology

2005-04-01

server at http://www.ncbi.nlm.nih.gov/BLAST/. There are many variants of BLAST, including: 1. BLASTN - Compares a DNA query to a DNA database. Searches ...database (3 reading frames from each strand of the DNA) searching . 13 4. TBLASTN - Compares a protein query to a DNA database, in the 6 possible...the molecular during this phase. After eliminating molecules that could not match the query , an atom-by-atom search for the molecules in conducted

Turbocharged molecular discovery of OLED emitters: from high-throughput quantum simulation to highly efficient TADF devices

NASA Astrophysics Data System (ADS)

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Ha, Dong-Gwang; Einzinger, Markus; Wu, Tony; Baldo, Marc A.; Aspuru-Guzik, Alán.

2016-09-01

Discovering new OLED emitters requires many experiments to synthesize candidates and test performance in devices. Large scale computer simulation can greatly speed this search process but the problem remains challenging enough that brute force application of massive computing power is not enough to successfully identify novel structures. We report a successful High Throughput Virtual Screening study that leveraged a range of methods to optimize the search process. The generation of candidate structures was constrained to contain combinatorial explosion. Simulations were tuned to the specific problem and calibrated with experimental results. Experimentalists and theorists actively collaborated such that experimental feedback was regularly utilized to update and shape the computational search. Supervised machine learning methods prioritized candidate structures prior to quantum chemistry simulation to prevent wasting compute on likely poor performers. With this combination of techniques, each multiplying the strength of the search, this effort managed to navigate an area of molecular space and identify hundreds of promising OLED candidate structures. An experimentally validated selection of this set shows emitters with external quantum efficiencies as high as 22%.

Quantum Teleportation and Grover's Algorithm Without the Wavefunction

NASA Astrophysics Data System (ADS)

Niestegge, Gerd

2017-02-01

In the same way as the quantum no-cloning theorem and quantum key distribution in two preceding papers, entanglement-assisted quantum teleportation and Grover's search algorithm are generalized by transferring them to an abstract setting, including usual quantum mechanics as a special case. This again shows that a much more general and abstract access to these quantum mechanical features is possible than commonly thought. A non-classical extension of conditional probability and, particularly, a very special type of state-independent conditional probability are used instead of Hilbert spaces and wavefunctions.

Multi-Database Searching in the Behavioral Sciences--Part I: Basic Techniques and Core Databases.

ERIC Educational Resources Information Center

Angier, Jennifer J.; Epstein, Barbara A.

1980-01-01

Outlines practical searching techniques in seven core behavioral science databases accessing psychological literature: Psychological Abstracts, Social Science Citation Index, Biosis, Medline, Excerpta Medica, Sociological Abstracts, ERIC. Use of individual files is discussed and their relative strengths/weaknesses are compared. Appended is a list…

Subject Specific Databases: A Powerful Research Tool

ERIC Educational Resources Information Center

Young, Terrence E., Jr.

2004-01-01

Subject specific databases, or vortals (vertical portals), are databases that provide highly detailed research information on a particular topic. They are the smallest, most focused search tools on the Internet and, in recent years, they've been on the rise. Currently, more of the so-called "mainstream" search engines, subject directories, and…

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,…

A Framework for Cloudy Model Optimization and Database Storage

NASA Astrophysics Data System (ADS)

Calvén, Emilia; Helton, Andrew; Sankrit, Ravi

2018-01-01

We present a framework for producing Cloudy photoionization models of the nebular emission from novae ejecta and storing a subset of the results in SQL database format for later usage. The database can be searched for models best fitting observed spectral line ratios. Additionally, the framework includes an optimization feature that can be used in tandem with the database to search for and improve on models by creating new Cloudy models while, varying the parameters. The database search and optimization can be used to explore the structures of nebulae by deriving their properties from the best-fit models. The goal is to provide the community with a large database of Cloudy photoionization models, generated from parameters reflecting conditions within novae ejecta, that can be easily fitted to observed spectral lines; either by directly accessing the database using the framework code or by usage of a website specifically made for this purpose.

Grover Search and the No-Signaling Principle

NASA Astrophysics Data System (ADS)

Bao, Ning; Bouland, Adam; Jordan, Stephen P.

2016-09-01

Two of the key properties of quantum physics are the no-signaling principle and the Grover search lower bound. That is, despite admitting stronger-than-classical correlations, quantum mechanics does not imply superluminal signaling, and despite a form of exponential parallelism, quantum mechanics does not imply polynomial-time brute force solution of NP-complete problems. Here, we investigate the degree to which these two properties are connected. We examine four classes of deviations from quantum mechanics, for which we draw inspiration from the literature on the black hole information paradox. We show that in these models, the physical resources required to send a superluminal signal scale polynomially with the resources needed to speed up Grover's algorithm. Hence the no-signaling principle is equivalent to the inability to solve NP-hard problems efficiently by brute force within the classes of theories analyzed.

Effectiveness of Motivational Interviewing Interventions for Adolescent Substance Use Behavior Change: A Meta-Analytic Review

ERIC Educational Resources Information Center

Jensen, Chad D.; Cushing, Christopher C.; Aylward, Brandon S.; Craig, James T.; Sorell, Danielle M.; Steele, Ric G.

2011-01-01

Objective: This study was designed to quantitatively evaluate the effectiveness of motivational interviewing (MI) interventions for adolescent substance use behavior change. Method: Literature searches of electronic databases were undertaken in addition to manual reference searches of identified review articles. Databases searched include…

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.

Quantum Gravitational Spectroscopy

DOE PAGES

Nesvizhevsky, Valery V.; Antoniadis, Ignatios; Baessler, Stefan; ...

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.

77 FR 6535 - Notice of Intent To Seek Approval To Collect Information

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-08

... information from participants: Contact information, affiliation, and database searching experience... and fax numbers, and email address. Six questions are asked regarding: database searching experience...

Searching mixed DNA profiles directly against profile databases.

PubMed

Bright, Jo-Anne; Taylor, Duncan; Curran, James; Buckleton, John

2014-03-01

DNA databases have revolutionised forensic science. They are a powerful investigative tool as they have the potential to identify persons of interest in criminal investigations. Routinely, a DNA profile generated from a crime sample could only be searched for in a database of individuals if the stain was from single contributor (single source) or if a contributor could unambiguously be determined from a mixed DNA profile. This meant that a significant number of samples were unsuitable for database searching. The advent of continuous methods for the interpretation of DNA profiles offers an advanced way to draw inferential power from the considerable investment made in DNA databases. Using these methods, each profile on the database may be considered a possible contributor to a mixture and a likelihood ratio (LR) can be formed. Those profiles which produce a sufficiently large LR can serve as an investigative lead. In this paper empirical studies are described to determine what constitutes a large LR. We investigate the effect on a database search of complex mixed DNA profiles with contributors in equal proportions with dropout as a consideration, and also the effect of an incorrect assignment of the number of contributors to a profile. In addition, we give, as a demonstration of the method, the results using two crime samples that were previously unsuitable for database comparison. We show that effective management of the selection of samples for searching and the interpretation of the output can be highly informative. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases

PubMed Central

Lee, Taein; Cheng, Chun-Huai; Ficklin, Stephen; Yu, Jing; Humann, Jodi; Main, Dorrie

2017-01-01

Abstract Tripal is an open-source database platform primarily used for development of genomic, genetic and breeding databases. We report here on the release of the Chado Loader, Chado Data Display and Chado Search modules to extend the functionality of the core Tripal modules. These new extension modules provide additional tools for (1) data loading, (2) customized visualization and (3) advanced search functions for supported data types such as organism, marker, QTL/Mendelian Trait Loci, germplasm, map, project, phenotype, genotype and their respective metadata. The Chado Loader module provides data collection templates in Excel with defined metadata and data loaders with front end forms. The Chado Data Display module contains tools to visualize each data type and the metadata which can be used as is or customized as desired. The Chado Search module provides search and download functionality for the supported data types. Also included are the tools to visualize map and species summary. The use of materialized views in the Chado Search module enables better performance as well as flexibility of data modeling in Chado, allowing existing Tripal databases with different metadata types to utilize the module. These Tripal Extension modules are implemented in the Genome Database for Rosaceae (rosaceae.org), CottonGen (cottongen.org), Citrus Genome Database (citrusgenomedb.org), Genome Database for Vaccinium (vaccinium.org) and the Cool Season Food Legume Database (coolseasonfoodlegume.org). Database URL: https://www.citrusgenomedb.org/, https://www.coolseasonfoodlegume.org/, https://www.cottongen.org/, https://www.rosaceae.org/, https://www.vaccinium.org/

Difficulties and challenges associated with literature searches in operating room management, complete with recommendations.

PubMed

Wachtel, Ruth E; Dexter, Franklin

2013-12-01

The purpose of this article is to teach operating room managers, financial analysts, and those with a limited knowledge of search engines, including PubMed, how to locate articles they need in the areas of operating room and anesthesia group management. Many physicians are unaware of current literature in their field and evidence-based practices. The most common source of information is colleagues. Many people making management decisions do not read published scientific articles. Databases such as PubMed are available to search for such articles. Other databases, such as citation indices and Google Scholar, can be used to uncover additional articles. Nevertheless, most people who do not know how to use these databases are reluctant to utilize help resources when they do not know how to accomplish a task. Most people are especially reluctant to use on-line help files. Help files and search databases are often difficult to use because they have been designed for users already familiar with the field. The help files and databases have specialized vocabularies unique to the application. MeSH terms in PubMed are not useful alternatives for operating room management, an important limitation, because MeSH is the default when search terms are entered in PubMed. Librarians or those trained in informatics can be valuable assets for searching unusual databases, but they must possess the domain knowledge relative to the subject they are searching. The search methods we review are especially important when the subject area (e.g., anesthesia group management) is so specific that only 1 or 2 articles address the topic of interest. The materials are presented broadly enough that the reader can extrapolate the findings to other areas of clinical and management issues in anesthesiology.

HBVPathDB: a database of HBV infection-related molecular interaction network.

PubMed

Zhang, Yi; Bo, Xiao-Chen; Yang, Jing; Wang, Sheng-Qi

2005-03-21

To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

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.

Undergraduate computational physics projects on quantum computing

NASA Astrophysics Data System (ADS)

Candela, D.

2015-08-01

Computational projects on quantum computing suitable for students in a junior-level quantum mechanics course are described. In these projects students write their own programs to simulate quantum computers. Knowledge is assumed of introductory quantum mechanics through the properties of spin 1/2. Initial, more easily programmed projects treat the basics of quantum computation, quantum gates, and Grover's quantum search algorithm. These are followed by more advanced projects to increase the number of qubits and implement Shor's quantum factoring algorithm. The projects can be run on a typical laptop or desktop computer, using most programming languages. Supplementing resources available elsewhere, the projects are presented here in a self-contained format especially suitable for a short computational module for physics students.

A design for the geoinformatics system

NASA Astrophysics Data System (ADS)

Allison, M. L.

2002-12-01

Informatics integrates and applies information technologies with scientific and technical disciplines. A geoinformatics system targets the spatially based sciences. The system is not a master database, but will collect pertinent information from disparate databases distributed around the world. Seamless interoperability of databases promises quantum leaps in productivity not only for scientific researchers but also for many areas of society including business and government. The system will incorporate: acquisition of analog and digital legacy data; efficient information and data retrieval mechanisms (via data mining and web services); accessibility to and application of visualization, analysis, and modeling capabilities; online workspace, software, and tutorials; GIS; integration with online scientific journal aggregates and digital libraries; access to real time data collection and dissemination; user-defined automatic notification and quality control filtering for selection of new resources; and application to field techniques such as mapping. In practical terms, such a system will provide the ability to gather data over the Web from a variety of distributed sources, regardless of computer operating systems, database formats, and servers. Search engines will gather data about any geographic location, above, on, or below ground, covering any geologic time, and at any scale or detail. A distributed network of digital geolibraries can archive permanent copies of databases at risk of being discontinued and those that continue to be maintained by the data authors. The geoinformatics system will generate results from widely distributed sources to function as a dynamic data network. Instead of posting a variety of pre-made tables, charts, or maps based on static databases, the interactive dynamic system creates these products on the fly, each time an inquiry is made, using the latest information in the appropriate databases. Thus, in the dynamic system, a map generated today may differ from one created yesterday and one to be created tomorrow, because the databases used to make it are constantly (and sometimes automatically) being updated.

Multi-source and ontology-based retrieval engine for maize mutant phenotypes

PubMed Central

Green, Jason M.; Harnsomburana, Jaturon; Schaeffer, Mary L.; Lawrence, Carolyn J.; Shyu, Chi-Ren

2011-01-01

Model Organism Databases, including the various plant genome databases, collect and enable access to massive amounts of heterogeneous information, including sequence data, gene product information, images of mutant phenotypes, etc, as well as textual descriptions of many of these entities. While a variety of basic browsing and search capabilities are available to allow researchers to query and peruse the names and attributes of phenotypic data, next-generation search mechanisms that allow querying and ranking of text descriptions are much less common. In addition, the plant community needs an innovative way to leverage the existing links in these databases to search groups of text descriptions simultaneously. Furthermore, though much time and effort have been afforded to the development of plant-related ontologies, the knowledge embedded in these ontologies remains largely unused in available plant search mechanisms. Addressing these issues, we have developed a unique search engine for mutant phenotypes from MaizeGDB. This advanced search mechanism integrates various text description sources in MaizeGDB to aid a user in retrieving desired mutant phenotype information. Currently, descriptions of mutant phenotypes, loci and gene products are utilized collectively for each search, though expansion of the search mechanism to include other sources is straightforward. The retrieval engine, to our knowledge, is the first engine to exploit the content and structure of available domain ontologies, currently the Plant and Gene Ontologies, to expand and enrich retrieval results in major plant genomic databases. Database URL: http:www.PhenomicsWorld.org/QBTA.php PMID:21558151

BLAST and FASTA similarity searching for multiple sequence alignment.

PubMed

Pearson, William R

2014-01-01

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

Concentrations of indoor pollutants database: User's manual

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

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author's last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user's needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

Concentrations of indoor pollutants database: User`s manual

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

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author`s last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user`s needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

DRUMS: a human disease related unique gene mutation search engine.

PubMed

Li, Zuofeng; Liu, Xingnan; Wen, Jingran; Xu, Ye; Zhao, Xin; Li, Xuan; Liu, Lei; Zhang, Xiaoyan

2011-10-01

With the completion of the human genome project and the development of new methods for gene variant detection, the integration of mutation data and its phenotypic consequences has become more important than ever. Among all available resources, locus-specific databases (LSDBs) curate one or more specific genes' mutation data along with high-quality phenotypes. Although some genotype-phenotype data from LSDB have been integrated into central databases little effort has been made to integrate all these data by a search engine approach. In this work, we have developed disease related unique gene mutation search engine (DRUMS), a search engine for human disease related unique gene mutation as a convenient tool for biologists or physicians to retrieve gene variant and related phenotype information. Gene variant and phenotype information were stored in a gene-centred relational database. Moreover, the relationships between mutations and diseases were indexed by the uniform resource identifier from LSDB, or another central database. By querying DRUMS, users can access the most popular mutation databases under one interface. DRUMS could be treated as a domain specific search engine. By using web crawling, indexing, and searching technologies, it provides a competitively efficient interface for searching and retrieving mutation data and their relationships to diseases. The present system is freely accessible at http://www.scbit.org/glif/new/drums/index.html. © 2011 Wiley-Liss, Inc.

Accelerating Information Retrieval from Profile Hidden Markov Model Databases.

PubMed

Tamimi, Ahmad; Ashhab, Yaqoub; Tamimi, Hashem

2016-01-01

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

THGS: a web-based database of Transmembrane Helices in Genome Sequences

PubMed Central

Fernando, S. A.; Selvarani, P.; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, S.; Sekar, K.

2004-01-01

Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs/ or http://144.16.71.10/thgs/. PMID:14681375

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.

Data-driven indexing mechanism for the recognition of polyhedral objects

NASA Astrophysics Data System (ADS)

McLean, Stewart; Horan, Peter; Caelli, Terry M.

1992-02-01

This paper is concerned with the problem of searching large model databases. To date, most object recognition systems have concentrated on the problem of matching using simple searching algorithms. This is quite acceptable when the number of object models is small. However, in the future, general purpose computer vision systems will be required to recognize hundreds or perhaps thousands of objects and, in such circumstances, efficient searching algorithms will be needed. The problem of searching a large model database is one which must be addressed if future computer vision systems are to be at all effective. In this paper we present a method we call data-driven feature-indexed hypothesis generation as one solution to the problem of searching large model databases.

Embracing the quantum limit in silicon computing.

PubMed

Morton, John J L; McCamey, Dane R; Eriksson, Mark A; Lyon, Stephen A

2011-11-16

Quantum computers hold the promise of massive performance enhancements across a range of applications, from cryptography and databases to revolutionary scientific simulation tools. Such computers would make use of the same quantum mechanical phenomena that pose limitations on the continued shrinking of conventional information processing devices. Many of the key requirements for quantum computing differ markedly from those of conventional computers. However, silicon, which plays a central part in conventional information processing, has many properties that make it a superb platform around which to build a quantum computer. © 2011 Macmillan Publishers Limited. All rights reserved

Novel LOVD databases for hereditary breast cancer and colorectal cancer genes in the Chinese population.

PubMed

Pan, Min; Cong, Peikuan; Wang, Yue; Lin, Changsong; Yuan, Ying; Dong, Jian; Banerjee, Santasree; Zhang, Tao; Chen, Yanling; Zhang, Ting; Chen, Mingqing; Hu, Peter; Zheng, Shu; Zhang, Jin; Qi, Ming

2011-12-01

The Human Variome Project (HVP) is an international consortium of clinicians, geneticists, and researchers from over 30 countries, aiming to facilitate the establishment and maintenance of standards, systems, and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The HVP-China Node will build new and supplement existing databases of genetic diseases. As the first effort, we have created a novel variant database of BRCA1 and BRCA2, mismatch repair genes (MMR), and APC genes for breast cancer, Lynch syndrome, and familial adenomatous polyposis (FAP), respectively, in the Chinese population using the Leiden Open Variation Database (LOVD) format. We searched PubMed and some Chinese search engines to collect all the variants of these genes in the Chinese population that have already been detected and reported. There are some differences in the gene variants between the Chinese population and that of other ethnicities. The database is available online at http://www.genomed.org/LOVD/. Our database will appear to users who survey other LOVD databases (e.g., by Google search, or by NCBI GeneTests search). Remote submissions are accepted, and the information is updated monthly. © 2011 Wiley Periodicals, Inc.

Comparison of CINAHL, EMBASE, and MEDLINE databases for the nurse researcher.

PubMed

Burnham, J; Shearer, B

1993-01-01

The purpose of this research was to determine which of three databases, CINAHL, EMBASE or MEDLINE, should be accessed when researching nursing topics. The three databases were searched for citations on topics selected by three nurse researchers and the results were compared. For the search of nursing care literature on a medical condition, it was helpful to search both CINAHL and MEDLINE. CINAHL provided the majority of relevant articles for the second search, on computers and privacy, but inclusion of MEDLINE and EMBASE enhanced retrieval somewhat. The search on substance abuse in pregnancy, not restricted to nursing literature, retrieved better results when searching both MEDLINE and EMBASE. Due to the nature and distribution of the nursing literature, it is especially important for the searcher to understand and respond to the focus of the researcher.

Choosing a Database for Social Work: A Comparison of Social Work Abstracts and Social Service Abstracts

ERIC Educational Resources Information Center

Flatley, Robert K.; Lilla, Rick; Widner, Jack

2007-01-01

This study compared Social Work Abstracts and Social Services Abstracts databases in terms of indexing, journal coverage, and searches. The authors interviewed editors, analyzed journal coverage, and compared searches. It was determined that the databases complement one another more than compete. The authors conclude with some considerations.

The Philip Morris Information Network: A Library Database on an In-House Timesharing System.

ERIC Educational Resources Information Center

DeBardeleben, Marian Z.; And Others

1983-01-01

Outlines a database constructed at Philip Morris Research Center Library which encompasses holdings and circulation and acquisitions records for all items in the library. Host computer (DECSYSTEM-2060), software (BASIC), database design, search methodology, cataloging, and accessibility are noted; sample search, circ-in profile, end user profiles,…

How Many People Search the ERIC Database Each Day?

ERIC Educational Resources Information Center

Rudner, Lawrence

This study estimated the number of people searching the ERIC database each day. The Educational Resources Information Center (ERIC) is a national information system designed to provide ready access to an extensive body of education-related literature. Federal funds traditionally have paid for the development of the database, but not the…

FirstSearch and NetFirst--Web and Dial-up Access: Plus Ca Change, Plus C'est la Meme Chose?

ERIC Educational Resources Information Center

Koehler, Wallace; Mincey, Danielle

1996-01-01

Compares and evaluates the differences between OCLC's dial-up and World Wide Web FirstSearch access methods and their interfaces with the underlying databases. Also examines NetFirst, OCLC's new Internet catalog, the only Internet tracking database from a "traditional" database service. (Author/PEN)

Ocean Drilling Program: Web Site Access Statistics

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main See statistics for JOIDES members. See statistics for Janus database. 1997 October November December accessible only on www-odp.tamu.edu. ** End of ODP, start of IODP. Privacy Policy ODP | Search | Database

Digging Deeper: The Deep Web.

ERIC Educational Resources Information Center

Turner, Laura

2001-01-01

Focuses on the Deep Web, defined as Web content in searchable databases of the type that can be found only by direct query. Discusses the problems of indexing; inability to find information not indexed in the search engine's database; and metasearch engines. Describes 10 sites created to access online databases or directly search them. Lists ways…

A practical approach for inexpensive searches of radiology report databases.

PubMed

Desjardins, Benoit; Hamilton, R Curtis

2007-06-01

We present a method to perform full text searches of radiology reports for the large number of departments that do not have this ability as part of their radiology or hospital information system. A tool written in Microsoft Access (front-end) has been designed to search a server (back-end) containing the indexed backup weekly copy of the full relational database extracted from a radiology information system (RIS). This front end-/back-end approach has been implemented in a large academic radiology department, and is used for teaching, research and administrative purposes. The weekly second backup of the 80 GB, 4 million record RIS database takes 2 hours. Further indexing of the exported radiology reports takes 6 hours. Individual searches of the indexed database typically take less than 1 minute on the indexed database and 30-60 minutes on the nonindexed database. Guidelines to properly address privacy and institutional review board issues are closely followed by all users. This method has potential to improve teaching, research, and administrative programs within radiology departments that cannot afford more expensive technology.

Decision making in family medicine: randomized trial of the effects of the InfoClinique and Trip database search engines.

PubMed

Labrecque, Michel; Ratté, Stéphane; Frémont, Pierre; Cauchon, Michel; Ouellet, Jérôme; Hogg, William; McGowan, Jessie; Gagnon, Marie-Pierre; Njoya, Merlin; Légaré, France

2013-10-01

To compare the ability of users of 2 medical search engines, InfoClinique and the Trip database, to provide correct answers to clinical questions and to explore the perceived effects of the tools on the clinical decision-making process. Randomized trial. Three family medicine units of the family medicine program of the Faculty of Medicine at Laval University in Quebec city, Que. Fifteen second-year family medicine residents. Residents generated 30 structured questions about therapy or preventive treatment (2 questions per resident) based on clinical encounters. Using an Internet platform designed for the trial, each resident answered 20 of these questions (their own 2, plus 18 of the questions formulated by other residents, selected randomly) before and after searching for information with 1 of the 2 search engines. For each question, 5 residents were randomly assigned to begin their search with InfoClinique and 5 with the Trip database. The ability of residents to provide correct answers to clinical questions using the search engines, as determined by third-party evaluation. After answering each question, participants completed a questionnaire to assess their perception of the engine's effect on the decision-making process in clinical practice. Of 300 possible pairs of answers (1 answer before and 1 after the initial search), 254 (85%) were produced by 14 residents. Of these, 132 (52%) and 122 (48%) pairs of answers concerned questions that had been assigned an initial search with InfoClinique and the Trip database, respectively. Both engines produced an important and similar absolute increase in the proportion of correct answers after searching (26% to 62% for InfoClinique, for an increase of 36%; 24% to 63% for the Trip database, for an increase of 39%; P = .68). For all 30 clinical questions, at least 1 resident produced the correct answer after searching with either search engine. The mean (SD) time of the initial search for each question was 23.5 (7.6) minutes with InfoClinique and 22.3 (7.8) minutes with the Trip database (P = .30). Participants' perceptions of each engine's effect on the decision-making process were very positive and similar for both search engines. Family medicine residents' ability to provide correct answers to clinical questions increased dramatically and similarly with the use of both InfoClinique and the Trip database. These tools have strong potential to increase the quality of medical care.

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

PubMed

Tai, David; Fang, Jianwen

2012-08-27

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

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.

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

PubMed

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

DOE Research and Development Accomplishments Website Policies/Important

Science.gov Websites

Links RSS Archive Videos XML DOE R&D Accomplishments DOE R&D Accomplishments searchQuery × Find searchQuery x Find DOE R&D Acccomplishments Navigation dropdown arrow The Basics Stories Snapshots R&D Nuggets Database dropdown arrow Search Tag Cloud Browse Reports Database Help

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…

Ocean Drilling Program: Mirror Sites

Science.gov Websites

Publication services and products Drilling services and tools Online Janus database Search the ODP/TAMU web information, see www.iodp-usio.org. ODP | Search | Database | Drilling | Publications | Science | Cruise Info

Ocean Drilling Program: TAMU Staff Directory

Science.gov Websites

products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main web site Employment Opportunities ODP | Search | Database | Drilling | Publications | Science | Cruise Info | Public

[A survey of the best bibliographic searching system in occupational medicine and discussion of its implementation].

PubMed

Inoue, J

1991-12-01

When occupational health personnel, especially occupational physicians search bibliographies, they usually have to search bibliographies by themselves. Also, if a library is not available because of the location of their work place, they might have to rely on online databases. Although there are many commercial databases in the world, people who seldom use them, will have problems with on-line searching, such as user-computer interface, keywords, and so on. The present study surveyed the best bibliographic searching system in the field of occupational medicine by questionnaire through the use of DIALOG OnDisc MEDLINE as a commercial database. In order to ascertain the problems involved in determining the best bibliographic searching system, a prototype bibliographic searching system was constructed and then evaluated. Finally, solutions for the problems were discussed. These led to the following conclusions: to construct the best bibliographic searching system at the present time, 1) a concept of micro-to-mainframe links (MML) is needed for the computer hardware network; 2) multi-lingual font standards and an excellent common user-computer interface are needed for the computer software; 3) a short course and education of database management systems, and support of personal information processing for retrieved data are necessary for the practical use of the system.

A Novel Quantum-Behaved Bat Algorithm with Mean Best Position Directed for Numerical Optimization

PubMed Central

Zhu, Wenyong; Liu, Zijuan; Duan, Qingyan; Cao, Long

2016-01-01

This paper proposes a novel quantum-behaved bat algorithm with the direction of mean best position (QMBA). In QMBA, the position of each bat is mainly updated by the current optimal solution in the early stage of searching and in the late search it also depends on the mean best position which can enhance the convergence speed of the algorithm. During the process of searching, quantum behavior of bats is introduced which is beneficial to jump out of local optimal solution and make the quantum-behaved bats not easily fall into local optimal solution, and it has better ability to adapt complex environment. Meanwhile, QMBA makes good use of statistical information of best position which bats had experienced to generate better quality solutions. This approach not only inherits the characteristic of quick convergence, simplicity, and easy implementation of original bat algorithm, but also increases the diversity of population and improves the accuracy of solution. Twenty-four benchmark test functions are tested and compared with other variant bat algorithms for numerical optimization the simulation results show that this approach is simple and efficient and can achieve a more accurate solution. PMID:27293424

Development of a One-Stop Data Search and Discovery Engine using Ontologies for Semantic Mappings (HydroSeek)

NASA Astrophysics Data System (ADS)

Piasecki, M.; Beran, B.

2007-12-01

Search engines have changed the way we see the Internet. The ability to find the information by just typing in keywords was a big contribution to the overall web experience. While the conventional search engine methodology worked well for textual documents, locating scientific data remains a problem since they are stored in databases not readily accessible by search engine bots. Considering different temporal, spatial and thematic coverage of different databases, especially for interdisciplinary research it is typically necessary to work with multiple data sources. These sources can be federal agencies which generally offer national coverage or regional sources which cover a smaller area with higher detail. However for a given geographic area of interest there often exists more than one database with relevant data. Thus being able to query multiple databases simultaneously is a desirable feature that would be tremendously useful for scientists. Development of such a search engine requires dealing with various heterogeneity issues. In scientific databases, systems often impose controlled vocabularies which ensure that they are generally homogeneous within themselves but are semantically heterogeneous when moving between different databases. This defines the boundaries of possible semantic related problems making it easier to solve than with the conventional search engines that deal with free text. We have developed a search engine that enables querying multiple data sources simultaneously and returns data in a standardized output despite the aforementioned heterogeneity issues between the underlying systems. This application relies mainly on metadata catalogs or indexing databases, ontologies and webservices with virtual globe and AJAX technologies for the graphical user interface. Users can trigger a search of dozens of different parameters over hundreds of thousands of stations from multiple agencies by providing a keyword, a spatial extent, i.e. a bounding box, and a temporal bracket. As part of this development we have also added an environment that allows users to do some of the semantic tagging, i.e. the linkage of a variable name (which can be anything they desire) to defined concepts in the ontology structure which in turn provides the backbone of the search engine.

What Searches Do Users Run on PEDro? An Analysis of 893,971 Search Commands Over a 6-Month Period.

PubMed

Stevens, Matthew L; Moseley, Anne; Elkins, Mark R; Lin, Christine C-W; Maher, Chris G

2016-08-05

Clinicians must be able to search effectively for relevant research if they are to provide evidence-based healthcare. It is therefore relevant to consider how users search databases of evidence in healthcare, including what information users look for and what search strategies they employ. To date such analyses have been restricted to the PubMed database. Although the Physiotherapy Evidence Database (PEDro) is searched millions of times each year, no studies have investigated how users search PEDro. To assess the content and quality of searches conducted on PEDro. Searches conducted on the PEDro website over 6 months were downloaded and the 'get' commands and page-views extracted. The following data were tabulated: the 25 most common searches; the number of search terms used; the frequency of use of simple and advanced searches, including the use of each advanced search field; and the frequency of use of various search strategies. Between August 2014 and January 2015, 893,971 search commands were entered on PEDro. Fewer than 18 % of these searches used the advanced search features of PEDro. 'Musculoskeletal' was the most common subdiscipline searched, while 'low back pain' was the most common individual search. Around 20 % of all searches contained errors. PEDro is a commonly used evidence resource, but searching appears to be sub-optimal in many cases. The effectiveness of searches conducted by users needs to improve, which could be facilitated by methods such as targeted training and amending the search interface.

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.

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

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

PubMed

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.

Exponential vanishing of the ground-state gap of the quantum random energy model via adiabatic quantum computing

NASA Astrophysics Data System (ADS)

Adame, J.; Warzel, S.

2015-11-01

In this note, we use ideas of Farhi et al. [Int. J. Quantum. Inf. 6, 503 (2008) and Quantum Inf. Comput. 11, 840 (2011)] who link a lower bound on the run time of their quantum adiabatic search algorithm to an upper bound on the energy gap above the ground-state of the generators of this algorithm. We apply these ideas to the quantum random energy model (QREM). Our main result is a simple proof of the conjectured exponential vanishing of the energy gap of the QREM.

Exponential vanishing of the ground-state gap of the quantum random energy model via adiabatic quantum computing

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

Adame, J.; Warzel, S., E-mail: warzel@ma.tum.de

In this note, we use ideas of Farhi et al. [Int. J. Quantum. Inf. 6, 503 (2008) and Quantum Inf. Comput. 11, 840 (2011)] who link a lower bound on the run time of their quantum adiabatic search algorithm to an upper bound on the energy gap above the ground-state of the generators of this algorithm. We apply these ideas to the quantum random energy model (QREM). Our main result is a simple proof of the conjectured exponential vanishing of the energy gap of the QREM.

MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.

PubMed

Gacesa, Ranko; Zucko, Jurica; Petursdottir, Solveig K; Gudmundsdottir, Elisabet Eik; Fridjonsson, Olafur H; Diminic, Janko; Long, Paul F; Cullum, John; Hranueli, Daslav; Hreggvidsson, Gudmundur O; Starcevic, Antonio

2017-06-01

The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya . The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described. In addition to standard assembly of reads, a novel 'functional' assembly was developed, in which screening of reads with the HMM profiles occurs before the assembly. The AMYLOMICS database incorporates additional HMM profiles for carbohydrate-modifying enzymes and it is illustrated how the combination of HMM and BLAST analyses helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.

Characterizing the genetic structure of a forensic DNA database using a latent variable approach.

PubMed

Kruijver, Maarten

2016-07-01

Several problems in forensic genetics require a representative model of a forensic DNA database. Obtaining an accurate representation of the offender database can be difficult, since databases typically contain groups of persons with unregistered ethnic origins in unknown proportions. We propose to estimate the allele frequencies of the subpopulations comprising the offender database and their proportions from the database itself using a latent variable approach. We present a model for which parameters can be estimated using the expectation maximization (EM) algorithm. This approach does not rely on relatively small and possibly unrepresentative population surveys, but is driven by the actual genetic composition of the database only. We fit the model to a snapshot of the Dutch offender database (2014), which contains close to 180,000 profiles, and find that three subpopulations suffice to describe a large fraction of the heterogeneity in the database. We demonstrate the utility and reliability of the approach with three applications. First, we use the model to predict the number of false leads obtained in database searches. We assess how well the model predicts the number of false leads obtained in mock searches in the Dutch offender database, both for the case of familial searching for first degree relatives of a donor and searching for contributors to three-person mixtures. Second, we study the degree of partial matching between all pairs of profiles in the Dutch database and compare this to what is predicted using the latent variable approach. Third, we use the model to provide evidence to support that the Dutch practice of estimating match probabilities using the Balding-Nichols formula with a native Dutch reference database and θ=0.03 is conservative. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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

PubMed

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

2015-01-01

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

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

PubMed

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

2014-06-10

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.

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

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…

Parallel database search and prime factorization with magnonic holographic memory devices

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

Khitun, Alexander

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 exploitmore » 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.« less

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.

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 discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/ .

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics

PubMed Central

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

2016-01-01

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 non-redundant 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 discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/. PMID:27577934

STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.

PubMed

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 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. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

Issac, Biju; Raghava, G P S

2002-09-01

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

Analysis of Users' Searches of CD-ROM Databases in the National and University Library in Zagreb.

ERIC Educational Resources Information Center

Jokic, Maja

1997-01-01

Investigates the search behavior of CD-ROM database users in Zagreb (Croatia) libraries: one group needed a minimum of technical assistance, and the other was completely independent. Highlights include the use of questionnaires and transaction log analysis and the need for end-user education. The questionnaire and definitions of search process…

Parallel simulations of Grover's algorithm for closest match search in neutron monitor data

NASA Astrophysics Data System (ADS)

Kussainov, Arman; White, Yelena

We are studying the parallel implementations of Grover's closest match search algorithm for neutron monitor data analysis. This includes data formatting, and matching quantum parameters to a conventional structure of a chosen programming language and selected experimental data type. We have employed several workload distribution models based on acquired data and search parameters. As a result of these simulations, we have an understanding of potential problems that may arise during configuration of real quantum computational devices and the way they could run tasks in parallel. The work was supported by the Science Committee of the Ministry of Science and Education of the Republic of Kazakhstan Grant #2532/GF3.

Tautomerism in chemical information management systems

NASA Astrophysics Data System (ADS)

Warr, Wendy A.

2010-06-01

Tautomerism has an impact on many of the processes in chemical information management systems including novelty checking during registration into chemical structure databases; storage of structures; exact and substructure searching in chemical structure databases; and depiction of structures retrieved by a search. The approaches taken by 27 different software vendors and database producers are compared. It is hoped that this comparison will act as a discussion document that could ultimately improve databases and software for researchers in the future.

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.

Mass measurement errors of Fourier-transform mass spectrometry (FTMS): distribution, recalibration, and application.

PubMed

Zhang, Jiyang; Ma, Jie; Dou, Lei; Wu, Songfeng; Qian, Xiaohong; Xie, Hongwei; Zhu, Yunping; He, Fuchu

2009-02-01

The hybrid linear trap quadrupole Fourier-transform (LTQ-FT) ion cyclotron resonance mass spectrometer, an instrument with high accuracy and resolution, is widely used in the identification and quantification of peptides and proteins. However, time-dependent errors in the system may lead to deterioration of the accuracy of these instruments, negatively influencing the determination of the mass error tolerance (MET) in database searches. Here, a comprehensive discussion of LTQ/FT precursor ion mass error is provided. On the basis of an investigation of the mass error distribution, we propose an improved recalibration formula and introduce a new tool, FTDR (Fourier-transform data recalibration), that employs a graphic user interface (GUI) for automatic calibration. It was found that the calibration could adjust the mass error distribution to more closely approximate a normal distribution and reduce the standard deviation (SD). Consequently, we present a new strategy, LDSF (Large MET database search and small MET filtration), for database search MET specification and validation of database search results. As the name implies, a large-MET database search is conducted and the search results are then filtered using the statistical MET estimated from high-confidence results. By applying this strategy to a standard protein data set and a complex data set, we demonstrate the LDSF can significantly improve the sensitivity of the result validation procedure.

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

PubMed

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

2009-01-01

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

Cost and Search Result Comparisons of BRS After Dark and Knowledge Index.

ERIC Educational Resources Information Center

Cloud, Gayla Staples; Hambric, Jacqueline

This two-part study was designed (1) to determine differences in the costs of searching BRS After Dark (BRS AD) and Knowledge Index (KI) generally and across ten selected databases, and (2) to determine whether there is a difference in the citations retrieved when the same search is conducted on the same database in both systems. Study methodology…

PubMed searches: overview and strategies for clinicians.

PubMed

Lindsey, Wesley T; Olin, Bernie R

2013-04-01

PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search.

Secure quantum private information retrieval using phase-encoded queries

NASA Astrophysics Data System (ADS)

Olejnik, Lukasz

2011-08-01

We propose a quantum solution to the classical private information retrieval (PIR) problem, which allows one to query a database in a private manner. The protocol offers privacy thresholds and allows the user to obtain information from a database in a way that offers the potential adversary, in this model the database owner, no possibility of deterministically establishing the query contents. This protocol may also be viewed as a solution to the symmetrically private information retrieval problem in that it can offer database security (inability for a querying user to steal its contents). Compared to classical solutions, the protocol offers substantial improvement in terms of communication complexity. In comparison with the recent quantum private queries [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.100.230502 100, 230502 (2008)] protocol, it is more efficient in terms of communication complexity and the number of rounds, while offering a clear privacy parameter. We discuss the security of the protocol and analyze its strengths and conclude that using this technique makes it challenging to obtain the unconditional (in the information-theoretic sense) privacy degree; nevertheless, in addition to being simple, the protocol still offers a privacy level. The oracle used in the protocol is inspired both by the classical computational PIR solutions as well as the Deutsch-Jozsa oracle.

Secure quantum private information retrieval using phase-encoded queries

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

Olejnik, Lukasz

We propose a quantum solution to the classical private information retrieval (PIR) problem, which allows one to query a database in a private manner. The protocol offers privacy thresholds and allows the user to obtain information from a database in a way that offers the potential adversary, in this model the database owner, no possibility of deterministically establishing the query contents. This protocol may also be viewed as a solution to the symmetrically private information retrieval problem in that it can offer database security (inability for a querying user to steal its contents). Compared to classical solutions, the protocol offersmore » substantial improvement in terms of communication complexity. In comparison with the recent quantum private queries [Phys. Rev. Lett. 100, 230502 (2008)] protocol, it is more efficient in terms of communication complexity and the number of rounds, while offering a clear privacy parameter. We discuss the security of the protocol and analyze its strengths and conclude that using this technique makes it challenging to obtain the unconditional (in the information-theoretic sense) privacy degree; nevertheless, in addition to being simple, the protocol still offers a privacy level. The oracle used in the protocol is inspired both by the classical computational PIR solutions as well as the Deutsch-Jozsa oracle.« less

An Efficient Quantum Somewhat Homomorphic Symmetric Searchable Encryption

NASA Astrophysics Data System (ADS)

Sun, Xiaoqiang; Wang, Ting; Sun, Zhiwei; Wang, Ping; Yu, Jianping; Xie, Weixin

2017-04-01

In 2009, Gentry first introduced an ideal lattices fully homomorphic encryption (FHE) scheme. Later, based on the approximate greatest common divisor problem, learning with errors problem or learning with errors over rings problem, FHE has developed rapidly, along with the low efficiency and computational security. Combined with quantum mechanics, Liang proposed a symmetric quantum somewhat homomorphic encryption (QSHE) scheme based on quantum one-time pad, which is unconditional security. And it was converted to a quantum fully homomorphic encryption scheme, whose evaluation algorithm is based on the secret key. Compared with Liang's QSHE scheme, we propose a more efficient QSHE scheme for classical input states with perfect security, which is used to encrypt the classical message, and the secret key is not required in the evaluation algorithm. Furthermore, an efficient symmetric searchable encryption (SSE) scheme is constructed based on our QSHE scheme. SSE is important in the cloud storage, which allows users to offload search queries to the untrusted cloud. Then the cloud is responsible for returning encrypted files that match search queries (also encrypted), which protects users' privacy.

Publication and Retrieval of Computational Chemical-Physical Data Via the Semantic Web. Final Technical Report

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

Ostlund, Neil

This research showed the feasibility of applying the concepts of the Semantic Web to Computation Chemistry. We have created the first web portal (www.chemsem.com) that allows data created in the calculations of quantum chemistry, and other such chemistry calculations to be placed on the web in a way that makes the data accessible to scientists in a semantic form never before possible. The semantic web nature of the portal allows data to be searched, found, and used as an advance over the usual approach of a relational database. The semantic data on our portal has the nature of a Giantmore » Global Graph (GGG) that can be easily merged with related data and searched globally via a SPARQL Protocol and RDF Query Language (SPARQL) that makes global searches for data easier than with traditional methods. Our Semantic Web Portal requires that the data be understood by a computer and hence defined by an ontology (vocabulary). This ontology is used by the computer in understanding the data. We have created such an ontology for computational chemistry (purl.org/gc) that encapsulates a broad knowledge of the field of computational chemistry. We refer to this ontology as the Gainesville Core. While it is perhaps the first ontology for computational chemistry and is used by our portal, it is only a start of what must be a long multi-partner effort to define computational chemistry. In conjunction with the above efforts we have defined a new potential file standard (Common Standard for eXchange – CSX for computational chemistry data). This CSX file is the precursor of data in the Resource Description Framework (RDF) form that the semantic web requires. Our portal translates CSX files (as well as other computational chemistry data files) into RDF files that are part of the graph database that the semantic web employs. We propose a CSX file as a convenient way to encapsulate computational chemistry data.« less

An ontology-based search engine for protein-protein interactions

PubMed Central

2010-01-01

Background Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. Results We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Conclusion Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology. PMID:20122195

An ontology-based search engine for protein-protein interactions.

PubMed

Park, Byungkyu; Han, Kyungsook

2010-01-18

Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.

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

LiverTox: Clinical and Research Information on Drug-Induced Liver Injury

MedlinePlus

... News Information Resources Glossary Abbreviations SEARCH THE LIVERTOX DATABASE Search for a specific medication, herbal or supplement: ... About Us . Disclaimer. Information presented in the LiverTox database is derived from the scientific literature and public ...

A comparison of the performance of seven key bibliographic databases in identifying all relevant systematic reviews of interventions for hypertension.

PubMed

Rathbone, John; Carter, Matt; Hoffmann, Tammy; Glasziou, Paul

2016-02-09

Bibliographic databases are the primary resource for identifying systematic reviews of health care interventions. Reliable retrieval of systematic reviews depends on the scope of indexing used by database providers. Therefore, searching one database may be insufficient, but it is unclear how many need to be searched. We sought to evaluate the performance of seven major bibliographic databases for the identification of systematic reviews for hypertension. We searched seven databases (Cochrane library, Database of Abstracts of Reviews of Effects (DARE), Excerpta Medica Database (EMBASE), Epistemonikos, Medical Literature Analysis and Retrieval System Online (MEDLINE), PubMed Health and Turning Research Into Practice (TRIP)) from 2003 to 2015 for systematic reviews of any intervention for hypertension. Citations retrieved were screened for relevance, coded and checked for screening consistency using a fuzzy text matching query. The performance of each database was assessed by calculating its sensitivity, precision, the number of missed reviews and the number of unique records retrieved. Four hundred systematic reviews were identified for inclusion from 11,381 citations retrieved from seven databases. No single database identified all the retrieved systematic reviews for hypertension. EMBASE identified the most reviews (sensitivity 69 %) but also retrieved the most irrelevant citations with 7.2 % precision (Pr). The sensitivity of the Cochrane library was 60 %, DARE 57 %, MEDLINE 57 %, PubMed Health 53 %, Epistemonikos 49 % and TRIP 33 %. EMBASE contained the highest number of unique records (n = 43). The Cochrane library identified seven unique records and had the highest precision (Pr = 30 %), followed by Epistemonikos (n = 2, Pr = 19 %). No unique records were found in PubMed Health (Pr = 24 %) DARE (Pr = 21 %), TRIP (Pr = 10 %) or MEDLINE (Pr = 10 %). Searching EMBASE and the Cochrane library identified 88 % of all systematic reviews in the reference set, and searching the freely available databases (Cochrane, Epistemonikos, MEDLINE) identified 83 % of all the reviews. The databases were re-analysed after systematic reviews of non-conventional interventions (e.g. yoga, acupuncture) were removed. Similarly, no database identified all the retrieved systematic reviews. EMBASE identified the most relevant systematic reviews (sensitivity 73 %) but also retrieved the most irrelevant citations with Pr = 5 %. The sensitivity of the Cochrane database was 62 %, followed by MEDLINE (60 %), DARE (55 %), PubMed Health (54 %), Epistemonikos (50 %) and TRIP (31 %). The precision of the Cochrane library was the highest (20 %), followed by PubMed Health (Pr = 16 %), DARE (Pr = 13 %), Epistemonikos (Pr = 12 %), MEDLINE (Pr = 6 %), TRIP (Pr = 6 %) and EMBASE (Pr = 5 %). EMBASE contained the most unique records (n = 34). The Cochrane library identified seven unique records. The other databases held no unique records. The coverage of bibliographic databases varies considerably due to differences in their scope and content. Researchers wishing to identify systematic reviews should not rely on one database but search multiple databases.

Quantum-secured blockchain

NASA Astrophysics Data System (ADS)

Kiktenko, E. O.; Pozhar, N. O.; Anufriev, M. N.; Trushechkin, A. S.; Yunusov, R. R.; Kurochkin, Y. V.; Lvovsky, A. I.; Fedorov, A. K.

2018-07-01

Blockchain is a distributed database which is cryptographically protected against malicious modifications. While promising for a wide range of applications, current blockchain platforms rely on digital signatures, which are vulnerable to attacks by means of quantum computers. The same, albeit to a lesser extent, applies to cryptographic hash functions that are used in preparing new blocks, so parties with access to quantum computation would have unfair advantage in procuring mining rewards. Here we propose a possible solution to the quantum era blockchain challenge and report an experimental realization of a quantum-safe blockchain platform that utilizes quantum key distribution across an urban fiber network for information-theoretically secure authentication. These results address important questions about realizability and scalability of quantum-safe blockchains for commercial and governmental applications.

Recommender engine for continuous-time quantum Monte Carlo methods

NASA Astrophysics Data System (ADS)

Huang, Li; Yang, Yi-feng; Wang, Lei

2017-03-01

Recommender systems play an essential role in the modern business world. They recommend favorable items such as books, movies, and search queries to users based on their past preferences. Applying similar ideas and techniques to Monte Carlo simulations of physical systems boosts their efficiency without sacrificing accuracy. Exploiting the quantum to classical mapping inherent in the continuous-time quantum Monte Carlo methods, we construct a classical molecular gas model to reproduce the quantum distributions. We then utilize powerful molecular simulation techniques to propose efficient quantum Monte Carlo updates. The recommender engine approach provides a general way to speed up the quantum impurity solvers.

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.

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases

PubMed Central

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-01-01

Background and Aims: The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Methods: Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. Results: The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. Conclusion: PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles. PMID:26236086

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases.

PubMed

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-06-01

The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles.

Prairie Resources

Science.gov Websites

Search Prairie Resources for Students Plant Database Plant Database Butterfly Info Butterfly Info Insects Insect Database Frogs Frog Info Bird Database Bird Database Online Prairie Data Online Prairie Data

The use of Research Electronic Data Capture (REDCap) software to create a database of librarian-mediated literature searches.

PubMed

Lyon, Jennifer A; Garcia-Milian, Rolando; Norton, Hannah F; Tennant, Michele R

2014-01-01

Expert-mediated literature searching, a keystone service in biomedical librarianship, would benefit significantly from regular methodical review. This article 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.

Efficient bibliographic searches on allergy using ISI databases.

PubMed

Sáez Gómez, J M; Annan, J W; Negro Alvarez, J M; Guillen-Grima, F; Bozzola, C M; Ivancevich, J C; Aguinaga Ontoso, E

2008-01-01

The aim of this article is to provide an introduction to using databases from the Thomson ISI Web of Knowledge, with special reference to Citation Indexes as an analysis tool for publications, and also to explain the meaning of the well-known Impact Factor. We present the partially modified new Consultation Interface to enhance information search routines of these databases. It introduces distinctive methods in search bibliography, including the correct application of analysis tools, paying particular attention to Journal Citation Reports and Impact Factor. We finish this article with comment on the consequences of using the Impact Factor as a quality indicator for the assessment of journals and publications, and how to ensure measures for indexing in the Thomson ISI Databases.

The MPI-Mainz UV/VIS Spectral Atlas of Gaseous Molecules of Atmospheric Interest

NASA Astrophysics Data System (ADS)

Sander, Rolf; Keller-Rudek, Hannelore; Moortgat, Geert; Sörensen, Rüdiger

2014-05-01

Measurements from satellites can be used to obtain global concentration maps of atmospheric trace constituents. Critical parameters needed in the analysis of the satellite data are the absorption cross sections of the observed molecules. Here, we present the MPI-Mainz UV/VIS Spectral Atlas, which is a large collection of more than 5000 absorption cross section and quantum yield data files in the ultraviolet and visible (UV/VIS) wavelength region for gaseous molecules and radicals primarily of atmospheric interest. The data files contain results of individual measurements, covering research of almost a whole century. To compare and visualize the data sets, multicoloured graphical representations have been created. The Spectral Atlas is available on the internet at http://www.uv-vis-spectral-atlas-mainz.org. It has been completely overhauled and now appears with improved browse and search options, based on PostgreSQL, Django and Python database software. The web pages are continuously updated.

The MPI-Mainz UV/VIS Spectral Atlas of Gaseous Molecules of Atmospheric Interest

NASA Astrophysics Data System (ADS)

Keller-Rudek, H.; Moortgat, G. K.; Sander, R.; Sörensen, R.

2013-08-01

We present the MPI-Mainz UV/VIS Spectral Atlas, which is a large collection of absorption cross sections and quantum yields in the ultraviolet and visible (UV/VIS) wavelength region for gaseous molecules and radicals primarily of atmospheric interest. The data files contain results of individual measurements, covering research of almost a whole century. To compare and visualize the data sets, multicoloured graphical representations have been created. The Spectral Atlas is available on the internet at http://www.uv-vis-spectral-atlas-mainz.org. It now appears with improved browse and search options, based on new database software. In addition to the web pages, which are continuously updated, a frozen version of the data is available under the doi:10.5281/zenodo.6951.

Use of instruments to evaluate leadership in nursing and health services.

PubMed

Carrara, Gisleangela Lima Rodrigues; Bernardes, Andrea; Balsanelli, Alexandre Pazetto; Camelo, Silvia Helena Henriques; Gabriel, Carmen Silvia; Zanetti, Ariane Cristina Barboza

2018-03-12

To identify the available scientific evidence about the use of instruments for the evaluation of leadership in health and nursing services and verify the use of leadership styles/models/theories in the construction of these tools. Integrative literature review of indexed studies in the LILACS, PUBMED, CINAHL and EMBASE databases from 2006 to 2016. Thirty-eight articles were analyzed, exhibiting 19 leadership evaluation tools; the most used were the Multifactor Leadership Questionnaire, the Global Transformational Leadership Scale, the Leadership Practices Inventory, the Servant Leadership Questionnaire, the Servant Leadership Survey and the Authentic Leadership Questionnaire. The literature search allowed to identify the main theories/styles/models of contemporary leadership and analyze their use in the design of leadership evaluation tools, with the transformational, situational, servant and authentic leadership categories standing out as the most prominent. To a lesser extent, the quantum, charismatic and clinical leadership types were evidenced.

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

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

Beer, Tjaart A. P. de; Laskowski, Roman A.; Duban, Mark-Eugene

LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews.

PubMed

Bramer, Wichor M; Giustini, Dean; Kramer, Bianca Mr; Anderson, Pf

2013-12-23

The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. GS' overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be performed by experienced searchers creating searches that maximize recall for as many databases as deemed necessary by the search expert.

The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews

PubMed Central

2013-01-01

Background The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. Methods The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. Results GS’ overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Conclusions Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be performed by experienced searchers creating searches that maximize recall for as many databases as deemed necessary by the search expert. PMID:24360284

An Adaptive Cultural Algorithm with Improved Quantum-behaved Particle Swarm Optimization for Sonar Image Detection.

PubMed

Wang, Xingmei; Hao, Wenqian; Li, Qiming

2017-12-18

This paper proposes an adaptive cultural algorithm with improved quantum-behaved particle swarm optimization (ACA-IQPSO) to detect the underwater sonar image. In the population space, to improve searching ability of particles, iterative times and the fitness value of particles are regarded as factors to adaptively adjust the contraction-expansion coefficient of the quantum-behaved particle swarm optimization algorithm (QPSO). The improved quantum-behaved particle swarm optimization algorithm (IQPSO) can make particles adjust their behaviours according to their quality. In the belief space, a new update strategy is adopted to update cultural individuals according to the idea of the update strategy in shuffled frog leaping algorithm (SFLA). Moreover, to enhance the utilization of information in the population space and belief space, accept function and influence function are redesigned in the new communication protocol. The experimental results show that ACA-IQPSO can obtain good clustering centres according to the grey distribution information of underwater sonar images, and accurately complete underwater objects detection. Compared with other algorithms, the proposed ACA-IQPSO has good effectiveness, excellent adaptability, a powerful searching ability and high convergence efficiency. Meanwhile, the experimental results of the benchmark functions can further demonstrate that the proposed ACA-IQPSO has better searching ability, convergence efficiency and stability.

Hospital nurses' information retrieval behaviours in relation to evidence based nursing: a literature review.

PubMed

Alving, Berit Elisabeth; Christensen, Janne Buck; Thrysøe, Lars

2018-03-01

The purpose of this literature review is to provide an overview of the information retrieval behaviour of clinical nurses, in terms of the use of databases and other information resources and their frequency of use. Systematic searches carried out in five databases and handsearching were used to identify the studies from 2010 to 2016, with a populations, exposures and outcomes (PEO) search strategy, focusing on the question: In which databases or other information resources do hospital nurses search for evidence based information, and how often? Of 5272 titles retrieved based on the search strategy, only nine studies fulfilled the criteria for inclusion. The studies are from the United States, Canada, Taiwan and Nigeria. The results show that hospital nurses' primary choice of source for evidence based information is Google and peers, while bibliographic databases such as PubMed are secondary choices. Data on frequency are only included in four of the studies, and data are heterogenous. The reasons for choosing Google and peers are primarily lack of time; lack of information; lack of retrieval skills; or lack of training in database searching. Only a few studies are published on clinical nurses' retrieval behaviours, and more studies are needed from Europe and Australia. © 2018 Health Libraries Group.

Robust QKD-based private database queries based on alternative sequences of single-qubit measurements

NASA Astrophysics Data System (ADS)

Yang, YuGuang; Liu, ZhiChao; Chen, XiuBo; Zhou, YiHua; Shi, WeiMin

2017-12-01

Quantum channel noise may cause the user to obtain a wrong answer and thus misunderstand the database holder for existing QKD-based quantum private query (QPQ) protocols. In addition, an outside attacker may conceal his attack by exploiting the channel noise. We propose a new, robust QPQ protocol based on four-qubit decoherence-free (DF) states. In contrast to existing QPQ protocols against channel noise, only an alternative fixed sequence of single-qubit measurements is needed by the user (Alice) to measure the received DF states. This property makes it easy to implement the proposed protocol by exploiting current technologies. Moreover, to retain the advantage of flexible database queries, we reconstruct Alice's measurement operators so that Alice needs only conditioned sequences of single-qubit measurements.

Scaling of the local quantum uncertainty at quantum phase transitions

NASA Astrophysics Data System (ADS)

Coulamy, I. B.; Warnes, J. H.; Sarandy, M. S.; Saguia, A.

2016-04-01

We investigate the local quantum uncertainty (LQU) between a block of L qubits and one single qubit in a composite system of n qubits driven through a quantum phase transition (QPT). A first-order QPT is analytically considered through a Hamiltonian implementation of the quantum search. In the case of second-order QPTs, we consider the transverse-field Ising chain via a numerical analysis through density matrix renormalization group. For both cases, we compute the LQU for finite-sizes as a function of L and of the coupling parameter, analyzing its pronounced behavior at the QPT.

PlantGI: a database for searching gene indices in agricultural plants developed at NIAB, Korea

PubMed Central

Kim, Chang Kug; Choi, Ji Weon; Park, DongSuk; Kang, Man Jung; Seol, Young-Joo; Hyun, Do Yoon; Hahn, Jang Ho

2008-01-01

The Plant Gene Index (PlantGI) database is developed as a web-based search system with search capabilities for keywords to provide information on gene indices specifically for agricultural plants. The database contains specific Gene Index information for ten agricultural species, namely, rice, Chinese cabbage, wheat, maize, soybean, barley, mushroom, Arabidopsis, hot pepper and tomato. PlantGI differs from other Gene Index databases in being specific to agricultural plant species and thus complements services from similar other developments. The database includes options for interactive mining of EST CONTIGS and assembled EST data for user specific keyword queries. The current version of PlantGI contains a total of 34,000 EST CONTIGS data for rice (8488 records), wheat (8560 records), maize (4570 records), soybean (3726 records), barley (3417 records), Chinese cabbage (3602 records), tomato (1236 records), hot pepper (998 records), mushroom (130 records) and Arabidopsis (8 records). Availability The database is available for free at http://www.niab.go.kr/nabic/. PMID:18685722

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.

Spatial search on a two-dimensional lattice with long-range interactions

NASA Astrophysics Data System (ADS)

Osada, Tomo; Sanaka, Kaoru; Munro, William J.; Nemoto, Kae

2018-06-01

Quantum-walk-based algorithms that search a marked location among N locations on a d -dimensional lattice succeeds in time O (√{N }) for d >2 , while this is not found to be possible when d =2 . In this paper, we consider a spatial search algorithm using continuous-time quantum walk on a two-dimensional square lattice with the existence of additional long-range edges. We examined such a search on a probabilistic graph model where an edge connecting non-nearest-neighbor lattice points i and j apart by a distance |i -j | is added by probability pi j=|i-j | -α(α ≥0 ) . Through numerical analysis, we found that the search succeeds in time O (√{N }) when α ≤αc=2.4 ±0.1 . For α >2 , the expectation value of the additional long-range edges on each node scales as a constant when N →∞ , which means that search time of O (√{N }) is achieved on a graph with average degree scaling as a constant.

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

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.

Generalized Grover's Algorithm for Multiple Phase Inversion States

NASA Astrophysics Data System (ADS)

Byrnes, Tim; Forster, Gary; Tessler, Louis

2018-02-01

Grover's algorithm is a quantum search algorithm that proceeds by repeated applications of the Grover operator and the Oracle until the state evolves to one of the target states. In the standard version of the algorithm, the Grover operator inverts the sign on only one state. Here we provide an exact solution to the problem of performing Grover's search where the Grover operator inverts the sign on N states. We show the underlying structure in terms of the eigenspectrum of the generalized Hamiltonian, and derive an appropriate initial state to perform the Grover evolution. This allows us to use the quantum phase estimation algorithm to solve the search problem in this generalized case, completely bypassing the Grover algorithm altogether. We obtain a time complexity of this case of √{D /Mα }, where D is the search space dimension, M is the number of target states, and α ≈1 , which is close to the optimal scaling.

SinEx DB: a database for single exon coding sequences in mammalian genomes.

PubMed

Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

2016-01-01

Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

Analysis of Patent Activity in the Field of Quantum Information Processing

NASA Astrophysics Data System (ADS)

Winiarczyk, Ryszard; Gawron, Piotr; Miszczak, Jarosław Adam; Pawela, Łukasz; Puchała, Zbigniew

2013-03-01

This paper provides an analysis of patent activity in the field of quantum information processing. Data from the PatentScope database from the years 1993-2011 was used. In order to predict the future trends in the number of filed patents time series models were used.

Database Access Systems.

ERIC Educational Resources Information Center

Dalrymple, Prudence W.; Roderer, Nancy K.

1994-01-01

Highlights the changes that have occurred from 1987-93 in database access systems. Topics addressed include types of databases, including CD-ROMs; enduser interface; database selection; database access management, including library instruction and use of primary literature; economic issues; database users; the search process; and improving…

Front-End/Gateway Software: Availability and Usefulness.

ERIC Educational Resources Information Center

Kesselman, Martin

1985-01-01

Reviews features of front-end software packages (interface between user and online system)--database selection, search strategy development, saving and downloading, hardware and software requirements, training and documentation, online systems and database accession, and costs--and discusses gateway services (user searches through intermediary…

Digital Equipment Corporation's CRDOM Software and Database Publications.

ERIC Educational Resources Information Center

Adams, Michael Q.

1986-01-01

Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

Complexity of the Quantum Adiabatic Algorithm

NASA Astrophysics Data System (ADS)

Hen, Itay

2013-03-01

The Quantum Adiabatic Algorithm (QAA) has been proposed as a mechanism for efficiently solving optimization problems on a quantum computer. Since adiabatic computation is analog in nature and does not require the design and use of quantum gates, it can be thought of as a simpler and perhaps more profound method for performing quantum computations that might also be easier to implement experimentally. While these features have generated substantial research in QAA, to date there is still a lack of solid evidence that the algorithm can outperform classical optimization algorihms. Here, we discuss several aspects of the quantum adiabatic algorithm: We analyze the efficiency of the algorithm on several ``hard'' (NP) computational problems. Studying the size dependence of the typical minimum energy gap of the Hamiltonians of these problems using quantum Monte Carlo methods, we find that while for most problems the minimum gap decreases exponentially with the size of the problem, indicating that the QAA is not more efficient than existing classical search algorithms, for other problems there is evidence to suggest that the gap may be polynomial near the phase transition. We also discuss applications of the QAA to ``real life'' problems and how they can be implemented on currently available (albeit prototypical) quantum hardware such as ``D-Wave One'', that impose serious restrictions as to which type of problems may be tested. Finally, we discuss different approaches to find improved implementations of the algorithm such as local adiabatic evolution, adaptive methods, local search in Hamiltonian space and others.

Competitive code-based fast palmprint identification using a set of cover trees

NASA Astrophysics Data System (ADS)

Yue, Feng; Zuo, Wangmeng; Zhang, David; Wang, Kuanquan

2009-06-01

A palmprint identification system recognizes a query palmprint image by searching for its nearest neighbor from among all the templates in a database. When applied on a large-scale identification system, it is often necessary to speed up the nearest-neighbor searching process. We use competitive code, which has very fast feature extraction and matching speed, for palmprint identification. To speed up the identification process, we extend the cover tree method and propose to use a set of cover trees to facilitate the fast and accurate nearest-neighbor searching. We can use the cover tree method because, as we show, the angular distance used in competitive code can be decomposed into a set of metrics. Using the Hong Kong PolyU palmprint database (version 2) and a large-scale palmprint database, our experimental results show that the proposed method searches for nearest neighbors faster than brute force searching.

MEDLINE versus EMBASE and CINAHL for telemedicine searches.

PubMed

Bahaadinbeigy, Kambiz; Yogesan, Kanagasingam; Wootton, Richard

2010-10-01

Researchers in the domain of telemedicine throughout the world tend to search multiple bibliographic databases to retrieve the highest possible number of publications when conducting review projects. Medical Literature Analysis and Retrieval System Online (MEDLINE), Excerpta Medica Database (EMBASE), and Cumulative Index to Nursing and Allied Health Literature (CINAHL) are three popular databases in the discipline of biomedicine that are used for conducting reviews. Access to the MEDLINE database is free and easy, whereas EMBASE and CINAHL are not free and sometimes not easy to access for researchers in small research centers. This project sought to compare MEDLINE with EMBASE and CINAHL to estimate what proportion of potentially relevant publications would be missed when only MEDLINE is used in a review project, in comparison to when EMBASE and CINAHL are also used. Twelve simple keywords relevant to 12 different telemedicine applications were searched using all three databases, and the results were compared. About 9%-18% of potentially relevant articles would have been missed if MEDLINE had been the only database used. It is preferable if all three or more databases are used when conducting a review in telemedicine. Researchers from developing countries or small research institutions could rely on only MEDLINE, but they would loose 9%-18% of the potentially relevant publications. Searching MEDLINE alone is not ideal, but in a resource-constrained situation, it is definitely better than nothing.

Improvements to the Magnetics Information Consortium (MagIC) Paleo and Rock Magnetic Database

NASA Astrophysics Data System (ADS)

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

2015-12-01

The Magnetic Information Consortium (MagIC) database (http://earthref.org/MagIC/) continues to improve the ease of data uploading and editing, the creation of complex searches, data visualization, and data downloads for the paleomagnetic, geomagnetic, and rock magnetic communities. Online data editing is now available and the need for proprietary spreadsheet software is therefore entirely negated. The data owner can change values in the database or delete entries through an HTML 5 web interface that resembles typical spreadsheets in behavior and uses. Additive uploading now allows for additions to data sets to be uploaded with a simple drag and drop interface. Searching the database has improved with the addition of more sophisticated search parameters and with the facility to use them in complex combinations. A comprehensive summary view of a search result has been added for increased quick data comprehension while a raw data view is available if one desires to see all data columns as stored in the database. Data visualization plots (ARAI, equal area, demagnetization, Zijderveld, etc.) are presented with the data when appropriate to aid the user in understanding the dataset. MagIC data associated with individual contributions or from online searches may be downloaded in the tab delimited MagIC text file format for susbsequent offline use and analysis. With input from the paleomagnetic, geomagnetic, and rock magnetic communities, the MagIC database will continue to improve as a data warehouse and resource.

An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values.

PubMed

Sakurai, Nozomu; Ara, Takeshi; Kanaya, Shigehiko; Nakamura, Yukiko; Iijima, Yoko; Enomoto, Mitsuo; Motegi, Takeshi; Aoki, Koh; Suzuki, Hideyuki; Shibata, Daisuke

2013-01-15

High-accuracy mass values detected by high-resolution mass spectrometry analysis enable prediction of elemental compositions, and thus are used for metabolite annotations in metabolomic studies. Here, we report an application of a relational database to significantly improve the rate of elemental composition predictions. By searching a database of pre-calculated elemental compositions with fixed kinds and numbers of atoms, the approach eliminates redundant evaluations of the same formula that occur in repeated calculations with other tools. When our approach is compared with HR2, which is one of the fastest tools available, our database search times were at least 109 times shorter than those of HR2. When a solid-state drive (SSD) was applied, the search time was 488 times shorter at 5 ppm mass tolerance and 1833 times at 0.1 ppm. Even if the search by HR2 was performed with 8 threads in a high-spec Windows 7 PC, the database search times were at least 26 and 115 times shorter without and with the SSD. These improvements were enhanced in a low spec Windows XP PC. We constructed a web service 'MFSearcher' to query the database in a RESTful manner. Available for free at http://webs2.kazusa.or.jp/mfsearcher. The web service is implemented in Java, MySQL, Apache and Tomcat, with all major browsers supported. sakurai@kazusa.or.jp Supplementary data are available at Bioinformatics online.

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.

CHERNOLITTM. Chernobyl Bibliographic Search System

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

Caff, F., Jr.; Kennedy, R.A.; Mahaffey, J.A.

1992-03-02

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world`s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

Chernobyl Bibliographic Search System

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

Carr, Jr, F.; Kennedy, R. A.; Mahaffey, J. A.

1992-05-11

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world''s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

NASA Image eXchange (NIX)

NASA Technical Reports Server (NTRS)

vonOfenheim. William H. C.; Heimerl, N. Lynn; Binkley, Robert L.; Curry, Marty A.; Slater, Richard T.; Nolan, Gerald J.; Griswold, T. Britt; Kovach, Robert D.; Corbin, Barney H.; Hewitt, Raymond W.

1998-01-01

This paper discusses the technical aspects of and the project background for the NASA Image exchange (NIX). NIX, which provides a single entry point to search selected image databases at the NASA Centers, is a meta-search engine (i.e., a search engine that communicates with other search engines). It uses these distributed digital image databases to access photographs, animations, and their associated descriptive information (meta-data). NIX is available for use at the following URL: http://nix.nasa.gov./NIX, which was sponsored by NASAs Scientific and Technical Information (STI) Program, currently serves images from seven NASA Centers. Plans are under way to link image databases from three additional NASA Centers. images and their associated meta-data, which are accessible by NIX, reside at the originating Centers, and NIX utilizes a virtual central site that communicates with each of these sites. Incorporated into the virtual central site are several protocols to support searches from a diverse collection of database engines. The searches are performed in parallel to ensure optimization of response times. To augment the search capability, browse functionality with pre-defined categories has been built into NIX, thereby ensuring dissemination of 'best-of-breed' imagery. As a final recourse, NIX offers access to a help desk via an on-line form to help locate images and information either within the scope of NIX or from available external sources.

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2011 CFR

2011-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2010 CFR

2010-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2014 CFR

2014-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2012 CFR

2012-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2013 CFR

2013-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture.

PubMed

Azman, Syafiq Kamarul; Anwar, Muhammad Zohaib; Henschel, Andreas

2017-07-24

Given the current influx of 16S rRNA profiles of microbiota samples, it is conceivable that large amounts of them eventually are available for search, comparison and contextualization with respect to novel samples. This process facilitates the identification of similar compositional features in microbiota elsewhere and therefore can help to understand driving factors for microbial community assembly. We present Visibiome, a microbiome search engine that can perform exhaustive, phylogeny based similarity search and contextualization of user-provided samples against a comprehensive dataset of 16S rRNA profiles environments, while tackling several computational challenges. In order to scale to high demands, we developed a distributed system that combines web framework technology, task queueing and scheduling, cloud computing and a dedicated database server. To further ensure speed and efficiency, we have deployed Nearest Neighbor search algorithms, capable of sublinear searches in high-dimensional metric spaces in combination with an optimized Earth Mover Distance based implementation of weighted UniFrac. The search also incorporates pairwise (adaptive) rarefaction and optionally, 16S rRNA copy number correction. The result of a query microbiome sample is the contextualization against a comprehensive database of microbiome samples from a diverse range of environments, visualized through a rich set of interactive figures and diagrams, including barchart-based compositional comparisons and ranking of the closest matches in the database. Visibiome is a convenient, scalable and efficient framework to search microbiomes against a comprehensive database of environmental samples. The search engine leverages a popular but computationally expensive, phylogeny based distance metric, while providing numerous advantages over the current state of the art tool.

Application of Quantum Gauss-Jordan Elimination Code to Quantum Secret Sharing Code

NASA Astrophysics Data System (ADS)

Diep, Do Ngoc; Giang, Do Hoang; Phu, Phan Huy

2017-12-01

The QSS codes associated with a MSP code are based on finding an invertible matrix V, solving the system vATMB (s a) = s. We propose a quantum Gauss-Jordan Elimination Procedure to produce such a pivotal matrix V by using the Grover search code. The complexity of solving is of square-root order of the cardinal number of the unauthorized set √ {2^{|B|}}.

Application of Quantum Gauss-Jordan Elimination Code to Quantum Secret Sharing Code

NASA Astrophysics Data System (ADS)

Diep, Do Ngoc; Giang, Do Hoang; Phu, Phan Huy

2018-03-01

The QSS codes associated with a MSP code are based on finding an invertible matrix V, solving the system vATMB (s a)=s. We propose a quantum Gauss-Jordan Elimination Procedure to produce such a pivotal matrix V by using the Grover search code. The complexity of solving is of square-root order of the cardinal number of the unauthorized set √ {2^{|B|}}.

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…

Decision making in family medicine

PubMed Central

Labrecque, Michel; Ratté, Stéphane; Frémont, Pierre; Cauchon, Michel; Ouellet, Jérôme; Hogg, William; McGowan, Jessie; Gagnon, Marie-Pierre; Njoya, Merlin; Légaré, France

2013-01-01

Abstract Objective To compare the ability of users of 2 medical search engines, InfoClinique and the Trip database, to provide correct answers to clinical questions and to explore the perceived effects of the tools on the clinical decision-making process. Design Randomized trial. Setting Three family medicine units of the family medicine program of the Faculty of Medicine at Laval University in Quebec city, Que. Participants Fifteen second-year family medicine residents. Intervention Residents generated 30 structured questions about therapy or preventive treatment (2 questions per resident) based on clinical encounters. Using an Internet platform designed for the trial, each resident answered 20 of these questions (their own 2, plus 18 of the questions formulated by other residents, selected randomly) before and after searching for information with 1 of the 2 search engines. For each question, 5 residents were randomly assigned to begin their search with InfoClinique and 5 with the Trip database. Main outcome measures The ability of residents to provide correct answers to clinical questions using the search engines, as determined by third-party evaluation. After answering each question, participants completed a questionnaire to assess their perception of the engine’s effect on the decision-making process in clinical practice. Results Of 300 possible pairs of answers (1 answer before and 1 after the initial search), 254 (85%) were produced by 14 residents. Of these, 132 (52%) and 122 (48%) pairs of answers concerned questions that had been assigned an initial search with InfoClinique and the Trip database, respectively. Both engines produced an important and similar absolute increase in the proportion of correct answers after searching (26% to 62% for InfoClinique, for an increase of 36%; 24% to 63% for the Trip database, for an increase of 39%; P = .68). For all 30 clinical questions, at least 1 resident produced the correct answer after searching with either search engine. The mean (SD) time of the initial search for each question was 23.5 (7.6) minutes with InfoClinique and 22.3 (7.8) minutes with the Trip database (P = .30). Participants’ perceptions of each engine’s effect on the decision-making process were very positive and similar for both search engines. Conclusion Family medicine residents’ ability to provide correct answers to clinical questions increased dramatically and similarly with the use of both InfoClinique and the Trip database. These tools have strong potential to increase the quality of medical care. PMID:24130286

Role of quantum correlations in light-matter quantum heat engines

NASA Astrophysics Data System (ADS)

Barrios, G. Alvarado; Albarrán-Arriagada, F.; Cárdenas-López, F. A.; Romero, G.; Retamal, J. C.

2017-11-01

We study a quantum Otto engine embedding a working substance composed of a two-level system interacting with a harmonic mode. The physical properties of the substance are described by a generalized quantum Rabi model arising in superconducting circuit realizations. We show that light-matter quantum correlation reduction during the hot bath stage and adiabatic stages act as an indicator for enhanced work extraction and efficiency, respectively. Also, we demonstrate that the anharmonic spectrum of the working substance has a direct impact on the transition from heat engine into refrigerator as the light-matter coupling is increased. These results shed light on the search for optimal conditions in the performance of quantum heat engines.

PLQP & Company: Decidable Logics for Quantum Algorithms

NASA Astrophysics Data System (ADS)

Baltag, Alexandru; Bergfeld, Jort; Kishida, Kohei; Sack, Joshua; Smets, Sonja; Zhong, Shengyang

2014-10-01

We introduce a probabilistic modal (dynamic-epistemic) quantum logic PLQP for reasoning about quantum algorithms. We illustrate its expressivity by using it to encode the correctness of the well-known quantum search algorithm, as well as of a quantum protocol known to solve one of the paradigmatic tasks from classical distributed computing (the leader election problem). We also provide a general method (extending an idea employed in the decidability proof in Dunn et al. (J. Symb. Log. 70:353-359, 2005)) for proving the decidability of a range of quantum logics, interpreted on finite-dimensional Hilbert spaces. We give general conditions for the applicability of this method, and in particular we apply it to prove the decidability of PLQP.

High School Students, Libraries, and the Search Process. An Analysis of Student Materials and Facilities Usage Patterns in Delaware Following Introduction of Online Bibliographic Database Searching.

ERIC Educational Resources Information Center

Mancall, Jacqueline C.; Deskins, Dreama

This report assesses the impact of instruction in online bibliographic database searching on high school students' use of library materials and facilities in three Delaware secondary schools (one public, one parochial, and one private) during the spring of 1984. Most students involved in the analysis were given a brief explanation of online…

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.

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. The method’s graphical environment, along with its computational and probabilistic architectures, represents a rich package that offers analysts and discussants with additional modes of interaction, concise representation, and coherent communication. PMID:22849390

Workflow of the Grover algorithm simulation incorporating CUDA and GPGPU

NASA Astrophysics Data System (ADS)

Lu, Xiangwen; Yuan, Jiabin; Zhang, Weiwei

2013-09-01

The Grover quantum search algorithm, one of only a few representative quantum algorithms, can speed up many classical algorithms that use search heuristics. No true quantum computer has yet been developed. For the present, simulation is one effective means of verifying the search algorithm. In this work, we focus on the simulation workflow using a compute unified device architecture (CUDA). Two simulation workflow schemes are proposed. These schemes combine the characteristics of the Grover algorithm and the parallelism of general-purpose computing on graphics processing units (GPGPU). We also analyzed the optimization of memory space and memory access from this perspective. We implemented four programs on CUDA to evaluate the performance of schemes and optimization. Through experimentation, we analyzed the organization of threads suited to Grover algorithm simulations, compared the storage costs of the four programs, and validated the effectiveness of optimization. Experimental results also showed that the distinguished program on CUDA outperformed the serial program of libquantum on a CPU with a speedup of up to 23 times (12 times on average), depending on the scale of the simulation.

Development of Concepts in the History of Quantum Theory

ERIC Educational Resources Information Center

Heisenberg, Werner

1975-01-01

Traces the development of quantum theory from the concept of the discrete stationary states, to the generalized concept of state, to the search for the elementary particle. States that the concept of the elementary particle should be replaced by the concept of a fundamental symmetry. (MLH)

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.

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.

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.

[International bibliographic databases--Current Contents on disk and in FTP format (Internet): presentation and guide].

PubMed

Bloch-Mouillet, E

1999-01-01

This paper aims to provide technical and practical advice about finding references using Current Contents on disk (Macintosh or PC) or via the Internet (FTP). Seven editions are published each week. They are all organized in the same way and have the same search engine. The Life Sciences edition, extensively used in medical research, is presented here in detail, as an example. This methodological note explains, in French, how to use this reference database. It is designed to be a practical guide for browsing and searching the database, and particularly for creating search profiles adapted to the needs of researchers.

A searching and reporting system for relational databases using a graph-based metadata representation.

PubMed

Hewitt, Robin; Gobbi, Alberto; Lee, Man-Ling

2005-01-01

Relational databases are the current standard for storing and retrieving data in the pharmaceutical and biotech industries. However, retrieving data from a relational database requires specialized knowledge of the database schema and of the SQL query language. At Anadys, we have developed an easy-to-use system for searching and reporting data in a relational database to support our drug discovery project teams. This system is fast and flexible and allows users to access all data without having to write SQL queries. This paper presents the hierarchical, graph-based metadata representation and SQL-construction methods that, together, are the basis of this system's capabilities.

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.

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

Vocabulary Control and the Humanities: A Case Study of the "MLA International Bibliography."

ERIC Educational Resources Information Center

Stebelman, Scott

1994-01-01

Discussion of research in the humanities focuses on the "MLA International Bibliography," the primary database for literary research. Highlights include comparisons to research in the sciences; humanities vocabulary; database search techniques; contextual indexing; examples of searches; thesauri; and software. (43 references) (LRW)

More Databases Searched by a Business Generalist--Part 2: A Veritable Cornucopia of Sources.

ERIC Educational Resources Information Center

Meredith, Meri

1986-01-01

This second installment describes databases irregularly searched in the Business Information Center, Cummins Engine Company (Columbus, Indiana). Highlights include typical research topics (happenings among similar manufacturers); government topics (Department of Defense contracts); market and industry topics; corporate intelligence; and personnel,…

Database systems for knowledge-based discovery.

PubMed

Jagarlapudi, Sarma A R P; Kishan, K V Radha

2009-01-01

Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery.

The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age.

PubMed

Adams, Sam; de Castro, Pablo; Echenique, Pablo; Estrada, Jorge; Hanwell, Marcus D; Murray-Rust, Peter; Sherwood, Paul; Thomas, Jens; Townsend, Joe

2011-10-14

Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education.The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage.Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science.

The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age

PubMed Central

2011-01-01

Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication. In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today. Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education. The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage. Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science. PMID:21999363

Decrease of Fisher information and the information geometry of evolution equations for quantum mechanical probability amplitudes.

PubMed

Cafaro, Carlo; Alsing, Paul M

2018-04-01

The relevance of the concept of Fisher information is increasing in both statistical physics and quantum computing. From a statistical mechanical standpoint, the application of Fisher information in the kinetic theory of gases is characterized by its decrease along the solutions of the Boltzmann equation for Maxwellian molecules in the two-dimensional case. From a quantum mechanical standpoint, the output state in Grover's quantum search algorithm follows a geodesic path obtained from the Fubini-Study metric on the manifold of Hilbert-space rays. Additionally, Grover's algorithm is specified by constant Fisher information. In this paper, we present an information geometric characterization of the oscillatory or monotonic behavior of statistically parametrized squared probability amplitudes originating from special functional forms of the Fisher information function: constant, exponential decay, and power-law decay. Furthermore, for each case, we compute both the computational speed and the availability loss of the corresponding physical processes by exploiting a convenient Riemannian geometrization of useful thermodynamical concepts. Finally, we briefly comment on the possibility of using the proposed methods of information geometry to help identify a suitable trade-off between speed and thermodynamic efficiency in quantum search algorithms.

Decrease of Fisher information and the information geometry of evolution equations for quantum mechanical probability amplitudes

NASA Astrophysics Data System (ADS)

Cafaro, Carlo; Alsing, Paul M.

2018-04-01

The relevance of the concept of Fisher information is increasing in both statistical physics and quantum computing. From a statistical mechanical standpoint, the application of Fisher information in the kinetic theory of gases is characterized by its decrease along the solutions of the Boltzmann equation for Maxwellian molecules in the two-dimensional case. From a quantum mechanical standpoint, the output state in Grover's quantum search algorithm follows a geodesic path obtained from the Fubini-Study metric on the manifold of Hilbert-space rays. Additionally, Grover's algorithm is specified by constant Fisher information. In this paper, we present an information geometric characterization of the oscillatory or monotonic behavior of statistically parametrized squared probability amplitudes originating from special functional forms of the Fisher information function: constant, exponential decay, and power-law decay. Furthermore, for each case, we compute both the computational speed and the availability loss of the corresponding physical processes by exploiting a convenient Riemannian geometrization of useful thermodynamical concepts. Finally, we briefly comment on the possibility of using the proposed methods of information geometry to help identify a suitable trade-off between speed and thermodynamic efficiency in quantum search algorithms.

Near-optimal quantum circuit for Grover's unstructured search using a transverse field

NASA Astrophysics Data System (ADS)

Jiang, Zhang; Rieffel, Eleanor G.; Wang, Zhihui

2017-06-01

Inspired by a class of algorithms proposed by Farhi et al. (arXiv:1411.4028), namely, the quantum approximate optimization algorithm (QAOA), we present a circuit-based quantum algorithm to search for a needle in a haystack, obtaining the same quadratic speedup achieved by Grover's original algorithm. In our algorithm, the problem Hamiltonian (oracle) and a transverse field are applied alternately to the system in a periodic manner. We introduce a technique, based on spin-coherent states, to analyze the composite unitary in a single period. This composite unitary drives a closed transition between two states that have high degrees of overlap with the initial state and the target state, respectively. The transition rate in our algorithm is of order Θ (1 /√{N }) , and the overlaps are of order Θ (1 ) , yielding a nearly optimal query complexity of T ≃√{N }(π /2 √{2 }) . Our algorithm is a QAOA circuit that demonstrates a quantum advantage with a large number of iterations that is not derived from Trotterization of an adiabatic quantum optimization (AQO) algorithm. It also suggests that the analysis required to understand QAOA circuits involves a very different process from estimating the energy gap of a Hamiltonian in AQO.

A New Interface for the Magnetics Information Consortium (MagIC) Paleo and Rock Magnetic Database

NASA Astrophysics Data System (ADS)

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

2014-12-01

The Magnetic Information Consortium (MagIC) database (http://earthref.org/MagIC/) continues to improve the ease of uploading data, the creation of complex searches, data visualization, and data downloads for the paleomagnetic, geomagnetic, and rock magnetic communities. Data uploading has been simplified and no longer requires the use of the Excel SmartBook interface. Instead, properly formatted MagIC text files can be dragged-and-dropped onto an HTML 5 web interface. Data can be uploaded one table at a time to facilitate ease of uploading and data error checking is done online on the whole dataset at once instead of incrementally in an Excel Console. Searching the database has improved with the addition of more sophisticated search parameters and with the ability to use them in complex combinations. Searches may also be saved as permanent URLs for easy reference or for use as a citation in a publication. Data visualization plots (ARAI, equal area, demagnetization, Zijderveld, etc.) are presented with the data when appropriate to aid the user in understanding the dataset. Data from the MagIC database may be downloaded from individual contributions or from online searches for offline use and analysis in the tab delimited MagIC text file format. With input from the paleomagnetic, geomagnetic, and rock magnetic communities, the MagIC database will continue to improve as a data warehouse and resource.

Elucidation of metabolic pathways from enzyme classification data.

PubMed

McDonald, Andrew G; Tipton, Keith F

2014-01-01

The IUBMB Enzyme List is widely used by other databases as a source for avoiding ambiguity in the recognition of enzymes as catalytic entities. However, it was not designed for metabolic pathway tracing, which has become increasingly important in systems biology. A Reactions Database has been created from the material in the Enzyme List to allow reactions to be searched by substrate/product, and pathways to be traced from any selected starting/seed substrate. An extensive synonym glossary allows searches by many of the alternative names, including accepted abbreviations, by which a chemical compound may be known. This database was necessary for the development of the application Reaction Explorer ( http://www.reaction-explorer.org ), which was written in Real Studio ( http://www.realsoftware.com/realstudio/ ) to search the Reactions Database and draw metabolic pathways from reactions selected by the user. Having input the name of the starting compound (the "seed"), the user is presented with a list of all reactions containing that compound and then selects the product of interest as the next point on the ensuing graph. The pathway diagram is then generated as the process iterates. A contextual menu is provided, which allows the user: (1) to remove a compound from the graph, along with all associated links; (2) to search the reactions database again for additional reactions involving the compound; (3) to search for the compound within the Enzyme List.

DB-PABP: a database of polyanion-binding proteins

PubMed Central

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Russell Middaugh, C.

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references. PMID:17916573

DB-PABP: a database of polyanion-binding proteins.

PubMed

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Middaugh, C Russell

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.

Adaptive hybrid optimal quantum control for imprecisely characterized systems.

PubMed

Egger, D J; Wilhelm, F K

2014-06-20

Optimal quantum control theory carries a huge promise for quantum technology. Its experimental application, however, is often hindered by imprecise knowledge of the input variables, the quantum system's parameters. We show how to overcome this by adaptive hybrid optimal control, using a protocol named Ad-HOC. This protocol combines open- and closed-loop optimal control by first performing a gradient search towards a near-optimal control pulse and then an experimental fidelity estimation with a gradient-free method. For typical settings in solid-state quantum information processing, adaptive hybrid optimal control enhances gate fidelities by an order of magnitude, making optimal control theory applicable and useful.

Practical quantum private query of blocks based on unbalanced-state Bennett-Brassard-1984 quantum-key-distribution protocol

NASA Astrophysics Data System (ADS)

Wei, Chun-Yan; Gao, Fei; Wen, Qiao-Yan; Wang, Tian-Yin

2014-12-01

Until now, the only kind of practical quantum private query (QPQ), quantum-key-distribution (QKD)-based QPQ, focuses on the retrieval of a single bit. In fact, meaningful message is generally composed of multiple adjacent bits (i.e., a multi-bit block). To obtain a message from database, the user Alice has to query l times to get each ai. In this condition, the server Bob could gain Alice's privacy once he obtains the address she queried in any of the l queries, since each ai contributes to the message Alice retrieves. Apparently, the longer the retrieved message is, the worse the user privacy becomes. To solve this problem, via an unbalanced-state technique and based on a variant of multi-level BB84 protocol, we present a protocol for QPQ of blocks, which allows the user to retrieve a multi-bit block from database in one query. Our protocol is somewhat like the high-dimension version of the first QKD-based QPQ protocol proposed by Jacobi et al., but some nontrivial modifications are necessary.

Practical quantum private query of blocks based on unbalanced-state Bennett-Brassard-1984 quantum-key-distribution protocol

PubMed Central

Wei, Chun-Yan; Gao, Fei; Wen, Qiao-Yan; Wang, Tian-Yin

2014-01-01

Until now, the only kind of practical quantum private query (QPQ), quantum-key-distribution (QKD)-based QPQ, focuses on the retrieval of a single bit. In fact, meaningful message is generally composed of multiple adjacent bits (i.e., a multi-bit block). To obtain a message from database, the user Alice has to query l times to get each ai. In this condition, the server Bob could gain Alice's privacy once he obtains the address she queried in any of the l queries, since each ai contributes to the message Alice retrieves. Apparently, the longer the retrieved message is, the worse the user privacy becomes. To solve this problem, via an unbalanced-state technique and based on a variant of multi-level BB84 protocol, we present a protocol for QPQ of blocks, which allows the user to retrieve a multi-bit block from database in one query. Our protocol is somewhat like the high-dimension version of the first QKD-based QPQ protocol proposed by Jacobi et al., but some nontrivial modifications are necessary. PMID:25518810

Loss-tolerant measurement-device-independent quantum private queries

NASA Astrophysics Data System (ADS)

Zhao, Liang-Yuan; Yin, Zhen-Qiang; Chen, Wei; Qian, Yong-Jun; Zhang, Chun-Mei; Guo, Guang-Can; Han, Zheng-Fu

2017-01-01

Quantum private queries (QPQ) is an important cryptography protocol aiming to protect both the user’s and database’s privacy when the database is queried privately. Recently, a variety of practical QPQ protocols based on quantum key distribution (QKD) have been proposed. However, for QKD-based QPQ the user’s imperfect detectors can be subjected to some detector- side-channel attacks launched by the dishonest owner of the database. Here, we present a simple example that shows how the detector-blinding attack can damage the security of QKD-based QPQ completely. To remove all the known and unknown detector side channels, we propose a solution of measurement-device-independent QPQ (MDI-QPQ) with single- photon sources. The security of the proposed protocol has been analyzed under some typical attacks. Moreover, we prove that its security is completely loss independent. The results show that practical QPQ will remain the same degree of privacy as before even with seriously uncharacterized detectors.

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)

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

Quantum Private Query Based on Bell State and Single Photons

NASA Astrophysics Data System (ADS)

Gao, Xiang; Chang, Yan; Zhang, Shi-Bin; Yang, Fan; Zhang, Yan

2018-03-01

Quantum private query (QPQ) can protect both user's and database holder's privacy. In this paper, we propose a novel quantum private query protocol based on Bell state and single photons. As far as we know, no one has ever proposed the QPQ based on Bell state. By using the decoherence-free (DF) states, our protocol can resist the collective noise. Besides that, our protocol is a one-way quantum protocol, which can resist the Trojan horse attack and reduce the communication complexity. Our protocol can not only guarantee the participants' privacy but also stand against an external eavesdropper.

Detection of alternative splice variants at the proteome level in Aspergillus flavus.

PubMed

Chang, Kung-Yen; Georgianna, D Ryan; Heber, Steffen; Payne, Gary A; Muddiman, David C

2010-03-05

Identification of proteins from proteolytic peptides or intact proteins plays an essential role in proteomics. Researchers use search engines to match the acquired peptide sequences to the target proteins. However, search engines depend on protein databases to provide candidates for consideration. Alternative splicing (AS), the mechanism where the exon of pre-mRNAs can be spliced and rearranged to generate distinct mRNA and therefore protein variants, enable higher eukaryotic organisms, with only a limited number of genes, to have the requisite complexity and diversity at the proteome level. Multiple alternative isoforms from one gene often share common segments of sequences. However, many protein databases only include a limited number of isoforms to keep minimal redundancy. As a result, the database search might not identify a target protein even with high quality tandem MS data and accurate intact precursor ion mass. We computationally predicted an exhaustive list of putative isoforms of Aspergillus flavus proteins from 20 371 expressed sequence tags to investigate whether an alternative splicing protein database can assign a greater proportion of mass spectrometry data. The newly constructed AS database provided 9807 new alternatively spliced variants in addition to 12 832 previously annotated proteins. The searches of the existing tandem MS spectra data set using the AS database identified 29 new proteins encoded by 26 genes. Nine fungal genes appeared to have multiple protein isoforms. In addition to the discovery of splice variants, AS database also showed potential to improve genome annotation. In summary, the introduction of an alternative splicing database helps identify more proteins and unveils more information about a proteome.

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

PubMed

Zeng, Victor; Extavour, Cassandra G

2012-01-01

The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics. Database URL: asgard.rc.fas.harvard.edu.

Methods and pitfalls in searching drug safety databases utilising the Medical Dictionary for Regulatory Activities (MedDRA).

PubMed

Brown, Elliot G

2003-01-01

The Medical Dictionary for Regulatory Activities (MedDRA) is a unified standard terminology for recording and reporting adverse drug event data. Its introduction is widely seen as a significant improvement on the previous situation, where a multitude of terminologies of widely varying scope and quality were in use. However, there are some complexities that may cause difficulties, and these will form the focus for this paper. Two methods of searching MedDRA-coded databases are described: searching based on term selection from all of MedDRA and searching based on terms in the safety database. There are several potential traps for the unwary in safety searches. There may be multiple locations of relevant terms within a system organ class (SOC) and lack of recognition of appropriate group terms; the user may think that group terms are more inclusive than is the case. MedDRA may distribute terms relevant to one medical condition across several primary SOCs. If the database supports the MedDRA model, it is possible to perform multiaxial searching: while this may help find terms that might have been missed, it is still necessary to consider the entire contents of the SOCs to find all relevant terms and there are many instances of incomplete secondary linkages. It is important to adjust for multiaxiality if data are presented using primary and secondary locations. Other sources for errors in searching are non-intuitive placement and the selection of terms as preferred terms (PTs) that may not be widely recognised. Some MedDRA rules could also result in errors in data retrieval if the individual is unaware of these: in particular, the lack of multiaxial linkages for the Investigations SOC, Social circumstances SOC and Surgical and medical procedures SOC and the requirement that a PT may only be present under one High Level Term (HLT) and one High Level Group Term (HLGT) within any single SOC. Special Search Categories (collections of PTs assembled from various SOCs by searching all of MedDRA) are limited by the small number available and by lack of clarity about criteria applied in their construction. Difficulties in database searching may be addressed by suitable user training and experience, and by central reporting of detected deficiencies in MedDRA. Other remedies may include regulatory guidance on implementation and use of MedDRA. Further systematic review of MedDRA is needed and generation of standardised searches that may be used 'off the shelf' will help, particularly where the same search is performed repeatedly on multiple data sets. Until these enhancements are widely available, MedDRA users should take great care when searching a safety database to ensure that cases are not inadvertently missed.

Quantum Simulation of Tunneling in Small Systems

PubMed Central

Sornborger, Andrew T.

2012-01-01

A number of quantum algorithms have been performed on small quantum computers; these include Shor's prime factorization algorithm, error correction, Grover's search algorithm and a number of analog and digital quantum simulations. Because of the number of gates and qubits necessary, however, digital quantum particle simulations remain untested. A contributing factor to the system size required is the number of ancillary qubits needed to implement matrix exponentials of the potential operator. Here, we show that a set of tunneling problems may be investigated with no ancillary qubits and a cost of one single-qubit operator per time step for the potential evolution, eliminating at least half of the quantum gates required for the algorithm and more than that in the general case. Such simulations are within reach of current quantum computer architectures. PMID:22916333

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…

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)

BIOREMEDIATION IN THE FIELD SEARCH SYSTEM (BFSS) - VERSION 2.0 (DISKETTE)

EPA Science Inventory

BFSS is a PC-based software product that provides access to a database of information on waste sites in the United States and Canada where bioremediation is being tested or implemented, or has been completed. BFSS allows users to search the database electronically, view data on s...

Development of a biomarkers database for the National Children's Study

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

Lobdell, Danelle T.; Mendola, Pauline

The National Children's Study (NCS) is a federally-sponsored, longitudinal study of environmental influences on the health and development of children across the United States (www.nationalchildrensstudy.gov). Current plans are to study approximately 100,000 children and their families beginning before birth up to age 21 years. To explore potential biomarkers that could be important measurements in the NCS, we compiled the relevant scientific literature to identify both routine or standardized biological markers as well as new and emerging biological markers. Although the search criteria encouraged examination of factors that influence the breadth of child health and development, attention was primarily focused onmore » exposure, susceptibility, and outcome biomarkers associated with four important child health outcomes: autism and neurobehavioral disorders, injury, cancer, and asthma. The Biomarkers Database was designed to allow users to: (1) search the biomarker records compiled by type of marker (susceptibility, exposure or effect), sampling media (e.g., blood, urine, etc.), and specific marker name; (2) search the citations file; and (3) read the abstract evaluations relative to our search criteria. A searchable, user-friendly database of over 2000 articles was created and is publicly available at: http://cfpub.epa.gov/ncea/cfm/recordisplay.cfm?deid=85844. PubMed was the primary source of references with some additional searches of Toxline, NTIS, and other reference databases. Our initial focus was on review articles, beginning as early as 1996, supplemented with searches of the recent primary research literature from 2001 to 2003. We anticipate this database will have applicability for the NCS as well as other studies of children's environmental health.« less

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.

Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

PubMed

Falagas, Matthew E; Pitsouni, Eleni I; Malietzis, George A; Pappas, Georgios

2008-02-01

The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.

The annotation-enriched non-redundant patent sequence databases.

PubMed

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/

The Annotation-enriched non-redundant patent sequence databases

PubMed Central

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/ PMID:23396323

A Taxonomic Search Engine: Federating taxonomic databases using web services

PubMed Central

Page, Roderic DM

2005-01-01

Background The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. Conclusion The Taxonomic Search Engine is available at and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names. PMID:15757517

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences.

PubMed

Padliya, Neerav D; Garrett, Wesley M; Campbell, Kimberly B; Tabb, David L; Cooper, Bret

2007-11-01

LC-MS/MS has demonstrated potential for detecting plant pathogens. Unlike PCR or ELISA, LC-MS/MS does not require pathogen-specific reagents for the detection of pathogen-specific proteins and peptides. However, the MS/MS approach we and others have explored does require a protein sequence reference database and database-search software to interpret tandem mass spectra. To evaluate the limitations of database composition on pathogen identification, we analyzed proteins from cultured Ustilago maydis, Phytophthora sojae, Fusarium graminearum, and Rhizoctonia solani by LC-MS/MS. When the search database did not contain sequences for a target pathogen, or contained sequences to related pathogens, target pathogen spectra were reliably matched to protein sequences from nontarget organisms, giving an illusion that proteins from nontarget organisms were identified. Our analysis demonstrates that when database-search software is used as part of the identification process, a paradox exists whereby additional sequences needed to detect a wide variety of possible organisms may lead to more cross-species protein matches and misidentification of pathogens.

Validated methods for identifying tuberculosis patients in health administrative databases: systematic review.

PubMed

Ronald, L A; Ling, D I; FitzGerald, J M; Schwartzman, K; Bartlett-Esquilant, G; Boivin, J-F; Benedetti, A; Menzies, D

2017-05-01

An increasing number of studies are using health administrative databases for tuberculosis (TB) research. However, there are limitations to using such databases for identifying patients with TB. To summarise validated methods for identifying TB in health administrative databases. We conducted a systematic literature search in two databases (Ovid Medline and Embase, January 1980-January 2016). We limited the search to diagnostic accuracy studies assessing algorithms derived from drug prescription, International Classification of Diseases (ICD) diagnostic code and/or laboratory data for identifying patients with TB in health administrative databases. The search identified 2413 unique citations. Of the 40 full-text articles reviewed, we included 14 in our review. Algorithms and diagnostic accuracy outcomes to identify TB varied widely across studies, with positive predictive value ranging from 1.3% to 100% and sensitivity ranging from 20% to 100%. Diagnostic accuracy measures of algorithms using out-patient, in-patient and/or laboratory data to identify patients with TB in health administrative databases vary widely across studies. Use solely of ICD diagnostic codes to identify TB, particularly when using out-patient records, is likely to lead to incorrect estimates of case numbers, given the current limitations of ICD systems in coding TB.

Searching fee and non-fee toxicology information resources: an overview of selected databases.

PubMed

Wright, L L

2001-01-12

Toxicology profiles organize information by broad subjects, the first of which affirms identity of the agent studied. Studies here show two non-fee databases (ChemFinder and ChemIDplus) verify the identity of compounds with high efficiency (63% and 73% respectively) with the fee-based Chemical Abstracts Registry file serving well to fill data gaps (100%). Continued searching proceeds using knowledge of structure, scope and content to select databases. Valuable sources for information are factual databases that collect data and facts in special subject areas organized in formats available for analysis or use. Some sources representative of factual files are RTECS, CCRIS, HSDB, GENE-TOX and IRIS. Numerous factual databases offer a wealth of reliable information; however, exhaustive searches probe information published in journal articles and/or technical reports with records residing in bibliographic databases such as BIOSIS, EMBASE, MEDLINE, TOXLINE and Web of Science. Listed with descriptions are numerous factual and bibliographic databases supplied by 11 producers. Given the multitude of options and resources, it is often necessary to seek service desk assistance. Questions were posed by telephone and e-mail to service desks at DIALOG, ISI, MEDLARS, Micromedex and STN International. Results of the survey are reported.

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.

PubMed

Liu, Yifeng; Liang, Yongjie; Wishart, David

2015-07-01

PolySearch2 (http://polysearch.ca) is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies. PolySearch2 supports a generalized 'Given X, find all associated Ys' query, where X and Y can be selected from the aforementioned biomedical entities. An example query might be: 'Find all diseases associated with Bisphenol A'. To find its answers, PolySearch2 searches for associations against comprehensive collections of free-text collections, including local versions of MEDLINE abstracts, PubMed Central full-text articles, Wikipedia full-text articles and US Patent application abstracts. PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage. PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more

PubMed Central

Liu, Yifeng; Liang, Yongjie; Wishart, David

2015-01-01

PolySearch2 (http://polysearch.ca) is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies. PolySearch2 supports a generalized ‘Given X, find all associated Ys’ query, where X and Y can be selected from the aforementioned biomedical entities. An example query might be: ‘Find all diseases associated with Bisphenol A’. To find its answers, PolySearch2 searches for associations against comprehensive collections of free-text collections, including local versions of MEDLINE abstracts, PubMed Central full-text articles, Wikipedia full-text articles and US Patent application abstracts. PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage. PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation. PMID:25925572

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

PubMed Central

2013-01-01

Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/. PMID:23452691

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information.

PubMed

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

2013-03-01

Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user's query, advanced data searching based on the specified user's query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/.

Enabling search over encrypted multimedia databases

NASA Astrophysics Data System (ADS)

Lu, Wenjun; Swaminathan, Ashwin; Varna, Avinash L.; Wu, Min

2009-02-01

Performing information retrieval tasks while preserving data confidentiality is a desirable capability when a database is stored on a server maintained by a third-party service provider. This paper addresses the problem of enabling content-based retrieval over encrypted multimedia databases. Search indexes, along with multimedia documents, are first encrypted by the content owner and then stored onto the server. Through jointly applying cryptographic techniques, such as order preserving encryption and randomized hash functions, with image processing and information retrieval techniques, secure indexing schemes are designed to provide both privacy protection and rank-ordered search capability. Retrieval results on an encrypted color image database and security analysis of the secure indexing schemes under different attack models show that data confidentiality can be preserved while retaining very good retrieval performance. This work has promising applications in secure multimedia management.

FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry.

PubMed

Akimoto, Nayumi; Ara, Takeshi; Nakajima, Daisuke; Suda, Kunihiro; Ikeda, Chiaki; Takahashi, Shingo; Muneto, Reiko; Yamada, Manabu; Suzuki, Hideyuki; Shibata, Daisuke; Sakurai, Nozomu

2017-04-28

Currently, in mass spectrometry-based metabolomics, limited reference mass spectra are available for flavonoid identification. In the present study, a database of probable mass fragments for 6,867 known flavonoids (FsDatabase) was manually constructed based on new structure- and fragmentation-related rules using new heuristics to overcome flavonoid complexity. We developed the FlavonoidSearch system for flavonoid annotation, which consists of the FsDatabase and a computational tool (FsTool) to automatically search the FsDatabase using the mass spectra of metabolite peaks as queries. This system showed the highest identification accuracy for the flavonoid aglycone when compared to existing tools and revealed accurate discrimination between the flavonoid aglycone and other compounds. Sixteen new flavonoids were found from parsley, and the diversity of the flavonoid aglycone among different fruits and vegetables was investigated.

Systematic review of the literature on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health: a study protocol

PubMed Central

Hashem, Kawther M; He, Feng J; MacGregor, Graham A

2016-01-01

Introduction Obesity, type 2 diabetes and dental caries are all major public health problems in the UK, with significant costs to the healthcare service. We aim to conduct a systematic review to summarise the evidence on the effectiveness of product reformulation measures to reduce the sugar content of food and drink on the population's sugar consumption and health. Methods and analysis Electronic database will be systematically searched using a combination of terms, tailored to optimise sensitivity, specificity, and the syntax and functionality of each database. The databases searched will include the Cochrane Library, EMBASE, MEDLINE (Ovid) and Scopus. The bibliographies of those papers that match inclusion criteria will be searched by hand to identify any further, relevant references, which will be subject to the same screening and selection process. The database search results will be supplemented by hand searches. In addition to the peer-reviewed literature, a number of grey literature searches will be undertaken using the broad search terms ‘sugar’ and ‘food’ or ‘drink’ and ‘reduction’, these searches will include key government and organisation websites as well as general searches in Google. The selection of the studies, data collection and quality appraisal will be performed independently by 2 reviewers. Data will be initially analysed through a narrative synthesis method. If a subset of data we analyse appears comparable, we will investigate the possibility of performing a meta-analysis. Ethics and dissemination Ethics approval will not be required as this is a protocol for a systematic review. The findings will be disseminated widely through conference presentations and published in a peer-reviewed journal. PROSPERO registration number CRD42016034022. PMID:27288379

CENTRAL, PEDro, PubMed, and EMBASE are the most comprehensive databases indexing randomized controlled trials of physical therapy interventions.

PubMed

Michaleff, Zoe A; Costa, Leonardo O P; Moseley, Anne M; Maher, Christopher G; Elkins, Mark R; Herbert, Robert D; Sherrington, Catherine

2011-02-01

Many bibliographic databases index research studies evaluating the effects of health care interventions. One study has concluded that the Physiotherapy Evidence Database (PEDro) has the most complete indexing of reports of randomized controlled trials of physical therapy interventions, but the design of that study may have exaggerated estimates of the completeness of indexing by PEDro. The purpose of this study was to compare the completeness of indexing of reports of randomized controlled trials of physical therapy interventions by 8 bibliographic databases. This study was an audit of bibliographic databases. Prespecified criteria were used to identify 400 reports of randomized controlled trials from the reference lists of systematic reviews published in 2008 that evaluated physical therapy interventions. Eight databases (AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO, and PubMed) were searched for each trial report. The proportion of the 400 trial reports indexed by each database was calculated. The proportions of the 400 trial reports indexed by the databases were as follows: CENTRAL, 95%; PEDro, 92%; PubMed, 89%; EMBASE, 88%; CINAHL, 53%; AMED, 50%; Hooked on Evidence, 45%; and PsycINFO, 6%. Almost all of the trial reports (99%) were found in at least 1 database, and 88% were indexed by 4 or more databases. Four trial reports were uniquely indexed by a single database only (2 in CENTRAL and 1 each in PEDro and PubMed). The results are only applicable to searching for English-language published reports of randomized controlled trials evaluating physical therapy interventions. The 4 most comprehensive databases of trial reports evaluating physical therapy interventions were CENTRAL, PEDro, PubMed, and EMBASE. Clinicians seeking quick answers to clinical questions could search any of these databases knowing that all are reasonably comprehensive. PEDro, unlike the other 3 most complete databases, is specific to physical therapy, so studies not relevant to physical therapy are less likely to be retrieved. Researchers could use CENTRAL, PEDro, PubMed, and EMBASE in combination to conduct exhaustive searches for randomized trials in physical therapy.

[A Terahertz Spectral Database Based on Browser/Server Technique].

PubMed

Zhang, Zhuo-yong; Song, Yue

2015-09-01

With the solution of key scientific and technical problems and development of instrumentation, the application of terahertz technology in various fields has been paid more and more attention. Owing to the unique characteristic advantages, terahertz technology has been showing a broad future in the fields of fast, non-damaging detections, as well as many other fields. Terahertz technology combined with other complementary methods can be used to cope with many difficult practical problems which could not be solved before. One of the critical points for further development of practical terahertz detection methods depends on a good and reliable terahertz spectral database. We developed a BS (browser/server) -based terahertz spectral database recently. We designed the main structure and main functions to fulfill practical requirements. The terahertz spectral database now includes more than 240 items, and the spectral information was collected based on three sources: (1) collection and citation from some other abroad terahertz spectral databases; (2) collected from published literatures; and (3) spectral data measured in our laboratory. The present paper introduced the basic structure and fundament functions of the terahertz spectral database developed in our laboratory. One of the key functions of this THz database is calculation of optical parameters. Some optical parameters including absorption coefficient, refractive index, etc. can be calculated based on the input THz time domain spectra. The other main functions and searching methods of the browser/server-based terahertz spectral database have been discussed. The database search system can provide users convenient functions including user registration, inquiry, displaying spectral figures and molecular structures, spectral matching, etc. The THz database system provides an on-line searching function for registered users. Registered users can compare the input THz spectrum with the spectra of database, according to the obtained correlation coefficient one can perform the searching task very fast and conveniently. Our terahertz spectral database can be accessed at http://www.teralibrary.com. The proposed terahertz spectral database is based on spectral information so far, and will be improved in the future. We hope this terahertz spectral database can provide users powerful, convenient, and high efficient functions, and could promote the broader applications of terahertz technology.

The CTBTO Link to the database of the International Seismological Centre (ISC)

NASA Astrophysics Data System (ADS)

Bondar, I.; Storchak, D. A.; Dando, B.; Harris, J.; Di Giacomo, D.

2011-12-01

The CTBTO Link to the database of the International Seismological Centre (ISC) is a project to provide access to seismological data sets maintained by the ISC using specially designed interactive tools. The Link is open to National Data Centres and to the CTBTO. By means of graphical interfaces and database queries tailored to the needs of the monitoring community, the users are given access to a multitude of products. These include the ISC and ISS bulletins, covering the seismicity of the Earth since 1904; nuclear and chemical explosions; the EHB bulletin; the IASPEI Reference Event list (ground truth database); and the IDC Reviewed Event Bulletin. The searches are divided into three main categories: The Area Based Search (a spatio-temporal search based on the ISC Bulletin), the REB search (a spatio-temporal search based on specific events in the REB) and the IMS Station Based Search (a search for historical patterns in the reports of seismic stations close to a particular IMS seismic station). The outputs are HTML based web-pages with a simplified version of the ISC Bulletin showing the most relevant parameters with access to ISC, GT, EHB and REB Bulletins in IMS1.0 format for single or multiple events. The CTBTO Link offers a tool to view REB events in context within the historical seismicity, look at observations reported by non-IMS networks, and investigate station histories and residual patterns for stations registered in the International Seismographic Station Registry.

Predicting the performance of fingerprint similarity searching.

PubMed

Vogt, Martin; Bajorath, Jürgen

2011-01-01

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

Searching for disability in electronic databases of published literature.

PubMed

Walsh, Emily S; Peterson, Jana J; Judkins, Dolores Z

2014-01-01

As researchers in disability and health conduct systematic reviews with greater frequency, the definition of disability used in these reviews gains importance. Translating a comprehensive conceptual definition of "disability" into an operational definition that utilizes electronic databases in the health sciences is a difficult step necessary for performing systematic literature reviews in the field. Consistency of definition across studies will help build a body of evidence that is comparable and amenable to synthesis. To illustrate a process for operationalizing the World Health Organization's International Classification of Disability, Functioning, and Health concept of disability for MEDLINE, PsycINFO, and CINAHL databases. We created an electronic search strategy in conjunction with a reference librarian and an expert panel. Quality control steps included comparison of search results to results of a search for a specific disabling condition and to articles nominated by the expert panel. The complete search strategy is presented. Results of the quality control steps indicated that our strategy was sufficiently sensitive and specific. Our search strategy will be valuable to researchers conducting literature reviews on broad populations with disabilities. Copyright © 2014 Elsevier Inc. All rights reserved.

Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database.

PubMed

Arita, Masanori; Suwa, Kazuhiro

2008-09-17

In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.

Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database

PubMed Central

Arita, Masanori; Suwa, Kazuhiro

2008-01-01

Background In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. Results To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. Conclusion This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated. PMID:18822113

Optimal approach to quantum communication using dynamic programming.

PubMed

Jiang, Liang; Taylor, Jacob M; Khaneja, Navin; Lukin, Mikhail D

2007-10-30

Reliable preparation of entanglement between distant systems is an outstanding problem in quantum information science and quantum communication. In practice, this has to be accomplished by noisy channels (such as optical fibers) that generally result in exponential attenuation of quantum signals at large distances. A special class of quantum error correction protocols, quantum repeater protocols, can be used to overcome such losses. In this work, we introduce a method for systematically optimizing existing protocols and developing more efficient protocols. Our approach makes use of a dynamic programming-based searching algorithm, the complexity of which scales only polynomially with the communication distance, letting us efficiently determine near-optimal solutions. We find significant improvements in both the speed and the final-state fidelity for preparing long-distance entangled states.

Home Page: Division of Mammals: Department of Vertebrate Zoology: NMNH

Science.gov Websites

Search Field: Search Submit: Submit {search_item} Advanced Search Plan Your Visit Exhibitions Education Resources Databases Marine Mammal Program Beaked Whale Identification Guide 3D Primates VZ Libraries Related

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

PubMed Central

2012-01-01

Background For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications with known masses. Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed. Results We present a sequence database search engine that is specifically designed to run efficiently on the Hadoop MapReduce distributed computing framework. The search engine implements the K-score algorithm, generating comparable output for the same input files as the original implementation. The scalability of the system is shown, and the architecture required for the development of such distributed processing is discussed. Conclusion The software is scalable in its ability to handle a large peptide database, numerous modifications and large numbers of spectra. Performance scales with the number of processors in the cluster, allowing throughput to expand with the available resources. PMID:23216909

Finding Qualitative Research Evidence for Health Technology Assessment.

PubMed

DeJean, Deirdre; Giacomini, Mita; Simeonov, Dorina; Smith, Andrea

2016-08-01

Health technology assessment (HTA) agencies increasingly use reviews of qualitative research as evidence for evaluating social, experiential, and ethical aspects of health technologies. We systematically searched three bibliographic databases (MEDLINE, CINAHL, and Social Science Citation Index [SSCI]) using published search filters or "hedges" and our hybrid filter to identify qualitative research studies pertaining to chronic obstructive pulmonary disease and early breast cancer. The search filters were compared in terms of sensitivity, specificity, and precision. Our screening by title and abstract revealed that qualitative research constituted only slightly more than 1% of all published research on each health topic. The performance of the published search filters varied greatly across topics and databases. Compared with existing search filters, our hybrid filter demonstrated a consistently high sensitivity across databases and topics, and minimized the resource-intensive process of sifting through false positives. We identify opportunities for qualitative health researchers to improve the uptake of qualitative research into evidence-informed policy making. © The Author(s) 2016.

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.

PubMed

Lewis, Steven; Csordas, Attila; Killcoyne, Sarah; Hermjakob, Henning; Hoopmann, Michael R; Moritz, Robert L; Deutsch, Eric W; Boyle, John

2012-12-05

For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications with known masses. Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed. We present a sequence database search engine that is specifically designed to run efficiently on the Hadoop MapReduce distributed computing framework. The search engine implements the K-score algorithm, generating comparable output for the same input files as the original implementation. The scalability of the system is shown, and the architecture required for the development of such distributed processing is discussed. The software is scalable in its ability to handle a large peptide database, numerous modifications and large numbers of spectra. Performance scales with the number of processors in the cluster, allowing throughput to expand with the available resources.

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.

MyMolDB: a micromolecular database solution with open source and free components.

PubMed

Xia, Bing; Tai, Zheng-Fu; Gu, Yu-Cheng; Li, Bang-Jing; Ding, Li-Sheng; Zhou, Yan

2011-10-01

To manage chemical structures in small laboratories is one of the important daily tasks. Few solutions are available on the internet, and most of them are closed source applications. The open-source applications typically have limited capability and basic cheminformatics functionalities. In this article, we describe an open-source solution to manage chemicals in research groups based on open source and free components. It has a user-friendly interface with the functions of chemical handling and intensive searching. MyMolDB is a micromolecular database solution that supports exact, substructure, similarity, and combined searching. This solution is mainly implemented using scripting language Python with a web-based interface for compound management and searching. Almost all the searches are in essence done with pure SQL on the database by using the high performance of the database engine. Thus, impressive searching speed has been archived in large data sets for no external Central Processing Unit (CPU) consuming languages were involved in the key procedure of the searching. MyMolDB is an open-source software and can be modified and/or redistributed under GNU General Public License version 3 published by the Free Software Foundation (Free Software Foundation Inc. The GNU General Public License, Version 3, 2007. Available at: http://www.gnu.org/licenses/gpl.html). The software itself can be found at http://code.google.com/p/mymoldb/. Copyright © 2011 Wiley Periodicals, Inc.

LymPHOS 2.0: an update of a phosphosite database of primary human T cells

PubMed Central

Nguyen, Tien Dung; Vidal-Cortes, Oriol; Gallardo, Oscar; Abian, Joaquin; Carrascal, Montserrat

2015-01-01

LymPHOS is a web-oriented database containing peptide and protein sequences and spectrometric information on the phosphoproteome of primary human T-Lymphocytes. Current release 2.0 contains 15 566 phosphorylation sites from 8273 unique phosphopeptides and 4937 proteins, which correspond to a 45-fold increase over the original database description. It now includes quantitative data on phosphorylation changes after time-dependent treatment with activators of the TCR-mediated signal transduction pathway. Sequence data quality has also been improved with the use of multiple search engines for database searching. LymPHOS can be publicly accessed at http://www.lymphos.org. Database URL: http://www.lymphos.org. PMID:26708986

TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University

PubMed Central

Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

2010-01-01

We developed, TNAURice: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx. PMID:21364829

TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University.

PubMed

Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

2010-11-27

WE DEVELOPED, TNAURICE: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx.

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.

Phenotip - a web-based instrument to help diagnosing fetal syndromes antenatally.

PubMed

Porat, Shay; de Rham, Maud; Giamboni, Davide; Van Mieghem, Tim; Baud, David

2014-12-10

Prenatal ultrasound can often reliably distinguish fetal anatomic anomalies, particularly in the hands of an experienced ultrasonographer. Given the large number of existing syndromes and the significant overlap in prenatal findings, antenatal differentiation for syndrome diagnosis is difficult. We constructed a hierarchic tree of 1140 sonographic markers and submarkers, organized per organ system. Subsequently, a database of prenatally diagnosable syndromes was built. An internet-based search engine was then designed to search the syndrome database based on a single or multiple sonographic markers. Future developments will include a database with magnetic resonance imaging findings as well as further refinements in the search engine to allow prioritization based on incidence of syndromes and markers.

The Fragment Network: A Chemistry Recommendation Engine Built Using a Graph Database.

PubMed

Hall, Richard J; Murray, Christopher W; Verdonk, Marcel L

2017-07-27

The hit validation stage of a fragment-based drug discovery campaign involves probing the SAR around one or more fragment hits. This often requires a search for similar compounds in a corporate collection or from commercial suppliers. The Fragment Network is a graph database that allows a user to efficiently search chemical space around a compound of interest. The result set is chemically intuitive, naturally grouped by substitution pattern and meaningfully sorted according to the number of observations of each transformation in medicinal chemistry databases. This paper describes the algorithms used to construct and search the Fragment Network and provides examples of how it may be used in a drug discovery context.

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

Quasi-experimental study designs series-paper 8: identifying quasi-experimental studies to inform systematic reviews.

PubMed

Glanville, Julie; Eyers, John; Jones, Andrew M; Shemilt, Ian; Wang, Grace; Johansen, Marit; Fiander, Michelle; Rothstein, Hannah

2017-09-01

This article reviews the available evidence and guidance on methods to identify reports of quasi-experimental (QE) studies to inform systematic reviews of health care, public health, international development, education, crime and justice, and social welfare. Research, guidance, and examples of search strategies were identified by searching a range of databases, key guidance documents, selected reviews, conference proceedings, and personal communication. Current practice and research evidence were summarized. Four thousand nine hundred twenty-four records were retrieved by database searches, and additional documents were obtained by other searches. QE studies are challenging to identify efficiently because they have no standardized nomenclature and may be indexed in various ways. Reliable search filters are not available. There is a lack of specific resources devoted to collecting QE studies and little evidence on where best to search. Searches to identify QE studies should search a range of resources and, until indexing improves, use strategies that focus on the topic rather than the study design. Better definitions, better indexing in databases, prospective registers, and reporting guidance are required to improve the retrieval of QE studies and promote systematic reviews of what works based on the evidence from such studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Standardization of search methods for guideline development: an international survey of evidence-based guideline development groups.

PubMed

Deurenberg, Rikie; Vlayen, Joan; Guillo, Sylvie; Oliver, Thomas K; Fervers, Beatrice; Burgers, Jako

2008-03-01

Effective literature searching is particularly important for clinical practice guideline development. Sophisticated searching and filtering mechanisms are needed to help ensure that all relevant research is reviewed. To assess the methods used for the selection of evidence for guideline development by evidence-based guideline development organizations. A semistructured questionnaire assessing the databases, search filters and evaluation methods used for literature retrieval was distributed to eight major organizations involved in evidence-based guideline development. All of the organizations used search filters as part of guideline development. The medline database was the primary source accessed for literature retrieval. The OVID or SilverPlatter interfaces were used in preference to the freely accessed PubMed interface. The Cochrane Library, embase, cinahl and psycinfo databases were also frequently used by the organizations. All organizations reported the intention to improve and validate their filters for finding literature specifically relevant for guidelines. In the first international survey of its kind, eight major guideline development organizations indicated a strong interest in identifying, improving and standardizing search filters to improve guideline development. It is to be hoped that this will result in the standardization of, and open access to, search filters, an improvement in literature searching outcomes and greater collaboration among guideline development organizations.

Methods and means used in programming intelligent searches of technical documents

NASA Technical Reports Server (NTRS)

Gross, David L.

1993-01-01

In order to meet the data research requirements of the Safety, Reliability & Quality Assurance activities at Kennedy Space Center (KSC), a new computer search method for technical data documents was developed. By their very nature, technical documents are partially encrypted because of the author's use of acronyms, abbreviations, and shortcut notations. This problem of computerized searching is compounded at KSC by the volume of documentation that is produced during normal Space Shuttle operations. The Centralized Document Database (CDD) is designed to solve this problem. It provides a common interface to an unlimited number of files of various sizes, with the capability to perform any diversified types and levels of data searches. The heart of the CDD is the nature and capability of its search algorithms. The most complex form of search that the program uses is with the use of a domain-specific database of acronyms, abbreviations, synonyms, and word frequency tables. This database, along with basic sentence parsing, is used to convert a request for information into a relational network. This network is used as a filter on the original document file to determine the most likely locations for the data requested. This type of search will locate information that traditional techniques, (i.e., Boolean structured key-word searching), would not find.

Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.

PubMed

Sadygov, Rovshan G; Cociorva, Daniel; Yates, John R

2004-12-01

Database searching is an essential element of large-scale proteomics. Because these methods are widely used, it is important to understand the rationale of the algorithms. Most algorithms are based on concepts first developed in SEQUEST and PeptideSearch. Four basic approaches are used to determine a match between a spectrum and sequence: descriptive, interpretative, stochastic and probability-based matching. We review the basic concepts used by most search algorithms, the computational modeling of peptide identification and current challenges and limitations of this approach for protein identification.

ScienceDirect through SciVerse: a new way to approach Elsevier.

PubMed

Bengtson, Jason

2011-01-01

SciVerse is the new combined portal from Elsevier that services their ScienceDirect collection, SciTopics, and their Scopus database. Using SciVerse to access ScienceDirect is the specific focus of this review. Along with advanced keyword searching and citation searching options, SciVerse also incorporates a very useful image search feature. The aim seems to be not only to create an interface that provides broad functionality on par with other database search tools that many searchers use regularly but also to create an open platform that could be changed to respond effectively to the needs of customers.

DOE Research and Development Accomplishments Help

Science.gov Websites

be used to search, locate, access, and electronically download full-text research and development (R Browse Downloading, Viewing, and/or Searching Full-text Documents/Pages Searching the Database Search Features Search allows you to search the OCRed full-text document and bibliographic information, the

Department of Pesticide Regulation Databases

Science.gov Websites

; Safety Report an Illness | Food Safety | Risk Assessment & Mitigation | Human Health | Physicians Endangered Species Enforcement Food Safety Forms Human Health Laws Licensing Mill Assessment Permitting Pest Statewide search: Search Search Search this site: Search Search DPR California Home Programs Health &

Building the Infrastructure of Resource Sharing: Union Catalogs, Distributed Search, and Cross-Database Linkage.

ERIC Educational Resources Information Center

Lynch, Clifford A.

1997-01-01

Union catalogs and distributed search systems are two ways users can locate materials in print and electronic formats. This article examines the advantages and limitations of both approaches and argues that they should be considered complementary rather than competitive. Discusses technologies creating linkage between catalogs and databases and…

28 CFR 25.6 - Accessing records in the system.

Code of Federal Regulations, 2010 CFR

2010-07-01

... through the FBI NICS Operations Center. FFLs may contact the NICS Operations Center by use of a toll-free...) Search the relevant databases (i.e., NICS Index, NCIC, III) for any matching records; and (iv) Provide..., it will search the relevant databases (i.e., NICS Index, NCIC, III) for any matching record(s) and...

77 FR 30433 - Privacy Act of 1974: Implementation of Exemptions; Automated Targeting System

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-23

... the combination of license plate, Department of Motor Vehicle (DMV) registration data and biographical...: ATS allows users to search data across many different databases and correlates it across the various... elements of certain CBP databases in order to minimize the processing time for searches on the operational...

ELNET--The Electronic Library Database System.

ERIC Educational Resources Information Center

King, Shirley V.

1991-01-01

ELNET (Electronic Library Network), a Japanese language database, allows searching of index terms and free text terms from articles and stores the full text of the articles on an optical disc system. Users can order fax copies of the text from the optical disc. This article also explains online searching and discusses machine translation. (LRW)

Systematically Retrieving Research: A Case Study Evaluating Seven Databases

ERIC Educational Resources Information Center

Taylor, Brian; Wylie, Emma; Dempster, Martin; Donnelly, Michael

2007-01-01

Objective: Developing the scientific underpinnings of social welfare requires effective and efficient methods of retrieving relevant items from the increasing volume of research. Method: We compared seven databases by running the nearest equivalent search on each. The search topic was chosen for relevance to social work practice with older people.…

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…

Extending the Online Public Access Catalog into the Microcomputer Environment.

ERIC Educational Resources Information Center

Sutton, Brett

1990-01-01

Describes PCBIS, a database program for MS-DOS microcomputers that features a utility for automatically converting online public access catalog search results stored as text files into structured database files that can be searched, sorted, edited, and printed. Topics covered include the general features of the program, record structure, record…

Identifying contributors of two-person DNA mixtures by familial database search.

PubMed

Chung, Yuk-Ka; Fung, Wing K

2013-01-01

The role of familial database search as a crime-solving tool has been increasingly recognized by forensic scientists. As an enhancement to the existing familial search approach on single source cases, this article presents our current progress in exploring the potential use of familial search to mixture cases. A novel method was established to predict the outcome of the search, from which a simple strategy for determining an appropriate scale of investigation by the police force is developed. Illustrated by an example using Swedish data, our approach is shown to have the potential for assisting the police force to decide on the scale of investigation, thereby achieving desirable crime-solving rate with reasonable cost.

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

Webb-Robertson, Bobbie-Jo M.

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 peptidemore » 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« less

Identifying the effective evidence sources to use in developing Clinical Guidelines for Acute Stroke Management: lived experiences of the search specialist and project manager.

PubMed

Parkhill, Anne; Hill, Kelvin

2009-03-01

The Australian National Stroke Foundation appointed a search specialist to find the best available evidence for the second edition of its Clinical Guidelines for Acute Stroke Management. To identify the relative effectiveness of differing evidence sources for the guideline update. We searched and reviewed references from five valid evidence sources for clinical and economic questions: (i) electronic databases; (ii) reference lists of relevant systematic reviews, guidelines, and/or primary studies; (iii) table of contents of a number of key journals for the last 6 months; (iv) internet/grey literature; and (v) experts. Reference sources were recorded, quantified, and analysed. In the clinical portion of the guidelines document, there was a greater use of previous knowledge and sources other than electronic databases for evidence, while there was a greater use of electronic databases for the economic section. The results confirmed that searchers need to be aware of the context and range of sources for evidence searches. For best available evidence, searchers cannot rely solely on electronic databases and need to encompass many different media and sources.

Exploiting Quantum Resonance to Solve Combinatorial Problems

NASA Technical Reports Server (NTRS)

Zak, Michail; Fijany, Amir

2006-01-01

Quantum resonance would be exploited in a proposed quantum-computing approach to the solution of combinatorial optimization problems. In quantum computing in general, one takes advantage of the fact that an algorithm cannot be decoupled from the physical effects available to implement it. Prior approaches to quantum computing have involved exploitation of only a subset of known quantum physical effects, notably including parallelism and entanglement, but not including resonance. In the proposed approach, one would utilize the combinatorial properties of tensor-product decomposability of unitary evolution of many-particle quantum systems for physically simulating solutions to NP-complete problems (a class of problems that are intractable with respect to classical methods of computation). In this approach, reinforcement and selection of a desired solution would be executed by means of quantum resonance. Classes of NP-complete problems that are important in practice and could be solved by the proposed approach include planning, scheduling, search, and optimal design.

Combined use of computational chemistry and chemoinformatics methods for chemical discovery

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

Sugimoto, Manabu, E-mail: sugimoto@kumamoto-u.ac.jp; Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012

2015-12-31

Data analysis on numerical data by the computational chemistry calculations is carried out to obtain knowledge information of molecules. A molecular database is developed to systematically store chemical, electronic-structure, and knowledge-based information. The database is used to find molecules related to a keyword of “cancer”. Then the electronic-structure calculations are performed to quantitatively evaluate quantum chemical similarity of the molecules. Among the 377 compounds registered in the database, 24 molecules are found to be “cancer”-related. This set of molecules includes both carcinogens and anticancer drugs. The quantum chemical similarity analysis, which is carried out by using numerical results of themore » density-functional theory calculations, shows that, when some energy spectra are referred to, carcinogens are reasonably distinguished from the anticancer drugs. Therefore these spectral properties are considered of as important measures for classification.« less

Searching for an exotic spin-dependent interaction with a single electron-spin quantum sensor.

PubMed

Rong, Xing; Wang, Mengqi; Geng, Jianpei; Qin, Xi; Guo, Maosen; Jiao, Man; Xie, Yijin; Wang, Pengfei; Huang, Pu; Shi, Fazhan; Cai, Yi-Fu; Zou, Chongwen; Du, Jiangfeng

2018-02-21

Searching for new particles beyond the standard model is crucial for understanding several fundamental conundrums in physics and astrophysics. Several hypothetical particles can mediate exotic spin-dependent interactions between ordinary fermions, which enable laboratory searches via the detection of the interactions. Most laboratory searches utilize a macroscopic source and detector, thus allowing the detection of interactions with submillimeter force range and above. It remains a challenge to detect the interactions at shorter force ranges. Here we propose and demonstrate that a near-surface nitrogen-vacancy center in diamond can be utilized as a quantum sensor to detect the monopole-dipole interaction between an electron spin and nucleons. Our result sets a constraint for the electron-nucleon coupling, [Formula: see text], with the force range 0.1-23 μm. The obtained upper bound of the coupling at 20 μm is [Formula: see text] < 6.24 × 10 -15 .

A Swarm Optimization Genetic Algorithm Based on Quantum-Behaved Particle Swarm Optimization.

PubMed

Sun, Tao; Xu, Ming-Hai

2017-01-01

Quantum-behaved particle swarm optimization (QPSO) algorithm is a variant of the traditional particle swarm optimization (PSO). The QPSO that was originally developed for continuous search spaces outperforms the traditional PSO in search ability. This paper analyzes the main factors that impact the search ability of QPSO and converts the particle movement formula to the mutation condition by introducing the rejection region, thus proposing a new binary algorithm, named swarm optimization genetic algorithm (SOGA), because it is more like genetic algorithm (GA) than PSO in form. SOGA has crossover and mutation operator as GA but does not need to set the crossover and mutation probability, so it has fewer parameters to control. The proposed algorithm was tested with several nonlinear high-dimension functions in the binary search space, and the results were compared with those from BPSO, BQPSO, and GA. The experimental results show that SOGA is distinctly superior to the other three algorithms in terms of solution accuracy and convergence.

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. Copyright © 2015 Central Police University.

Determination of the atmospheric neutrino flux and searches for new physics with AMANDA-II

NASA Astrophysics Data System (ADS)

Abbasi, R.; Abdou, Y.; Ackermann, M.; Adams, J.; Ahlers, M.; Andeen, K.; Auffenberg, J.; Bai, X.; Baker, M.; Barwick, S. W.; Bay, R.; Bazo Alba, J. L.; Beattie, K.; Bechet, S.; Becker, J. K.; Becker, K.-H.; Benabderrahmane, M. L.; Berdermann, J.; Berghaus, P.; Berley, D.; Bernardini, E.; Bertrand, D.; Besson, D. Z.; Bissok, M.; Blaufuss, E.; Boersma, D. J.; Bohm, C.; Bolmont, J.; Böser, S.; Botner, O.; Bradley, L.; Braun, J.; Breder, D.; Burgess, T.; Castermans, T.; Chirkin, D.; Christy, B.; Clem, J.; Cohen, S.; Cowen, D. F.; D'Agostino, M. V.; Danninger, M.; Day, C. T.; de Clercq, C.; Demirörs, L.; Depaepe, O.; Descamps, F.; Desiati, P.; de Vries-Uiterweerd, G.; De Young, T.; Diaz-Velez, J. C.; Dreyer, J.; Dumm, J. P.; Duvoort, M. R.; Edwards, W. R.; Ehrlich, R.; Eisch, J.; Ellsworth, R. W.; Engdegård, O.; Euler, S.; Evenson, P. A.; Fadiran, O.; Fazely, A. R.; Feusels, T.; Filimonov, K.; Finley, C.; Foerster, M. M.; Fox, B. D.; Franckowiak, A.; Franke, R.; Gaisser, T. K.; Gallagher, J.; Ganugapati, R.; Gerhardt, L.; Gladstone, L.; Goldschmidt, A.; Goodman, J. A.; Gozzini, R.; Grant, D.; Griesel, T.; Groß, A.; Grullon, S.; Gunasingha, R. M.; Gurtner, M.; Ha, C.; Hallgren, A.; Halzen, F.; Han, K.; Hanson, K.; Hasegawa, Y.; Heise, J.; Helbing, K.; Herquet, P.; Hickford, S.; Hill, G. C.; Hoffman, K. D.; Hoshina, K.; Hubert, D.; Huelsnitz, W.; Hülß, J.-P.; Hulth, P. O.; Hultqvist, K.; Hussain, S.; Imlay, R. L.; Inaba, M.; Ishihara, A.; Jacobsen, J.; Japaridze, G. S.; Johansson, H.; Joseph, J. M.; Kampert, K.-H.; Kappes, A.; Karg, T.; Karle, A.; Kelley, J. L.; Kenny, P.; Kiryluk, J.; Kislat, F.; Klein, S. R.; Klepser, S.; Knops, S.; Kohnen, G.; Kolanoski, H.; Köpke, L.; Kowalski, M.; Kowarik, T.; Krasberg, M.; Kuehn, K.; Kuwabara, T.; Labare, M.; Laihem, K.; Landsman, H.; Lauer, R.; Leich, H.; Lennarz, D.; Lucke, A.; Lundberg, J.; Lünemann, J.; Madsen, J.; Majumdar, P.; Maruyama, R.; Mase, K.; Matis, H. S.; McParland, C. P.; Meagher, K.; Merck, M.; Mészáros, P.; Middell, E.; Milke, N.; Miyamoto, H.; Mohr, A.; Montaruli, T.; Morse, R.; Movit, S. M.; Münich, K.; Nahnhauer, R.; Nam, J. W.; Nießen, P.; Nygren, D. R.; Odrowski, S.; Olivas, A.; Olivo, M.; Ono, M.; Panknin, S.; Patton, S.; Pérez de Los Heros, C.; Petrovic, J.; Piegsa, A.; Pieloth, D.; Pohl, A. C.; Porrata, R.; Potthoff, N.; Price, P. B.; Prikockis, M.; Przybylski, G. T.; Rawlins, K.; Redl, P.; Resconi, E.; Rhode, W.; Ribordy, M.; Rizzo, A.; Rodrigues, J. P.; Roth, P.; Rothmaier, F.; Rott, C.; Roucelle, C.; Rutledge, D.; Ryckbosch, D.; Sander, H.-G.; Sarkar, S.; Satalecka, K.; Schlenstedt, S.; Schmidt, T.; Schneider, D.; Schukraft, A.; Schulz, O.; Schunck, M.; Seckel, D.; Semburg, B.; Seo, S. H.; Sestayo, Y.; Seunarine, S.; Silvestri, A.; Slipak, A.; Spiczak, G. M.; Spiering, C.; Stanev, T.; Stephens, G.; Stezelberger, T.; Stokstad, R. G.; Stoufer, M. C.; Stoyanov, S.; Strahler, E. A.; Straszheim, T.; Sulanke, K.-H.; Sullivan, G. W.; Swillens, Q.; Taboada, I.; Tarasova, O.; Tepe, A.; Ter-Antonyan, S.; Terranova, C.; Tilav, S.; Tluczykont, M.; Toale, P. A.; Tosi, D.; Turčan, D.; van Eijndhoven, N.; Vandenbroucke, J.; van Overloop, A.; Voigt, B.; Walck, C.; Waldenmaier, T.; Walter, M.; Wendt, C.; Westerhoff, S.; Whitehorn, N.; Wiebusch, C. H.; Wiedemann, A.; Wikström, G.; Williams, D. R.; Wischnewski, R.; Wissing, H.; Woschnagg, K.; Xu, X. W.; Yodh, G.; Yoshida, S.

2009-05-01

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 or quantum decoherence. 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 violation of Lorentz invariance and quantum decoherence parameters using a maximum likelihood method. Given the absence of evidence for new flavor-changing physics, we use the same methodology to determine the conventional atmospheric muon neutrino flux above 100 GeV.

Determination of the atmospheric neutrino flux and searches for new physics with AMANDA-II

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

Abbasi, R.; Andeen, K.; Baker, M.

2009-05-15

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 or quantum decoherence. 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 violation of Lorentzmore » invariance and quantum decoherence parameters using a maximum likelihood method. Given the absence of evidence for new flavor-changing physics, we use the same methodology to determine the conventional atmospheric muon neutrino flux above 100 GeV.« less

32 CFR 518.18 - Judicial actions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... procedures used to search for the requested records, (manual search of records, computer database search, etc... deliberate consideration of the institutional, commercial, and personal privacy interests that could be...

32 CFR 518.18 - Judicial actions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... procedures used to search for the requested records, (manual search of records, computer database search, etc... deliberate consideration of the institutional, commercial, and personal privacy interests that could be...

32 CFR 518.18 - Judicial actions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... procedures used to search for the requested records, (manual search of records, computer database search, etc... deliberate consideration of the institutional, commercial, and personal privacy interests that could be...

Cooperative quantum-behaved particle swarm optimization with dynamic varying search areas and Lévy flight disturbance.

PubMed

Li, Desheng

2014-01-01

This paper proposes a novel variant of cooperative quantum-behaved particle swarm optimization (CQPSO) algorithm with two mechanisms to reduce the search space and avoid the stagnation, called CQPSO-DVSA-LFD. One mechanism is called Dynamic Varying Search Area (DVSA), which takes charge of limiting the ranges of particles' activity into a reduced area. On the other hand, in order to escape the local optima, Lévy flights are used to generate the stochastic disturbance in the movement of particles. To test the performance of CQPSO-DVSA-LFD, numerical experiments are conducted to compare the proposed algorithm with different variants of PSO. According to the experimental results, the proposed method performs better than other variants of PSO on both benchmark test functions and the combinatorial optimization issue, that is, the job-shop scheduling problem.

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…

Aerodynamic Optimization of Rocket Control Surface Geometry Using Cartesian Methods and CAD Geometry

NASA Technical Reports Server (NTRS)

Nelson, Andrea; Aftosmis, Michael J.; Nemec, Marian; Pulliam, Thomas H.

2004-01-01

Aerodynamic design is an iterative process involving geometry manipulation and complex computational analysis subject to physical constraints and aerodynamic objectives. A design cycle consists of first establishing the performance of a baseline design, which is usually created with low-fidelity engineering tools, and then progressively optimizing the design to maximize its performance. Optimization techniques have evolved from relying exclusively on designer intuition and insight in traditional trial and error methods, to sophisticated local and global search methods. Recent attempts at automating the search through a large design space with formal optimization methods include both database driven and direct evaluation schemes. Databases are being used in conjunction with surrogate and neural network models as a basis on which to run optimization algorithms. Optimization algorithms are also being driven by the direct evaluation of objectives and constraints using high-fidelity simulations. Surrogate methods use data points obtained from simulations, and possibly gradients evaluated at the data points, to create mathematical approximations of a database. Neural network models work in a similar fashion, using a number of high-fidelity database calculations as training iterations to create a database model. Optimal designs are obtained by coupling an optimization algorithm to the database model. Evaluation of the current best design then gives either a new local optima and/or increases the fidelity of the approximation model for the next iteration. Surrogate methods have also been developed that iterate on the selection of data points to decrease the uncertainty of the approximation model prior to searching for an optimal design. The database approximation models for each of these cases, however, become computationally expensive with increase in dimensionality. Thus the method of using optimization algorithms to search a database model becomes problematic as the number of design variables is increased.

Development of a Publicly Available, Comprehensive Database of Fiber and Health Outcomes: Rationale and Methods

PubMed Central

Livingston, Kara A.; Chung, Mei; Sawicki, Caleigh M.; Lyle, Barbara J.; Wang, Ding Ding; Roberts, Susan B.; McKeown, Nicola M.

2016-01-01

Background Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes. Objectives (1) Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2) Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information. Methods To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™), a web-based, publicly available application. Conclusions A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome) data on published studies and as a searchable tool through which this data can be extracted and updated. PMID:27348733

GenderMedDB: an interactive database of sex and gender-specific medical literature.

PubMed

Oertelt-Prigione, Sabine; Gohlke, Björn-Oliver; Dunkel, Mathias; Preissner, Robert; Regitz-Zagrosek, Vera

2014-01-01

Searches for sex and gender-specific publications are complicated by the absence of a specific algorithm within search engines and by the lack of adequate archives to collect the retrieved results. We previously addressed this issue by initiating the first systematic archive of medical literature containing sex and/or gender-specific analyses. This initial collection has now been greatly enlarged and re-organized as a free user-friendly database with multiple functions: GenderMedDB (http://gendermeddb.charite.de). GenderMedDB retrieves the included publications from the PubMed database. Manuscripts containing sex and/or gender-specific analysis are continuously screened and the relevant findings organized systematically into disciplines and diseases. Publications are furthermore classified by research type, subject and participant numbers. More than 11,000 abstracts are currently included in the database, after screening more than 40,000 publications. The main functions of the database include searches by publication data or content analysis based on pre-defined classifications. In addition, registrants are enabled to upload relevant publications, access descriptive publication statistics and interact in an open user forum. Overall, GenderMedDB offers the advantages of a discipline-specific search engine as well as the functions of a participative tool for the gender medicine community.

Web-based Electronic Sharing and RE-allocation of Assets

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

Leverett, Dave; Miller, Robert A.; Berlin, Gary J.

2002-09-09

The Electronic Asses Sharing Program is a web-based application that provides the capability for complex-wide sharing and reallocation of assets that are excess, under utilized, or un-utilized. through a web-based fron-end and supporting has database with a search engine, users can search for assets that they need, search for assets needed by others, enter assets they need, and enter assets they have available for reallocation. In addition, entire listings of available assets and needed assets can be viewed. The application is written in Java, the hash database and search engine are in Object-oriented Java Database Management (OJDBM). The application willmore » be hosted on an SRS-managed server outside the Firewall and access will be controlled via a protected realm. An example of the application can be viewed at the followinig (temporary) URL: http://idgdev.srs.gov/servlet/srs.weshare.WeShare« less

Google Scholar versus PubMed in locating primary literature to answer drug-related questions.

PubMed

Freeman, Maisha Kelly; Lauderdale, Stacy A; Kendrach, Michael G; Woolley, Thomas W

2009-03-01

Google Scholar linked more visitors to biomedical journal Web sites than did PubMed after the database's initial release; however, its usefulness in locating primary literature articles is unknown. To assess in both databases the availability of primary literature target articles; total number of citations; availability of free, full-text journal articles; and number of primary literature target articles retrieved by year within the first 100 citations of the search results. Drug information question reviews published in The Annals of Pharmacotherapy Drug Information Rounds column served as targets to determine the retrieval ability of Google Scholar and PubMed searches. Reviews printed in this column from January 2006 to June 2007 were eligible for study inclusion. Articles were chosen if at least 2 key words of the printed article were included in the PubMed Medical Subject Heading (MeSH) database, and these terms were searched in both databases. Twenty-two of 33 (67%) eligible Drug Information Rounds articles met the inclusion criteria. The median number of primary literature articles used in each of these articles was 6.5 (IQR 4.8, 8.3; mean +/- SD 8 +/- 5.4). No significant differences were found for the mean number of target primary literature articles located within the first 100 citations in Google Scholar and PubMed searches (5.1 +/- 3.9 vs 5.3 +/- 3.3; p = 0.868). Google Scholar searches located more total results than PubMed (2211.6 +/- 3999.5 vs 44.2 +/- 47.4; p = 0.019). The availability of free, full-text journal articles per Drug Information Rounds article was similar between the databases (1.8 +/- 1.7 vs 2.3 +/- 1.7; p = 0.325). More primary literature articles published prior to 2000 were located with Google Scholar searches compared with PubMed (62.8% vs 34.9%; p = 0.017); however, no statistically significant differences between the databases were observed for articles published after 2000 (66.4 vs 77.1; p = 0.074). No significant differences were identified in the number of target primary literature articles located between databases. PubMed searches yielded fewer total citations than Google Scholar results; however, PubMed appears to be more specific than Google Scholar for locating relevant primary literature articles.

Users’ guide to the surgical literature: how to perform a high-quality literature search

PubMed Central

Waltho, Daniel; Kaur, Manraj Nirmal; Haynes, R. Brian; Farrokhyar, Forough; Thoma, Achilleas

2015-01-01

Summary The article “Users’ guide to the surgical literature: how to perform a literature search” was published in 2003, but the continuing technological developments in databases and search filters have rendered that guide out of date. The present guide fills an existing gap in this area; it provides the reader with strategies for developing a searchable clinical question, creating an efficient search strategy, accessing appropriate databases, and skillfully retrieving the best evidence to address the research question. PMID:26384150

Structator: fast index-based search for RNA sequence-structure patterns

PubMed Central

2011-01-01

Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. Conclusions The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator. PMID:21619640

Validation of SmartRank: A likelihood ratio software for searching national DNA databases with complex DNA profiles.

PubMed

Benschop, Corina C G; van de Merwe, Linda; de Jong, Jeroen; Vanvooren, Vanessa; Kempenaers, Morgane; Kees van der Beek, C P; Barni, Filippo; Reyes, Eusebio López; Moulin, Léa; Pene, Laurent; Haned, Hinda; Sijen, Titia

2017-07-01

Searching a national DNA database with complex and incomplete profiles usually yields very large numbers of possible matches that can present many candidate suspects to be further investigated by the forensic scientist and/or police. Current practice in most forensic laboratories consists of ordering these 'hits' based on the number of matching alleles with the searched profile. Thus, candidate profiles that share the same number of matching alleles are not differentiated and due to the lack of other ranking criteria for the candidate list it may be difficult to discern a true match from the false positives or notice that all candidates are in fact false positives. SmartRank was developed to put forward only relevant candidates and rank them accordingly. The SmartRank software computes a likelihood ratio (LR) for the searched profile and each profile in the DNA database and ranks database entries above a defined LR threshold according to the calculated LR. In this study, we examined for mixed DNA profiles of variable complexity whether the true donors are retrieved, what the number of false positives above an LR threshold is and the ranking position of the true donors. Using 343 mixed DNA profiles over 750 SmartRank searches were performed. In addition, the performance of SmartRank and CODIS were compared regarding DNA database searches and SmartRank was found complementary to CODIS. We also describe the applicable domain of SmartRank and provide guidelines. The SmartRank software is open-source and freely available. Using the best practice guidelines, SmartRank enables obtaining investigative leads in criminal cases lacking a suspect. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantum private query with perfect user privacy against a joint-measurement attack

NASA Astrophysics Data System (ADS)

Yang, Yu-Guang; Liu, Zhi-Chao; Li, Jian; Chen, Xiu-Bo; Zuo, Hui-Juan; Zhou, Yi-Hua; Shi, Wei-Min

2016-12-01

The joint-measurement (JM) attack is the most powerful threat to the database security for existing quantum-key-distribution (QKD)-based quantum private query (QPQ) protocols. Wei et al. (2016) [28] proposed a novel QPQ protocol against the JM attack. However, their protocol relies on two-way quantum communication thereby affecting its real implementation and communication efficiency. Moreover, it cannot ensure perfect user privacy. In this paper, we present a new one-way QPQ protocol in which the special way of classical post-processing of oblivious key ensures the security against the JM attack. Furthermore, it realizes perfect user privacy and lower complexity of communication.

Moving Beyond Quantum Mechanics in Search for a Generalized Theory of Superconductivity

NASA Astrophysics Data System (ADS)

Akpojotor, Godfrey; Animalu, Alexander

2012-02-01

Though there are infinite number of theories currently in the literature in the search for a generalized theory of superconductivity (SC), there may be three domineering mechanisms for the Cooper pair formation (CPF) and their emergent theories of SC. Two of these mechanisms, electron-phonon interactions and electron-electron correlations which are based on the quantum theory axiom of action-at-a distance, may be only an approximation of the third mechanism which is contact interaction of the wavepackets of the two electrons forming the Cooper pair as envisaged in hadronic mechanics to be responsible for natural bonding of elements. The application of this hydronic --type interaction to the superconducting cuprates, iron based compounds and heavy fermions leads to interesting results. It is therefore suggested that the future of the search for the theory of SC may be considered from this natural possible bonding that at short distances, the CPF is by a nonlinear, nonlocal and nonhamiltonian strong hadronic-type interactions due to deep wave-overlapping of spinning particles leading to Hulthen potential that is attractive between two electrons in singlet couplings while at large distances the CPF is by superexchange interaction which is purely a quantum mechanical affairs.

Quantum Phase Transitions in Cavity Coupled Dot systems

NASA Astrophysics Data System (ADS)

Kasisomayajula, Vijay; Russo, Onofrio

2011-03-01

We investigate a Quantum Dot System, in which the transconductance, in part, is due to spin coupling, with each dot subjected to a biasing voltage. When this system is housed in a QED cavity, the cavity dot coupling alters the spin coupling of the coupled dots significantly via the Purcell Effect. In this paper we show the extent to which one can control the various coupling parameters: the inter dot coupling, the individual dots coupling with the cavity and the coupled dots coupling with the cavity as a single entity. We show that the dots coupled to each other and to the cavity, the spin transport can be controlled selectively. We derive the conditions for such control explicitly. Further, we discuss the Quantum phase transition effects due to the charge and spin transport through the dots. The electron transport through the dots, electron-electron spin interaction and the electron-photon interaction are treated using the Non-equilibrium Green's Function Formalism. http://publish.aps.org/search/field/author/Trif_Mircea (Trif Mircea), http://publish.aps.org/search/field/author/Golovach_Vitaly_N (Vitaly N. Golovach), and http://publish.aps.org/search/field/author/Loss_Daniel (Daniel Loss), Phys. Rev. B 75, 085307 (2007)

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.

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…

Universal measurement-based quantum computation in two-dimensional symmetry-protected topological phases

NASA Astrophysics Data System (ADS)

Wei, Tzu-Chieh; Huang, Ching-Yu

2017-09-01

Recent progress in the characterization of gapped quantum phases has also triggered the search for a universal resource for quantum computation in symmetric gapped phases. Prior works in one dimension suggest that it is a feature more common than previously thought, in that nontrivial one-dimensional symmetry-protected topological (SPT) phases provide quantum computational power characterized by the algebraic structure defining these phases. Progress in two and higher dimensions so far has been limited to special fixed points. Here we provide two families of two-dimensional Z2 symmetric wave functions such that there exists a finite region of the parameter in the SPT phases that supports universal quantum computation. The quantum computational power appears to lose its universality at the boundary between the SPT and the symmetry-breaking phases.

Coined quantum walks on weighted graphs

NASA Astrophysics Data System (ADS)

Wong, Thomas G.

2017-11-01

We define a discrete-time, coined quantum walk on weighted graphs that is inspired by Szegedy’s quantum walk. Using this, we prove that many lackadaisical quantum walks, where each vertex has l integer self-loops, can be generalized to a quantum walk where each vertex has a single self-loop of real-valued weight l. We apply this real-valued lackadaisical quantum walk to two problems. First, we analyze it on the line or one-dimensional lattice, showing that it is exactly equivalent to a continuous deformation of the three-state Grover walk with faster ballistic dispersion. Second, we generalize Grover’s algorithm, or search on the complete graph, to have a weighted self-loop at each vertex, yielding an improved success probability when l < 3 + 2\\sqrt{2} ≈ 5.828 .

Fidelity-Based Ant Colony Algorithm with Q-learning of Quantum System

NASA Astrophysics Data System (ADS)

Liao, Qin; Guo, Ying; Tu, Yifeng; Zhang, Hang

2018-03-01

Quantum ant colony algorithm (ACA) has potential applications in quantum information processing, such as solutions of traveling salesman problem, zero-one knapsack problem, robot route planning problem, and so on. To shorten the search time of the ACA, we suggest the fidelity-based ant colony algorithm (FACA) for the control of quantum system. Motivated by structure of the Q-learning algorithm, we demonstrate the combination of a FACA with the Q-learning algorithm and suggest the design of a fidelity-based ant colony algorithm with the Q-learning to improve the performance of the FACA in a spin-1/2 quantum system. The numeric simulation results show that the FACA with the Q-learning can efficiently avoid trapping into local optimal policies and increase the speed of convergence process of quantum system.

Fidelity-Based Ant Colony Algorithm with Q-learning of Quantum System

NASA Astrophysics Data System (ADS)

Liao, Qin; Guo, Ying; Tu, Yifeng; Zhang, Hang

2017-12-01

Quantum ant colony algorithm (ACA) has potential applications in quantum information processing, such as solutions of traveling salesman problem, zero-one knapsack problem, robot route planning problem, and so on. To shorten the search time of the ACA, we suggest the fidelity-based ant colony algorithm (FACA) for the control of quantum system. Motivated by structure of the Q-learning algorithm, we demonstrate the combination of a FACA with the Q-learning algorithm and suggest the design of a fidelity-based ant colony algorithm with the Q-learning to improve the performance of the FACA in a spin-1/2 quantum system. The numeric simulation results show that the FACA with the Q-learning can efficiently avoid trapping into local optimal policies and increase the speed of convergence process of quantum system.

Supplementary search methods were more effective and offered better value than bibliographic database searching: A case study from public health and environmental enhancement.

PubMed

Cooper, Chris; Lovell, Rebecca; Husk, Kerryn; Booth, Andrew; Garside, Ruth

2018-06-01

We undertook a systematic review to evaluate the health benefits of environmental enhancement and conservation activities. We were concerned that a conventional process of study identification, focusing on exhaustive searches of bibliographic databases as the primary search method, would be ineffective, offering limited value. The focus of this study is comparing study identification methods. We compare (1) an approach led by searches of bibliographic databases with (2) an approach led by supplementary search methods. We retrospectively assessed the effectiveness and value of both approaches. Effectiveness was determined by comparing (1) the total number of studies identified and screened and (2) the number of includable studies uniquely identified by each approach. Value was determined by comparing included study quality and by using qualitative sensitivity analysis to explore the contribution of studies to the synthesis. The bibliographic databases approach identified 21 409 studies to screen and 2 included qualitative studies were uniquely identified. Study quality was moderate, and contribution to the synthesis was minimal. The supplementary search approach identified 453 studies to screen and 9 included studies were uniquely identified. Four quantitative studies were poor quality but made a substantive contribution to the synthesis; 5 studies were qualitative: 3 studies were good quality, one was moderate quality, and 1 study was excluded from the synthesis due to poor quality. All 4 included qualitative studies made significant contributions to the synthesis. This case study found value in aligning primary methods of study identification to maximise location of relevant evidence. Copyright © 2017 John Wiley & Sons, Ltd.

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.…

Prediction of enzyme binding: human thrombin inhibition study by quantum chemical and artificial intelligence methods based on X-ray structures.

PubMed

Mlinsek, G; Novic, M; Hodoscek, M; Solmajer, T

2001-01-01

Thrombin is a serine protease which plays important roles in the human body, the key one being the control of thrombus formation. The inhibition of thrombin has become a target for new antithrombotics. The aim of our work was to (i) construct a model which would enable us to predict Ki values for the binding of an inhibitor into the active site of thrombin based on a database of known X-ray structures of inhibitor-enzyme complexes and (ii) to identify the structural and electrostatic characteristics of inhibitor molecules crucially important to their effective binding. To retain as much of the 3D structural information of the bound inhibitor as possible, we implemented the quantum mechanical/molecular mechanical (QM/MM) procedure for calculating the molecular electrostatic potential (MEP) at the van der Waals surfaces of atoms in the protein's active site. The inhibitor was treated quantum mechanically, while the rest of the complex was treated by classical means. The obtained MEP values served as inputs into the counter-propagation artificial neural network (CP-ANN), and a genetic algorithm was subsequently used to search for the combination of atoms that predominantly influences the binding. The constructed CP-ANN model yielded Ki values predictions with a correlation coefficient of 0.96, with Ki values extended over 7 orders of magnitude. Our approach also shows the relative importance of the various amino acid residues present in the active site of the enzyme for inhibitor binding. The list of residues selected by our automatic procedure is in good correlation with the current consensus regarding the importance of certain crucial residues in thrombin's active site.

Search Fermilab Insect Database

Science.gov Websites

data reflects observations at Fermilab. Search Clear Choices Find All Insects |Help| |Glossary | |Advanced Search| How it's named and classified: Common Name: Insect Order: equals contains begins with ends

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

Hierarchies in Quantum Gravity: Large Numbers, Small Numbers, and Axions

NASA Astrophysics Data System (ADS)

Stout, John Eldon

Our knowledge of the physical world is mediated by relatively simple, effective descriptions of complex processes. By their very nature, these effective theories obscure any phenomena outside their finite range of validity, discarding information crucial to understanding the full, quantum gravitational theory. However, we may gain enormous insight into the full theory by understanding how effective theories with extreme characteristics--for example, those which realize large-field inflation or have disparate hierarchies of scales--can be naturally realized in consistent theories of quantum gravity. The work in this dissertation focuses on understanding the quantum gravitational constraints on these "extreme" theories in well-controlled corners of string theory. Axion monodromy provides one mechanism for realizing large-field inflation in quantum gravity. These models spontaneously break an axion's discrete shift symmetry and, assuming that the corrections induced by this breaking remain small throughout the excursion, create a long, quasi-flat direction in field space. This weakly-broken shift symmetry has been used to construct a dynamical solution to the Higgs hierarchy problem, dubbed the "relaxion." We study this relaxion mechanism and show that--without major modifications--it can not be naturally embedded within string theory. In particular, we find corrections to the relaxion potential--due to the ten-dimensional backreaction of monodromy charge--that conflict with naive notions of technical naturalness and render the mechanism ineffective. The super-Planckian field displacements necessary for large-field inflation may also be realized via the collective motion of many aligned axions. However, it is not clear that string theory provides the structures necessary for this to occur. We search for these structures by explicitly constructing the leading order potential for C4 axions and computing the maximum possible field displacement in all compactifications of type IIB string theory on toric Calabi-Yau hypersurfaces with h1,1 ≤ 4 in the Kreuzer-Skarke database. While none of these examples can sustain a super-Planckian displacement--the largest possible is 0.3 Mpl--we find an alignment mechanism responsible for large displacements in random matrix models at large h 1,1 >> 1, indicating that large-field inflation may be feasible in compactifications with tens or hundreds of axions. These results represent a modest step toward a complete understanding of large hierarchies and naturalness in quantum gravity.

VaProS: a database-integration approach for protein/genome information retrieval.

PubMed

Gojobori, Takashi; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei

2016-12-01

Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein-protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts' knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/ .

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.

PubMed

Stephens, Susie M; Chen, Jake Y; Davidson, Marcel G; Thomas, Shiby; Trute, Barry M

2005-01-01

As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.

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…

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.

Preference vs. Authority: A Comparison of Student Searching in a Subject-Specific Indexing and Abstracting Database and a Customized Discovery Layer

ERIC Educational Resources Information Center

Dahlen, Sarah P. C.; Hanson, Kathlene

2017-01-01

Discovery layers provide a simplified interface for searching library resources. Libraries with limited finances make decisions about retaining indexing and abstracting databases when similar information is available in discovery layers. These decisions should be informed by student success at finding quality information as well as satisfaction…

77 FR 31237 - Electronic Filing in the Copyright Office of Notices of Intention To Obtain a Section 115...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-25

... multiple nondramatic musical works may be submitted electronically as XML files. Electronically submitted Notices will be maintained in a database that can be searched using any of the included fields of... the Licensing Division for a search of the database during the interim period. As such, the Office...

100 Colleges Sign Up with Google to Speed Access to Library Resources

ERIC Educational Resources Information Center

Young, Jeffrey R.

2005-01-01

More than 100 colleges and universities have arranged to give people using the Google Scholar search engine on their campuses more-direct access to library materials. Google Scholar is a free tool that searches scholarly materials on the Web and in academic databases. The new arrangements essentially let Google know which online databases the…

LSE-Sign: A lexical database for Spanish Sign Language.

PubMed

Gutierrez-Sigut, Eva; Costello, Brendan; Baus, Cristina; Carreiras, Manuel

2016-03-01

The LSE-Sign database is a free online tool for selecting Spanish Sign Language stimulus materials to be used in experiments. It contains 2,400 individual signs taken from a recent standardized LSE dictionary, and a further 2,700 related nonsigns. Each entry is coded for a wide range of grammatical, phonological, and articulatory information, including handshape, location, movement, and non-manual elements. The database is accessible via a graphically based search facility which is highly flexible both in terms of the search options available and the way the results are displayed. LSE-Sign is available at the following website: http://www.bcbl.eu/databases/lse/.

Molecular Dynamics Simulation of the Thermophysical Properties of Quantum Liquid Helium Using the Feynman-Hibbs Potential

NASA Astrophysics Data System (ADS)

Liu, J.; Lu, W. Q.

2010-03-01

This paper presents the detailed MD simulation on the properties including the thermal conductivities and viscosities of the quantum fluid helium at different state points. The molecular interactions are represented by the Lennard-Jones pair potentials supplemented by quantum corrections following the Feynman-Hibbs approach and the properties are calculated using the Green-Kubo equations. A comparison is made among the numerical results using LJ and QFH potentials and the existing database and shows that the LJ model is not quantitatively correct for the supercritical liquid helium, thereby the quantum effect must be taken into account when the quantum fluid helium is studied. The comparison of the thermal conductivity is also made as a function of temperatures and pressure and the results show quantum effect correction is an efficient tool to get the thermal conductivities.

Beyond relevance and recall: testing new user-centred measures of database performance.

PubMed

Stokes, Peter; Foster, Allen; Urquhart, Christine

2009-09-01

Measures of the effectiveness of databases have traditionally focused on recall, precision, with some debate on how relevance can be assessed, and by whom. New measures of database performance are required when users are familiar with search engines, and expect full text availability. This research ascertained which of four bibliographic databases (BNI, CINAHL, MEDLINE and EMBASE) could be considered most useful to nursing and midwifery students searching for information for an undergraduate dissertation. Searches on title were performed for dissertation topics supplied by nursing students (n = 9), who made the relevance judgements. Measures of recall and precision were combined with additional factors to provide measures of effectiveness, while efficiency combined measures of novelty and originality and accessibility combined measures for availability and retrievability, based on obtainability. There were significant differences among the databases in precision, originality and availability, but other differences were not significant (Friedman test). Odds ratio tests indicated that BNI, followed by CINAHL were the most effective, CINAHL the most efficient, and BNI the most accessible. The methodology could help library services in purchase decisions as the measure for accessibility, and odds ratio testing helped to differentiate database performance.

HepSEQ: International Public Health Repository for Hepatitis B

PubMed Central

Gnaneshan, Saravanamuttu; Ijaz, Samreen; Moran, Joanne; Ramsay, Mary; Green, Jonathan

2007-01-01

HepSEQ is a repository for an extensive library of public health and molecular data relating to hepatitis B virus (HBV) infection collected from international sources. It is hosted by the Centre for Infections, Health Protection Agency (HPA), England, United Kingdom. This repository has been developed as a web-enabled, quality-controlled database to act as a tool for surveillance, HBV case management and for research. The web front-end for the database system can be accessed from . The format of the database system allows for comprehensive molecular, clinical and epidemiological data to be deposited into a functional database, to search and manipulate the stored data and to extract and visualize the information on epidemiological, virological, clinical, nucleotide sequence and mutational aspects of HBV infection through web front-end. Specific tools, built into the database, can be utilized to analyse deposited data and provide information on HBV genotype, identify mutations with known clinical significance (e.g. vaccine escape, precore and antiviral-resistant mutations) and carry out sequence homology searches against other deposited strains. Further mechanisms are also in place to allow specific tailored searches of the database to be undertaken. PMID:17130143

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

Electronic Biomedical Literature Search for Budding Researcher

PubMed Central

Thakre, Subhash B.; Thakre S, Sushama S.; Thakre, Amol D.

2013-01-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, 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, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. 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, levels of evidence, and detail about features of search engine as 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. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research. PMID:24179937

Electronic biomedical literature search for budding researcher.

PubMed

Thakre, Subhash B; Thakre S, Sushama S; Thakre, Amol D

2013-09-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, 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, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. 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, levels of evidence, and detail about features of search engine as 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. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research.

A survey of existing and proposed classical and quantum approaches to the photon mass

NASA Astrophysics Data System (ADS)

Spavieri, G.; Quintero, J.; Gillies, G. T.; Rodríguez, M.

2011-02-01

Over the past twenty years, there have been several careful experimental, observational and phenomenological investigations aimed at searching for and establishing ever tighter bounds on the possible mass of the photon. There are many fascinating and paradoxical physical implications that would arise from the presence of even a very small value for it, and thus such searches have always been well motivated in terms of the new physics that would result. We provide a brief overview of the theoretical background and classical motivations for this work and the early tests of the exactness of Coulomb's law that underlie it. We then go on to address the modern situation, in which quantum physics approaches come to attention. Among them we focus especially on the implications that the Aharonov-Bohm and Aharonov-Casher class of effects have on searches for a photon mass. These arise in several different ways and can lead to experiments that might involve the interaction of magnetic dipoles, electric dipoles, or charged particles with suitable potentials. Still other quantum-based approaches employ measurements of the g-factor of the electron. Plausible target sensitivities for limits on the photon mass as sought by the various quantum approaches are in the range of 10-53 to 10-54 g. Possible experimental arrangements for the associated experiments are discussed. We close with an assessment of the state of the art and a prognosis for future work.

Practical quantum private query of blocks based on unbalanced-state Bennett-Brassard-1984 quantum-key-distribution protocol.

PubMed

Wei, Chun-Yan; Gao, Fei; Wen, Qiao-Yan; Wang, Tian-Yin

2014-12-18

Until now, the only kind of practical quantum private query (QPQ), quantum-key-distribution (QKD)-based QPQ, focuses on the retrieval of a single bit. In fact, meaningful message is generally composed of multiple adjacent bits (i.e., a multi-bit block). To obtain a message a1a2···al from database, the user Alice has to query l times to get each ai. In this condition, the server Bob could gain Alice's privacy once he obtains the address she queried in any of the l queries, since each a(i) contributes to the message Alice retrieves. Apparently, the longer the retrieved message is, the worse the user privacy becomes. To solve this problem, via an unbalanced-state technique and based on a variant of multi-level BB84 protocol, we present a protocol for QPQ of blocks, which allows the user to retrieve a multi-bit block from database in one query. Our protocol is somewhat like the high-dimension version of the first QKD-based QPQ protocol proposed by Jacobi et al., but some nontrivial modifications are necessary.

Library Search Prefilters for Vehicle Manufacturers to Assist in the Forensic Examination of Automotive Paints.

PubMed

Lavine, Barry K; White, Collin G; Ding, Tao

2018-03-01

Pattern recognition techniques have been applied to the infrared (IR) spectral libraries of the Paint Data Query (PDQ) database to differentiate between nonidentical but similar IR spectra of automotive paints. To tackle the problem of library searching, search prefilters were developed to identify the vehicle make from IR spectra of the clear coat, surfacer-primer, and e-coat layers. To develop these search prefilters with the appropriate degree of accuracy, IR spectra from the PDQ database were preprocessed using the discrete wavelet transform to enhance subtle but significant features in the IR spectral data. Wavelet coefficients characteristic of vehicle make were identified using a genetic algorithm for pattern recognition and feature selection. Search prefilters to identify automotive manufacturer through IR spectra obtained from a paint chip recovered at a crime scene were developed using 1596 original manufacturer's paint systems spanning six makes (General Motors, Chrysler, Ford, Honda, Nissan, and Toyota) within a limited production year range (2000-2006). Search prefilters for vehicle manufacturer that were developed as part of this study were successfully validated using IR spectra obtained directly from the PDQ database. Information obtained from these search prefilters can serve to quantify the discrimination power of original automotive paint encountered in casework and further efforts to succinctly communicate trace evidential significance to the courts.

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…

Evaluation of an open source tool for indexing and searching enterprise radiology and pathology reports

NASA Astrophysics Data System (ADS)

Kim, Woojin; Boonn, William

2010-03-01

Data mining of existing radiology and pathology reports within an enterprise health system can be used for clinical decision support, research, education, as well as operational analyses. In our health system, the database of radiology and pathology reports exceeds 13 million entries combined. We are building a web-based tool to allow search and data analysis of these combined databases using freely available and open source tools. This presentation will compare performance of an open source full-text indexing tool to MySQL's full-text indexing and searching and describe implementation procedures to incorporate these capabilities into a radiology-pathology search engine.

USGS launches online database: Lichens in National Parks

USGS Publications Warehouse

Bennett, Jim

2005-01-01

If you are interested in lichens and National Parks, now you can query a lichen database that combines these two elements. Using pull-down menus you can: search by park, specifying either species list or the references used for that area; search by species (a report will show the parks in which species are found); and search by reference codes, which are available from the first query. The reference code search allows you to obtain the complete citation for each lichen species listed in a National Park.The result pages from these queries can be printed directly from the web browser, or can be copied and pasted into a word processor.

Fast Multivariate Search on Large Aviation Datasets

NASA Technical Reports Server (NTRS)

Bhaduri, Kanishka; Zhu, Qiang; Oza, Nikunj C.; Srivastava, Ashok N.

2010-01-01

Multivariate Time-Series (MTS) are ubiquitous, and are generated in areas as disparate as sensor recordings in aerospace systems, music and video streams, medical monitoring, and financial systems. Domain experts are often interested in searching for interesting multivariate patterns from these MTS databases which can contain up to several gigabytes of data. Surprisingly, research on MTS search is very limited. Most existing work only supports queries with the same length of data, or queries on a fixed set of variables. In this paper, we propose an efficient and flexible subsequence search framework for massive MTS databases, that, for the first time, enables querying on any subset of variables with arbitrary time delays between them. We propose two provably correct algorithms to solve this problem (1) an R-tree Based Search (RBS) which uses Minimum Bounding Rectangles (MBR) to organize the subsequences, and (2) a List Based Search (LBS) algorithm which uses sorted lists for indexing. We demonstrate the performance of these algorithms using two large MTS databases from the aviation domain, each containing several millions of observations Both these tests show that our algorithms have very high prune rates (>95%) thus needing actual