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.

Review of availability of food composition data for fish and shellfish.

PubMed

Rittenschober, Doris; Nowak, Verena; Charrondiere, U Ruth

2013-12-15

The FAO/INFOODS database on fish and shellfish (aFiSh) is a collection of analytical data from primary sources and holds values for 2,277 entries on raw and processed food with sufficient quality. Most data were entered on fatty acids (60%), followed by macronutrients and their fractions (16%), minerals (10%), amino acids (7%), (pro)vitamins (2%), heavy metals (2%) and other components (3%). Information on several factors that contribute to the variation of compositional data (e.g., biodiversity, catch season, habitat, size and part of fish/shellfish analysed) as well as the bibliographic references are presented alongside with each food entry. The data were published in the FAO/INFOODS Food Composition Database for Biodiversity (BioFoodComp2.0) and in the FAO/INFOODS Analytical Food Composition Database (AnFooD1.0), freely available at the INFOODS webpage http://www.fao.org/infoods/biodiversity/index_en.stm. The provision of easy accessible, analytical compositional data should be seen as stimulation for researchers and compilers to incorporate more analytical and detailed data of fish and shellfish into future food composition tables and databases and to improve dietary assessment tools. Copyright © 2013 Food and Agriculture Organization of the United Nations. Published by Elsevier Ltd.. All rights reserved.

Polyunsaturated fatty acids (PUFAs) for children with specific learning disorders.

PubMed

Tan, May Loong; Ho, Jacqueline J; Teh, Keng Hwang

2012-12-12

About 5% of schoolchildren have a specific learning disorder, defined as an unexpected failure to acquire adequate abilities in reading, writing or mathematic skills not as a result of reduced intellectual ability, inadequate teaching or social deprivation. Of these, 80% are reading disorders. Polyunsaturated fatty acids (PUFAs), in particular omega-3 and omega-6 fatty acids, which are found abundantly in the brain and retina are important for learning. Some children with specific learning disorders have been found to be deficient in these PUFAs, and it is argued that supplementation of PUFAs may help these children improve their learning abilities. To assess the effects of polyunsaturated fatty acids (PUFAs) supplementation for children with specific learning disorders, on learning outcomes. We searched the following databases in April 2012: CENTRAL (2012, Issue 4), MEDLINE (1948 to April Week 2 2012), EMBASE (1980 to 2012 Week 16), PsycINFO (1806 to April 2012), ERIC (1966 to April 2012), Science Citation Index (1970 to 20 April 2012), Social Science Citation Index (1970 to 20 April 2012), Conference Proceedings Citation Index-Science (1970 to 20 April 2012), Conference Proceedings Citation Index-Social Sciences and Humanites (1970 to 20 April 2012), Cochrane Database of Systematic Reviews (2012, Issue 4), DARE (2012, Issue 2) , ZETOC (24 April 2012) and WorldCat (24 April 2012). We searched the WHO International Clinical Trials Registry Platform and ClinicalTrials.gov on 24 April 2012. We also searched the reference lists of relevant articles identified by the searches. Randomised or quasi-randomised controlled trials comparing polyunsaturated fatty acids (PUFAs) with placebo or no treatment in children aged below 18 years with specific learning disabilities diagnosed using DSM-IV, ICD-10 or equivalent criteria. We intended to include participants with co-existing developmental disorders such as attention deficit hyperactivity disorder (ADHD) or autism. Two authors (ML and KH) independently screened the titles and abstracts of the search results and eliminated all studies that did not meet the inclusion criteria. Authors were contacted for missing information and clarifications when needed. We did not find any studies suitable for inclusion in the review. One study is awaiting classification as we were unable to get any information from the study author. There is insufficient evidence to draw any conclusion about the use of PUFAs for children with specific learning disorders. There is a need for well designed randomised studies to support or refute the use of PUFAs in this group of children.

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.

New generic indexing technology

NASA Technical Reports Server (NTRS)

Freeston, Michael

1996-01-01

There has been no fundamental change in the dynamic indexing methods supporting database systems since the invention of the B-tree twenty-five years ago. And yet the whole classical approach to dynamic database indexing has long since become inappropriate and increasingly inadequate. We are moving rapidly from the conventional one-dimensional world of fixed-structure text and numbers to a multi-dimensional world of variable structures, objects and images, in space and time. But, even before leaving the confines of conventional database indexing, the situation is highly unsatisfactory. In fact, our research has led us to question the basic assumptions of conventional database indexing. We have spent the past ten years studying the properties of multi-dimensional indexing methods, and in this paper we draw the strands of a number of developments together - some quite old, some very new, to show how we now have the basis for a new generic indexing technology for the next generation of database systems.

Protein binding hot spots prediction from sequence only by a new ensemble learning method.

PubMed

Hu, Shan-Shan; Chen, Peng; Wang, Bing; Li, Jinyan

2017-10-01

Hot spots are interfacial core areas of binding proteins, which have been applied as targets in drug design. Experimental methods are costly in both time and expense to locate hot spot areas. Recently, in-silicon computational methods have been widely used for hot spot prediction through sequence or structure characterization. As the structural information of proteins is not always solved, and thus hot spot identification from amino acid sequences only is more useful for real-life applications. This work proposes a new sequence-based model that combines physicochemical features with the relative accessible surface area of amino acid sequences for hot spot prediction. The model consists of 83 classifiers involving the IBk (Instance-based k means) algorithm, where instances are encoded by important properties extracted from a total of 544 properties in the AAindex1 (Amino Acid Index) database. Then top-performance classifiers are selected to form an ensemble by a majority voting technique. The ensemble classifier outperforms the state-of-the-art computational methods, yielding an F1 score of 0.80 on the benchmark binding interface database (BID) test set. http://www2.ahu.edu.cn/pchen/web/HotspotEC.htm .

Semantic Similarities between a Keyword Database and a Controlled Vocabulary Database: An Investigation in the Antibiotic Resistance Literature.

ERIC Educational Resources Information Center

Qin, Jian

2000-01-01

Explores similarities or dissimilarities between citation-semantic and analytic indexing based on a study of records in the Science Citation Index and MEDLINE databases on antibiotic resistance in pneumonia. Concludes that disparate indexing terms may be an advantage for better recall and precision in information retrieval. (Contains 42…

46 CFR 515.34 - Regulated Persons Index.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Commission § 515.34 Regulated Persons Index. The Regulated Persons Index is a database containing the names...-regulated entities. The database may be purchased for $108 by contacting the Bureau of Certification and...

46 CFR 515.34 - Regulated Persons Index.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Commission § 515.34 Regulated Persons Index. The Regulated Persons Index is a database containing the names...-regulated entities. The database may be purchased for $108 by contacting the Bureau of Certification and...

46 CFR 515.34 - Regulated Persons Index.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Commission § 515.34 Regulated Persons Index. The Regulated Persons Index is a database containing the names...-regulated entities. The database may be purchased for $108 by contacting the Bureau of Certification and...

46 CFR 515.34 - Regulated Persons Index.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Commission § 515.34 Regulated Persons Index. The Regulated Persons Index is a database containing the names...-regulated entities. The database may be purchased for $108 by contacting the Bureau of Certification and...

46 CFR 515.34 - Regulated Persons Index.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Commission § 515.34 Regulated Persons Index. The Regulated Persons Index is a database containing the names...-regulated entities. The database may be purchased for $108 by contacting the Bureau of Certification and...

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

Hydrophobicity diversity in globular and nonglobular proteins measured with the Gini index.

PubMed

Carugo, Oliviero

2017-12-01

Amino acids and their properties are variably distributed in proteins and different compositions determine all protein features, ranging from solubility to stability and functionality. Gini index, a tool to estimate distribution uniformity, is widely used in macroeconomics and has numerous statistical applications. Here, Gini index is used to analyze the distribution of hydrophobicity in proteins and to compare hydrophobicity distribution in globular and intrinsically disordered proteins. Based on the analysis of carefully selected high-quality data sets of proteins extracted from the Protein Data Bank (http://www.rcsb.org) and from the DisProt database (http://www.disprot.org/), it is observed that hydrophobicity is distributed in a more diverse way in intrinsically disordered proteins than in folded and soluble globular proteins. This correlates with the observation that the amino acid composition deviates from the uniformity (estimate with the Shannon and the Gini-Simpson indices) more in intrinsically disordered proteins than in globular and soluble proteins. Although statistical tools tike the Gini index have received little attention in molecular biology, these results show that they allow one to estimate sequence diversity and that they are useful to delineate trends that can hardly be described, otherwise, in simple and concise ways. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Indexing of Patents of Pharmaceutical Composition in Online Databases

NASA Astrophysics Data System (ADS)

Online searching of patents of pharmaceutical composition is generally considered to be very difficult. It is due to the fact that the patent databases include extensive technical information as well as legal information so that they are not likely to have index proper to the pharmaceutical composition or even if they have such index, the scope and coverage of indexing is ambiguous. This paper discusses how patents of pharmaceutical composition are indexed in online databases such as WPl, CA, CLAIMS, USP and PATOLIS. Online searching of patents of pharmaceutical composition are also discussed in some detail.

VIEWCACHE: An incremental pointer-base access method for distributed databases. Part 1: The universal index system design document. Part 2: The universal index system low-level design document. Part 3: User's guide. Part 4: Reference manual. Part 5: UIMS test suite

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos

1992-01-01

The goal of the Universal Index System (UIS), is to provide an easy-to-use and reliable interface to many different kinds of database systems. The impetus for this system was to simplify database index management for users, thus encouraging the use of indexes. As the idea grew into an actual system design, the concept of increasing database performance by facilitating the use of time-saving techniques at the user level became a theme for the project. This Final Report describes the Design, the Implementation of UIS, and its Language Interfaces. It also includes the User's Guide and the Reference Manual.

Urate levels predict survival in amyotrophic lateral sclerosis: Analysis of the expanded Pooled Resource Open-Access ALS clinical trials database.

PubMed

Paganoni, Sabrina; Nicholson, Katharine; Chan, James; Shui, Amy; Schoenfeld, David; Sherman, Alexander; Berry, James; Cudkowicz, Merit; Atassi, Nazem

2018-03-01

Urate has been identified as a predictor of amyotrophic lateral sclerosis (ALS) survival in some but not all studies. Here we leverage the recent expansion of the Pooled Resource Open-Access ALS Clinical Trials (PRO-ACT) database to study the association between urate levels and ALS survival. Pooled data of 1,736 ALS participants from the PRO-ACT database were analyzed. Cox proportional hazards regression models were used to evaluate associations between urate levels at trial entry and survival. After adjustment for potential confounders (i.e., creatinine and body mass index), there was an 11% reduction in risk of reaching a survival endpoint during the study with each 1-mg/dL increase in uric acid levels (adjusted hazard ratio 0.89, 95% confidence interval 0.82-0.97, P < 0.01). Our pooled analysis provides further support for urate as a prognostic factor for survival in ALS and confirms the utility of the PRO-ACT database as a powerful resource for ALS epidemiological research. Muscle Nerve 57: 430-434, 2018. © 2017 Wiley Periodicals, Inc.

The effect of long chain polyunsaturated fatty acid supplementation on intelligence in low birth weight infant during lactation: A meta-analysis

PubMed Central

Song, Yuan; Liu, Ya; Pan, Yun; Yuan, Xiaofeng; Chang, Pengyu; Tian, Yuan; Cui, Weiwei

2018-01-01

Background Low birth weight infant (LBWIs) are prone to mental and behavioural problems. As an important constituent of the brain and retina, long chain polyunsaturated fatty acids are essential for foetal infant mental and visual development. The effect of lactation supplemented with long chain polyunsaturated fatty acids (LCPUFA) on the improvement of intelligence in low birth weight children requires further validation. Methods In this study, a comprehensive search of multiple databases was performed to identify studies focused the association between intelligence and long chain polyunsaturated fatty acid supplementation in LBWIs. Studies that compared the Bayley Scales of Infant Development (BSID) or the Wechsler Abbreviated Scale of Intelligence for Children (WISC) scores between LBWIs who were supplemented and controls that were not supplemented with LCPUFA during lactation were selected for inclusion in the meta-analysis. Results The main outcome was the mean difference in the mental development index (MDI) and psychomotor development index (PDI) of the BSID and the full scale intelligence quotient (FSIQ), verbal intelligence quotient (VIQ) and performance intelligence quotient (PIQ) of the WISC between LBWIs and controls. Our findings indicated that the mean BSID or WISC scores in LBWIs did not differ between the supplemented groups and controls. Conclusion This meta-analysis does not reveal that LCPUFA supplementation has a significant impact on the level of intelligence in LBWIs. PMID:29634752

A Study of the Efficiency of Spatial Indexing Methods Applied to Large Astronomical Databases

NASA Astrophysics Data System (ADS)

Donaldson, Tom; Berriman, G. Bruce; Good, John; Shiao, Bernie

2018-01-01

Spatial indexing of astronomical databases generally uses quadrature methods, which partition the sky into cells used to create an index (usually a B-tree) written as database column. We report the results of a study to compare the performance of two common indexing methods, HTM and HEALPix, on Solaris and Windows database servers installed with a PostgreSQL database, and a Windows Server installed with MS SQL Server. The indexing was applied to the 2MASS All-Sky Catalog and to the Hubble Source catalog. On each server, the study compared indexing performance by submitting 1 million queries at each index level with random sky positions and random cone search radius, which was computed on a logarithmic scale between 1 arcsec and 1 degree, and measuring the time to complete the query and write the output. These simulated queries, intended to model realistic use patterns, were run in a uniform way on many combinations of indexing method and indexing level. The query times in all simulations are strongly I/O-bound and are linear with number of records returned for large numbers of sources. There are, however, considerable differences between simulations, which reveal that hardware I/O throughput is a more important factor in managing the performance of a DBMS than the choice of indexing scheme. The choice of index itself is relatively unimportant: for comparable index levels, the performance is consistent within the scatter of the timings. At small index levels (large cells; e.g. level 4; cell size 3.7 deg), there is large scatter in the timings because of wide variations in the number of sources found in the cells. At larger index levels, performance improves and scatter decreases, but the improvement at level 8 (14 min) and higher is masked to some extent in the timing scatter caused by the range of query sizes. At very high levels (20; 0.0004 arsec), the granularity of the cells becomes so high that a large number of extraneous empty cells begin to degrade performance. Thus, for the use patterns studied here the database performance is not critically dependent on the exact choices of index or level.

Folic acid supplements and colorectal cancer risk: meta-analysis of randomized controlled trials

NASA Astrophysics Data System (ADS)

Qin, Tingting; Du, Mulong; Du, Haina; Shu, Yongqian; Wang, Meilin; Zhu, Lingjun

2015-07-01

Numerous studies have investigated the effects of folic acid supplementation on colorectal cancer risk, but conflicting results were reported. We herein performed a meta-analysis based on relevant studies to reach a more definitive conclusion. The PubMed and Embase databases were searched for quality randomized controlled trials (RCTs) published before October 2014. Eight articles met the inclusion criteria and were subsequently analyzed. The results suggested that folic acid treatment was not associated with colorectal cancer risk in the total population (relative risk [RR] = 1.00, 95% confidence interval [CI] = 0.82-1.22, P = 0.974). Moreover, no statistical effect was identified in further subgroup analyses stratified by ethnicity, gender, body mass index (BMI) and potential confounding factors. No significant heterogeneity or publication bias was observed. In conclusion, our meta-analysis demonstrated that folic acid supplementation had no effect on colorectal cancer risk. However, this finding must be validated by further large studies.

A structured vocabulary for indexing dietary supplements in databases in the United States

USDA-ARS?s Scientific Manuscript database

Food composition databases are critical to assess and plan dietary intakes. Dietary supplement databases are also needed because dietary supplements make significant contributions to total nutrient intakes. However, no uniform system exists for classifying dietary supplement products and indexing ...

Subscribing to Databases: How Important Is Depth and Quality of Indexing?

ERIC Educational Resources Information Center

Delong, Linwood

2007-01-01

This paper compares the subject indexing on articles pertaining to Immanuel Kant, agriculture, and aging that are found simultaneously in Humanities Index, Academic Search Elite (EBSCO) and Periodicals Research II (Micromedia ProQuest), in order to show that there are substantial variations in the depth and quality of indexing in these databases.…

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.

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.

Assignment of adverse event indexing terms in randomized clinical trials involving spinal manipulative therapy: an audit of records in MEDLINE and EMBASE databases.

PubMed

Gorrell, Lindsay M; Engel, Roger M; Lystad, Reidar P; Brown, Benjamin T

2017-03-14

Reporting of adverse events in randomized clinical trials (RCTs) is encouraged by the authors of The Consolidated Standards of Reporting Trials (CONSORT) statement. With robust methodological design and adequate reporting, RCTs have the potential to provide useful evidence on the incidence of adverse events associated with spinal manipulative therapy (SMT). During a previous investigation, it became apparent that comprehensive search strategies combining text words with indexing terms was not sufficiently sensitive for retrieving records that were known to contain reports on adverse events. The aim of this analysis was to compare the proportion of articles containing data on adverse events associated with SMT that were indexed in MEDLINE and/or EMBASE and the proportion of those that included adverse event-related words in their title or abstract. A sample of 140 RCT articles previously identified as containing data on adverse events associated with SMT was used. Articles were checked to determine if: (1) they had been indexed with relevant terms describing adverse events in the MEDLINE and EMBASE databases; and (2) they mentioned adverse events (or any related terms) in the title or abstract. Of the 140 papers, 91% were MEDLINE records, 85% were EMBASE records, 81% were found in both MEDLINE and EMBASE records, and 4% were not in either database. Only 19% mentioned adverse event-related text words in the title or abstract. There was no significant difference between MEDLINE and EMBASE records in the proportion of available papers (p = 0.078). Of the 113 papers that were found in both MEDLINE and EMBASE records, only 3% had adverse event-related indexing terms assigned to them in both databases, while 81% were not assigned an adverse event-related indexing term in either database. While there was effective indexing of RCTs involving SMT in the MEDLINE and EMBASE databases, there was a failure of allocation of adverse event indexing terms in both databases. We recommend the development of standardized definitions and reporting tools for adverse events associated with SMT. Adequate reporting of adverse events associated with SMT will facilitate accurate indexing of these types of manuscripts in the databases.

Universal Index System

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos; Wallace, Sarah

1993-01-01

The Universal Index System (UIS) is an index management system that uses a uniform interface to solve the heterogeneity problem among database management systems. UIS provides an easy-to-use common interface to access all underlying data, but also allows different underlying database management systems, storage representations, and access methods.

Off-Site Indexing: A Cottage Industry.

ERIC Educational Resources Information Center

Fay, Catherine H.

1984-01-01

Briefly describes use of off-site staffing--indexers, abstractors, editors--in the production of two major databases: Management Contents and The Computer Data Base. Discussion covers the production sequence; database administrator; off-site indexer; savings (office space, furniture and equipment costs, salaries, and overhead); and problems…

IMPROVED SEARCH OF PRINCIPAL COMPONENT ANALYSIS DATABASES FOR SPECTRO-POLARIMETRIC INVERSION

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

Casini, R.; Lites, B. W.; Ramos, A. Asensio

2013-08-20

We describe a simple technique for the acceleration of spectro-polarimetric inversions based on principal component analysis (PCA) of Stokes profiles. This technique involves the indexing of the database models based on the sign of the projections (PCA coefficients) of the first few relevant orders of principal components of the four Stokes parameters. In this way, each model in the database can be attributed a distinctive binary number of 2{sup 4n} bits, where n is the number of PCA orders used for the indexing. Each of these binary numbers (indices) identifies a group of ''compatible'' models for the inversion of amore » given set of observed Stokes profiles sharing the same index. The complete set of the binary numbers so constructed evidently determines a partition of the database. The search of the database for the PCA inversion of spectro-polarimetric data can profit greatly from this indexing. In practical cases it becomes possible to approach the ideal acceleration factor of 2{sup 4n} as compared to the systematic search of a non-indexed database for a traditional PCA inversion. This indexing method relies on the existence of a physical meaning in the sign of the PCA coefficients of a model. For this reason, the presence of model ambiguities and of spectro-polarimetric noise in the observations limits in practice the number n of relevant PCA orders that can be used for the indexing.« less

Population groups: indexing, coverage, and retrieval effectiveness of ethnically related health care issues in health sciences databases.

PubMed Central

Efthimiadis, E N; Afifi, M

1996-01-01

OBJECTIVES: This study examined methods of accessing (for indexing and retrieval purposes) medical research on population groups in the major abstracting and indexing services of the health sciences literature. DESIGN: The study of diseases in specific population groups is facilitated by the indexing of both diseases and populations in a database. The MEDLINE, PsycINFO, and Embase databases were selected for the study. The published thesauri for these databases were examined to establish the vocabulary in use. Indexing terms were identified and examined as to their representation in the current literature. Terms were clustered further into groups thought to reflect an end user's perspective and to facilitate subsequent analysis. The medical literature contained in the three online databases was searched with both controlled vocabulary and natural language terms. RESULTS: The three thesauri revealed shallow pre-coordinated hierarchical structures, rather difficult-to-use terms for post-coordination, and a blurring of cultural, genetic, and racial facets of populations. Post-coordination is difficult because of the system-oriented terminology, which is intended mostly for information professionals. The terminology unintentionally restricts access by the end users who lack the knowledge needed to use the thesauri effectively for information retrieval. CONCLUSIONS: Population groups are not represented adequately in the index languages of health sciences databases. Users of these databases need to be alerted to the difficulties that may be encountered in searching for information on population groups. Information and health professionals may not be able to access the literature if they are not familiar with the indexing policies on population groups. Consequently, the study points to a problem that needs to be addressed, through either the redesign of existing systems or the design of new ones to meet the goals of Healthy People 2000 and beyond. PMID:8883987

Integrating Borrowed Records into a Database: Impact on Thesaurus Development and Retrieval.

ERIC Educational Resources Information Center

And Others; Kirtland, Monika

1980-01-01

Discusses three approaches to thesaurus and indexing/retrieval language maintenance for combined databases: reindexing, merging, and initial standardization. Two thesauri for a combined database are evaluated in terms of their compatibility, and indexing practices are compared. Tables and figures help illustrate aspects of the comparison. (SW)

Indexing Temporal XML Using FIX

NASA Astrophysics Data System (ADS)

Zheng, Tiankun; Wang, Xinjun; Zhou, Yingchun

XML has become an important criterion for description and exchange of information. It is of practical significance to introduce the temporal information on this basis, because time has penetrated into all walks of life as an important property information .Such kind of database can track document history and recover information to state of any time before, and is called Temporal XML database. We advise a new feature vector on the basis of FIX which is a feature-based XML index, and build an index on temporal XML database using B+ tree, donated TFIX. We also put forward a new query algorithm upon it for temporal query. Our experiments proved that this index has better performance over other kinds of XML indexes. The index can satisfy all TXPath queries with depth up to K(>0).

Tranexamic acid for reducing mortality in emergency and urgent surgery.

PubMed

Perel, Pablo; Ker, Katharine; Morales Uribe, Carlos Hernando; Roberts, Ian

2013-01-31

Emergency or urgent surgery, which can be defined as surgery which must be done promptly to save life, limb, or functional capacity, is associated with a high risk of bleeding and death. Antifibrinolytic agents, such as tranexamic acid, inhibit blood clot breakdown (fibrinolysis) and can reduce perioperative bleeding. Tranexamic acid has been shown to reduce the need for a blood transfusion in adult patients undergoing elective surgery but its effects in patients undergoing emergency or urgent surgery is unclear.   To assess the effects of tranexamic acid on mortality, blood transfusion and thromboembolic events in adults undergoing emergency or urgent surgery. We searched the following electronic databases: the Cochrane Injuries Group's Specialised Register (22 August 2012); Cochrane Central Register of Controlled Trials (2012, issue 8 of 12); MEDLINE (Ovid SP) 1950 to August Week 2, 2012; PubMed 1 June 2012 to 22 August 2012; EMBASE (Ovid SP) 1980 to 2012 Week 33; ISI Web of Science: Conference Proceedings Citation Index-Science (CPCI-S) 1990 to 22 August 2012; ISI Web of Science: Science Citation Index Expanded (SCI-EXPANDED) 1970 to 22 August 2012. We also searched online trial registers on 22 August 2012 to identify unpublished studies. Randomised controlled trials comparing tranexamic acid with no tranexamic acid or placebo in adults undergoing emergency or urgent surgery. Two authors examined titles, abstracts and keywords of citations from the electronic databases for eligibility and extracted data for analysis and risk of bias assessment. Outcome measures of interest were mortality, receipt of a blood transfusion, units of blood transfused, reoperation, seizures and thromboembolic events (myocardial infarction, stroke, deep vein thrombosis and pulmonary embolism). We identified five trials involving 372 people that met the inclusion criteria. Three trials (260 patients) contributed data to the analyses. The effect of tranexamic acid on mortality (RR 1.01; 95% CI 0.14 to 7.3) is uncertain. However, tranexamic acid reduces the probability of receiving a blood transfusion by 30% although the estimate is imprecise (RR 0.70; 95% CI 0.52 to 0.94). The effect on deep venous thrombosis (RR 2.29; 95% CI 0.68 to 7.66), and stroke (RR 2.79; 95% CI 0.12 to 67.10) is uncertain. There were no events of pulmonary embolism or myocardial infarction. None of the trials reported units of blood transfused, reoperation, or seizure outcomes. There is evidence that tranexamic acid reduces blood transfusion in patients undergoing emergency or urgent surgery. There is a need for a large pragmatic clinical trial to assess the effects of routine use of tranexamic acid on mortality in a heterogeneous group of urgent and emergency surgical patients.

Exploration of the Chemical Space of Public Genomic Databases

EPA Science Inventory

The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information.

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.

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…

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.

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.

Glycemic Index Diet: What's Behind the Claims

MedlinePlus

... choices for people with diabetes. An international GI database is maintained by Sydney University Glycemic Index Research Services in Sydney, Australia. The database contains the results of studies conducted there and ...

Retrieving Online Information on Drugs: An Analysis of Four Databases.

ERIC Educational Resources Information Center

Lavengood, Kathryn A.

This study examines the indexing of drugs in the literature and compares actual drug indexing to stated indexing policies in selected databases. The goal is to aid health science information specialists, end-users, and/or non-subject experts to improve recall and comprehensiveness when searching for drug information by identifying the most useful…

Compression of Index Term Dictionary in an Inverted-File-Oriented Database: Some Effective Algorithms.

ERIC Educational Resources Information Center

Wisniewski, Janusz L.

1986-01-01

Discussion of a new method of index term dictionary compression in an inverted-file-oriented database highlights a technique of word coding, which generates short fixed-length codes obtained from the index terms themselves by analysis of monogram and bigram statistical distributions. Substantial savings in communication channel utilization are…

Indexation Rules for Metallurgy in PASCAL. Original Title: Regles d'Indexation de la Metallurgie'--Technical Note Issued by Informascience--January 1980. Translated by Marie Wallin.

ERIC Educational Resources Information Center

Royal Inst. of Tech., Stockholm (Sweden). Library.

The indexing rules presented are designed for use with a new French-German database on metallurgy being developed under an agreement by CNRS (Centre National de la Recherche Scientifique, Paris) and BAM (Bundesanstalt fur Materialprufung, Berlin). The new database, which will feature multilingual titles and index terms (French-German-English-) and…

Coverage of Google Scholar, Scopus, and Web of Science: a case study of the h-index in nursing.

PubMed

De Groote, Sandra L; Raszewski, Rebecca

2012-01-01

This study compares the articles cited in CINAHL, Scopus, Web of Science (WOS), and Google Scholar and the h-index ratings provided by Scopus, WOS, and Google Scholar. The publications of 30 College of Nursing faculty at a large urban university were examined. Searches by author name were executed in Scopus, WOS, and POP (Publish or Perish, which searches Google Scholar), and the h-index for each author from each database was recorded. In addition, the citing articles of their published articles were imported into a bibliographic management program. This data was used to determine an aggregated h-index for each author. Scopus, WOS, and Google Scholar provided different h-index ratings for authors and each database found unique and duplicate citing references. More than one tool should be used to calculate the h-index for nursing faculty because one tool alone cannot be relied on to provide a thorough assessment of a researcher's impact. If researchers are interested in a comprehensive h-index, they should aggregate the citing references located by WOS and Scopus. Because h-index rankings differ among databases, comparisons between researchers should be done only within a specified database. Copyright © 2012 Elsevier Inc. All rights reserved.

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

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

Liu, Ling; Xiong, Yi; Gao, Hongyun

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

DOE PAGES

Liu, Ling; Xiong, Yi; Gao, Hongyun; ...

2018-04-02

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

Database Overlap vs. Complementary Coverage in Forestry and Forest Products: Factors in Database Acquisition.

ERIC Educational Resources Information Center

Hoover, Ryan E.

This study examines (1) subject content, (2) file size, (3) types of documents indexed, (4) range of years spanned, and (5) level of indexing and abstracting in five databases which collectively provide extensive coverage of the forestry and forest products industries: AGRICOLA, CAB ABSTRACTS, FOREST PRODUCTS (AIDS), PAPERCHEM, and PIRA. The…

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection.

PubMed

Rigden, Daniel J; Fernández, Xosé M

2018-01-04

The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest. In the area of metabolism, HMDB and Reactome both report new features while PULDB appears in NAR for the first time. This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE. Update papers from the IUPHAR/BPS Guide to Pharmacology and DrugBank are highlights of the drug and drug target section while a number of proteomics databases including proteomicsDB are also covered. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 138 entries, adding 88 new resources and eliminating 47 discontinued URLs, bringing the current total to 1737 databases. It is available at http://www.oxfordjournals.org/nar/database/c/. © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

PubMed Central

Kumar Mishra, Subodh; Kumar, Amit

2016-01-01

Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php PMID:26896846

Citations and the h index of soil researchers and journals in the Web of Science, Scopus, and Google Scholar

PubMed Central

Hartemink, Alfred E.; McBratney, Alex; Jang, Ho-Jun

2013-01-01

Citation metrics and h indices differ using different bibliometric databases. We compiled the number of publications, number of citations, h index and year since the first publication from 340 soil researchers from all over the world. On average, Google Scholar has the highest h index, number of publications and citations per researcher, and the Web of Science the lowest. The number of papers in Google Scholar is on average 2.3 times higher and the number of citations is 1.9 times higher compared to the data in the Web of Science. Scopus metrics are slightly higher than that of the Web of Science. The h index in Google Scholar is on average 1.4 times larger than Web of Science, and the h index in Scopus is on average 1.1 times larger than Web of Science. Over time, the metrics increase in all three databases but fastest in Google Scholar. The h index of an individual soil scientist is about 0.7 times the number of years since his/her first publication. There is a large difference between the number of citations, number of publications and the h index using the three databases. From this analysis it can be concluded that the choice of the database affects widely-used citation and evaluation metrics but that bibliometric transfer functions exist to relate the metrics from these three databases. We also investigated the relationship between journal’s impact factor and Google Scholar’s h5-index. The h5-index is a better measure of a journal’s citation than the 2 or 5 year window impact factor. PMID:24167778

Citations and the h index of soil researchers and journals in the Web of Science, Scopus, and Google Scholar.

PubMed

Minasny, Budiman; Hartemink, Alfred E; McBratney, Alex; Jang, Ho-Jun

2013-01-01

Citation metrics and h indices differ using different bibliometric databases. We compiled the number of publications, number of citations, h index and year since the first publication from 340 soil researchers from all over the world. On average, Google Scholar has the highest h index, number of publications and citations per researcher, and the Web of Science the lowest. The number of papers in Google Scholar is on average 2.3 times higher and the number of citations is 1.9 times higher compared to the data in the Web of Science. Scopus metrics are slightly higher than that of the Web of Science. The h index in Google Scholar is on average 1.4 times larger than Web of Science, and the h index in Scopus is on average 1.1 times larger than Web of Science. Over time, the metrics increase in all three databases but fastest in Google Scholar. The h index of an individual soil scientist is about 0.7 times the number of years since his/her first publication. There is a large difference between the number of citations, number of publications and the h index using the three databases. From this analysis it can be concluded that the choice of the database affects widely-used citation and evaluation metrics but that bibliometric transfer functions exist to relate the metrics from these three databases. We also investigated the relationship between journal's impact factor and Google Scholar's h5-index. The h5-index is a better measure of a journal's citation than the 2 or 5 year window impact factor.

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

Data management of a multilaboratory field program using distributed processing. [PRECP

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

Tichler, J.L.

The PRECP program is a multilaboratory research effort conducted by the US Department of Energy as a part of the National Acid Precipitation Assessment Program (NAPAP). The primary objective of PRECP is to provide essential information for the quantitative description of chemical wet deposition as a function of air pollution loadings, geograpic location, and atmospheric processing. The program is broken into four closely interrelated sectors: Diagnostic Modeling; Field Measurements; Laboratory Measurements; and Climatological Evaluation. Data management tasks are: compile databases of the data collected in field studies; verify the contents of data sets; make data available to program participants eithermore » on-line or by means of computer tapes; perform requested analyses, graphical displays, and data aggregations; provide an index of what data is available; and provide documentation for field programs both as part of the computer database and as data reports.« less

Mapping the literature of transcultural nursing*

PubMed Central

Murphy, Sharon C.

2006-01-01

Overview: No bibliometric studies of the literature of the field of transcultural nursing have been published. This paper describes a citation analysis as part of the project undertaken by the Nursing and Allied Health Resources Section of the Medical Library Association to map the literature of nursing. Objective: The purpose of this study was to identify the core literature and determine which databases provided the most complete access to the transcultural nursing literature. Methods: Cited references from essential source journals were analyzed for a three-year period. Eight major databases were compared for indexing coverage of the identified core list of journals. Results: This study identifies 138 core journals. Transcultural nursing relies on journal literature from associated health sciences fields in addition to nursing. Books provide an important format. Nearly all cited references were from the previous 18 years. In comparing indexing coverage among 8 major databases, 3 databases rose to the top. Conclusions: No single database can claim comprehensive indexing coverage for this broad field. It is essential to search multiple databases. Based on this study, PubMed/MEDLINE, Social Sciences Citation Index, and CINAHL provide the best coverage. Collections supporting transcultural nursing require robust access to literature beyond nursing publications. PMID:16710461

Polymorphisms in FFAR4 (GPR120) Gene Modulate Insulin Levels and Sensitivity after Fish Oil Supplementation.

PubMed

Vallée Marcotte, Bastien; Cormier, Hubert; Rudkowska, Iwona; Lemieux, Simone; Couture, Patrick; Vohl, Marie-Claude

2017-11-06

The objective was to test whether FFAR4 single nucleotide polymorphisms (SNPs) are associated with glycemic control-related traits in humans following fish oil supplementation. A total of 210 participants were given 3 g/day of omega-3 (n-3) fatty acids (FA) (1.9-2.2 g of eicosapentaenoic acid (EPA) and 1.1 g of docosahexaenoic acid (DHA)) during six weeks. Biochemical parameters were taken before and after the supplementation. Using the HapMap database and the tagger procedure in Haploview, 12 tagging SNPs in FFAR4 were selected and then genotyped using TaqMan technology. Transcript expression levels were measured for 30 participants in peripheral mononuclear blood cells. DNA methylation levels were measured for 35 participants in leukocytes. In silico analyses were also performed. Four gene-diet interactions on fasting insulin levels and homeostatic model assessment of insulin resistance (HOMA-IR) index values were found. rs17108973 explained a significant proportion of the variance of insulin levels (3.0%) and HOMA-IR (2.03%) index values. Splice site prediction was different depending on the allele for rs11187527. rs17108973 and rs17484310 had different affinity for transcription factors depending on the allele. n-3 FAs effectively improve insulin-related traits for major allele homozygotes of four FFAR4 SNPs as opposed to carriers of the minor alleles.

Polymorphisms in FFAR4 (GPR120) Gene Modulate Insulin Levels and Sensitivity after Fish Oil Supplementation

PubMed Central

Vallée Marcotte, Bastien; Cormier, Hubert; Rudkowska, Iwona; Lemieux, Simone; Couture, Patrick

2017-01-01

The objective was to test whether FFAR4 single nucleotide polymorphisms (SNPs) are associated with glycemic control-related traits in humans following fish oil supplementation. A total of 210 participants were given 3 g/day of omega-3 (n-3) fatty acids (FA) (1.9–2.2 g of eicosapentaenoic acid (EPA) and 1.1 g of docosahexaenoic acid (DHA)) during six weeks. Biochemical parameters were taken before and after the supplementation. Using the HapMap database and the tagger procedure in Haploview, 12 tagging SNPs in FFAR4 were selected and then genotyped using TaqMan technology. Transcript expression levels were measured for 30 participants in peripheral mononuclear blood cells. DNA methylation levels were measured for 35 participants in leukocytes. In silico analyses were also performed. Four gene–diet interactions on fasting insulin levels and homeostatic model assessment of insulin resistance (HOMA-IR) index values were found. rs17108973 explained a significant proportion of the variance of insulin levels (3.0%) and HOMA-IR (2.03%) index values. Splice site prediction was different depending on the allele for rs11187527. rs17108973 and rs17484310 had different affinity for transcription factors depending on the allele. n-3 FAs effectively improve insulin-related traits for major allele homozygotes of four FFAR4 SNPs as opposed to carriers of the minor alleles. PMID:29113108

Molecular Diversity of Lactic Acid Bacteria on Ileum and Coecum Broiler Chicken Fed by Chrysonilia crassa Fermentation

NASA Astrophysics Data System (ADS)

Nur Jannah, Siti; Khotimah, Husnul; Siti Ferniah, Rejeki; Sugiharto

2018-05-01

The Lactid Acid Bakteria (LAB) are microflora in the digestive tract which has positive roles in poultry’s health. One of the factors diversity of LAB in the gatrointestinal tract are influenced by feeding factor. The purpose of this study was to analyze the LAB diversity in ileum and coecum after being fed on fermented Chrysonilia crassa molecularly. LAB species diversity was analysed to provide a baseline profile of the microbial community database on the ileum and coecum digestive tract of broiler chicken of control (commercial feed) and treatment (feed with Chrysonilia crassa fermentation) by the method of Terminal Restriction Fragment Lenght Polymorphism The calculated values werethe number of phylotypes, relative abundace, Shannon-Wiener diversity index (H’), evennes index (E’), and similarity. Group of LAB detected in the control group were Lactobacillus delbrueckii (180 bp), Lactobacillus sp. (187 bp), Lactobacillus plantarum (572 bp), uncultured bacterium (87 bp) and unidentified (50 bp, 582bp). The result of this study showed that by feeding on the fermented Chrysonilia crassa feed had resulted in the decreasing of LAB diversity, i.e. ileum (0.66), coecum (0.48) compared with commercial feed (control) that was ileum (0.84), coecum (1.05).

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

PubMed

Galperin, Michael Y; Rigden, Daniel J; Fernández-Suárez, Xosé M

2015-01-01

The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

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

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

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…

Iris indexing based on local intensity order pattern

NASA Astrophysics Data System (ADS)

Emerich, Simina; Malutan, Raul; Crisan, Septimiu; Lefkovits, Laszlo

2017-03-01

In recent years, iris biometric systems have increased in popularity and have been proven that are capable of handling large-scale databases. The main advantage of these systems is accuracy and reliability. A proper iris patterns classification is expected to reduce the matching time in huge databases. This paper presents an iris indexing technique based on Local Intensity Order Pattern. The performance of the present approach is evaluated on UPOL database and is compared with other recent systems designed for iris indexing. The results illustrate the potential of the proposed method for large scale iris identification.

Waist to hip ratio is a better predictor of esophageal acid exposure than body mass index.

PubMed

Ringhofer, C; Lenglinger, J; Riegler, M; Kristo, I; Kainz, A; Schoppmann, S F

2017-07-01

Obesity and gastroesophageal reflux disease (GERD) are major health problems showing an inconstant relationship in the literature. Therefore, anthropometric parameters which are predictive and can simply be assessed at first patient presentation may lead to a better patient selection for ambulatory reflux monitoring. We aimed to examine the association of body mass index (BMI) and waist to hip ratio (WHR) with gastroesophageal reflux activity during 24 hour-pH-impedance monitoring. Seven hundred and seventy-one patients with GERD symptoms underwent 24 hour-pH-impedance monitoring and high resolution manometry off proton pump inhibitors. Patients with known primary motility disorders of the esophagus and pre-existing endoscopic or operative procedure on esophagus or stomach were excluded from the study. Reflux parameters and anthropometric and demographic data from our prospectively gathered database were analyzed. We performed univariate and multivariate regression analysis to evaluate the associations of BMI and WHR with reflux parameters measured with 24 hour-pH-impedance monitoring. WHR showed a significantly stronger association with esophageal acid exposure than BMI (P<.001). Our data show that 6.9% of the percentage of endoluminal pH<4 in the distal esophagus is attributable to WHR. Furthermore, an association of WHR with impaired esophageal acid clearance was observed. Additionally, we observed an inverse relationship between lower esophageal sphincter integrity (P=.05) and esophageal acid exposure. WHR is a better predictor for esophageal acid exposure than BMI. Biomechanical and metabolic mechanisms of central fat distribution may influence reflux parameters in 24 hour pH impedance monitoring, which may affect patient selection for ambulatory reflux monitoring. © 2017 John Wiley & Sons Ltd.

Attribute index and uniform design based multiobjective association rule mining with evolutionary algorithm.

PubMed

Zhang, Jie; Wang, Yuping; Feng, Junhong

2013-01-01

In association rule mining, evaluating an association rule needs to repeatedly scan database to compare the whole database with the antecedent, consequent of a rule and the whole rule. In order to decrease the number of comparisons and time consuming, we present an attribute index strategy. It only needs to scan database once to create the attribute index of each attribute. Then all metrics values to evaluate an association rule do not need to scan database any further, but acquire data only by means of the attribute indices. The paper visualizes association rule mining as a multiobjective problem rather than a single objective one. In order to make the acquired solutions scatter uniformly toward the Pareto frontier in the objective space, elitism policy and uniform design are introduced. The paper presents the algorithm of attribute index and uniform design based multiobjective association rule mining with evolutionary algorithm, abbreviated as IUARMMEA. It does not require the user-specified minimum support and minimum confidence anymore, but uses a simple attribute index. It uses a well-designed real encoding so as to extend its application scope. Experiments performed on several databases demonstrate that the proposed algorithm has excellent performance, and it can significantly reduce the number of comparisons and time consumption.

Attribute Index and Uniform Design Based Multiobjective Association Rule Mining with Evolutionary Algorithm

PubMed Central

Wang, Yuping; Feng, Junhong

2013-01-01

In association rule mining, evaluating an association rule needs to repeatedly scan database to compare the whole database with the antecedent, consequent of a rule and the whole rule. In order to decrease the number of comparisons and time consuming, we present an attribute index strategy. It only needs to scan database once to create the attribute index of each attribute. Then all metrics values to evaluate an association rule do not need to scan database any further, but acquire data only by means of the attribute indices. The paper visualizes association rule mining as a multiobjective problem rather than a single objective one. In order to make the acquired solutions scatter uniformly toward the Pareto frontier in the objective space, elitism policy and uniform design are introduced. The paper presents the algorithm of attribute index and uniform design based multiobjective association rule mining with evolutionary algorithm, abbreviated as IUARMMEA. It does not require the user-specified minimum support and minimum confidence anymore, but uses a simple attribute index. It uses a well-designed real encoding so as to extend its application scope. Experiments performed on several databases demonstrate that the proposed algorithm has excellent performance, and it can significantly reduce the number of comparisons and time consumption. PMID:23766683

A structured vocabulary for indexing dietary supplements in databases in the United States

PubMed Central

Saldanha, Leila G; Dwyer, Johanna T; Holden, Joanne M; Ireland, Jayne D.; Andrews, Karen W; Bailey, Regan L; Gahche, Jaime J.; Hardy, Constance J; Møller, Anders; Pilch, Susan M.; Roseland, Janet M

2011-01-01

Food composition databases are critical to assess and plan dietary intakes. Dietary supplement databases are also needed because dietary supplements make significant contributions to total nutrient intakes. However, no uniform system exists for classifying dietary supplement products and indexing their ingredients in such databases. Differing approaches to classifying these products make it difficult to retrieve or link information effectively. A consistent approach to classifying information within food composition databases led to the development of LanguaL™, a structured vocabulary. LanguaL™ is being adapted as an interface tool for classifying and retrieving product information in dietary supplement databases. This paper outlines proposed changes to the LanguaL™ thesaurus for indexing dietary supplement products and ingredients in databases. The choice of 12 of the original 14 LanguaL™ facets pertinent to dietary supplements, modifications to their scopes, and applications are described. The 12 chosen facets are: Product Type; Source; Part of Source; Physical State, Shape or Form; Ingredients; Preservation Method, Packing Medium, Container or Wrapping; Contact Surface; Consumer Group/Dietary Use/Label Claim; Geographic Places and Regions; and Adjunct Characteristics of food. PMID:22611303

A reservoir morphology database for the conterminous United States

USGS Publications Warehouse

Rodgers, Kirk D.

2017-09-13

The U.S. Geological Survey, in cooperation with the Reservoir Fisheries Habitat Partnership, combined multiple national databases to create one comprehensive national reservoir database and to calculate new morphological metrics for 3,828 reservoirs. These new metrics include, but are not limited to, shoreline development index, index of basin permanence, development of volume, and other descriptive metrics based on established morphometric formulas. The new database also contains modeled chemical and physical metrics. Because of the nature of the existing databases used to compile the Reservoir Morphology Database and the inherent missing data, some metrics were not populated. One comprehensive database will assist water-resource managers in their understanding of local reservoir morphology and water chemistry characteristics throughout the continental United States.

Incomplete evidence: the inadequacy of databases in tracing published adverse drug reactions in clinical trials

PubMed Central

Derry, Sheena; Kong Loke, Yoon; Aronson, Jeffrey K

2001-01-01

Background We would expect information on adverse drug reactions in randomised clinical trials to be easily retrievable from specific searches of electronic databases. However, complete retrieval of such information may not be straightforward, for two reasons. First, not all clinical drug trials provide data on the frequency of adverse effects. Secondly, not all electronic records of trials include terms in the abstract or indexing fields that enable us to select those with adverse effects data. We have determined how often automated search methods, using indexing terms and/or textwords in the title or abstract, would fail to retrieve trials with adverse effects data. Methods We used a sample set of 107 trials known to report frequencies of adverse drug effects, and measured the proportion that (i) were not assigned the appropriate adverse effects indexing terms in the electronic databases, and (ii) did not contain identifiable adverse effects textwords in the title or abstract. Results Of the 81 trials with records on both MEDLINE and EMBASE, 25 were not indexed for adverse effects in either database. Twenty-six trials were indexed in one database but not the other. Only 66 of the 107 trials reporting adverse effects data mentioned this in the abstract or title of the paper. Simultaneous use of textword and indexing terms retrieved only 82/107 (77%) papers. Conclusions Specific search strategies based on adverse effects textwords and indexing terms will fail to identify nearly a quarter of trials that report on the rate of drug adverse effects. PMID:11591220

Spanish personal name variations in national and international biomedical databases: implications for information retrieval and bibliometric studies

PubMed Central

Ruiz-Pérez, R.; López-Cózar, E. Delgado; Jiménez-Contreras, E.

2002-01-01

Objectives: The study sought to investigate how Spanish names are handled by national and international databases and to identify mistakes that can undermine the usefulness of these databases for locating and retrieving works by Spanish authors. Methods: The authors sampled 172 articles published by authors from the University of Granada Medical School between 1987 and 1996 and analyzed the variations in how each of their names was indexed in Science Citation Index (SCI), MEDLINE, and Índice Médico Español (IME). The number and types of variants that appeared for each author's name were recorded and compared across databases to identify inconsistencies in indexing practices. We analyzed the relationship between variability (number of variants of an author's name) and productivity (number of items the name was associated with as an author), the consequences for retrieval of information, and the most frequent indexing structures used for Spanish names. Results: The proportion of authors who appeared under more then one name was 48.1% in SCI, 50.7% in MEDLINE, and 69.0% in IME. Productivity correlated directly with variability: more than 50% of the authors listed on five to ten items appeared under more than one name in any given database, and close to 100% of the authors listed on more than ten items appeared under two or more variants. Productivity correlated inversely with retrievability: as the number of variants for a name increased, the number of items retrieved under each variant decreased. For the most highly productive authors, the number of items retrieved under each variant tended toward one. The most frequent indexing methods varied between databases. In MEDLINE and IME, names were indexed correctly as “first surname second surname, first name initial middle name initial” (if present) in 41.7% and 49.5% of the records, respectively. However, in SCI, the most frequent method was “first surname, first name initial second name initial” (48.0% of the records) and first surname and second surname run together, first name initial (18.3%). Conclusions: Retrievability on the basis of author's name was poor in all three databases. Each database uses accurate indexing methods, but these methods fail to result in consistency or coherence for specific entries. The likely causes of inconsistency are: (1) use by authors of variants of their names during their publication careers, (2) lack of authority control in all three databases, (3) the use of an inappropriate indexing method for Spanish names in SCI, (4) authors' inconsistent behaviors, and (5) possible editorial interventions by some journals. We offer some suggestions as to how to avert the proliferation of author name variants in the databases. PMID:12398248

For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases.

PubMed

Liljekvist, Mads Svane; Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

2015-01-01

Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases' criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ's coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general.

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.

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.

Optimal Embedding for Shape Indexing in Medical Image Databases

PubMed Central

Qian, Xiaoning; Tagare, Hemant D.; Fulbright, Robert K.; Long, Rodney; Antani, Sameer

2010-01-01

This paper addresses the problem of indexing shapes in medical image databases. Shapes of organs are often indicative of disease, making shape similarity queries important in medical image databases. Mathematically, shapes with landmarks belong to shape spaces which are curved manifolds with a well defined metric. The challenge in shape indexing is to index data in such curved spaces. One natural indexing scheme is to use metric trees, but metric trees are prone to inefficiency. This paper proposes a more efficient alternative. We show that it is possible to optimally embed finite sets of shapes in shape space into a Euclidean space. After embedding, classical coordinate-based trees can be used for efficient shape retrieval. The embedding proposed in the paper is optimal in the sense that it least distorts the partial Procrustes shape distance. The proposed indexing technique is used to retrieve images by vertebral shape from the NHANES II database of cervical and lumbar spine x-ray images maintained at the National Library of Medicine. Vertebral shape strongly correlates with the presence of osteophytes, and shape similarity retrieval is proposed as a tool for retrieval by osteophyte presence and severity. Experimental results included in the paper evaluate (1) the usefulness of shape-similarity as a proxy for osteophytes, (2) the computational and disk access efficiency of the new indexing scheme, (3) the relative performance of indexing with embedding to the performance of indexing without embedding, and (4) the computational cost of indexing using the proposed embedding versus the cost of an alternate embedding. The experimental results clearly show the relevance of shape indexing and the advantage of using the proposed embedding. PMID:20163981

Optimal embedding for shape indexing in medical image databases.

PubMed

Qian, Xiaoning; Tagare, Hemant D; Fulbright, Robert K; Long, Rodney; Antani, Sameer

2010-06-01

This paper addresses the problem of indexing shapes in medical image databases. Shapes of organs are often indicative of disease, making shape similarity queries important in medical image databases. Mathematically, shapes with landmarks belong to shape spaces which are curved manifolds with a well defined metric. The challenge in shape indexing is to index data in such curved spaces. One natural indexing scheme is to use metric trees, but metric trees are prone to inefficiency. This paper proposes a more efficient alternative. We show that it is possible to optimally embed finite sets of shapes in shape space into a Euclidean space. After embedding, classical coordinate-based trees can be used for efficient shape retrieval. The embedding proposed in the paper is optimal in the sense that it least distorts the partial Procrustes shape distance. The proposed indexing technique is used to retrieve images by vertebral shape from the NHANES II database of cervical and lumbar spine X-ray images maintained at the National Library of Medicine. Vertebral shape strongly correlates with the presence of osteophytes, and shape similarity retrieval is proposed as a tool for retrieval by osteophyte presence and severity. Experimental results included in the paper evaluate (1) the usefulness of shape similarity as a proxy for osteophytes, (2) the computational and disk access efficiency of the new indexing scheme, (3) the relative performance of indexing with embedding to the performance of indexing without embedding, and (4) the computational cost of indexing using the proposed embedding versus the cost of an alternate embedding. The experimental results clearly show the relevance of shape indexing and the advantage of using the proposed embedding. Copyright (c) 2010 Elsevier B.V. All rights reserved.

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid.

PubMed

Kumar Mishra, Subodh; Kumar, Amit

2016-01-01

Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php. © The Author(s) 2016. Published by Oxford University Press.

Maslinic acid in olive fruit alleviates mild knee joint pain and improves quality of life by promoting weight loss in the elderly

PubMed Central

Fukumitsu, Satoshi; Villareal, Myra O; Aida, Kazuhiko; Hino, Akihiro; Hori, Noriya; Isoda, Hiroko; Naito, Yuji

2016-01-01

Consumption of olives (Olea europaea L.) is associated with a low incidence of inflammation-related diseases. Olive fruit is rich in bioactive pentacyclic triterpenoids, mainly maslinic acid. This study, a randomized, double-blind, and placebo-controlled trial, examined the effects of an orally administered maslinic acid supplement, olive fruit extract, on 20 middle-aged and elderly volunteers with mild knee joint pain. Each subject (58 ± 7 years) received either olive fruit extract, containing 50 mg maslinic acid (n = 12), or placebo (n = 8) daily for 12 weeks and evaluated for pain and physical functions as primary outcome measures. Secondary outcome measures included body composition and inflammatory biomarkers in serum. Although both groups exhibited improved pain visual analogue scale score and quality of life after supplementation, symptoms were better in the maslinic acid group than in the placebo group. After 12 weeks, maslinic acid group exhibited significant decrease in body weight and body mass index suggesting that maslinic acid affected the weight of volunteers with mild knee joint pain. Therefore, olive products containing maslinic acid may be useful as a new preventive and therapeutic food ingredient for arthritic diseases. Since this clinical study is a preliminary study, it was not registered in a publicly accessible database. PMID:27895390

3DSDSCAR--a three dimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation.

PubMed

Veluraja, Kasinadar; Selvin, Jeyasigamani F A; Venkateshwari, Selvakumar; Priyadarzini, Thanu R K

2010-09-23

The inherent flexibility and lack of strong intramolecular interactions of oligosaccharides demand the use of theoretical methods for their structural elucidation. In spite of the developments of theoretical methods, not much research on glycoinformatics is done so far when compared to bioinformatics research on proteins and nucleic acids. We have developed three dimensional structural database for a sialic acid-containing carbohydrates (3DSDSCAR). This is an open-access database that provides 3D structural models of a given sialic acid-containing carbohydrate. At present, 3DSDSCAR contains 60 conformational models, belonging to 14 different sialic acid-containing carbohydrates, deduced through 10 ns molecular dynamics (MD) simulations. The database is available at the URL: http://www.3dsdscar.org. Copyright 2010 Elsevier Ltd. All rights reserved.

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

PubMed

Fernández-Suárez, Xosé M; Rigden, Daniel J; Galperin, Michael Y

2014-01-01

The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI's MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/).

SuperSweet—a resource on natural and artificial sweetening agents

PubMed Central

Ahmed, Jessica; Preissner, Saskia; Dunkel, Mathias; Worth, Catherine L.; Eckert, Andreas; Preissner, Robert

2011-01-01

A vast number of sweet tasting molecules are known, encompassing small compounds, carbohydrates, d-amino acids and large proteins. Carbohydrates play a particularly big role in human diet. The replacement of sugars in food with artificial sweeteners is common and is a general approach to prevent cavities, obesity and associated diseases such as diabetes and hyperlipidemia. Knowledge about the molecular basis of taste may reveal new strategies to overcome diet-induced diseases. In this context, the design of safe, low-calorie sweeteners is particularly important. Here, we provide a comprehensive collection of carbohydrates, artificial sweeteners and other sweet tasting agents like proteins and peptides. Additionally, structural information and properties such as number of calories, therapeutic annotations and a sweetness-index are stored in SuperSweet. Currently, the database consists of more than 8000 sweet molecules. Moreover, the database provides a modeled 3D structure of the sweet taste receptor and binding poses of the small sweet molecules. These binding poses provide hints for the design of new sweeteners. A user-friendly graphical interface allows similarity searching, visualization of docked sweeteners into the receptor etc. A sweetener classification tree and browsing features allow quick requests to be made to the database. The database is freely available at: http://bioinformatics.charite.de/sweet/. PMID:20952410

SuperSweet--a resource on natural and artificial sweetening agents.

PubMed

Ahmed, Jessica; Preissner, Saskia; Dunkel, Mathias; Worth, Catherine L; Eckert, Andreas; Preissner, Robert

2011-01-01

A vast number of sweet tasting molecules are known, encompassing small compounds, carbohydrates, d-amino acids and large proteins. Carbohydrates play a particularly big role in human diet. The replacement of sugars in food with artificial sweeteners is common and is a general approach to prevent cavities, obesity and associated diseases such as diabetes and hyperlipidemia. Knowledge about the molecular basis of taste may reveal new strategies to overcome diet-induced diseases. In this context, the design of safe, low-calorie sweeteners is particularly important. Here, we provide a comprehensive collection of carbohydrates, artificial sweeteners and other sweet tasting agents like proteins and peptides. Additionally, structural information and properties such as number of calories, therapeutic annotations and a sweetness-index are stored in SuperSweet. Currently, the database consists of more than 8000 sweet molecules. Moreover, the database provides a modeled 3D structure of the sweet taste receptor and binding poses of the small sweet molecules. These binding poses provide hints for the design of new sweeteners. A user-friendly graphical interface allows similarity searching, visualization of docked sweeteners into the receptor etc. A sweetener classification tree and browsing features allow quick requests to be made to the database. The database is freely available at: http://bioinformatics.charite.de/sweet/.

Antimicrobial Peptides of Meat Origin - An In silico and In vitro Analysis.

PubMed

Keska, Paulina; Stadnik, Joanna

2017-01-01

The aim of this study was to evaluate the antimicrobial activity of meat protein-derived peptides against selected Gram-positive and Gram-negative bacteria. The in silico and in vitro approach was combined to determine the potency of antimicrobial peptides derived from pig (Sus scrofa) and cow (Bos taurus) proteins. The in silico studies consisted of an analysis of the amino acid composition of peptides obtained from the CAMPR database, their molecular weight and other physicochemical properties (isoelectric point, molar extinction coefficient, instability index, aliphatic index, hydropathy index and net charge). The degree of similarity was estimated between the antimicrobial peptide sequences derived from the slaughtered animals and the main meat proteins. Antimicrobial activity of peptides isolated from dry-cured meat products was analysed (in vitro) against two strains of pathogenic bacteria using the disc diffusion method. There was no evidence of growthinhibitory properties of peptides isolated from dry-cured meat products against Escherichia coli K12 ATCC 10798 and Staphylococcus aureus ATCC 25923. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

DOGMA: A Disk-Oriented Graph Matching Algorithm for RDF Databases

NASA Astrophysics Data System (ADS)

Bröcheler, Matthias; Pugliese, Andrea; Subrahmanian, V. S.

RDF is an increasingly important paradigm for the representation of information on the Web. As RDF databases increase in size to approach tens of millions of triples, and as sophisticated graph matching queries expressible in languages like SPARQL become increasingly important, scalability becomes an issue. To date, there is no graph-based indexing method for RDF data where the index was designed in a way that makes it disk-resident. There is therefore a growing need for indexes that can operate efficiently when the index itself resides on disk. In this paper, we first propose the DOGMA index for fast subgraph matching on disk and then develop a basic algorithm to answer queries over this index. This algorithm is then significantly sped up via an optimized algorithm that uses efficient (but correct) pruning strategies when combined with two different extensions of the index. We have implemented a preliminary system and tested it against four existing RDF database systems developed by others. Our experiments show that our algorithm performs very well compared to these systems, with orders of magnitude improvements for complex graph queries.

Finding European bioethical literature: an evaluation of the leading abstracting and indexing services

PubMed Central

Fangerau, H

2004-01-01

Objectives: In this study the author aimed to provide information for researchers to help them with the selection of suitable databases for finding medical ethics literature. The quantity of medical ethical literature that is indexed in different existing electronic bibliographies was ascertained. Method: Using the international journal index Ulrich's Periodicals Directory, journals on medical ethics were identified. The electronic bibliographies indexing these journals were analysed. In an additional analysis documentalists indexing bioethical literature were asked to name European journals on medical ethics. The bibliographies indexing these journals were examined. Results: Of 290 journals on medical ethics 173 were indexed in at least one bibliography. Current Contents showed the highest coverage with 66 (22.8%) journals indexed followed by MEDLINE (22.1%). By a combined search in the top ten bibliographies with the highest coverage, a maximum coverage of 45.2% of all journals could be reached. All the bibliographies showed a tendency to index more North American than European literature. This result was verified by the supplementary analysis of a sample of continental European journals. Here EMBASE covered the highest number of journals (20.6%) followed by the Russian Academy of Sciences Bibliographies (19.2%). Conclusion: A medical ethics literature search has to be carried out in several databases in order to reach an adequate collection of literature. The databases one wishes to combine should be carefully chosen. There seems to be a regional bias in the most popular databases, favouring North American periodicals compared with European literature on medical ethics. PMID:15173367

For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases

PubMed Central

Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

2015-01-01

Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases’ criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ’s coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases. However, DOAJ only indexes articles for half of the biomedical journals listed, making it an incomplete source for biomedical research papers in general. PMID:26038727

Indexation of psychiatric journals from low- and middle-income countries: a survey and a case study

PubMed Central

KIELING, CHRISTIAN; HERRMAN, HELEN; PATEL, VIKRAM; MARI, JAIR DE JESUS

2009-01-01

There is a marked underepresentation of low- and middle-income countries (LAMIC) in the psychiatric literature, which may reflect an overall low representation of LAMIC publications in databases of indexed journals. This paper investigates the worldwide distribution of indexed psychiatric journals. A survey in both Medline and ISI Web of Science was performed in order to identify journals in the field of psychiatry according to their country of origin. Two hundred and twenty-two indexed psychiatric journals were found. Of these, 213 originated from high-income countries and only nine (4.1%) from middle-income countries. None were found in low-income countries. We also present the experience of a LAMIC psychiatric journal, the Revista Brasileira de Psiquiatria, in its recent indexation process. This case study may serve as an example for other LAMIC journals to pursue indexation in major databases as a strategy to widen the international foundation of psychiatric research. There is an important need for the inclusion of LAMIC psychiatric publications in the major indexation databases. This process will require multiple agents to partner with journals from LAMIC to improve their quality and strengthen their chances of being indexed. PMID:19293959

dbDSM: a manually curated database for deleterious synonymous mutations.

PubMed

Wen, Pengbo; Xiao, Peng; Xia, Junfeng

2016-06-15

Synonymous mutations (SMs), which changed the sequence of a gene without directly altering the amino acid sequence of the encoded protein, were thought to have no functional consequences for a long time. They are often assumed to be neutral in models of mutation and selection and were completely ignored in many studies. However, accumulating experimental evidence has demonstrated that these mutations exert their impact on gene functions via splicing accuracy, mRNA stability, translation fidelity, protein folding and expression, and some of these mutations are implicated in human diseases. To the best of our knowledge, there is still no database specially focusing on disease-related SMs. We have developed a new database called dbDSM (database of Deleterious Synonymous Mutation), a continually updated database that collects, curates and manages available human disease-related SM data obtained from published literature. In the current release, dbDSM collects 1936 SM-disease association entries, including 1289 SMs and 443 human diseases from ClinVar, GRASP, GWAS Catalog, GWASdb, PolymiRTS database, PubMed database and Web of Knowledge. Additionally, we provided users a link to download all the data in the dbDSM and a link to submit novel data into the database. We hope dbDSM will be a useful resource for investigating the roles of SMs in human disease. dbDSM is freely available online at http://bioinfo.ahu.edu.cn:8080/dbDSM/index.jsp with all major browser supported. jfxia@ahu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

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.

Creating Your Own Database.

ERIC Educational Resources Information Center

Blair, John C., Jr.

1982-01-01

Outlines the important factors to be considered in selecting a database management system for use with a microcomputer and presents a series of guidelines for developing a database. General procedures, report generation, data manipulation, information storage, word processing, data entry, database indexes, and relational databases are among the…

Optimization of the efficiency of search operations in the relational database of radio electronic systems

NASA Astrophysics Data System (ADS)

Wajszczyk, Bronisław; Biernacki, Konrad

2018-04-01

The increase of interoperability of radio electronic systems used in the Armed Forces requires the processing of very large amounts of data. Requirements for the integration of information from many systems and sensors, including radar recognition, electronic and optical recognition, force to look for more efficient methods to support information retrieval in even-larger database resources. This paper presents the results of research on methods of improving the efficiency of databases using various types of indexes. The data structure indexing technique is a solution used in RDBMS systems (relational database management system). However, the analysis of the performance of indices, the description of potential applications, and in particular the presentation of a specific scale of performance growth for individual indices are limited to few studies in this field. This paper contains analysis of methods affecting the work efficiency of a relational database management system. As a result of the research, a significant increase in the efficiency of operations on data was achieved through the strategy of indexing data structures. The presentation of the research topic discussed in this paper mainly consists of testing the operation of various indexes against the background of different queries and data structures. The conclusions from the conducted experiments allow to assess the effectiveness of the solutions proposed and applied in the research. The results of the research indicate the existence of a real increase in the performance of operations on data using indexation of data structures. In addition, the level of this growth is presented, broken down by index types.

Species identification of corynebacteria by cellular fatty acid analysis.

PubMed

Van den Velde, Sandra; Lagrou, Katrien; Desmet, Koen; Wauters, Georges; Verhaegen, Jan

2006-02-01

We evaluated the usefulness of cellular fatty acid analysis for the identification of corynebacteria. Therefore, 219 well-characterized strains belonging to 21 Corynebacterium species were analyzed with the Sherlock System of MIDI (Newark, DE). Most Corynebacterium species have a qualitative different fatty acid profile. Corynebacterium coyleae (subgroup 1), Corynebacterium riegelii, Corynebacterium simulans, and Corynebacterium imitans differ only quantitatively. Corynebacterium afermentans afermentans and C. coyleae (subgroup 2) have both a similar qualitative and quantitative profile. The commercially available database (CLIN 40, MIDI) identified only one third of the 219 strains correctly at the species level. We created a new database with these 219 strains. This new database was tested with 34 clinical isolates and could identify 29 strains correctly. Strains that remained unidentified were 2 Corynebacterium aurimucosum (not included in our database), 1 C. afermentans afermentans, and 2 Corynebacterium pseudodiphtheriticum. Cellular fatty acid analysis with a self-created database can be used for the identification and differentiation of corynebacteria.

The LSST Data Mining Research Agenda

NASA Astrophysics Data System (ADS)

Borne, K.; Becla, J.; Davidson, I.; Szalay, A.; Tyson, J. A.

2008-12-01

We describe features of the LSST science database that are amenable to scientific data mining, object classification, outlier identification, anomaly detection, image quality assurance, and survey science validation. The data mining research agenda includes: scalability (at petabytes scales) of existing machine learning and data mining algorithms; development of grid-enabled parallel data mining algorithms; designing a robust system for brokering classifications from the LSST event pipeline (which may produce 10,000 or more event alerts per night) multi-resolution methods for exploration of petascale databases; indexing of multi-attribute multi-dimensional astronomical databases (beyond spatial indexing) for rapid querying of petabyte databases; and more.

Efficacy and safety of curcumin and its combination with boswellic acid in osteoarthritis: a comparative, randomized, double-blind, placebo-controlled study.

PubMed

Haroyan, Armine; Mukuchyan, Vahan; Mkrtchyan, Nana; Minasyan, Naira; Gasparyan, Srbuhi; Sargsyan, Aida; Narimanyan, Mikael; Hovhannisyan, Areg

2018-01-09

The aim of this clinical trial was to assess the efficacy and safety of curcuminoid complex extract from turmeric rhizome with turmeric volatile oil (CuraMed®) and its combination with boswellic acid extract from Indian frankincense root (Curamin®) vs placebo for the treatment of 40- to 70-year-old patients with osteoarthritis (OA). The effects of CuraMed® 500-mg capsules (333 mg curcuminoids) and Curamin® 500-mg capsules (350 mg curcuminoids and 150 mg boswellic acid) taken orally three times a day for 12 weeks in 201 patients was investigated in a three-arm, parallel-group, randomized, double-blinded, placebo-controlled trial. Primary outcome efficacy measures included OA physical function performance-based tests, the WOMAC recommended index of joint pain, morning stiffness, limitations of physical function, and the patients' global assessment of disease severity. Favorable effects of both preparations compared to placebo were observed after only 3 months of continuous treatment. A significant effect of Curamin® compared to placebo was observed both in physical performance tests and the WOMAC joint pain index, while superior efficacy of CuraMed vs placebo was observed only in physical performance tests. The effect size compared to placebo was comparable for both treatment groups but was superior in the Curamin® group. The treatments were well tolerated. Twelve-week use of curcumin complex or its combination with boswellic acid reduces pain-related symptoms in patients with OA. Curcumin in combination with boswellic acid is more effective. Combining Curcuma longa and Boswellia serrata extracts in Curamin® increases the efficacy of OA treatment presumably due to synergistic effects of curcumin and boswellic acid. This trial is registered at the database www.clinicaltrials.gov . https://clinicaltrials.gov/ct2/show/NCT02390349?term=EuroPharma&rank=1 . Study registration number: NCT02390349 .

The allelopathic effects of invasive plant Solidago canadensis on seed germination and growth of Lactuca sativa enhanced by different types of acid deposition.

PubMed

Wang, Congyan; Xiao, Hongguang; Zhao, Lulu; Liu, Jun; Wang, Lei; Zhang, Fei; Shi, Yanchun; Du, Daolin

2016-04-01

Invasive species can exhibit allelopathic effects on native species. Meanwhile, the types of acid deposition are gradually changing. Thus, the allelopathic effects of invasive species on seed germination and growth of native species may be altered or even enhanced under conditions with diversified acid deposition. This study aims to assess the allelopathic effects (using leaves extracts) of invasive plant Solidago canadensis on seed germination and growth of native species Lactuca sativa treated with five types of acid deposition with different SO4(2-) to NO3(-) ratios (1:0, sulfuric acid; 5:1, sulfuric-rich acid; 1:1, mixed acid; 1:5, nitric-rich acid; 0:1, nitric acid). Solidago canadensis leaf extracts exhibited significantly allelopathic effects on germination index, vigor index, and germination rate index of L. sativa. High concentration of S. canadensis leaf extracts also similarly exhibited significantly allelopathic effects on root length of L. sativa. This may be due to that S. canadensis could release allelochemicals and then trigger allelopathic effects on seed germination and growth of L. sativa. Acid deposition exhibited significantly negative effects on seedling biomass, root length, seedling height, germination index, vigor index, and germination rate index of L. sativa. This may be ascribed to the decreased soil pH values mediated by acid deposition which could produce toxic effects on seedling growth. Sulfuric acid deposition triggered more toxic effects on seedling biomass and vigor index of L. sativa than nitric acid deposition. This may be attributing to the difference in exchange capacity with hydroxyl groups (OH(-)) between SO4(2-) and NO3(-) as well as the fertilizing effects mediated by nitric deposition. All types of acid deposition significantly enhanced the allelopathic effects of S. canadensis on root length, germination index, vigor index, and germination rate index of L. sativa. This may be due to the negatively synergistic effects of acid deposition and S. canadensis on seed germination and growth of L. sativa. The ratio of SO4(2-) to NO3(-) in acid deposition was an important factor that profoundly affected the allelopathic effects of S. canadensis on the seed germination and growth of L. sativa possibly because the difference in exchange capacity with hydroxyl groups (OH(-)) between SO4(2-) and NO3(-) as well as the fertilizing effects triggered by nitric deposition. Thus, the allelopathic effects of invasive species on seed germination and growth of native plants might be enhanced under increased and diversified acid deposition.

Indexing and retrieval of MPEG compressed video

NASA Astrophysics Data System (ADS)

Kobla, Vikrant; Doermann, David S.

1998-04-01

To keep pace with the increased popularity of digital video as an archival medium, the development of techniques for fast and efficient analysis of ideo streams is essential. In particular, solutions to the problems of storing, indexing, browsing, and retrieving video data from large multimedia databases are necessary to a low access to these collections. Given that video is often stored efficiently in a compressed format, the costly overhead of decompression can be reduced by analyzing the compressed representation directly. In earlier work, we presented compressed domain parsing techniques which identified shots, subshots, and scenes. In this article, we present efficient key frame selection, feature extraction, indexing, and retrieval techniques that are directly applicable to MPEG compressed video. We develop a frame type independent representation which normalizes spatial and temporal features including frame type, frame size, macroblock encoding, and motion compensation vectors. Features for indexing are derived directly from this representation and mapped to a low- dimensional space where they can be accessed using standard database techniques. Spatial information is used as primary index into the database and temporal information is used to rank retrieved clips and enhance the robustness of the system. The techniques presented enable efficient indexing, querying, and retrieval of compressed video as demonstrated by our system which typically takes a fraction of a second to retrieve similar video scenes from a database, with over 95 percent recall.

AFAL: a web service for profiling amino acids surrounding ligands in proteins

NASA Astrophysics Data System (ADS)

Arenas-Salinas, Mauricio; Ortega-Salazar, Samuel; Gonzales-Nilo, Fernando; Pohl, Ehmke; Holmes, David S.; Quatrini, Raquel

2014-11-01

With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5'-triphosphate.

AFAL: a web service for profiling amino acids surrounding ligands in proteins.

PubMed

Arenas-Salinas, Mauricio; Ortega-Salazar, Samuel; Gonzales-Nilo, Fernando; Pohl, Ehmke; Holmes, David S; Quatrini, Raquel

2014-11-01

With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html ). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5'-triphosphate.

Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data

PubMed Central

Freire, Sergio Miranda; Teodoro, Douglas; Wei-Kleiner, Fang; Sundvall, Erik; Karlsson, Daniel; Lambrix, Patrick

2016-01-01

This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest. PMID:26958859

Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data.

PubMed

Freire, Sergio Miranda; Teodoro, Douglas; Wei-Kleiner, Fang; Sundvall, Erik; Karlsson, Daniel; Lambrix, Patrick

2016-01-01

This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest.

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...

The Status of Cognitive Psychology Journals: An Impact Factor Approach

ERIC Educational Resources Information Center

Togia, Aspasia

2013-01-01

The purpose of this study was to examine the impact factor of cognitive psychology journals indexed in the Science and Social Sciences edition of "Journal Citation Reports" ("JCR") database over a period of 10 consecutive years. Cognitive psychology journals were indexed in 11 different subject categories of the database. Their mean impact factor…

Comparing IndexedHBase and Riak for Serving Truthy: Performance of Data Loading and Query Evaluation

DTIC Science & Technology

2013-08-01

Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS performance evaluation, distributed database, noSQL , HBase, indexing Xiaoming Gao, Judy Qiu...common hashtags created during a given time window. With the purpose of finding a solution for these challenges, we evaluate NoSQL databases such as

Febuxostat for the treatment of gout.

PubMed

Bridgeman, Mary Barna; Chavez, Benjamin

2015-02-01

Gout is a rheumatologic condition associated with elevated serum uric acid levels and deposition of monosodium urate crystals in joints and soft tissues. The xanthine oxidase inhibitor, allopurinol, has historically been the principle agent utilized for reducing elevated uric acid levels and treating underlying cause of gout symptoms; the availability of febuxostat, a newer non-purine selective xanthine oxidase inhibitor, represents an alternative therapy for those patients with contraindications or intolerance to allopurinol. This article reviews the published literature on the pharmacologic characteristics and clinical safety and efficacy data on the use of febuxostat in the treatment of gout. A literature search of MEDLINE and MEDLINE In-Process & Other Non-Indexed Citations Databases (1996-November 2014) was conducted utilizing the key words 'febuxostat', 'allopurinol', and 'gout'. All published articles regarding febuxostat were evaluated. References of selected articles, data from poster presentations, and abstract publications were additionally reviewed. Febuxostat has shown benefit with respect to symptomatic relief and uric acid level reduction. The safety profile of this agent makes it an ideal alternative in those patients with contraindications to or who are intolerant of allopurinol.

Visibility of medical informatics regarding bibliometric indices and databases

PubMed Central

2011-01-01

Background The quantitative study of the publication output (bibliometrics) deeply influences how scientific work is perceived (bibliometric visibility). Recently, new bibliometric indices and databases have been established, which may change the visibility of disciplines, institutions and individuals. This study examines the effects of the new indices on the visibility of Medical Informatics. Methods By objective criteria, three sets of journals are chosen, two representing Medical Informatics and a third addressing Internal Medicine as a benchmark. The availability of index data (index coverage) and the aggregate scores of these corpora are compared for journal-related (Journal impact factor, Eigenfactor metrics, SCImago journal rank) and author-related indices (Hirsch-index, Egghes G-index). Correlation analysis compares the dependence of author-related indices. Results The bibliometric visibility depended on the research focus and the citation database: Scopus covers more journals relevant for Medical Informatics than ISI/Thomson Reuters. Journals focused on Medical Informatics' methodology were negatively affected by the Eigenfactor metrics, while the visibility profited from an interdisciplinary research focus. The correlation between Hirsch-indices computed on citation databases and the Internet was strong. Conclusions The visibility of smaller technology-oriented disciplines like Medical Informatics is changed by the new bibliometric indices and databases possibly leading to suitably changed publication strategies. Freely accessible author-related indices enable an easy and adequate individual assessment. PMID:21496230

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.

PubMed

Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2017-01-04

The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is useful for macroevolutionary studies. The ATGC database includes many forms of pre-computed data, in particular ATGC-COGs (Clusters of Orthologous Genes), multiple sequence alignments, a set of 'index' orthologs representing the most well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc. Although the ATGC database contains several million proteins from thousands of genomes organized into hundreds of clusters (roughly a 4-fold increase since the last version of the ATGC database), it is now built with completely automated methods and will be regularly updated following new releases of the NCBI RefSeq database. The ATGC database is hosted jointly at the University of Iowa at dmk-brain.ecn.uiowa.edu/ATGC/ and the NCBI at ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Content-based video indexing and searching with wavelet transformation

NASA Astrophysics Data System (ADS)

Stumpf, Florian; Al-Jawad, Naseer; Du, Hongbo; Jassim, Sabah

2006-05-01

Biometric databases form an essential tool in the fight against international terrorism, organised crime and fraud. Various government and law enforcement agencies have their own biometric databases consisting of combination of fingerprints, Iris codes, face images/videos and speech records for an increasing number of persons. In many cases personal data linked to biometric records are incomplete and/or inaccurate. Besides, biometric data in different databases for the same individual may be recorded with different personal details. Following the recent terrorist atrocities, law enforcing agencies collaborate more than before and have greater reliance on database sharing. In such an environment, reliable biometric-based identification must not only determine who you are but also who else you are. In this paper we propose a compact content-based video signature and indexing scheme that can facilitate retrieval of multiple records in face biometric databases that belong to the same person even if their associated personal data are inconsistent. We shall assess the performance of our system using a benchmark audio visual face biometric database that has multiple videos for each subject but with different identity claims. We shall demonstrate that retrieval of relatively small number of videos that are nearest, in terms of the proposed index, to any video in the database results in significant proportion of that individual biometric data.

Transportation-markings database : composite categories, classification & index. Part I 5, Volume 3, additional studies

DOT National Transportation Integrated Search

2006-01-01

The Transportation-Markings Database project (within the T-M Monograph Series) began in 1997 with the publishing of the initial component, Transportation-Markings Database: Marine. That study was joined by T-M Database: Traffic Control Devices (1998)...

Automated indexing for making of a newspaper article database

NASA Astrophysics Data System (ADS)

Kamio, Tatsuo

Automated indexing has been widely employed in the process of making newspaper article databases. It is essential to speed up the compiling time of the said databases for the large amount of articles come out daily, and save manpower involved in it, with the aid of computers. However, indexed terms which are extracted by the current automated indexing systems have no links with subject analysis, so that they are not considered to be keywords in a strict sense. Thus, the system of Nihon Keizai Shimbun KK enables to justify keywords to certain extent based on the two clues ; 1) at which location the extracted term occurred, and 2) whether or not subject area of the article corresponds to thesaurus class of the extracted term, by using characteristics peculiar to newspaper articles. Also the experiment of assigning keywords which are not occurred in articles was conducted. The fairly good result was obtained.

(BARS) -- Bibliographic Retrieval System Sandia Shock Compression (SSC) database Shock Physics Index (SPHINX) database. Volume 1: UNIX version query guide customized application for INGRES

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

Herrmann, W.; von Laven, G.M.; Parker, T.

1993-09-01

The Bibliographic Retrieval System (BARS) is a data base management system specially designed to retrieve bibliographic references. Two databases are available, (i) the Sandia Shock Compression (SSC) database which contains over 5700 references to the literature related to stress waves in solids and their applications, and (ii) the Shock Physics Index (SPHINX) which includes over 8000 further references to stress waves in solids, material properties at intermediate and low rates, ballistic and hypervelocity impact, and explosive or shock fabrication methods. There is some overlap in the information in the two data bases.

Information-theoretic CAD system in mammography: Entropy-based indexing for computational efficiency and robust performance

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

Tourassi, Georgia D.; Harrawood, Brian; Singh, Swatee

2007-08-15

We have previously presented a knowledge-based computer-assisted detection (KB-CADe) system for the detection of mammographic masses. The system is designed to compare a query mammographic region with mammographic templates of known ground truth. The templates are stored in an adaptive knowledge database. Image similarity is assessed with information theoretic measures (e.g., mutual information) derived directly from the image histograms. A previous study suggested that the diagnostic performance of the system steadily improves as the knowledge database is initially enriched with more templates. However, as the database increases in size, an exhaustive comparison of the query case with each stored templatemore » becomes computationally burdensome. Furthermore, blind storing of new templates may result in redundancies that do not necessarily improve diagnostic performance. To address these concerns we investigated an entropy-based indexing scheme for improving the speed of analysis and for satisfying database storage restrictions without compromising the overall diagnostic performance of our KB-CADe system. The indexing scheme was evaluated on two different datasets as (i) a search mechanism to sort through the knowledge database, and (ii) a selection mechanism to build a smaller, concise knowledge database that is easier to maintain but still effective. There were two important findings in the study. First, entropy-based indexing is an effective strategy to identify fast a subset of templates that are most relevant to a given query. Only this subset could be analyzed in more detail using mutual information for optimized decision making regarding the query. Second, a selective entropy-based deposit strategy may be preferable where only high entropy cases are maintained in the knowledge database. Overall, the proposed entropy-based indexing scheme was shown to reduce the computational cost of our KB-CADe system by 55% to 80% while maintaining the system's diagnostic performance.« less

MRNIDX - Marine Data Index: Database Description, Operation, Retrieval, and Display

USGS Publications Warehouse

Paskevich, Valerie F.

1982-01-01

A database referencing the location and content of data stored on magnetic medium was designed to assist in the indexing of time-series and spatially dependent marine geophysical data collected or processed by the U. S. Geological Survey. The database was designed and created for input to the Geologic Retrieval and Synopsis Program (GRASP) to allow selective retrievals of information pertaining to location of data, data format, cruise, geographical bounds and collection dates of data. This information is then used to locate the stored data for administrative purposes or further processing. Database utilization is divided into three distinct operations. The first is the inventorying of the data and the updating of the database, the second is the retrieval of information from the database, and the third is the graphic display of the geographical boundaries to which the retrieved information pertains.

Ten Most Searched Databases by a Business Generalist--Part 1 or A Day in the Life of....

ERIC Educational Resources Information Center

Meredith, Meri

1986-01-01

Describes databases frequently used in Business Information Center, Cummins Engine Company (Columbus, Indiana): Dun and Bradstreet Business Information Report System, Newsearch, Dun and Bradstreet Market Identifiers, Trade and Industry Index, PTS PROMT, Bureau of Labor Statistics files, ABI/INFORM, Magazine Index, NEXIS, Dow Jones News/Retrieval.…

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…

A survey of the current status of web-based databases indexing Iranian journals.

PubMed

Merat, Shahin; Khatibzadeh, Shahab; Mesgarpour, Bita; Malekzadeh, Reza

2009-05-01

The scientific output of Iran is increasing rapidly during the recent years. Unfortunately, most papers are published in journals which are not indexed by popular indexing systems and many of them are in Persian without English translation. This makes the results of Iranian scientific research unavailable to other researchers, including Iranians. The aim of this study was to evaluate the quality of current web-based databases indexing scientific articles published in Iran. We identified web-based databases which indexed scientific journals published in Iran using popular search engines. The sites were then subjected to a series of tests to evaluate their coverage, search capabilities, stability, accuracy of information, consistency, accessibility, ease of use, and other features. Results were compared with each other to identify strengths and shortcomings of each site. Five web sites were indentified. None had a complete coverage on scientific Iranian journals. The search capabilities were less than optimal in most sites. English translations of research titles, author names, keywords, and abstracts of Persian-language articles did not follow standards. Some sites did not cover abstracts. Numerous typing errors make searches ineffective and citation indexing unreliable. None of the currently available indexing sites are capable of presenting Iranian research to the international scientific community. The government should intervene by enforcing policies designed to facilitate indexing through a systematic approach. The policies should address Iranian journals, authors, and indexing sites. Iranian journals should be required to provide their indexing data, including references, electronically; authors should provide correct indexing information to journals; and indexing sites should improve their software to meet standards set by the government.

Characterising droughts in Central America with uncertain hydro-meteorological data

NASA Astrophysics Data System (ADS)

Quesada Montano, B.; Westerberg, I.; Wetterhall, F.; Hidalgo, H. G.; Halldin, S.

2015-12-01

Droughts studies are scarce in Central America, a region frequently affected by droughts that cause significant socio-economic and environmental problems. Drought characterisation is important for water management and planning and can be done with the help of drought indices. Many indices have been developed in the last decades but their ability to suitably characterise droughts depends on the region of application. In Central America, comprehensive and high-quality observational networks of meteorological and hydrological data are not available. This limits the choice of drought indices and denotes the need to evaluate the quality of the data used in their calculation. This paper aimed to find which combination(s) of drought index and meteorological database are most suitable for characterising droughts in Central America. The drought indices evaluated were the standardised precipitation index (SPI), deciles (DI), the standardised precipitation evapotranspiration index (SPEI) and the effective drought index (EDI). These were calculated using precipitation data from the Climate Hazards Group Infra-Red Precipitation with station (CHIRPS), CRN073, the Climate Research Unit (CRU), ERA-Interim and station databases, and temperature data from the CRU database. All the indices were calculated at 1-, 3-, 6-, 9- and 12-month accumulation times. As a first step, the large-scale meteorological precipitation datasets were compared to have an overview of the level of agreement between them and find possible quality problems. Then, the performance of all the combinations of drought indices and meteorological datasets were evaluated against independent river discharge data, in form of the standardised streamflow index (SSI). Results revealed the large disagreement between the precipitation datasets; we found the selection of database to be more important than the selection of drought index. We found that the best combinations of meteorological drought index and database were obtained using the SPI and DI, calculated with CHIRPS and station data.

ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs.

PubMed

Meiler, Arno; Klinger, Claudia; Kaufmann, Michael

2012-09-08

The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC's NUCOCOG dataset as the largest one available for that purpose thus far. Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

PubMed Central

2012-01-01

Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills. PMID:22958836

A population health approach to reducing observational intensity bias in health risk adjustment: cross sectional analysis of insurance claims.

PubMed

Wennberg, David E; Sharp, Sandra M; Bevan, Gwyn; Skinner, Jonathan S; Gottlieb, Daniel J; Wennberg, John E

2014-04-10

To compare the performance of two new approaches to risk adjustment that are free of the influence of observational intensity with methods that depend on diagnoses listed in administrative databases. Administrative data from the US Medicare program for services provided in 2007 among 306 US hospital referral regions. Cross sectional analysis. 20% sample of fee for service Medicare beneficiaries residing in one of 306 hospital referral regions in the United States in 2007 (n = 5,153,877). The effect of health risk adjustment on age, sex, and race adjusted mortality and spending rates among hospital referral regions using four indices: the standard Centers for Medicare and Medicaid Services--Hierarchical Condition Categories (HCC) index used by the US Medicare program (calculated from diagnoses listed in Medicare's administrative database); a visit corrected HCC index (to reduce the effects of observational intensity on frequency of diagnoses); a poverty index (based on US census); and a population health index (calculated using data on incidence of hip fractures and strokes, and responses from a population based annual survey of health from the Centers for Disease Control and Prevention). Estimated variation in age, sex, and race adjusted mortality rates across hospital referral regions was reduced using the indices based on population health, poverty, and visit corrected HCC, but increased using the standard HCC index. Most of the residual variation in age, sex, and race adjusted mortality was explained (in terms of weighted R2) by the population health index: R2=0.65. The other indices explained less: R2=0.20 for the visit corrected HCC index; 0.19 for the poverty index, and 0.02 for the standard HCC index. The residual variation in age, sex, race, and price adjusted spending per capita across the 306 hospital referral regions explained by the indices (in terms of weighted R2) were 0.50 for the standard HCC index, 0.21 for the population health index, 0.12 for the poverty index, and 0.07 for the visit corrected HCC index, implying that only a modest amount of the variation in spending can be explained by factors most closely related to mortality. Further, once the HCC index is visit corrected it accounts for almost none of the residual variation in age, sex, and race adjusted spending. Health risk adjustment using either the poverty index or the population health index performed substantially better in terms of explaining actual mortality than the indices that relied on diagnoses from administrative databases; the population health index explained the majority of residual variation in age, sex, and race adjusted mortality. Owing to the influence of observational intensity on diagnoses from administrative databases, the standard HCC index over-adjusts for regional differences in spending. Research to improve health risk adjustment methods should focus on developing measures of risk that do not depend on observation influenced diagnoses recorded in administrative databases.

Three Library and Information Science Databases Revisited: Currency, Coverage and Overlap, Interindexing Consistency.

ERIC Educational Resources Information Center

Blackwell, Michael Lind

This study evaluates the "Education Resources Information Center" (ERIC), "Library and Information Science Abstracts" (LISA), and "Library Literature" (LL) databases, determining how long the databases take to enter records (indexing delay), how much duplication of effort exists among the three databases (indexing…

A controlled nursing vocabulary for indexing and information retrieval.

PubMed

Pekkala, Eila; Saranto, Kaija; Tallberg, Marianne; Ensio, Anneli; Junttila, Kristiina

2006-01-01

The lack of a nursing thesaurus in Finnish has emerged among nursing professionals searching nursing knowledge and librarians when indexing literature to databases. The Finnish Nursing Education Society launched a project focusing on the development of a nursing vocabulary and the compilation of a thesaurus. The content of a vocabulary was created by six experts using Delphi-technique. The validity of the vocabulary was twice tested for indexing nursing research and has afterwards been revised. The vocabulary can be used for indexing and information retrieval purposes. The main challenge is that nurses easily can find national as well as international nursing research from databases and enhance research utilization.

NPIDB: Nucleic acid-Protein Interaction DataBase.

PubMed

Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

2013-01-01

The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

A high performance, ad-hoc, fuzzy query processing system for relational databases

NASA Technical Reports Server (NTRS)

Mansfield, William H., Jr.; Fleischman, Robert M.

1992-01-01

Database queries involving imprecise or fuzzy predicates are currently an evolving area of academic and industrial research. Such queries place severe stress on the indexing and I/O subsystems of conventional database environments since they involve the search of large numbers of records. The Datacycle architecture and research prototype is a database environment that uses filtering technology to perform an efficient, exhaustive search of an entire database. It has recently been modified to include fuzzy predicates in its query processing. The approach obviates the need for complex index structures, provides unlimited query throughput, permits the use of ad-hoc fuzzy membership functions, and provides a deterministic response time largely independent of query complexity and load. This paper describes the Datacycle prototype implementation of fuzzy queries and some recent performance results.

Reflective random indexing for semi-automatic indexing of the biomedical literature.

PubMed

Vasuki, Vidya; Cohen, Trevor

2010-10-01

The rapid growth of biomedical literature is evident in the increasing size of the MEDLINE research database. Medical Subject Headings (MeSH), a controlled set of keywords, are used to index all the citations contained in the database to facilitate search and retrieval. This volume of citations calls for efficient tools to assist indexers at the US National Library of Medicine (NLM). Currently, the Medical Text Indexer (MTI) system provides assistance by recommending MeSH terms based on the title and abstract of an article using a combination of distributional and vocabulary-based methods. In this paper, we evaluate a novel approach toward indexer assistance by using nearest neighbor classification in combination with Reflective Random Indexing (RRI), a scalable alternative to the established methods of distributional semantics. On a test set provided by the NLM, our approach significantly outperforms the MTI system, suggesting that the RRI approach would make a useful addition to the current methodologies.

Walkability Index

EPA Pesticide Factsheets

The Walkability Index dataset characterizes every Census 2010 block group in the U.S. based on its relative walkability. Walkability depends upon characteristics of the built environment that influence the likelihood of walking being used as a mode of travel. The Walkability Index is based on the EPA's previous data product, the Smart Location Database (SLD). Block group data from the SLD was the only input into the Walkability Index, and consisted of four variables from the SLD weighted in a formula to create the new Walkability Index. This dataset shares the SLD's block group boundary definitions from Census 2010. The methodology describing the process of creating the Walkability Index can be found in the documents located at ftp://newftp.epa.gov/EPADataCommons/OP/WalkabilityIndex.zip. You can also learn more about the Smart Location Database at https://edg.epa.gov/data/Public/OP/Smart_Location_DB_v02b.zip.

Effective nonvaccine interventions to be considered alongside human papilloma virus vaccine delivery.

PubMed

Hindin, Michelle J; Bloem, Paul; Ferguson, Jane

2015-01-01

World Health Organization recommends that girls, ages 9-13 years, get the human papilloma virus (HPV) vaccine. Global Alliance for Vaccines Initiative, which provides low-cost vaccine to eligible countries, requires that an additional intervention to be offered alongside the vaccine. We systematically searched and assessed the published literature in lower- and middle-income countries to identify effective interventions. We conducted systematic searches of four databases: PubMed, EMBASE, Global Index Medicus Regional Databases, and Cochrane Reviews for effective adolescent health interventions that could be delivered with the HPV vaccine in the following areas: (1) iron and folic acid supplementation (iron alone or with folic acid); (2) voucher delivery and cash transfer programs; (3) hand washing and soap provision; (4) vision screening; (5) promotion of physical activity/exercise; (6) menstrual hygiene education; (7) sexual and reproductive health education; (8) human immunodeficiency virus prevention activities; and (9) condom promotion, condom use skill building, and demonstration. We found limited evidence of consistent positive impact. Iron supplementation reduced iron-deficiency anemia and raised serum ferritin levels. Promotion of physical activity lowered blood pressure and reduced weight gain. Sexual and reproductive health and human immunodeficiency virus interventions improved adolescent communication with adults but did not influence behavioral outcomes. Countries should consider locally relevant and proven interventions to be offered alongside the HPV vaccine. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

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…

An Updated Site Index Equation for Naturally Regenerated Longleaf Pine Stands

Treesearch

Jyoti N. Rayamajhi; John S. Kush; Ralph S. Meldahl

1999-01-01

From 1964 to 1967. the U.S. Forest Service established the Regional Longleaf Growth Study (RLGS) in the Gulf States with the objective of obtaining a database for the development of prediction systems for naturally regenerated, even-aged. longleaf pine stands. The database has been used for numerous quantitative studies. One of these efforts was a site index equation...

PrimateLit Database: Submit Literature for Indexing

Science.gov Websites

Access PrimateLit Using this Site About the Project Submit Literature for Indexing Copyright Info Center WI Regional Primate Resource Center Submit Literature for Indexing PrimateLit has not been

MIPS: a database for genomes and protein sequences

PubMed Central

Mewes, H. W.; Frishman, D.; Güldener, U.; Mannhaupt, G.; Mayer, K.; Mokrejs, M.; Morgenstern, B.; Münsterkötter, M.; Rudd, S.; Weil, B.

2002-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz–Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91–93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155–158; Barker et al. (2001) Nucleic Acids Res., 29, 29–32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de). PMID:11752246

MIPS: a database for genomes and protein sequences.

PubMed

Mewes, H W; Frishman, D; Güldener, U; Mannhaupt, G; Mayer, K; Mokrejs, M; Morgenstern, B; Münsterkötter, M; Rudd, S; Weil, B

2002-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

Drug–drug interactions between antithrombotic medications and the risk of gastrointestinal bleeding

PubMed Central

Delaney, Joseph A.; Opatrny, Lucie; Brophy, James M.; Suissa, Samy

2007-01-01

Background Anticoagulants and antiplatelet drugs (e.g., warfarin, clopidogrel and acetylsalicylic acid) are key therapeutic agents in the treatment of cardiovascular diseases. However, drug–drug interactions may lead to a greatly increased risk of gastrointestinal bleeding when these drugs are combined. We assessed whether antithrombotic drug combinations increased the risk of such bleeding in a general practice population. Methods We conducted a population-based, retrospective case–control study using records in the United Kingdom General Practice Research Database from 2000 through 2005. Cases were identified as patients over 18 years of age with a first-ever diagnosis of gastrointestinal bleeding. They were matched with controls by physician practice, patient age and index date (date of diagnosis of bleeding). All eligible patients had to have at least 3 years of follow-up data in the database. Drug exposure was considered to be any prescription issued in the 90 days before the index date. Results There were 4028 cases with a diagnosis of gastrointestinal bleeding and 40 171 matched controls. The prescribing of acetylsalicylic acid with either clopidogrel (adjusted rate ratio [RR] 3.90, 95% confidence interval [CI] 2.78–5.47) or warfarin (adjusted RR 6.48, 95% CI 4.25–9.87) was associated with a greater risk of gastrointestinal bleeding than that observed with each drug alone. The same was true when a nonsteroidal anti-inflammatory drug was combined with either clopidogrel (adjusted RR 2.93, 95% CI 1.74–4.93) or warfarin (RR 4.60, 95% CI 2.77–7.64). Interpretation Drug combinations involving antiplatelets and anticoagulants are associated with a high risk of gastrointestinal bleeding beyond that associated with each drug used alone. Physicians should be aware of these risks to better assess their patients' therapeutic risk–benefit profiles. PMID:17698822

Scientometrics of drug discovery efforts: pain-related molecular targets.

PubMed

Kissin, Igor

2015-01-01

The aim of this study was to make a scientometric assessment of drug discovery efforts centered on pain-related molecular targets. The following scientometric indices were used: the popularity index, representing the share of articles (or patents) on a specific topic among all articles (or patents) on pain over the same 5-year period; the index of change, representing the change in the number of articles (or patents) on a topic from one 5-year period to the next; the index of expectations, representing the ratio of the number of all types of articles on a topic in the top 20 journals relative to the number of articles in all (>5,000) biomedical journals covered by PubMed over a 5-year period; the total number of articles representing Phase I-III trials of investigational drugs over a 5-year period; and the trial balance index, a ratio of Phase I-II publications to Phase III publications. Articles (PubMed database) and patents (US Patent and Trademark Office database) on 17 topics related to pain mechanisms were assessed during six 5-year periods from 1984 to 2013. During the most recent 5-year period (2009-2013), seven of 17 topics have demonstrated high research activity (purinergic receptors, serotonin, transient receptor potential channels, cytokines, gamma aminobutyric acid, glutamate, and protein kinases). However, even with these seven topics, the index of expectations decreased or did not change compared with the 2004-2008 period. In addition, publications representing Phase I-III trials of investigational drugs (2009-2013) did not indicate great enthusiasm on the part of the pharmaceutical industry regarding drugs specifically designed for treatment of pain. A promising development related to the new tool of molecular targeting, ie, monoclonal antibodies, for pain treatment has not yet resulted in real success. This approach has not yet demonstrated clinical effectiveness (at least with nerve growth factor) much beyond conventional analgesics, when its potential cost is more than an order of magnitude higher than that of conventional treatments. This scientometric assessment demonstrated a lack of real breakthrough developments.

Scientometrics of drug discovery efforts: pain-related molecular targets

PubMed Central

Kissin, Igor

2015-01-01

The aim of this study was to make a scientometric assessment of drug discovery efforts centered on pain-related molecular targets. The following scientometric indices were used: the popularity index, representing the share of articles (or patents) on a specific topic among all articles (or patents) on pain over the same 5-year period; the index of change, representing the change in the number of articles (or patents) on a topic from one 5-year period to the next; the index of expectations, representing the ratio of the number of all types of articles on a topic in the top 20 journals relative to the number of articles in all (>5,000) biomedical journals covered by PubMed over a 5-year period; the total number of articles representing Phase I–III trials of investigational drugs over a 5-year period; and the trial balance index, a ratio of Phase I–II publications to Phase III publications. Articles (PubMed database) and patents (US Patent and Trademark Office database) on 17 topics related to pain mechanisms were assessed during six 5-year periods from 1984 to 2013. During the most recent 5-year period (2009–2013), seven of 17 topics have demonstrated high research activity (purinergic receptors, serotonin, transient receptor potential channels, cytokines, gamma aminobutyric acid, glutamate, and protein kinases). However, even with these seven topics, the index of expectations decreased or did not change compared with the 2004–2008 period. In addition, publications representing Phase I–III trials of investigational drugs (2009–2013) did not indicate great enthusiasm on the part of the pharmaceutical industry regarding drugs specifically designed for treatment of pain. A promising development related to the new tool of molecular targeting, ie, monoclonal antibodies, for pain treatment has not yet resulted in real success. This approach has not yet demonstrated clinical effectiveness (at least with nerve growth factor) much beyond conventional analgesics, when its potential cost is more than an order of magnitude higher than that of conventional treatments. This scientometric assessment demonstrated a lack of real breakthrough developments. PMID:26170624

Rehabilitation of asbestos mining waste: a Rehabilitation Prioritisation Index (RPI) for South Africa

NASA Astrophysics Data System (ADS)

van Rensburg, L.; Claassens, S.; Bezuidenhout, J. J.; Jansen van Rensburg, P. J.

2009-03-01

The much publicised problem with major asbestos pollution and related health issues in South Africa, has called for action to be taken to negate the situation. The aim of this project was to establish a prioritisation index that would provide a scientifically based sequence in which polluted asbestos mines in Southern Africa ought to be rehabilitated. It was reasoned that a computerised database capable of calculating such a Rehabilitation Prioritisation Index (RPI) would be a fruitful departure from the previously used subjective selection prone to human bias. The database was developed in Microsoft Access and both quantitative and qualitative data were used for the calculation of the RPI value. The logical database structure consists of a number of mines, each consisting of a number of dumps, for which a number of samples have been analysed to determine asbestos fibre contents. For this system to be accurate as well as relevant, the data in the database should be revalidated and updated on a regular basis.

Providing R-Tree Support for Mongodb

NASA Astrophysics Data System (ADS)

Xiang, Longgang; Shao, Xiaotian; Wang, Dehao

2016-06-01

Supporting large amounts of spatial data is a significant characteristic of modern databases. However, unlike some mature relational databases, such as Oracle and PostgreSQL, most of current burgeoning NoSQL databases are not well designed for storing geospatial data, which is becoming increasingly important in various fields. In this paper, we propose a novel method to provide R-tree index, as well as corresponding spatial range query and nearest neighbour query functions, for MongoDB, one of the most prevalent NoSQL databases. First, after in-depth analysis of MongoDB's features, we devise an efficient tabular document structure which flattens R-tree index into MongoDB collections. Further, relevant mechanisms of R-tree operations are issued, and then we discuss in detail how to integrate R-tree into MongoDB. Finally, we present the experimental results which show that our proposed method out-performs the built-in spatial index of MongoDB. Our research will greatly facilitate big data management issues with MongoDB in a variety of geospatial information applications.

CDS - Database Administrator's Guide

NASA Astrophysics Data System (ADS)

Day, J. P.

This guide aims to instruct the CDS database administrator in: o The CDS file system. o The CDS index files. o The procedure for assimilating a new CDS tape into the database. It is assumed that the administrator has read SUN/79.

[New bibliometric indicators for the scientific literature: an evolving panorama].

PubMed

La Torre, G; Sciarra, I; Chiappetta, M; Monteduro, A

2017-01-01

Bibliometrics is a science which evaluates the impact of the scientific work of a journal or of an author, using mathematical and statistical tools. Impact Factor (IF) is the first bibliometric parameter created, and after it many others have been progressively conceived in order to go beyond its limits. Currently bibliometric indexes are used for academic purposes, among them to evaluate the eligibility of a researcher to compete for the National Scientific Qualification, in order to access to competitive exams to become professor. Aim of this study is to identify the most relevant bibliometric indexes and to summarized their characteristics. A revision of bibliometric indexes as been conducted, starting from the classic ones and completing with the most recent ones. The two most used bibliometric indexes are the IF, which measures the scientific impact of a periodical and bases on Web of Science citation database, and the h-index, which measures the impact of the scientific work of a researcher, basing on Scopus database. Besides them other indexes have been created more recently, such as the SCImago Journal Rank Indicator (SJR), the Source Normalised Impact per Paper (SNIP) and the CiteScore index. They are all based on Scopus database and evaluate, in different ways, the citational impact of a periodic. The i10-index instead is provided from Google Scholar database and allows to evaluate the impact of the scientific production of a researcher. Recently two softwares have been introduced: the first one, Publish or Perish, allows to evaluate the scientific work of a researcher, through the assessment of many indexes; the second one, Altmetric, measure the use in the Web of the academic papers, instead of measuring citations, by means of alternative metrics respect to the traditional ones. Each analized index shows advantages but also criticalities. Therefore the combined use of more than one indexes, citational and not, should be preferred, in order to correctly evaluate the work of reserchers and to finally improve the quality and the development of scientific research.

Analysis of short-chain fatty acids in human feces: A scoping review.

PubMed

Primec, Maša; Mičetić-Turk, Dušanka; Langerholc, Tomaž

2017-06-01

Short-chain fatty acids (SCFAs) play a crucial role in maintaining homeostasis in humans, therefore the importance of a good and reliable SCFAs analytical detection has raised a lot in the past few years. The aim of this scoping review is to show the trends in the development of different methods of SCFAs analysis in feces, based on the literature published in the last eleven years in all major indexing databases. The search criteria included analytical quantification techniques of SCFAs in different human clinical and in vivo studies. SCFAs analysis is still predominantly performed using gas chromatography (GC), followed by high performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR) and capillary electrophoresis (CE). Performances, drawbacks and advantages of these methods are discussed, especially in the light of choosing a proper pretreatment, as feces is a complex biological material. Further optimization to develop a simple, cost effective and robust method for routine use is needed. Copyright © 2017 Elsevier Inc. All rights reserved.

Economic evaluation of manual therapy for musculoskeletal diseases: a protocol for a systematic review and narrative synthesis of evidence.

PubMed

Kim, Chang-Gon; Mun, Su-Jeong; Kim, Ka-Na; Shin, Byung-Cheul; Kim, Nam-Kwen; Lee, Dong-Hyo; Lee, Jung-Han

2016-05-13

Manual therapy is the non-surgical conservative management of musculoskeletal disorders using the practitioner's hands on the patient's body for diagnosing and treating disease. The aim of this study is to systematically review trial-based economic evaluations of manual therapy relative to other interventions used for the management of musculoskeletal diseases. Randomised clinical trials (RCTs) on the economic evaluation of manual therapy for musculoskeletal diseases will be included in the review. The following databases will be searched from their inception: Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Econlit, Mantis, Index to Chiropractic Literature, Science Citation Index, Social Science Citation Index, Allied and Complementary Medicine Database (AMED), Cochrane Database of Systematic Reviews (CDSR), National Health Service Database of Abstracts of Reviews of Effects (NHS DARE), National Health Service Health Technology Assessment Database (NHS HTA), National Health Service Economic Evaluation Database (NHS EED), CENTRAL, five Korean medical databases (Oriental Medicine Advanced Searching Integrated System (OASIS), Research Information Service System (RISS), DBPIA, Korean Traditional Knowledge Portal (KTKP) and KoreaMed) and three Chinese databases (China National Knowledge Infrastructure (CNKI), VIP and Wanfang). The evidence for the cost-effectiveness, cost-utility and cost-benefit of manual therapy for musculoskeletal diseases will be assessed as the primary outcome. Health-related quality of life and adverse effects will be assessed as secondary outcomes. We will critically appraise the included studies using the Cochrane risk of bias tool and the Drummond checklist. Results will be summarised using Slavin's qualitative best-evidence synthesis approach. The results of the study will be disseminated via a peer-reviewed journal and/or conference presentations. PROSPERO CRD42015026757. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Assessing values of air quality and visibility at risk from wildland fires.

Treesearch

Sue A. Ferguson; Steven J. McKay; David E. Nagel; Trent Piepho; Miriam L. Rorig; Casey Anderson; Lara Kellogg

2003-01-01

To assess values of air quality and visibility at risk from wildland fire in the United States, we generated a 40-year database that includes twice daily values of wind, mixing height, and a ventilation index that is the product of windspeed and mixing height. The database provides the first nationally consistent map of surface wind and ventilation index. In addition,...

Introduction to the DISRUPT postprandial database: subjects, studies and methodologies.

PubMed

Jackson, Kim G; Clarke, Dave T; Murray, Peter; Lovegrove, Julie A; O'Malley, Brendan; Minihane, Anne M; Williams, Christine M

2010-03-01

Dysregulation of lipid and glucose metabolism in the postprandial state are recognised as important risk factors for the development of cardiovascular disease and type 2 diabetes. Our objective was to create a comprehensive, standardised database of postprandial studies to provide insights into the physiological factors that influence postprandial lipid and glucose responses. Data were collated from subjects (n = 467) taking part in single and sequential meal postprandial studies conducted by researchers at the University of Reading, to form the DISRUPT (DIetary Studies: Reading Unilever Postprandial Trials) database. Subject attributes including age, gender, genotype, menopausal status, body mass index, blood pressure and a fasting biochemical profile, together with postprandial measurements of triacylglycerol (TAG), non-esterified fatty acids, glucose, insulin and TAG-rich lipoprotein composition are recorded. A particular strength of the studies is the frequency of blood sampling, with on average 10-13 blood samples taken during each postprandial assessment, and the fact that identical test meal protocols were used in a number of studies, allowing pooling of data to increase statistical power. The DISRUPT database is the most comprehensive postprandial metabolism database that exists worldwide and preliminary analysis of the pooled sequential meal postprandial dataset has revealed both confirmatory and novel observations with respect to the impact of gender and age on the postprandial TAG response. Further analysis of the dataset using conventional statistical techniques along with integrated mathematical models and clustering analysis will provide a unique opportunity to greatly expand current knowledge of the aetiology of inter-individual variability in postprandial lipid and glucose responses.

A population health approach to reducing observational intensity bias in health risk adjustment: cross sectional analysis of insurance claims

PubMed Central

Sharp, Sandra M; Bevan, Gwyn; Skinner, Jonathan S; Gottlieb, Daniel J

2014-01-01

Objective To compare the performance of two new approaches to risk adjustment that are free of the influence of observational intensity with methods that depend on diagnoses listed in administrative databases. Setting Administrative data from the US Medicare program for services provided in 2007 among 306 US hospital referral regions. Design Cross sectional analysis. Participants 20% sample of fee for service Medicare beneficiaries residing in one of 306 hospital referral regions in the United States in 2007 (n=5 153 877). Main outcome measures The effect of health risk adjustment on age, sex, and race adjusted mortality and spending rates among hospital referral regions using four indices: the standard Centers for Medicare and Medicaid Services—Hierarchical Condition Categories (HCC) index used by the US Medicare program (calculated from diagnoses listed in Medicare’s administrative database); a visit corrected HCC index (to reduce the effects of observational intensity on frequency of diagnoses); a poverty index (based on US census); and a population health index (calculated using data on incidence of hip fractures and strokes, and responses from a population based annual survey of health from the Centers for Disease Control and Prevention). Results Estimated variation in age, sex, and race adjusted mortality rates across hospital referral regions was reduced using the indices based on population health, poverty, and visit corrected HCC, but increased using the standard HCC index. Most of the residual variation in age, sex, and race adjusted mortality was explained (in terms of weighted R2) by the population health index: R2=0.65. The other indices explained less: R2=0.20 for the visit corrected HCC index; 0.19 for the poverty index, and 0.02 for the standard HCC index. The residual variation in age, sex, race, and price adjusted spending per capita across the 306 hospital referral regions explained by the indices (in terms of weighted R2) were 0.50 for the standard HCC index, 0.21 for the population health index, 0.12 for the poverty index, and 0.07 for the visit corrected HCC index, implying that only a modest amount of the variation in spending can be explained by factors most closely related to mortality. Further, once the HCC index is visit corrected it accounts for almost none of the residual variation in age, sex, and race adjusted spending. Conclusion Health risk adjustment using either the poverty index or the population health index performed substantially better in terms of explaining actual mortality than the indices that relied on diagnoses from administrative databases; the population health index explained the majority of residual variation in age, sex, and race adjusted mortality. Owing to the influence of observational intensity on diagnoses from administrative databases, the standard HCC index over-adjusts for regional differences in spending. Research to improve health risk adjustment methods should focus on developing measures of risk that do not depend on observation influenced diagnoses recorded in administrative databases. PMID:24721838

PGSB PlantsDB: updates to the database framework for comparative plant genome research.

PubMed

Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai C; Martis, Mihaela M; Seidel, Michael; Kugler, Karl G; Gundlach, Heidrun; Mayer, Klaus F X

2016-01-04

PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/). © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multifactorial risk index for prediction of intraoperative blood transfusion in endovascular aneurysm repair.

PubMed

Mahmood, Eitezaz; Matyal, Robina; Mueller, Ariel; Mahmood, Feroze; Tung, Avery; Montealegre-Gallegos, Mario; Schermerhorn, Marc; Shahul, Sajid

2018-03-01

In some institutions, the current blood ordering practice does not discriminate minimally invasive endovascular aneurysm repair (EVAR) from open procedures, with consequent increasing costs and likelihood of blood product wastage for EVARs. This limitation in practice can possibly be addressed with the development of a reliable prediction model for transfusion risk in EVAR patients. We used the American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) database to create a model for prediction of intraoperative blood transfusion occurrence in patients undergoing EVAR. Afterward, we tested our predictive model on the Vascular Study Group of New England (VSGNE) database. We used the ACS NSQIP database for patients who underwent EVAR from 2011 to 2013 (N = 4709) as our derivation set for identifying a risk index for predicting intraoperative blood transfusion. We then developed a clinical risk score and validated this model using patients who underwent EVAR from 2003 to 2014 in the VSGNE database (N = 4478). The transfusion rates were 8.4% and 6.1% for the ACS NSQIP (derivation set) and VSGNE (validation) databases, respectively. Hemoglobin concentration, American Society of Anesthesiologists class, age, and aneurysm diameter predicted blood transfusion in the derivation set. When it was applied on the validation set, our risk index demonstrated good discrimination in both the derivation and validation set (C statistic = 0.73 and 0.70, respectively) and calibration using the Hosmer-Lemeshow test (P = .27 and 0.31) for both data sets. We developed and validated a risk index for predicting the likelihood of intraoperative blood transfusion in EVAR patients. Implementation of this index may facilitate the blood management strategies specific for EVAR. Copyright © 2017 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

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.

Topical application of tranexamic acid for the reduction of bleeding.

PubMed

Ker, Katharine; Beecher, Deirdre; Roberts, Ian

2013-07-23

Intravenous tranexamic acid reduces bleeding in surgery, however, its effect on the risk of thromboembolic events is uncertain and an increased risk remains a theoretical concern. Because there is less systemic absorption following topical administration, the direct application of tranexamic acid to the bleeding surface has the potential to reduce bleeding with minimal systemic effects. To assess the effects of the topical administration of tranexamic acid in the control of bleeding. We searched the Cochrane Injuries Group Specialised Register; Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library; Ovid MEDLINE®, Ovid MEDLINE® In-Process & Other Non-Indexed Citations, Ovid MEDLINE® Daily and Ovid OLDMEDLINE®; Embase Classic + Embase (OvidSP); PubMed and ISI Web of Science (including Science Citation Index Expanded and Social Science Citation Index (SCI-EXPANDED & CPCI-S)). We also searched online trials registers to identify ongoing or unpublished trials. The search was run on the 31st May 2013. Randomised controlled trials comparing topical tranexamic acid with no topical tranexamic acid or placebo in bleeding patients. Two authors examined the titles and abstracts of citations from the electronic databases for eligibility. Two authors extracted the data and assessed the risk of bias for each trial. Outcome measures of interest were blood loss, mortality, thromboembolic events (myocardial infarction, stroke, deep vein thrombosis and pulmonary embolism) and receipt of a blood transfusion. We included 29 trials involving 2612 participants. Twenty-eight trials involved patients undergoing surgery and one trial involved patients with epistaxis (nosebleed). Tranexamic acid (TXA) reduced blood loss by 29% (pooled ratio 0.71, 95% confidence interval (CI) 0.69 to 0.72; P < 0.0001). There was uncertainty regarding the effect on death (risk ratio (RR) 0.28, 95% CI 0.06 to 1.34; P = 0.11), myocardial infarction (RR 0.33, 95% CI 0.04 to 3.08; P = 0.33), stroke (RR 0.33, 95% CI 0.01 to 7.96; P = 0.49), deep vein thrombosis (RR 0.69, 95% CI 0.31 to 1.57; P = 0.38) and pulmonary embolism (RR 0.52, 95% CI 0.09 to 3.15; P = 0.48). TXA reduced the risk of receiving a blood transfusion by a relative 45% (RR 0.55, 95% CI 0.55 to 0.46; P < 0.0001). There was substantial statistical heterogeneity between trials for the blood loss and blood transfusion outcomes. There is reliable evidence that topical application of tranexamic acid reduces bleeding and blood transfusion in surgical patients, however the effect on the risk of thromboembolic events is uncertain. The effects of topical tranexamic acid in patients with bleeding from non-surgical causes has yet to be reliably assessed. Further high-quality trials are warranted to resolve these uncertainties before topical tranexamic acid can be recommended for routine use.

Content based image retrieval using local binary pattern operator and data mining techniques.

PubMed

Vatamanu, Oana Astrid; Frandeş, Mirela; Lungeanu, Diana; Mihalaş, Gheorghe-Ioan

2015-01-01

Content based image retrieval (CBIR) concerns the retrieval of similar images from image databases, using feature vectors extracted from images. These feature vectors globally define the visual content present in an image, defined by e.g., texture, colour, shape, and spatial relations between vectors. Herein, we propose the definition of feature vectors using the Local Binary Pattern (LBP) operator. A study was performed in order to determine the optimum LBP variant for the general definition of image feature vectors. The chosen LBP variant is then subsequently used to build an ultrasound image database, and a database with images obtained from Wireless Capsule Endoscopy. The image indexing process is optimized using data clustering techniques for images belonging to the same class. Finally, the proposed indexing method is compared to the classical indexing technique, which is nowadays widely used.

Online Database Coverage of Pharmaceutical Journals.

ERIC Educational Resources Information Center

Snow, Bonnie

1984-01-01

Describes compilation of data concerning pharmaceutical journal coverage in online databases which aid information providers in collection development and database selection. Methodology, results (a core collection, overlap, timeliness, geographic scope), and implications are discussed. Eight references and a list of 337 journals indexed online in…

Comparison of Various Databases for Estimation of Dietary Polyphenol Intake in the Population of Polish Adults.

PubMed

Witkowska, Anna M; Zujko, Małgorzata E; Waśkiewicz, Anna; Terlikowska, Katarzyna M; Piotrowski, Walerian

2015-11-11

The primary aim of the study was to estimate the consumption of polyphenols in a population of 6661 subjects aged between 20 and 74 years representing a cross-section of the Polish society, and the second objective was to compare the intakes of flavonoids calculated on the basis of the two commonly used databases. Daily food consumption data were collected in 2003-2005 using a single 24-hour dietary recall. Intake of total polyphenols was estimated using an online Phenol-Explorer database, and flavonoid intake was determined using following data sources: the United States Department of Agriculture (USDA) database combined of flavonoid and isoflavone databases, and the Phenol-Explorer database. Total polyphenol intake, which was calculated with the Phenol-Explorer database, was 989 mg/day with the major contributions of phenolic acids 556 mg/day and flavonoids 403.5 mg/day. The flavonoid intake calculated on the basis of the USDA databases was 525 mg/day. This study found that tea is the primary source of polyphenols and flavonoids for the studied population, including mainly flavanols, while coffee is the most important contributor of phenolic acids, mostly hydroxycinnamic acids. Our study also demonstrated that flavonoid intakes estimated according to various databases may substantially differ. Further work should be undertaken to expand polyphenol databases to better reflect their food contents.

Lecturers’ Understanding on Indexing Databases of SINTA, DOAJ, Google Scholar, SCOPUS, and Web of Science: A Study of Indonesians

NASA Astrophysics Data System (ADS)

Saleh Ahmar, Ansari; Kurniasih, Nuning; Irawan, Dasapta Erwin; Utami Sutiksno, Dian; Napitupulu, Darmawan; Ikhsan Setiawan, Muhammad; Simarmata, Janner; Hidayat, Rahmat; Busro; Abdullah, Dahlan; Rahim, Robbi; Abraham, Juneman

2018-01-01

The Ministry of Research, Technology and Higher Education of Indonesia has introduced several national and international indexers of scientific works. This policy becomes a guideline for lecturers and researchers in choosing the reputable publications. This study aimed to describe the understanding level of Indonesian lecturers related to indexing databases, i.e. SINTA, DOAJ, Scopus, Web of Science, and Google Scholar. This research used descriptive design and survey method. The populations in this study were Indonesian lecturers and researchers. The primary data were obtained from a questionnaire filled by 316 lecturers and researchers from 33 Provinces in Indonesia recruited with convenience sampling technique on October-November 2017. The data analysis was performed using frequency distribution tables, cross tabulation and descriptive analysis. The results of this study showed that the understanding of Indonesian lecturers and researchers regarding publications in indexing databases SINTA, DOAJ, Scopus, Web of Science and Google Scholar is that, on average, 66,5% have known about SINTA, DOAJ, Scopus, Web of Science and Google Scholar. However, based on empirical frequency 76% of them have never published with journals or proceedings indexed in Scopus.

Role of amino acid supplementation in the prevention of necrotizing enterocolitis in preterm neonates - a review of current evidences.

PubMed

Garg, Bhawan Deep; Kabra, Nandkishor S

2018-09-01

Necrotizing enterocolitis (NEC) is one of the most common acute and fatal gastrointestinal emergency in very low birth weight (VLBW) preterm neonates with mortality range from 15 to 30%. NEC is likely due to multifactorial process such as oxidative injury, ischemic necrosis, and over-reactive inflammatory response to intestinal microbes. To evaluate the role of amino acid supplementation for reduction of neonatal NEC in preterm neonates. The literature search was done for various randomized control trial (RCT) by searching the Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, EMBASE, Web of Science, Scopus, Index Copernicus, African Index Medicus (AIM), Thomson Reuters (ESCI), Chemical Abstracts Service (CAS) and other database. This review included 15 RCTs that fulfilled inclusion criteria. The total neonates enrolled in these different RCT are 3424 (amino acid group 1711 and control 1713). Almost all participating neonates were of VLBW or extremely low birth weight (ELBW). In two trials, birth weight was between 1500-2000 grams. The intervention was started within first few days after birth and continued up to 30th day of postnatal age in most of the trials. In two trials, intervention was continued up to 120th day of postnatal age. Arginine, glutamine and N-acetyl cysteine (NAC) were used at the dose of 1.5 mol/kg/day (261 mg/kg/day), 0.3 grams/kg/day and 16-32 mg/kg/day, respectively. Role of amino acid in the prevention of neonatal NEC is not exclusively supported by the current evidence. Only three studies were able to show reduction in the incidence of NEC with amino acid supplementation (arginine, glutamine), and the remaining studies did not report any positive effect. Amino acid supplementation was not associated with significant reduction in mortality due to any causes. However, arginine supplementation was associated with significant reduction in mortality due to NEC. Two studies on glutamine were reported significant reduction in the incidence of invasive infection. Only one study reported significant positive effects on growth parameters and less time to reach full enteral feeds. None of the studies showed any effect on the duration of hospital stay.

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.

A Practical Standardized Composite Nutrition Score Based on Lean Tissue Index: Application in Nutrition Screening and Prediction of Outcome in Hemodialysis Population.

PubMed

Chen, Huan-Sheng; Cheng, Chun-Ting; Hou, Chun-Cheng; Liou, Hung-Hsiang; Chang, Cheng-Tsung; Lin, Chun-Ju; Wu, Tsai-Kun; Chen, Chang-Hsu; Lim, Paik-Seong

2017-07-01

Rapid screening and monitoring of nutritional status is mandatory in hemodialysis population because of the increasingly encountered nutritional problems. Considering the limitations of previous composite nutrition scores applied in this population, we tried to develop a standardized composite nutrition score (SCNS) using low lean tissue index as a marker of protein wasting to facilitate clinical screening and monitoring and to predict outcome. This retrospective cohort used 2 databases of dialysis populations from Taiwan between 2011 and 2014. First database consisting of data from 629 maintenance hemodialysis patients was used to develop the SCNS and the second database containing data from 297 maintenance hemodialysis patients was used to validate this developed score. SCNS containing albumin, creatinine, potassium, and body mass index was developed from the first database using low lean tissue index as a marker of protein wasting. When applying this score in the original database, significantly higher risk of developing protein wasting was found for patients with lower SCNS (odds ratio 1.38 [middle tertile vs highest tertile, P < .0001] and 2.40 [lowest tertile vs middle tertile, P < .0001]). The risk of death was also shown to be higher for patients with lower SCNS (hazard ratio 4.45 [below median level vs above median level, P < .0001]). These results were validated in the second database. We developed an SCNS consisting of 4 easily available biochemical parameters. This kind of scoring system can be easily applied in different dialysis facilities for screening and monitoring of protein wasting. The wide application of body composition monitor in dialysis population will also facilitate the development of specific nutrition scoring model for individual facility. Copyright © 2017 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

PceRBase: a database of plant competing endogenous RNA.

PubMed

Yuan, Chunhui; Meng, Xianwen; Li, Xue; Illing, Nicola; Ingle, Robert A; Wang, Jingjing; Chen, Ming

2017-01-04

Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants. We have developed a Plant ceRNA database (PceRBase, http://bis.zju.edu.cn/pcernadb/index.jsp) which contains potential ceRNA target-target, and ceRNA target-mimic pairs from 26 plant species. For example, in Arabidopsis lyrata, 311 candidate ceRNAs are identified which could affect 2646 target-miRNA-target interactions. Predicted pairing structure between miRNAs and their target mRNA transcripts, expression levels of ceRNA pairs and associated GO annotations are also stored in the database. A web interface provides convenient browsing and searching for specific genes of interest. Tools are available for the visualization and enrichment analysis of genes in the ceRNA networks. Moreover, users can use PceRBase to predict novel competing mimic-target and target-target interactions from their own data. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Applications of Technology to CAS Data-Base Production.

ERIC Educational Resources Information Center

Weisgerber, David W.

1984-01-01

Reviews the economic importance of applying computer technology to Chemical Abstracts Service database production from 1973 to 1983. Database building, technological applications for editorial processing (online editing, Author Index Manufacturing System), and benefits (increased staff productivity, reduced rate of increase of cost of services,…

Evaluation of relational and NoSQL database architectures to manage genomic annotations.

PubMed

Schulz, Wade L; Nelson, Brent G; Felker, Donn K; Durant, Thomas J S; Torres, Richard

2016-12-01

While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architectures may provide significant advantages in storage and query efficiency, thereby reducing the cost of data management. But their relative advantage when applied to biomedical data sets, such as genetic data, has not been characterized. To this end, we compared the storage, indexing, and query efficiency of a common relational database (MySQL), a document-oriented NoSQL database (MongoDB), and a relational database with NoSQL support (PostgreSQL). When used to store genomic annotations from the dbSNP database, we found the NoSQL architectures to outperform traditional, relational models for speed of data storage, indexing, and query retrieval in nearly every operation. These findings strongly support the use of novel database technologies to improve the efficiency of data management within the biological sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

Spatial variation of stratospheric aerosol acidity and model refractive index - Implications of recent results

NASA Technical Reports Server (NTRS)

Russell, P. B.; Hamill, P.

1984-01-01

Recent experimental results indicate that little or no solid ammonium sulfate is present in background stratospheric aerosols. Other results allow straightforward calculation of sulfuric acid/water droplet properties (acidity, specific gravity, refractive index) as functions of stratospheric temperature and humidity. These results are combined with a variety of latitudinal and seasonal temperature and humidity profiles to obtain corresponding profiles of droplet properties. These profiles are used to update a previous model of stratospheric aerosol refractive index. The new model retains the simplifying approximation of vertically constant refractive index in the inner stratosphere, but has sulfuric acid/water refractive index values that significantly exceed the previously used room temperature values. Mean conversion ratios (e.g., extinction-to-number, backscatter-to-volume) obtained using Mie scattering calculations with the new refractive indices are very similar to those obtained for the old indices, because the effects of deleting ammonium sulfate and increasing acid indices tend to cancel each other.

Context indexing of digital cardiac ultrasound records in PACS

NASA Astrophysics Data System (ADS)

Lobodzinski, S. Suave; Meszaros, Georg N.

1998-07-01

Recent wide adoption of the DICOM 3.0 standard by ultrasound equipment vendors created a need for practical clinical implementations of cardiac imaging study visualization, management and archiving, DICOM 3.0 defines only a logical and physical format for exchanging image data (still images, video, patient and study demographics). All DICOM compliant imaging studies must presently be archived on a 650 Mb recordable compact disk. This is a severe limitation for ultrasound applications where studies of 3 to 10 minutes long are a common practice. In addition, DICOM digital echocardiography objects require physiological signal indexing, content segmentation and characterization. Since DICOM 3.0 is an interchange standard only, it does not define how to database composite video objects. The goal of this research was therefore to address the issues of efficient storage, retrieval and management of DICOM compliant cardiac video studies in a distributed PACS environment. Our Web based implementation has the advantage of accommodating both DICOM defined entity-relation modules (equipment data, patient data, video format, etc.) in standard relational database tables and digital indexed video with its attributes in an object relational database. Object relational data model facilitates content indexing of full motion cardiac imaging studies through bi-directional hyperlink generation that tie searchable video attributes and related objects to individual video frames in the temporal domain. Benefits realized from use of bi-directionally hyperlinked data models in an object relational database include: (1) real time video indexing during image acquisition, (2) random access and frame accurate instant playback of previously recorded full motion imaging data, and (3) time savings from faster and more accurate access to data through multiple navigation mechanisms such as multidimensional queries on an index, queries on a hyperlink attribute, free search and browsing.

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…

Visualization of semantic indexing similarity over MeSH.

PubMed

Du, Haixia; Yoo, Terry S

2007-10-11

We present an interactive visualization system for the evaluation of indexing results of the MEDLINE data-base over the Medical Subject Headings (MeSH) structure in a graphical radial-tree layout. It displays indexing similarity measurements with 2D color coding and a 3D height field permitting the evaluation of the automatic Medical Text Indexer (MTI), compared with human indexers.

Selecting CD-ROM databases for nursing students: a comparison of MEDLINE and the Cumulative Index to Nursing and Allied Health Literature (CINAHL).

PubMed

Okuma, E

1994-01-01

With the introduction of the Cumulative Index to Nursing and Allied Health Literature (CINAHL) on CD-ROM, research was initiated to compare coverage of nursing journals by CINAHL and MEDLINE in this format, expanding on previous comparison of these databases in print and online. The study assessed search results for eight topics in 1989 and 1990 citations in both databases, each produced by SilverPlatter. Results were tallied and analyzed for number of records retrieved, unique and overlapping records, relevance, and appropriateness. An overall precision score was developed. The goal of the research was to develop quantifiable tools to help determine which database to purchase for an academic library serving an undergraduate nursing program.

Selecting CD-ROM databases for nursing students: a comparison of MEDLINE and the Cumulative Index to Nursing and Allied Health Literature (CINAHL).

PubMed Central

Okuma, E

1994-01-01

With the introduction of the Cumulative Index to Nursing and Allied Health Literature (CINAHL) on CD-ROM, research was initiated to compare coverage of nursing journals by CINAHL and MEDLINE in this format, expanding on previous comparison of these databases in print and online. The study assessed search results for eight topics in 1989 and 1990 citations in both databases, each produced by SilverPlatter. Results were tallied and analyzed for number of records retrieved, unique and overlapping records, relevance, and appropriateness. An overall precision score was developed. The goal of the research was to develop quantifiable tools to help determine which database to purchase for an academic library serving an undergraduate nursing program. PMID:8136757

The use of the Hirsch index in benchmarking hepatic surgery research.

PubMed

Cucchetti, Alessandro; Mazzotti, Federico; Pellegrini, Sara; Cescon, Matteo; Maroni, Lorenzo; Ercolani, Giorgio; Pinna, Antonio Daniele

2013-10-01

The Hirsch index (h-index) is recognized as an effective way to summarize an individual's scientific research output. However, a benchmark for evaluating surgeon scientists in the field of hepatic surgery is still not available. A total of 3,251 authors who published between 1949 and 2011 were identified using the Scopus identification number. The h-index, the total number of cited document, the total number of citations, and the scientific age were calculated for each author using both Scopus and Google Scholar. The median h-index was 6 and the median scientific age, assessed with Google Scholar, was 19 years. The numbers of cited documents, numbers of citations, and h-indexes obtained from Scopus and Google Scholar showed good correlation with one another; however, the results from the 2 databases were modified in different ways by scientific age. By plotting scientific age against h-index percentiles an h-index growth chart for both Scopus database and Google Scholar was provided. This analysis provides a first benchmark to assess surgeon scientists' productivity in the field of liver surgery. Copyright © 2013 Elsevier Inc. All rights reserved.

Performance of Point and Range Queries for In-memory Databases using Radix Trees on GPUs

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

Alam, Maksudul; Yoginath, Srikanth B; Perumalla, Kalyan S

In in-memory database systems augmented by hardware accelerators, accelerating the index searching operations can greatly increase the runtime performance of database queries. Recently, adaptive radix trees (ART) have been shown to provide very fast index search implementation on the CPU. Here, we focus on an accelerator-based implementation of ART. We present a detailed performance study of our GPU-based adaptive radix tree (GRT) implementation over a variety of key distributions, synthetic benchmarks, and actual keys from music and book data sets. The performance is also compared with other index-searching schemes on the GPU. GRT on modern GPUs achieves some of themore » highest rates of index searches reported in the literature. For point queries, a throughput of up to 106 million and 130 million lookups per second is achieved for sparse and dense keys, respectively. For range queries, GRT yields 600 million and 1000 million lookups per second for sparse and dense keys, respectively, on a large dataset of 64 million 32-bit keys.« less

Reference System of DNA and Protein Sequences on CD-ROM

NASA Astrophysics Data System (ADS)

Nasu, Hisanori; Ito, Toshiaki

DNASIS-DBREF31 is a database for DNA and Protein sequences in the form of optical Compact Disk (CD) ROM, developed and commercialized by Hitachi Software Engineering Co., Ltd. Both nucleic acid base sequences and protein amino acid sequences can be retrieved from a single CD-ROM. Existing database is offered in the form of on-line service, floppy disks, or magnetic tape, all of which have some problems or other, such as usability or storage capacity. DNASIS-DBREF31 newly adopt a CD-ROM as a database device to realize a mass storage and personal use of the database.

Document creation, linking, and maintenance system

DOEpatents

Claghorn, Ronald [Pasco, WA

2011-02-15

A document creation and citation system designed to maintain a database of reference documents. The content of a selected document may be automatically scanned and indexed by the system. The selected documents may also be manually indexed by a user prior to the upload. The indexed documents may be uploaded and stored within a database for later use. The system allows a user to generate new documents by selecting content within the reference documents stored within the database and inserting the selected content into a new document. The system allows the user to customize and augment the content of the new document. The system also generates citations to the selected content retrieved from the reference documents. The citations may be inserted into the new document in the appropriate location and format, as directed by the user. The new document may be uploaded into the database and included with the other reference documents. The system also maintains the database of reference documents so that when changes are made to a reference document, the author of a document referencing the changed document will be alerted to make appropriate changes to his document. The system also allows visual comparison of documents so that the user may see differences in the text of the documents.

Literature information in PubChem: associations between PubChem records and scientific articles.

PubMed

Kim, Sunghwan; Thiessen, Paul A; Cheng, Tiejun; Yu, Bo; Shoemaker, Benjamin A; Wang, Jiyao; Bolton, Evan E; Wang, Yanli; Bryant, Stephen H

2016-01-01

PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided chemical substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results provided from over 1 million biological assay records. Many PubChem records (substances, compounds, and assays) include depositor-provided cross-references to scientific articles in PubMed. Some PubChem contributors provide bioactivity data extracted from scientific articles. Literature-derived bioactivity data complement high-throughput screening (HTS) data from the concluded NIH Molecular Libraries Program and other HTS projects. Some journals provide PubChem with information on chemicals that appear in their newly published articles, enabling concurrent publication of scientific articles in journals and associated data in public databases. In addition, PubChem links records to PubMed articles indexed with the Medical Subject Heading (MeSH) controlled vocabulary thesaurus. Literature information, both provided by depositors and derived from MeSH annotations, can be accessed using PubChem's web interfaces, enabling users to explore information available in literature related to PubChem records beyond typical web search results. Graphical abstractLiterature information for PubChem records is derived from various sources.

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…

Thematic video indexing to support video database retrieval and query processing

NASA Astrophysics Data System (ADS)

Khoja, Shakeel A.; Hall, Wendy

1999-08-01

This paper presents a novel video database system, which caters for complex and long videos, such as documentaries, educational videos, etc. As compared to relatively structured format videos like CNN news or commercial advertisements, this database system has the capacity to work with long and unstructured videos.

An Introduction to Database Management Systems.

ERIC Educational Resources Information Center

Warden, William H., III; Warden, Bette M.

1984-01-01

Description of database management systems for microcomputers highlights system features and factors to consider in microcomputer system selection. A method for ranking database management systems is explained and applied to a defined need, i.e., software support for indexing a weekly newspaper. A glossary of terms and 32-item bibliography are…

Blood docosahexaenoic acid and eicosapentaenoic acid in vegans: Associations with age and gender and effects of an algal-derived omega-3 fatty acid supplement.

PubMed

Sarter, Barbara; Kelsey, Kristine S; Schwartz, Todd A; Harris, William S

2015-04-01

Several studies have demonstrated that vegetarians and vegans have much lower plasma concentrations of omega-3 fatty acids (i.e., docosahexaenoic and eicosapentaenoic acids) when compared to those who eat fish. The purposes of this study were 1) to define the age and/or sex-specific docosahexaenoic plus eicosapentaenoic acids levels in red blood cell membranes (expressed as a percent of total fatty acids; hereafter the omega-3 index) in long-term vegans, and 2) to determine the effects of a vegetarian omega-3 supplement (254 mg docosahexaenoic plus eicosapentaenoic acids/day for 4 months) on the omega-3 index. A sample (n = 165) of vegans was recruited, and their omega-3 index was determined using a dried blood spot methodology. A subset of 46 subjects with a baseline omega-3 index of <4% was given a vegetarian omega-3 supplement for 4 months and then retested. The mean ± SD omega-3 index was 3.7 ± 1.0% which was similar to that of a cohort of omnivores (deployed US soldiers) from a recently-reported study. Among the vegan cohort, the index was significantly higher in females than males (3.9 ± 1.0% vs. 3.5 ± 1.0%; p = 0.026) and was directly related to age (p for trend = 0.009). The omega-3 index increased from 3.1 ± 0.6% to 4.8 ± 0.8% (p = 0.009) in the supplementation study. We conclude that vegans have low baseline omega-3 levels, but not lower than omnivores who also consume very little docosahexaenoic and eicosapentaenoic acids. The vegans responded robustly to a relatively low dose of a vegetarian omega-3 supplement. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Assessing animal welfare in sow herds using data on meat inspection, medication and mortality.

PubMed

Knage-Rasmussen, K M; Rousing, T; Sørensen, J T; Houe, H

2015-03-01

This paper aims to contribute to the development of a cost-effective alternative to expensive on-farm animal-based welfare assessment systems. The objective of the study was to design an animal welfare index based on central database information (DBWI), and to validate it against an animal welfare index based on-farm animal-based measurements (AWI). Data on 63 Danish sow herds with herd-sizes of 80 to 2500 sows and an average herd size of 501 were collected from three central databases containing: Meat inspection data collected at animal level in the abattoir, mortality data at herd level from the rendering plants of DAKA, and medicine records at both herd and animal group level (sow with piglets, weaners or finishers) from the central database Vetstat. Selected measurements taken from these central databases were used to construct the DBWI. The relative welfare impacts of both individual database measurements and the databases overall were assigned in consultation with a panel consisting of 12 experts. The experts were drawn from production advisory activities, animal science and in one case an animal welfare organization. The expert panel weighted each measurement on a scale from 1 (not-important) to 5 (very important). The experts also gave opinions on the relative weightings of measurements for each of the three databases by stating a relative weight of each database in the DBWI. On the basis of this, the aggregated DBWI was normalized. The aggregation of AWI was based on weighted summary of herd prevalence's of 20 clinical and behavioural measurements originating from a 1 day data collection. AWI did not show linear dependency of DBWI. This suggests that DBWI is not suited to replace an animal welfare index using on-farm animal-based measurements.

The inclusion of an online journal in PubMed central - a difficult path.

PubMed

Grech, Victor

2016-01-01

The indexing of a journal in a prominent database (such as PubMed) is an important imprimatur. Journals accepted for inclusion in PubMed Central (PMC) are automatically indexed in PubMed but must provide the entire contents of their publications as XML-tagged (Extensible Markup Language) data files compliant with PubMed's document type definition (DTD). This paper describes the various attempts that the journal Images in Paediatric Cardiology made in its efforts to convert the journal contents (including all of the extant backlog) to PMC-compliant XML for archiving and indexing in PubMed after the journal was accepted for inclusion by the database.

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.

Performance of Malaysian Medical Journals

PubMed Central

Abrizah, Abdullah

2016-01-01

Indexation status matters for scholarly journal prestige and trust. The performance of Malaysian medical journals at the international level is gauged through the global citation databases, and at the national level through MyCite, a national citation indexing system. The performance indicators include journals publication productivity, the citations they garner, and their scores on other bibliometric indices such as journal impact factor (IF), and h-index. There is a growing consciousness amongst journal editorials to improve quality and increase chances of getting indexed in MyCite. Although it is now possible to gauge journal performance within Malaysia, through MyCite, the government and public are concerned about journal performance in international databases. Knowing the performance of journals in MyCite will help the editors and publishers to improve the quality and visibility of Malaysian journals and strategise to bring their journal to the international level of indexation. PMID:27547108

Database and new models based on a group contribution method to predict the refractive index of ionic liquids.

PubMed

Wang, Xinxin; Lu, Xingmei; Zhou, Qing; Zhao, Yongsheng; Li, Xiaoqian; Zhang, Suojiang

2017-08-02

Refractive index is one of the important physical properties, which is widely used in separation and purification. In this study, the refractive index data of ILs were collected to establish a comprehensive database, which included about 2138 pieces of data from 1996 to 2014. The Group Contribution-Artificial Neural Network (GC-ANN) model and Group Contribution (GC) method were employed to predict the refractive index of ILs at different temperatures from 283.15 K to 368.15 K. Average absolute relative deviations (AARD) of the GC-ANN model and the GC method were 0.179% and 0.628%, respectively. The results showed that a GC-ANN model provided an effective way to estimate the refractive index of ILs, whereas the GC method was simple and extensive. In summary, both of the models were accurate and efficient approaches for estimating refractive indices of ILs.

Adding glycaemic index and glycaemic load functionality to DietPLUS, a Malaysian food composition database and diet intake calculator.

PubMed

Shyam, Sangeetha; Wai, Tony Ng Kock; Arshad, Fatimah

2012-01-01

This paper outlines the methodology to add glycaemic index (GI) and glycaemic load (GL) functionality to food DietPLUS, a Microsoft Excel-based Malaysian food composition database and diet intake calculator. Locally determined GI values and published international GI databases were used as the source of GI values. Previously published methodology for GI value assignment was modified to add GI and GL calculators to the database. Two popular local low GI foods were added to the DietPLUS database, bringing up the total number of foods in the database to 838 foods. Overall, in relation to the 539 major carbohydrate foods in the Malaysian Food Composition Database, 243 (45%) food items had local Malaysian values or were directly matched to International GI database and another 180 (33%) of the foods were linked to closely-related foods in the GI databases used. The mean ± SD dietary GI and GL of the dietary intake of 63 women with previous gestational diabetes mellitus, calculated using DietPLUS version3 were, 62 ± 6 and 142 ± 45, respectively. These values were comparable to those reported from other local studies. DietPLUS version3, a simple Microsoft Excel-based programme aids calculation of diet GI and GL for Malaysian diets based on food records.

Refractive index modulation in polymer film doped with diazo Meldrum's acid

NASA Astrophysics Data System (ADS)

Zanutta, Alessio; Villa, Filippo; Bertarelli, Chiara; Bianco, Andrea

2016-08-01

Diazo Meldrum's acid undergoes a photoreaction induced by UV light and it is used as photosensitizer in photoresists. Upon photoreaction, a change in refractive index occurs, which makes this system interesting for volume holography. We report on the sublimation effect at room temperature and the effect of photoirradiation on the refractive index in thin films of CAB (Cellulose acetate butyrate) doped with different amount of diazo Meldrum's acid. A net modulation of the refractive index of 0.01 is achieved with 40% of doping ratio together with a reduction of the film thickness.

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…

Historical Space Climate Data from Finland: Compilation and Analysis

NASA Astrophysics Data System (ADS)

Nevanlinna, Heikki

2004-10-01

We have compiled archived geomagnetic observations from the Helsinki magnetic observatory as well as visual sightings of auroral occurrence in Finland. The magnetic database comprises about 2 000 000 observations of H- and D-components measured during 1844-1909 with time resolution of 10 min to 1 h. In addition, magnetic observations carried out in the First and Second Polar Years in Finland have been recompiled. Magnetic activity indices (three-hour K-and daily Ak-figures) have been derived from the magnetic observations. Comparisons between the Finnish indices and simultaneous global aa-index (starting in 1868) show a good mutual correlation. The Helsinki activity index series can be used as a (pseudo) extension of the aa-index series for about two solar cycles 1844d -1868. On the annual level the correlation coefficient is about 0.9 during the overlapped time interval 1868-1897. The auroral database consists of about 20 000 single observations observed in Finland since the year 1748. The database of visual auroras has been completed by auroral occurrence (AO) index data derived from the Finnish all-sky camera recordings during 1973 -1997 at several sites in Lapland. The AO-index reveals both spatial and temporal variations of auroras from diurnal to solar cycle time scales in different space weather conditions.

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

PubMed

Miao, Zhichao; Westhof, Eric

2016-07-08

RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A statistical view of FMRFamide neuropeptide diversity.

PubMed

Espinoza, E; Carrigan, M; Thomas, S G; Shaw, G; Edison, A S

2000-01-01

FMRFamide-like peptide (FLP) amino acid sequences have been collected and statistically analyzed. FLP amino acid composition as a function of position in the peptide is graphically presented for several major phyla. Results of total amino acid composition and frequencies of pairs of FLP amino acids have been computed and compared with corresponding values from the entire GenBank protein sequence database. The data for pairwise distributions of amino acids should help in future structure-function studies of FLPs. To aid in future peptide discovery, a computer program and search protocol was developed to identify FLPs from the GenBank protein database without the use of keywords.

Omega-3 fatty acids supplementation for autism spectrum disorders (ASD).

PubMed

James, Stephen; Montgomery, Paul; Williams, Katrina

2011-11-09

It has been suggested that impairments associated with autism spectrum disorders (ASD) may be partially explained by deficits of omega-3 fatty acids, and that supplementation of these essential fatty acids may lead to improvement of symptoms. To review the efficacy of omega-3 fatty acids for improving core features of ASD (for example, social interaction, communication, and stereotypies) and associated symptoms. We searched the following databases on 2 June 2010: CENTRAL (2010, Issue 2), MEDLINE (1950 to May Week 3 2010), EMBASE (1980 to 2010 Week 21), PsycINFO (1806 to current), BIOSIS (1985 to current), CINAHL (1982 to current), Science Citation Index (1970 to current), Social Science Citation Index (1970 to current), metaRegister of Controlled Trials (20 November 2008) and ClinicalTrials.gov (10 December 2010). Dissertation Abstracts International was searched on 10 December 2008, but was no longer available to the authors or editorial base in 2010. All randomised controlled trials of omega-3 fatty acids supplementation compared to placebo in individuals with ASD. Three authors independently selected studies, assessed them for risk of bias and extracted relevant data. We conducted meta-analysis of the included studies for three primary outcomes (social interaction, communication, and stereotypy) and one secondary outcome (hyperactivity). We included two trials with a total of 37 children diagnosed with ASD who were randomised into groups that received either omega-3 fatty acids supplementation or a placebo. We excluded six trials because they were either non-randomised controlled trials, did not contain a control group, or the control group did not receive a placebo. Overall, there was no evidence that omega-3 supplements had an effect on social interaction (mean difference (MD) 0.82, 95% confidence interval (CI) -2.84 to 4.48, I(2) = 0%), communication (MD 0.62, 95% CI -0.89 to 2.14, I(2) = 0%), stereotypy (MD 0.77, 95% CI -0.69 to 2.22, I(2) = 8%), or hyperactivity (MD 3.46, 95% CI -0.79 to 7.70, I(2) = 0%). To date there is no high quality evidence that omega-3 fatty acids supplementation is effective for improving core and associated symptoms of ASD. Given the paucity of rigorous studies in this area, there is a need for large well-conducted randomised controlled trials that examine both high and low functioning individuals with ASD, and that have longer follow-up periods.

Compilation of geothermal information: exploration

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

Not Available

1978-01-01

The Database for Geothermal Energy Exploration and Evaluation is a printout of selected references to publications covering the development of geothermal resources from the identification of an area to the production of elecric power. This annotated bibliography contains four sections: references, author index, author affiliation index, and descriptor index.

Determinants of Blood Cell Omega-3 Fatty Acid Content

PubMed Central

Block, Robert C.; Harris, William S.; Pottala, James V.

2009-01-01

Background Although red blood cell eicosapentaenoic acid (EPA) plus docosahexaenoic acid (DHA) content (the Omega-3 Index) predicts cardiovascular death, the factors determining the Index are unknown. Methods In 704 outpatients, we undertook an investigation of the clinical determinants of the Index. Results Factors associated with the Index in decreasing order were: EPA+DHA supplement use, fish consumption frequency, triglyceride level, age, high cholesterol history, and smoking. These factors explained 59% of Index variability, with capsules/fish intake together accounting for 47%. The Index increased by 13% (p< 0.0001) for each serving level increase in fish intake and EPA+DHA supplementation correlated with a 58% increase (p< 0.0001) regardless of background fish intake (p=0.25; test for interaction). A 100 mg/dL decrease in serum triglycerides was associated with a 15% higher (p<0.0001) Index. Conclusions The intake of EPA+DHA-rich foods and supplements principally determined the Omega-3 Index, but explained only about half of the variability. PMID:19953197

modlAMP: Python for antimicrobial peptides.

PubMed

Müller, Alex T; Gabernet, Gisela; Hiss, Jan A; Schneider, Gisbert

2017-09-01

We have implemented the lecular esign aboratory's nti icrobial eptides package ( ), a Python-based software package for the design, classification and visual representation of peptide data. modlAMP offers functions for molecular descriptor calculation and the retrieval of amino acid sequences from public or local sequence databases, and provides instant access to precompiled datasets for machine learning. The package also contains methods for the analysis and representation of circular dichroism spectra. The modlAMP Python package is available under the BSD license from URL http://doi.org/10.5905/ethz-1007-72 or via pip from the Python Package Index (PyPI). gisbert.schneider@pharma.ethz.ch. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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 California Oak Disease and Arthropod (CODA) Database

Treesearch

Tedmund J. Swiecki; Elizabeth A. Bernhardt; Richard A. Arnold

1997-01-01

The California Oak Disease and Arthropod (CODA) host index database is a compilation of information on agents that colonize or feed on oaks in California. Agents in the database include plant-feeding insects and mites, nematodes, microorganisms, viruses, and abiotic disease agents. CODA contains summarized information on hosts, agents, information sources, and the...

Image Engine: an object-oriented multimedia database for storing, retrieving and sharing medical images and text.

PubMed Central

Lowe, H. J.

1993-01-01

This paper describes Image Engine, an object-oriented, microcomputer-based, multimedia database designed to facilitate the storage and retrieval of digitized biomedical still images, video, and text using inexpensive desktop computers. The current prototype runs on Apple Macintosh computers and allows network database access via peer to peer file sharing protocols. Image Engine supports both free text and controlled vocabulary indexing of multimedia objects. The latter is implemented using the TView thesaurus model developed by the author. The current prototype of Image Engine uses the National Library of Medicine's Medical Subject Headings (MeSH) vocabulary (with UMLS Meta-1 extensions) as its indexing thesaurus. PMID:8130596

Effects of tranexamic acid on coagulation indexes of patients undergoing heart valve replacement surgery under cardiopulmonary bypass

PubMed Central

Liu, Fei; Xu, Dong; Zhang, Kefeng; Zhang, Jian

2016-01-01

This study aims to explore the effects of tranexamic acid on the coagulation indexes of patients undergoing heart valve replacement surgery under the condition of cardiopulmonary bypass (CPB). One hundred patients who conformed to the inclusive criteria were selected and divided into a tranexamic acid group and a non-tranexamic acid group. They all underwent heart valve replacement surgery under CPB. Patients in the tranexamic acid group were intravenously injected with 1 g of tranexamic acid (100 mL) at the time point after anesthesia induction and before skin incision and at the time point after the neutralization of heparin. Patients in the non-tranexamic acid group were given 100 mL of normal saline at corresponding time points, respectively. Then the coagulation indexes of the two groups were analyzed. The activated blood clotting time (ACT) of the two groups was within normal scope before CPB, while four coagulation indexes including prothrombin time (PT), activated partial thromboplastin time (APTT), international normalized ratio (INR), and fibrinogen (FIB) had significant increases after surgery; the PT and INR of the tranexamic acid group had a remarkable decline after surgery. All the findings suggest that the application of tranexamic acid in heart valve replacement surgery under CPB can effectively reduce intraoperative and postoperative blood loss. PMID:27694613

A global characterization and identification of multifunctional enzymes.

PubMed

Cheng, Xian-Ying; Huang, Wei-Juan; Hu, Shi-Chang; Zhang, Hai-Lei; Wang, Hao; Zhang, Jing-Xian; Lin, Hong-Huang; Chen, Yu-Zong; Zou, Quan; Ji, Zhi-Liang

2012-01-01

Multi-functional enzymes are enzymes that perform multiple physiological functions. Characterization and identification of multi-functional enzymes are critical for communication and cooperation between different functions and pathways within a complex cellular system or between cells. In present study, we collected literature-reported 6,799 multi-functional enzymes and systematically characterized them in structural, functional, and evolutionary aspects. It was found that four physiochemical properties, that is, charge, polarizability, hydrophobicity, and solvent accessibility, are important for characterization of multi-functional enzymes. Accordingly, a combinational model of support vector machine and random forest model was constructed, based on which 6,956 potential novel multi-functional enzymes were successfully identified from the ENZYME database. Moreover, it was observed that multi-functional enzymes are non-evenly distributed in species, and that Bacteria have relatively more multi-functional enzymes than Archaebacteria and Eukaryota. Comparative analysis indicated that the multi-functional enzymes experienced a fluctuation of gene gain and loss during the evolution from S. cerevisiae to H. sapiens. Further pathway analyses indicated that a majority of multi-functional enzymes were well preserved in catalyzing several essential cellular processes, for example, metabolisms of carbohydrates, nucleotides, and amino acids. What's more, a database of known multi-functional enzymes and a server for novel multi-functional enzyme prediction were also constructed for free access at http://bioinf.xmu.edu.cn/databases/MFEs/index.htm.

Tempest: GPU-CPU computing for high-throughput database spectral matching.

PubMed

Milloy, Jeffrey A; Faherty, Brendan K; Gerber, Scott A

2012-07-06

Modern mass spectrometers are now capable of producing hundreds of thousands of tandem (MS/MS) spectra per experiment, making the translation of these fragmentation spectra into peptide matches a common bottleneck in proteomics research. When coupled with experimental designs that enrich for post-translational modifications such as phosphorylation and/or include isotopically labeled amino acids for quantification, additional burdens are placed on this computational infrastructure by shotgun sequencing. To address this issue, we have developed a new database searching program that utilizes the massively parallel compute capabilities of a graphical processing unit (GPU) to produce peptide spectral matches in a very high throughput fashion. Our program, named Tempest, combines efficient database digestion and MS/MS spectral indexing on a CPU with fast similarity scoring on a GPU. In our implementation, the entire similarity score, including the generation of full theoretical peptide candidate fragmentation spectra and its comparison to experimental spectra, is conducted on the GPU. Although Tempest uses the classical SEQUEST XCorr score as a primary metric for evaluating similarity for spectra collected at unit resolution, we have developed a new "Accelerated Score" for MS/MS spectra collected at high resolution that is based on a computationally inexpensive dot product but exhibits scoring accuracy similar to that of the classical XCorr. In our experience, Tempest provides compute-cluster level performance in an affordable desktop computer.

Efficient Single-Pass Index Construction for Text Databases.

ERIC Educational Resources Information Center

Heinz, Steffen; Zobel, Justin

2003-01-01

Discusses index construction for text collections, reviews principal approaches to inverted indexes, analyzes their theoretical cost, and presents experimental results of the use of a single-pass inversion method on Web document collections. Shows that the single-pass approach is faster and does not require the complete vocabulary of the indexed…

Plasma free amino acid profiles evaluate risk of metabolic syndrome, diabetes, dyslipidemia, and hypertension in a large Asian population.

PubMed

Yamaguchi, Natsu; Mahbub, M H; Takahashi, Hidekazu; Hase, Ryosuke; Ishimaru, Yasutaka; Sunagawa, Hiroshi; Amano, Hiroki; Kobayashi-Miura, Mikiko; Kanda, Hideyuki; Fujita, Yasuyuki; Yamamoto, Hiroshi; Yamamoto, Mai; Kikuchi, Shinya; Ikeda, Atsuko; Takasu, Mariko; Kageyama, Naoko; Nakamura, Mina; Tanabe, Tsuyoshi

2017-04-07

Recently, the association of plasma free amino acid (PFAA) profile and lifestyle-related diseases has been reported. However, few studies have been reported in large Asian populations, about the usefulness of PFAAs for evaluating disease risks. We examined the ability of PFAA profiles to evaluate lifestyle-related diseases in so far the largest Asian population. We examined plasma concentrations of 19 amino acids in 8589 Japanese subjects, and determined the association with variables associated with obesity, blood glucose, lipid, and blood pressure. We also evaluated the PFAA indexes that reflect visceral fat obesity and insulin resistance. The contribution of single PFAA level and relevant PFAA indexes was also examined in the risk assessment of lifestyle-related diseases. Of the 19 amino acids, branched-chain amino acids and aromatic amino acids showed association with obesity and lipid variables. The PFAA index related to visceral fat obesity showed relatively higher correlation with variables than that of any PFAA. In the evaluation of lifestyle-related disease risks, the odds ratios of the PFAA index related to visceral fat obesity or insulin resistance with the diseases were higher than most of those of individual amino acid levels even after adjusting for potential confounding factors. The association pattern of the indexes and PFAA with each lifestyle-related disease was distinct. We confirmed the usefulness of PFAA profiles and indexes as markers for evaluating the risks of lifestyle-related diseases, including diabetes mellitus, metabolic syndrome, dyslipidemia, and hypertension in a large Asian population.

The 5/95 gap in the indexation of psychiatric journals of low- and middle-income countries

PubMed Central

Mari, J J; Patel, V; Kieling, C; Razzouk, D; Tyrer, P; Herrman, H

2010-01-01

Mari JJ, Patel V, Kieling C, Razzouk D, Tyrer P, Herrman H. The 5/95 gap in the indexation of psychiatric journals of low- and middle-income countries. Objective: To investigate the relationship between science production and the indexation level of low- and middle-income countries (LAMIC) journals in international databases. Method: Indicators of productivity in research were based on the number of articles produced over the 1994–2004 period. A survey in both Medline and ISI/Thomson was conducted to identify journals according to their country of origin. A WPA Task Force designed a collaborative process to assess distribution and quality of non-indexed LAMIC journals. Results: Twenty LAMIC were found to present more than 100 publications and a total of 222 indexed psychiatric journals were found, but only nine were from LAMIC. The Task Force received 26 questionnaires from editors of non-indexed journals, and concluded that five journals would meet criteria for indexation. Conclusion: Barriers to indexation of journals contribute to the difficulties in achieving fair representation in the main literature databases for the scientific production in these countries. PMID:19764927

Research progress in muscle-derived stem cells: Literature retrieval results based on international database.

PubMed

Zhang, Li; Wang, Wei

2012-04-05

To identify global research trends of muscle-derived stem cells (MDSCs) using a bibliometric analysis of the Web of Science, Research Portfolio Online Reporting Tools of the National Institutes of Health (NIH), and the Clinical Trials registry database (ClinicalTrials.gov). We performed a bibliometric analysis of data retrievals for MDSCs from 2002 to 2011 using the Web of Science, NIH, and ClinicalTrials.gov. (1) Web of Science: (a) peer-reviewed articles on MDSCs that were published and indexed in the Web of Science. (b) Type of articles: original research articles, reviews, meeting abstracts, proceedings papers, book chapters, editorial material and news items. (c) Year of publication: 2002-2011. (d) Citation databases: Science Citation Index-Expanded (SCI-E), 1899-present; Conference Proceedings Citation Index-Science (CPCI-S), 1991-present; Book Citation Index-Science (BKCI-S), 2005-present. (2) NIH: (a) Projects on MDSCs supported by the NIH. (b) Fiscal year: 1988-present. (3) ClinicalTrials.gov: All clinical trials relating to MDSCs were searched in this database. (1) Web of Science: (a) Articles that required manual searching or telephone access. (b) We excluded documents that were not published in the public domain. (c) We excluded a number of corrected papers from the total number of articles. (d) We excluded articles from the following databases: Social Sciences Citation Index (SSCI), 1898-present; Arts & Humanities Citation Index (A&HCI), 1975-present; Conference Proceedings Citation Index - Social Science & Humanities (CPCI-SSH), 1991-present; Book Citation Index - Social Sciences & Humanities (BKCI-SSH), 2005-present; Current Chemical Reactions (CCR-EXPANDED), 1985-present; Index Chemicus (IC), 1993-present. (2) NIH: (a) We excluded publications related to MDSCs that were supported by the NIH. (b) We limited the keyword search to studies that included MDSCs within the title or abstract. (3) ClinicalTrials.gov: (a) We excluded clinical trials that were not in the ClinicalTrials.gov database. (b) We excluded clinical trials that dealt with stem cells other than MDSCs in the ClinicalTrials.gov database. (1) Type of literature; (2) annual publication output; (3) distribution according to journals; (4) distribution according to country; (5) distribution according to institution; (6) top cited authors over the last 10 years; (7) projects financially supported by the NIH; and (8) clinical trials registered. (1) In all, 802 studies on MDSCs appeared in the Web of Science from 2002 to 2011, almost half of which derived from American authors and institutes. The number of studies on MDSCs has gradually increased over the past 10 years. Most papers on MDSCs appeared in journals with a particular focus on cell biology research, such as Experimental Cell Research, Journal of Cell Science, and PLoS One. (2) Eight MDSC research projects have received over US$6 billion in funding from the NIH. The current project led by Dr. Johnny Huard of the University of Pittsburgh-"Muscle-Based Tissue Engineering to Improve Bone Healing"-is supported by the NIH. Dr. Huard has been the most productive and top-cited author in the field of gene therapy and adult stem cell research in the Web of Science over last 10 years. (3) On ClinicalTrials.gov, "Muscle Derived Cell Therapy for Bladder Exstrophy Epispadias Induced Incontinence" Phase 1 is registered and sponsored by Johns Hopkins University and has been led by Dr. John P. Gearhart since November 2009. From our analysis of the literature and research trends, we found that MDSCs may offer further benefits in regenerative medicine.

Metabolic Profiles of Obesity in American Indians: The Strong Heart Family Study.

PubMed

Zhao, Qi; Zhu, Yun; Best, Lyle G; Umans, Jason G; Uppal, Karan; Tran, ViLinh T; Jones, Dean P; Lee, Elisa T; Howard, Barbara V; Zhao, Jinying

2016-01-01

Obesity is a typical metabolic disorder resulting from the imbalance between energy intake and expenditure. American Indians suffer disproportionately high rates of obesity and diabetes. The goal of this study is to identify metabolic profiles of obesity in 431 normoglycemic American Indians participating in the Strong Heart Family Study. Using an untargeted liquid chromatography-mass spectrometry, we detected 1,364 distinct m/z features matched to known compounds in the current metabolomics databases. We conducted multivariate analysis to identify metabolic profiles for obesity, adjusting for standard obesity indicators. After adjusting for covariates and multiple testing, five metabolites were associated with body mass index and seven were associated with waist circumference. Of them, three were associated with both. Majority of the obesity-related metabolites belongs to lipids, e.g., fatty amides, sphingolipids, prenol lipids, and steroid derivatives. Other identified metabolites are amino acids or peptides. Of the nine identified metabolites, five metabolites (oleoylethanolamide, mannosyl-diinositol-phosphorylceramide, pristanic acid, glutamate, and kynurenine) have been previously implicated in obesity or its related pathways. Future studies are warranted to replicate these findings in larger populations or other ethnic groups.

Metabolic Profiles of Obesity in American Indians: The Strong Heart Family Study

PubMed Central

Best, Lyle G.; Umans, Jason G.; Uppal, Karan; Tran, ViLinh T.; Jones, Dean P.; Lee, Elisa T.; Howard, Barbara V.; Zhao, Jinying

2016-01-01

Obesity is a typical metabolic disorder resulting from the imbalance between energy intake and expenditure. American Indians suffer disproportionately high rates of obesity and diabetes. The goal of this study is to identify metabolic profiles of obesity in 431 normoglycemic American Indians participating in the Strong Heart Family Study. Using an untargeted liquid chromatography–mass spectrometry, we detected 1,364 distinct m/z features matched to known compounds in the current metabolomics databases. We conducted multivariate analysis to identify metabolic profiles for obesity, adjusting for standard obesity indicators. After adjusting for covariates and multiple testing, five metabolites were associated with body mass index and seven were associated with waist circumference. Of them, three were associated with both. Majority of the obesity-related metabolites belongs to lipids, e.g., fatty amides, sphingolipids, prenol lipids, and steroid derivatives. Other identified metabolites are amino acids or peptides. Of the nine identified metabolites, five metabolites (oleoylethanolamide, mannosyl-diinositol-phosphorylceramide, pristanic acid, glutamate, and kynurenine) have been previously implicated in obesity or its related pathways. Future studies are warranted to replicate these findings in larger populations or other ethnic groups. PMID:27434237

NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids

PubMed Central

Revilla-López, Guillem; Torras, Juan; Curcó, David; Casanovas, Jordi; Calaza, M. Isabel; Zanuy, David; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Grodzinski, Piotr; Alemán, Carlos

2010-01-01

Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids –also called non-coded, non-canonical or non-standard– is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, α-tetrasubstituted α-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example. PMID:20455555

Where are Romanian biomedical journals now and what does the future hold for them? A scientometric analysis.

PubMed

Dumitrascu, Dan L

2018-01-01

There is a competition between scientific journals in order to achieve leadership in their scientific field. There are several Romanian biomedical journals which are published in English and a smaller number in Romanian. We need a periodical analysis of their visibility and ranking according to scientometric measures. We searched all biomedical journals indexed on international data bases: Web of Science, PubMed, Scopus, Embase, Google Scholar. We analyzed their evaluation factors. Several journals from Romania in the biomedical field are indexed in international databases. Their scientometric indexes are not high. The best journal was acquired by an international publisher and is no longer listed for Romania. There are several Romanian biomedical journals indexed in international databases that deserve periodical analysis. There is a need to improve their ranking.

[Analysis of the academic level and impact of ophthalmological periodicals in China].

PubMed

Xu, Xiao-quan; Mao, Wen-ming; Zheng, Jun-hai; Qu, Jia

2009-04-01

To analyse the whole level and impact of ophthalmological periodicals in China. It was studied by using bibliometrics analysis method. According to the data of CAJCCR in 2002 to 2007 and Chinese Citation Database in 2001 to 2007. The impact factor (IF), non-self-citing impact factor, total cited frequency, cited articles, immediacy index, rate of fund papers, web immediacy download rate, average value of h index were analysed and the non-self-citing rate, h(2)/n, high cited articles were calculated. In addition, the results of cited by cole databases at home and abroad. The average value of IF and cited frequency of 13 kinds of ophthalmological periodicals were 0.3940 and 657 respectively in 2001 to 2006, which were higher than that of D part of CAJCCR. The periodicals which the five indexes of IF, non-self-citing impact factor, total cited frequency, the non-self-citing rate, immediacy index, rate of fund papers, web immediacy download rate, average value of h index and h(2)/n, high cited articles were Top 5 and cited by five or more than five kinds of the cole databases at home and abroad were Chinese Journal of Ophthalmology, Chinese Journal of Ocular Fundus Diseases, Practical Chinese Journal of Ophthalmology and Chinese Journal of Optometry & Ophthalmology. Most of indexes of Chinese Journal of Ophthalmology were the first. There are big difference between the 13 kinds of ophthalmological periodicals. The qualities of some ophthalmological periodicals should be improved.

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.

Assessment of indexing trends with specific and general terms for herbal medicine.

PubMed

Bartol, Tomaz

2012-12-01

Concepts for medicinal plants are represented by a variety of associated general terms with specific indexing patterns in databases, which may not consistently reflect growth of records. The objectives of this study are to assess the development in databases by identifying general terms that describe herbal medicine with optimal retrieval recall and to identify possible special trends in co-occurrence of specific and general concepts. Different search strategies are tested in cab abstracts, medline and web of science. Specific terms (Origanum and Salvia) are employed. Relevant general terms (e.g. 'Plants, Medicinal', Phytotherapy, Herbal drugs) are identified, along with indexing trends and co-occurrences. Growth trends, in specific (narrower) terms, are similar among databases. General terms, however, exhibit dissimilar trends, sometimes almost opposing one another. Co-occurrence of specific and general terms is changing over time. General terms may not denote definite development of trends as the use of terms differs amongst databases, making it difficult to correctly assess possible numbers of relevant records. Perceived increase can, sometimes, be attributed to an increased occurrence of a more general term alongside the specific one. Thesaurus-controlled databases may yield more hits, because of 'up-posted' (broader) terms. Use of broader terms is helpful as it enhances retrieval of relevant documents. © 2012 The authors. Health Information and Libraries Journal © 2012 Health Libraries Group.

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database

PubMed Central

Drabkin, Harold J.; Blake, Judith A.

2012-01-01

The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as ‘GO’ or ‘homology’ or ‘phenotype’. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as ‘papers selected for GO that refer to genes with NO GO annotation’. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications. PMID:23110975

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database.

PubMed

Drabkin, Harold J; Blake, Judith A

2012-01-01

The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as 'GO' or 'homology' or 'phenotype'. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as 'papers selected for GO that refer to genes with NO GO annotation'. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications.

Digitizing Olin Eggen's Card Database

NASA Astrophysics Data System (ADS)

Crast, J.; Silvis, G.

2017-06-01

The goal of the Eggen Card Database Project is to recover as many of the photometric observations from Olin Eggen's Card Database as possible and preserve these observations, in digital forms that are accessible by anyone. Any observations of interest to the AAVSO will be added to the AAVSO International Database (AID). Given to the AAVSO on long-term loan by the Cerro Tololo Inter-American Observatory, the database is a collection of over 78,000 index cards holding all Eggen's observations made between 1960 and 1990. The cards were electronically scanned and the resulting 108,000 card images have been published as a series of 2,216 PDF files, which are available from the AAVSO web site. The same images are also stored in an AAVSO online database where they are indexed by star name and card content. These images can be viewed using the eggen card portal online tool. Eggen made observations using filter bands from five different photometric systems. He documented these observations using 15 different data recording formats. Each format represents a combination of filter magnitudes and color indexes. These observations are being transcribed onto spreadsheets, from which observations of value to the AAVSO are added to the AID. A total of 506 U, B, V, R, and I observations were added to the AID for the variable stars S Car and l Car. We would like the reader to search through the card database using the eggen card portal for stars of particular interest. If such stars are found and retrieval of the observations is desired, e-mail the authors, and we will be happy to help retrieve those data for the reader.

Identification of Oxygenated Fatty Acid as a Side Chain of Lipo-Alkaloids in Aconitum carmichaelii by UHPLC-Q-TOF-MS and a Database.

PubMed

Liang, Ying; Wu, Jian-Lin; Leung, Elaine Lai-Han; Zhou, Hua; Liu, Zhongqiu; Yan, Guanyu; Liu, Ying; Liu, Liang; Li, Na

2016-03-31

Lipo-alkaloid is a kind of C19-norditerpenoid alkaloid usually found in Aconitum species. Structurally, they contain an aconitane skeleton and one or two fatty acid moieties of 3-25 carbon chains with 1-6 unsaturated degrees. Analysis of the lipo-alkaloids in roots of Aconitum carmichaelii resulted in the isolation of six known pure lipo-alkaloids (A1-A6) and a lipo-alkaloid mixture (A7). The mixture shared the same aconitane skeleton of 14-benzoylmesaconine, but their side chains were determined to be 9-hydroxy-octadecadienoic acid, 13-hydroxy-octadecadienoic acid and 10-hydroxy-octadecadienoic acid, respectively, by MS/MS analysis after alkaline hydrolysis. To our knowledge, this is the first time of the reporting of the oxygenated fatty acids as the side chains in naturally-occurring lipo-alkaloids. In order to identify more lipo-alkaloids, a compound database was established based on various combinations between the aconitane skeleton and the fatty acid chain, and then, the identification of lipo-alkaloids was conducted using the database, UHPLC-Q-TOF-MS and MS/MS. Finally, 148 lipo-alkaloids were identified from A. carmichaelii after intensive MS/MS analysis, including 93 potential new compounds and 38 compounds with oxygenated fatty acid moieties.

Annotations of Mexican bullfighting videos for semantic index

NASA Astrophysics Data System (ADS)

Montoya Obeso, Abraham; Oropesa Morales, Lester Arturo; Fernando Vázquez, Luis; Cocolán Almeda, Sara Ivonne; Stoian, Andrei; García Vázquez, Mireya Saraí; Zamudio Fuentes, Luis Miguel; Montiel Perez, Jesús Yalja; de la O Torres, Saul; Ramírez Acosta, Alejandro Alvaro

2015-09-01

The video annotation is important for web indexing and browsing systems. Indeed, in order to evaluate the performance of video query and mining techniques, databases with concept annotations are required. Therefore, it is necessary generate a database with a semantic indexing that represents the digital content of the Mexican bullfighting atmosphere. This paper proposes a scheme to make complex annotations in a video in the frame of multimedia search engine project. Each video is partitioned using our segmentation algorithm that creates shots of different length and different number of frames. In order to make complex annotations about the video, we use ELAN software. The annotations are done in two steps: First, we take note about the whole content in each shot. Second, we describe the actions as parameters of the camera like direction, position and deepness. As a consequence, we obtain a more complete descriptor of every action. In both cases we use the concepts of the TRECVid 2014 dataset. We also propose new concepts. This methodology allows to generate a database with the necessary information to create descriptors and algorithms capable to detect actions to automatically index and classify new bullfighting multimedia content.

Higher lipophilic index indicates higher risk of coronary heart disease in postmenopausal women

USDA-ARS?s Scientific Manuscript database

Fatty acids are essential components of cell membranes and play an integral role in membrane fluidity. The lipophilic index (LI, defined as the sum of the products between fatty acid levels and melting points (degrees Celsius), divided by the total amount of fatty acids is thought to reflect membran...

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

Myers, G.; Korber, B.; Wain-Hobson, S.

This compendium, including accompanying floppy diskettes, is the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts it comprises: (I) Nucleic Acid Alignments and Sequences; (II) Amino Acid Alignments; (III) Analysis; (IV) Related Sequences; (V) Database communications.

A secure data outsourcing scheme based on Asmuth-Bloom secret sharing

NASA Astrophysics Data System (ADS)

Idris Muhammad, Yusuf; Kaiiali, Mustafa; Habbal, Adib; Wazan, A. S.; Sani Ilyasu, Auwal

2016-11-01

Data outsourcing is an emerging paradigm for data management in which a database is provided as a service by third-party service providers. One of the major benefits of offering database as a service is to provide organisations, which are unable to purchase expensive hardware and software to host their databases, with efficient data storage accessible online at a cheap rate. Despite that, several issues of data confidentiality, integrity, availability and efficient indexing of users' queries at the server side have to be addressed in the data outsourcing paradigm. Service providers have to guarantee that their clients' data are secured against internal (insider) and external attacks. This paper briefly analyses the existing indexing schemes in data outsourcing and highlights their advantages and disadvantages. Then, this paper proposes a secure data outsourcing scheme based on Asmuth-Bloom secret sharing which tries to address the issues in data outsourcing such as data confidentiality, availability and order preservation for efficient indexing.

ERIC: Sphinx or Golden Griffin?

ERIC Educational Resources Information Center

Lopez, Manuel D.

1989-01-01

Evaluates the Educational Resources Information Center (ERIC) database. Summarizes ERIC's history and organization, and discusses criticisms concerning access, currency, and database content. Reviews role of component clearinghouses, indexing practices, thesaurus structure, international coverage, and comparative studies. Finds ERIC a valuable…

Patent Family Databases.

ERIC Educational Resources Information Center

Simmons, Edlyn S.

1985-01-01

Reports on retrieval of patent information online and includes definition of patent family, basic and equivalent patents, "parents and children" applications, designated states, patent family databases--International Patent Documentation Center, World Patents Index, APIPAT (American Petroleum Institute), CLAIMS (IFI/Plenum). A table…

Unexpected similarity in RBC DHA and AA levels between bottlenose dolphins and humans.

PubMed

Harris, William S; Schmitt, Todd L

2014-01-01

The Omega-3 Index [red blood cell (RBC) content of eicosapentaenoic acid (EPA)+docosahexaenoic acid (DHA)] is inversely related to risk of cardiovascular disease in humans. In the U.S., the average Omega-3 Index is about 4-6% of RBC fatty acids, whereas in Japan it is 9-10%. The range of physiologically-possible levels for the Omega-3 Index in other mammals is unknown. To compare the RBC fatty acid composition of a common piscivorous mammal, the bottlenose dolphin (Tursiops truncatus), with that of (U.S.) humans, and to examine the extent to which dietary fatty acid patterns were reflected in RBCs. RBCs were isolated from routine blood samples collected from 35 healthy dolphins at two display facilities and were analyzed by gas chromatography. For humans, historic, deidentified RBC fatty acid data from our laboratory were used (n=11,329; mean age 58). The mean Omega-3 Index of the dolphins was 19.9% compared with 6.0% for humans. EPA levels were 15.3% vs 1.2%, respectively, but DHA levels were virtually identical (4.6% vs 4.8%). Linoleic acid (LNA) levels were much lower in dolphins vs humans (0.5% vs 12.5%) whereas arachidonic acid (ARA) levels were similar (12.3% vs 14.5%). In a subgroup of humans with an Omega-3 Index in the >99.2 percentile, the mean index was similar to that of the dolphins. Based on an analysis of their food, the dolphins consumed about 60g of EPA+DHA per day as compared to about 0.1g in humans. Dolphins have an Omega-3 Index that is (only) 3-4× higher than that of U.S. adults despite their intake of EPA+DHA being about 165× higher (as a percent of kcal). RBC, EPA and LNA levels are relatively more reflective of dietary intakes than are DHA and ARA levels. The mechanisms by which certain fatty acid levels appear to be fixed and others may vary in RBC membranes are unknown. Copyright © 2013 Elsevier Ltd. All rights reserved.

HLLV avionics requirements study and electronic filing system database development

NASA Technical Reports Server (NTRS)

1994-01-01

This final report provides a summary of achievements and activities performed under Contract NAS8-39215. The contract's objective was to explore a new way of delivering, storing, accessing, and archiving study products and information and to define top level system requirements for Heavy Lift Launch Vehicle (HLLV) avionics that incorporate Vehicle Health Management (VHM). This report includes technical objectives, methods, assumptions, recommendations, sample data, and issues as specified by DPD No. 772, DR-3. The report is organized into two major subsections, one specific to each of the two tasks defined in the Statement of Work: the Index Database Task and the HLLV Avionics Requirements Task. The Index Database Task resulted in the selection and modification of a commercial database software tool to contain the data developed during the HLLV Avionics Requirements Task. All summary information is addressed within each task's section.

Importance of being indexed in important databases--effect on the quantity of published articles in JBUON.

PubMed

Vuckovic-Dekic, Ljiljana; Gavrilovic, Dusica

2016-01-01

To investigate the dynamics of indexing the Journal of the Balkan Union of Oncology (JBUON) in important biomedical databases, the effects on the quantity and type of published articles, and also the countries of the (co)authors of these papers. The process of the JBUON indexing started with EMBASE/Excerpta Medica, followed in 2006 (PUBMED/MEDLINE) and continued every second year in other important biomedical databases, until 2012 when JBUON became Open Access Journal (for even more information please visit www.jbuon.com). Including the next two years for monitoring the effect of the last indexing, we analyzed 9 volumes consisting of 36 issues that were published from January 2006 to December 2014, with regard to the number and category of articles, the contribution of authors from Balkan and non-Balkan countries, and the (co)authorship in the published articles. In the period 2006-2014, 1165 articles of different categories were published in J BUON. The indexing progress of JBUON immediately increased the submission rate, and enlarged the number of publications, original papers in particular, in every volume of JBUON. Authors from Balkan countries contributed in 80.7% of all articles. The average number of coauthors per original article grew slowly and was higher at the end of the investigated period than at the start (6.6 and 5.8, respectively). The progressing covering of JBUON in important biomedical databases and its visibility on international level attracted the attention of a large readership, and submission rate and the number of published articles grew significantly, particularly the number of original papers. This is the most important consequence of the editorial policy which will hopefully lead to even more progress of JBUON in the near future.

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

Effect of fiber sources on fatty acids profile, glycemic index, and phenolic compound content of in vitro digested fortified wheat bread.

PubMed

Kurek, Marcin Andrzej; Wyrwisz, Jarosław; Karp, Sabina; Wierzbicka, Agnieszka

2018-05-01

In this study, some dietary fiber (DF) sources were investigated as fortifiers of wheat bread: oat (OB), flax (FB), and apple (AB). Adding oat and flax fibers to bread significantly changed the fatty acid profiles. OB was highest in oleic acid (33.83% of lipids) and linoleic acid (24.31% of lipids). Only in FB, γ-linolenic fatty acid was present in a significant amount-18.32%. The bioaccessibility trails revealed that the DF slow down the intake of saturated fatty acids. PUFA were least bioaccessible from all fatty acids groups in the range of (72% in OB to 87% in FB). The control bread had the greatest value (80.5) and was significantly higher than values for OB, FB, and AB in terms of glycemic index. OB, FB and AB addition led to obtain low glycemic index. AB had a significant highest value of total phenolic (897.2 mg/kg) with the lowest values in FB (541.2 mg/kg). The only significant lowering of caloric values in this study was observed in AB. The study could address the gap in the area of research about taking into consideration glycemic index, fatty acid profile and phenolic content in parallel in terms of DF application in breads.

Effects of tranexamic acid on coagulation indexes of patients undergoing heart valve replacement surgery under cardiopulmonary bypass.

PubMed

Liu, Fei; Xu, Dong; Zhang, Kefeng; Zhang, Jian

2016-12-01

This study aims to explore the effects of tranexamic acid on the coagulation indexes of patients undergoing heart valve replacement surgery under the condition of cardiopulmonary bypass (CPB). One hundred patients who conformed to the inclusive criteria were selected and divided into a tranexamic acid group and a non-tranexamic acid group. They all underwent heart valve replacement surgery under CPB. Patients in the tranexamic acid group were intravenously injected with 1 g of tranexamic acid (100 mL) at the time point after anesthesia induction and before skin incision and at the time point after the neutralization of heparin. Patients in the non-tranexamic acid group were given 100 mL of normal saline at corresponding time points, respectively. Then the coagulation indexes of the two groups were analyzed. The activated blood clotting time (ACT) of the two groups was within normal scope before CPB, while four coagulation indexes including prothrombin time (PT), activated partial thromboplastin time (APTT), international normalized ratio (INR), and fibrinogen (FIB) had significant increases after surgery; the PT and INR of the tranexamic acid group had a remarkable decline after surgery. All the findings suggest that the application of tranexamic acid in heart valve replacement surgery under CPB can effectively reduce intraoperative and postoperative blood loss. © The Author(s) 2016.

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.

Cardiovascular benefits of omega-3 fatty acids.

PubMed

von Schacky, Clemens; Harris, William S

2007-01-15

Cardiac societies recommend the intake of 1 g/day of the two omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) for cardiovascular disease prevention, treatment after a myocardial infarction, prevention of sudden death, and secondary prevention of cardiovascular disease. These recommendations are based on a body of scientific evidence that encompasses literally thousands of publications. Of four large scale intervention studies three also support the recommendations of these cardiac societies. One methodologically questionable study with a negative result led a Cochrane meta-analysis to a null conclusion. This null conclusion, however, has not swayed the recommendations of the cardiac societies mentioned, and has been refuted with good reason by scientific societies. Based on the scientific evidence just mentioned, we propose a new risk factor to be considered for sudden cardiac death, the omega-3 index. It is measured in red blood cells, and is expressed as a percentage of EPA + DHA of total fatty acids. An omega-3 index of >8% is associated with 90% less risk for sudden cardiac death, as compared to an omega-3 index of <4%. The omega-3 index as a risk factor for sudden cardiac death has striking similarities to LDL as a risk factor for coronary artery disease. Moreover, the omega-3 index reflects the omega-3 fatty acid status of a given individual (analogous to HbA1c reflecting glucose homeostasis). The omega-3 index can therefore be used as a goal for treatment with EPA and DHA. As is the case now for LDL, in the future, the cardiac societies might very well recommend treatment with EPA and DHA to become goal oriented (e.g. an omega-3 index>8%).

Omega-3 Index of Canadian adults.

PubMed

Langlois, Kellie; Ratnayake, Walisundera M N

2015-11-01

Cardioprotective properties have been associated with two fatty acids-eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The Omega-3 Index indicates the percentage of EPA+DHA in red blood cell fatty acids. Omega-3 Index levels of the Canadian population have not been directly measured. Data for respondents aged 20 to 79 from cycle 3 (2012/2013) of the Canadian Health Measures Survey were used to calculate means and the prevalence of Omega-3 Index coronary heart disease (CHD) risk cut-offs-high (4% or less), moderate (more than 4% to less than 8%), and low (8% or more)-by sociodemographic and lifestyle characteristics, including fish consumption and use of omega-3 supplements. Associations between the Omega-3 Index and CHD-related factors including biomarkers, risk factors, and previous CHD events, were examined in multivariate regression models. The mean Omega-3 Index level of Canadians aged 20 to 79 was 4.5%. Levels were higher for women, older adults, Asians and other non-white Canadians, omega-3 supplement users, and fish consumers; levels were lower for smokers and people who were obese. Fewer than 3% of adults had levels associated with low CHD risk; 43% had levels associated with high risk. No CHD-related factor was associated with the Omega-3 Index when control variables were taken into account. Omega-3 Index levels among Canadian adults were strongly related to age, race, supplement use, fish consumption, smoking status and obesity. Fewer than 3% of adults had Omega-3 Index levels associated with low risk for CHD.

Reference intervals for plasma-free amino acid in a Japanese population.

PubMed

Yamamoto, Hiroyuki; Kondo, Kazuhiro; Tanaka, Takayuki; Muramatsu, Takahiko; Yoshida, Hiroo; Imaizumi, Akira; Nagao, Kenji; Noguchi, Yasushi; Miyano, Hiroshi

2016-05-01

Plasma amino acid concentrations vary with various diseases. Although reference intervals are useful in daily clinical practice, no reference intervals have been reported for plasma amino acids in a large Japanese population. Reference individuals were selected from 7685 subjects examined with the Japanese Ningen Dock in 2008. A total of 1890 individuals were selected based on exclusion criteria, and the reference samples were selected after the outlier samples for each amino acid concentration were excluded. The lower limit of the reference intervals for the plasma amino acid concentrations was set at the 2.5th percentile and the upper limit at the 97.5th percentile. By use of the nested analysis of variance, we analysed a large dataset of plasma samples and the effects of background factors (sex, age and body mass index [BMI]) on the plasma amino acid concentrations. Most amino acid concentrations were related to sex, especially those of branched-chained amino acid. The citrulline, glutamine, ornithine and lysine concentrations were related to age. The glutamate concentration was related to body mass index. The concentrations of most amino acids are more strongly related to sex than to age or body mass index. Our results indicate that the reference intervals for plasma amino acid concentrations should be stratified by sex when the background factors of age and body mass index are considered. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Extension of the COG and arCOG databases by amino acid and nucleotide sequences

PubMed Central

Meereis, Florian; Kaufmann, Michael

2008-01-01

Background The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequences corresponding to their protein or protein domain entries. Results Using sequence information obtained from GenBank flat files covering the completely sequenced genomes of the COG and arCOG databases, we constructed NUCOCOG (nucleotide sequences containing COG databases) as an extended version including all nucleotide sequences and in addition the amino acid sequences originally utilized to construct the current COG and arCOG databases. We make available three comprehensive single XML files containing the complete databases including all sequence information. In addition, we provide a web interface as a utility suitable to browse the NUCOCOG database for sequence retrieval. The database is accessible at . Conclusion NUCOCOG offers the possibility to analyze any sequence related property in the context of the COG and arCOG framework simply by using script languages such as PERL applied to a large but single XML document. PMID:19014535

Application of the h-Index in Academic Plastic Surgery.

PubMed

Therattil, Paul J; Hoppe, Ian C; Granick, Mark S; Lee, Edward S

2016-05-01

The h-index is a measure designed to assess the quantity and significance of an individual's academic contributions. The objective of this study was to determine whether the h-index of plastic surgeons correlates with academic rank and whether there is a difference based on academic rank, residency training model, sex, geographic region, faculty size, and departmental status. A database of all US academic plastic surgeons was created. The rank and sex of each surgeon were obtained, as were characteristics of their plastic surgery program. The Scopus database was queried to determine each surgeon's h-index. The 592 plastic surgeons in our database had a mean h-index of 8.97. The h-index increased with academic rank: 4.59 for assistant professors, 9.10 for associate professors, and 15.30 for professors. There was no significant difference in the h-index between chairpersons and chiefs. Plastic surgeons on faculty in integrated plastic surgery programs had significantly higher h-indices (9.64) than those at traditional programs (6.28). Those who were on faculty at larger programs also had higher h-indices. Male plastic surgeons had higher h-indices (9.57) than did female plastic surgeons (6.07), although this was insignificant when taking other variables into account. There was no correlation between the h-index and location or departmental status. The h-index of plastic surgeons seems to correlate with academic rank and has potential as a tool to measure academic productivity within plastic surgery. Plastic surgeons on faculty in integrated plastic surgery programs, those at larger programs, and male plastic surgeons tend to have higher h-indices. The difference between sexes seems to be, at least in part, due to the higher number of men in high academic positions. There does not seem to be a regional difference with regard to h-indices or a difference with regard to departmental status.

Korean association of medical journal editors at the forefront of improving the quality and indexing chances of its member journals.

PubMed

Suh, Chang-Ok; Oh, Se Jeong; Hong, Sung-Tae

2013-05-01

The article overviews some achievements and problems of Korean medical journals published in the highly competitive journal environment. Activities of Korean Association of Medical Journal Editors (KAMJE) are viewed as instrumental for improving the quality of Korean articles, indexing large number of local journals in prestigious bibliographic databases and launching new abstract and citation tracking databases or platforms (eg KoreaMed, KoreaMed Synapse, the Western Pacific Regional Index Medicus [WPRIM]). KAMJE encourages its member journals to upgrade science editing standards and to legitimately increase citation rates, primarily by publishing more great articles with global influence. Experience gained by KAMJE and problems faced by Korean editors may have global implications.

Data, knowledge and method bases in chemical sciences. Part IV. Current status in databases.

PubMed

Braibanti, Antonio; Rao, Rupenaguntla Sambasiva; Rao, Gollapalli Nagesvara; Ramam, Veluri Anantha; Rao, Sattiraju Veera Venkata Satyanarayana

2002-01-01

Computer readable databases have become an integral part of chemical research right from planning data acquisition to interpretation of the information generated. The databases available today are numerical, spectral and bibliographic. Data representation by different schemes--relational, hierarchical and objects--is demonstrated. Quality index (QI) throws light on the quality of data. The objective, prospects and impact of database activity on expert systems are discussed. The number and size of corporate databases available on international networks crossed manageable number leading to databases about their contents. Subsets of corporate or small databases have been developed by groups of chemists. The features and role of knowledge-based or intelligent databases are described.

Online Databases. Ingenta Grows in the U.S. Market.

ERIC Educational Resources Information Center

Tenopir, Carol

2002-01-01

Focuses on the growth of the United Kingdom company Ingenta in the United States. Highlights include a new partnership with Gale Group related to their InfoTrac databases; indexing and full text coverage; standards; and other Ingenta acquisitions. (LRW)

A database of natural products and chemical entities from marine habitat

PubMed Central

Babu, Padavala Ajay; Puppala, Suma Sree; Aswini, Satyavarapu Lakshmi; Vani, Metta Ramya; Kumar, Chinta Narasimha; Prasanna, Tallapragada

2008-01-01

Marine compound database consists of marine natural products and chemical entities, collected from various literature sources, which are known to possess bioactivity against human diseases. The database is constructed using html code. The 12 categories of 182 compounds are provided with the source, compound name, 2-dimensional structure, bioactivity and clinical trial information. The database is freely available online and can be accessed at http://www.progenebio.in/mcdb/index.htm PMID:19238254

Database of amino acid-nucleotide contacts in contacts in DNA-homeodomain protein

NASA Astrophysics Data System (ADS)

Grokhlina, T. I.; Zrelov, P. V.; Ivanov, V. V.; Polozov, R. V.; Chirgadze, Yu. N.; Sivozhelezov, V. S.

2013-09-01

The analysis of amino acid-nucleotide contacts in interfaces of the protein-DNA complexes, intended to find consistencies in the protein-DNA recognition, is a complex problem that requires an analysis of the physicochemical characteristics of these contacts and the positions of the participating amino acids and nucleotides in the chains of the protein and the DNA, respectively, as well as conservatism of these contacts. Thus, those heterogeneous data should be systematized. For this purpose we have developed a database of amino acid-nucleotide contacts ANTPC (Amino acid Nucleotide Type Position Conservation) following the archetypal example of the proteins in the homeodomain family. We show that it can be used to compare and classify the interfaces of the protein-DNA complexes.

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.

Tests of methods for evaluating bibliographic databases: an analysis of the National Library of Medicine's handling of literatures in the medical behavioral sciences.

PubMed

Griffith, B C; White, H D; Drott, M C; Saye, J D

1986-07-01

This article reports on five separate studies designed for the National Library of Medicine (NLM) to develop and test methodologies for evaluating the products of large databases. The methodologies were tested on literatures of the medical behavioral sciences (MBS). One of these studies examined how well NLM covered MBS monographic literature using CATLINE and OCLC. Another examined MBS journal and serial literature coverage in MEDLINE and other MBS-related databases available through DIALOG. These two studies used 1010 items derived from the reference lists of sixty-one journals, and tested for gaps and overlaps in coverage in the various databases. A third study examined the quality of the indexing NLM provides to MBS literatures and developed a measure of indexing as a system component. The final two studies explored how well MEDLINE retrieved documents on topics submitted by MBS professionals and how online searchers viewed MEDLINE (and other systems and databases) in handling MBS topics. The five studies yielded both broad research outcomes and specific recommendations to NLM.

Coverage and quality: A comparison of Web of Science and Scopus databases for reporting faculty nursing publication metrics.

PubMed

Powell, Kimberly R; Peterson, Shenita R

Web of Science and Scopus are the leading databases of scholarly impact. Recent studies outside the field of nursing report differences in journal coverage and quality. A comparative analysis of nursing publications reported impact. Journal coverage by each database for the field of nursing was compared. Additionally, publications by 2014 nursing faculty were collected in both databases and compared for overall coverage and reported quality, as modeled by Scimajo Journal Rank, peer review status, and MEDLINE inclusion. Individual author impact, modeled by the h-index, was calculated by each database for comparison. Scopus offered significantly higher journal coverage. For 2014 faculty publications, 100% of journals were found in Scopus, Web of Science offered 82%. No significant difference was found in the quality of reported journals. Author h-index was found to be higher in Scopus. When reporting faculty publications and scholarly impact, academic nursing programs may be better represented by Scopus, without compromising journal quality. Programs with strong interdisciplinary work should examine all areas of strength to ensure appropriate coverage. Copyright © 2017 Elsevier Inc. All rights reserved.

Is ursodeoxycholic acid effective for intrahepatic cholestasis of pregnancy?

PubMed

Sepúlveda Marín, Sebastián; Contreras Maragaño, Valeria; Vera, Claudio

2016-01-08

Intrahepatic cholestasis of pregnancy is a condition associated with fetal morbidity and mortality. Ursodeoxycholic acid has been proposed as a treatment alternative, but its use remains controversial. Searching in Epistemonikos database, which is maintained by screening 30 databases, we identified three systematic reviews including eight randomized trials. We combined the evidence using meta-analysis and generated a summary of findings table following the GRADE approach. We concluded ursodeoxycholic acid reduces prematurity risk and need for admission in neonatal intensive care units. It might also reduce maternal pruritus.

International Energy: Subject Thesaurus. Revision 1

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

Not Available

The International Energy Agency: Subject Thesaurus contains the standard vocabulary of indexing terms (descriptors) developed and structured to build and maintain energy information databases. Involved in this cooperative task are (1) the technical staff of the USDOE Office of Scientific and Technical Information (OSTI) in cooperation with the member countries of the International Energy Agency`s Energy Technology Data Exchange (ETDE) and (2) the International Atomic Energy Agency`s International Nuclear Information System (INIS) staff representing the more than 100 countries and organizations that record and index information for the international nuclear information community. ETDE member countries are also members of INIS.more » Nuclear information prepared for INIS by ETDE member countries is included in the ETDE Energy Database, which contains the online equivalent of the printed INIS Atomindex. Indexing terminology is therefore cooperatively standardized for use in both information systems. This structured vocabulary reflects thscope of international energy research, development, and technological programs. The terminology of this thesaurus aids in subject searching on commercial systems, such as ``Energy Science & Technology`` by DIALOG Information Services, ``Energy`` by STN International and the ``ETDE Energy Database`` by SilverPlatter. It is also the thesaurus for the Integrated Technical Information System (ITIS) online databases of the US Department of Energy.« less

Mapping selected general literature of international nursing.

PubMed

Shams, Marie-Lise Antoun; Dixon, Lana S

2007-01-01

This study, part of a wider project to map the literature of nursing, identifies core journals cited in non-US nursing journals and determines the extent of their coverage by indexing services. Four general English-language journals were analyzed for format types and publication dates. Core titles were identified and nine bibliographic databases were scanned for indexing coverage. Findings show that 57.5% (13,391/23,271) of the cited references from the 4 core journals were to journal articles, 27.8% (6,471/23,271) to books, 9.5% (2,208/23,271) to government documents, 4.9% (1,131/23,271) to miscellaneous sources, and less than 1% (70/23,271) to Internet resources. Eleven journals produced one-third of the citations; the next third included 146 journals, followed by a dispersion of 1,622 titles. PubMed received the best database coverage scores, followed by CINAHL and Science Citation Index. None of the databases provided complete coverage of all 11 core titles. The four source journals contain a diverse group of cited references. The currency of citations to government documents makes these journals a good source for regulatory and legislative awareness. Nurses consult nursing and biomedical journals and must search both nursing and biomedical databases to cover the literature.

Nutrition Education and Body Mass Index in Grades K-12: A Systematic Review

ERIC Educational Resources Information Center

Price, Cayla; Cohen, Deborah; Pribis, Peter; Cerami, Jean

2017-01-01

Background: Overweight and obese body mass index (BMI) status affects an increasing number of children in the United States. The school setting has been identified as a focus area to implement obesity prevention programs. Methods: A database search of PubMed, Education Search Complete, and Cumulative Index to Nursing and Allied Health Literature…

Planning Ahead by Thinking Backwards.

ERIC Educational Resources Information Center

Farmer, Lesley S. J.

1996-01-01

Suggests evaluation criteria for selecting CD-ROMs and describes some typical titles along with examples of learning activities. Highlights include reference titles, including encyclopedias, magazine indexes, newspaper databases, subject-specific indexes, timetables and almanacs, and atlases; and curriculum-specific titles. (LRW)

Tranexamic acid use and postoperative outcomes in patients undergoing total hip or knee arthroplasty in the United States: retrospective analysis of effectiveness and safety

PubMed Central

Poeran, Jashvant; Rasul, Rehana; Suzuki, Suzuko; Danninger, Thomas; Mazumdar, Madhu; Opperer, Mathias; Boettner, Friedrich

2014-01-01

Objective To determine the effectiveness and safety of perioperative tranexamic acid use in patients undergoing total hip or knee arthroplasty in the United States. Design Retrospective cohort study; multilevel multivariable logistic regression models measured the association between tranexamic acid use in the perioperative period and outcomes. Setting 510 US hospitals from the claims based Premier Perspective database for 2006-12. Participants 872 416 patients who had total hip or knee arthroplasty. Intervention Perioperative intravenous tranexamic acid use by dose categories (none, ≤1000 mg, 2000 mg, and ≥3000 mg). Main outcome measures Allogeneic or autologous transfusion, thromboembolic complications (pulmonary embolism, deep venous thrombosis), acute renal failure, and combined complications (thromboembolic complications, acute renal failure, cerebrovascular events, myocardial infarction, in-hospital mortality). Results While comparable regarding average age and comorbidity index, patients receiving tranexamic acid (versus those who did not) showed lower rates of allogeneic or autologous transfusion (7.7% v 20.1%), thromboembolic complications (0.6% v 0.8%), acute renal failure (1.2% v 1.6%), and combined complications (1.9% v 2.6%); all P<0.01. In the multilevel models, tranexamic acid dose categories (versus no tranexamic acid use) were associated with significantly (P<0.001) decreased odds for allogeneic or autologous blood transfusions (odds ratio 0.31 to 0.38 by dose category) and no significantly increased risk for complications: thromboembolic complications (odds ratio 0.85 to 1.02), acute renal failure (0.70 to 1.11), and combined complications (0.75 to 0.98). Conclusions Tranexamic acid was effective in reducing the need for blood transfusions while not increasing the risk of complications, including thromboembolic events and renal failure. Thus our data provide incremental evidence of the potential effectiveness and safety of tranexamic acid in patients requiring orthopedic surgery. PMID:25116268

JANE, A new information retrieval system for the Radiation Shielding Information Center

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

Trubey, D.K.

A new information storage and retrieval system has been developed for the Radiation Shielding Information Center (RSIC) at Oak Ridge National Laboratory to replace mainframe systems that have become obsolete. The database contains citations and abstracts of literature which were selected by RSIC analysts and indexed with terms from a controlled vocabulary. The database, begun in 1963, has been maintained continuously since that time. The new system, called JANE, incorporates automatic indexing techniques and on-line retrieval using the RSIC Data General Eclipse MV/4000 minicomputer, Automatic indexing and retrieval techniques based on fuzzy-set theory allow the presentation of results in ordermore » of Retrieval Status Value. The fuzzy-set membership function depends on term frequency in the titles and abstracts and on Term Discrimination Values which indicate the resolving power of the individual terms. These values are determined by the Cover Coefficient method. The use of a commercial database base to store and retrieve the indexing information permits rapid retrieval of the stored documents. Comparisons of the new and presently-used systems for actual searches of the literature indicate that it is practical to replace the mainframe systems with a minicomputer system similar to the present version of JANE. 18 refs., 10 figs.« less

Designing for Peta-Scale in the LSST Database

NASA Astrophysics Data System (ADS)

Kantor, J.; Axelrod, T.; Becla, J.; Cook, K.; Nikolaev, S.; Gray, J.; Plante, R.; Nieto-Santisteban, M.; Szalay, A.; Thakar, A.

2007-10-01

The Large Synoptic Survey Telescope (LSST), a proposed ground-based 8.4 m telescope with a 10 deg^2 field of view, will generate 15 TB of raw images every observing night. When calibration and processed data are added, the image archive, catalogs, and meta-data will grow 15 PB yr^{-1} on average. The LSST Data Management System (DMS) must capture, process, store, index, replicate, and provide open access to this data. Alerts must be triggered within 30 s of data acquisition. To do this in real-time at these data volumes will require advances in data management, database, and file system techniques. This paper describes the design of the LSST DMS and emphasizes features for peta-scale data. The LSST DMS will employ a combination of distributed database and file systems, with schema, partitioning, and indexing oriented for parallel operations. Image files are stored in a distributed file system with references to, and meta-data from, each file stored in the databases. The schema design supports pipeline processing, rapid ingest, and efficient query. Vertical partitioning reduces disk input/output requirements, horizontal partitioning allows parallel data access using arrays of servers and disks. Indexing is extensive, utilizing both conventional RAM-resident indexes and column-narrow, row-deep tag tables/covering indices that are extracted from tables that contain many more attributes. The DMS Data Access Framework is encapsulated in a middleware framework to provide a uniform service interface to all framework capabilities. This framework will provide the automated work-flow, replication, and data analysis capabilities necessary to make data processing and data quality analysis feasible at this scale.

Biological age as a health index for mortality and major age-related disease incidence in Koreans: National Health Insurance Service – Health screening 11-year follow-up study

PubMed Central

Kang, Young Gon; Suh, Eunkyung; Lee, Jae-woo; Kim, Dong Wook; Cho, Kyung Hee; Bae, Chul-Young

2018-01-01

Purpose A comprehensive health index is needed to measure an individual’s overall health and aging status and predict the risk of death and age-related disease incidence, and evaluate the effect of a health management program. The purpose of this study is to demonstrate the validity of estimated biological age (BA) in relation to all-cause mortality and age-related disease incidence based on National Sample Cohort database. Patients and methods This study was based on National Sample Cohort database of the National Health Insurance Service – Eligibility database and the National Health Insurance Service – Medical and Health Examination database of the year 2002 through 2013. BA model was developed based on the National Health Insurance Service – National Sample Cohort (NHIS – NSC) database and Cox proportional hazard analysis was done for mortality and major age-related disease incidence. Results For every 1 year increase of the calculated BA and chronological age difference, the hazard ratio for mortality significantly increased by 1.6% (1.5% in men and 2.0% in women) and also for hypertension, diabetes mellitus, heart disease, stroke, and cancer incidence by 2.5%, 4.2%, 1.3%, 1.6%, and 0.4%, respectively (p<0.001). Conclusion Estimated BA by the developed BA model based on NHIS – NSC database is expected to be used not only as an index for assessing health and aging status and predicting mortality and major age-related disease incidence, but can also be applied to various health care fields. PMID:29593385

[Topological models of retention index of thin-layer chromatogram for chiral organic acids].

PubMed

Li, Mingjian; Wang, Yuxiao; Feng, Hui; Feng, Changjun

2014-03-01

On the basis of Kier's molecular connectivity indices and conjugated matrix, novel molecular connectivity indices ((m) G(t)(v)) were defined and calculated for 18 chiral hydroxyl acids and amino acids. The chiral connectivity indices ((m)C(t)(v)) were introduced by extending (m)G(t)(v): (m)C(t)(v) = (m)G(t)(v) x w(j), where w(j) is the chiral index. The quantitative structure-retention index relationship (QSRR) between the retention index (R(M)) of thin-layer chromatogram for the chiral organic acids and (m)C(t)(v) was studied by multivariate statistical regression. By leaps-and-bounds regression analysis, the best four-parameter QSRR model was set up, and the traditional correlation coefficient (R2) and the cross-validation correlation coefficient (Q2) of leave-one-out (LOO) were 0.973 and 0.950, respectively. The results demonstrated that the model was highly reliable and had good predictive ability from the point of view of statistics. From the four parameters (0C(p)(v), 2C(p)(v), C(ch),(v), 5C(p)(v)) of the model, it is known that the dominant influence factors of the retention index were the molecular structure characteristics of two-dimensional and the space factors: the chiral characteristics, the flexibility and the puckered degree of molecules for the chiral organic acids. The results showed that the new parameter mC(t)(v) had good rationality and efficiency for the retention indices of the chiral organic acids. Therefore, an effective method was provided to predict the retention indices of the chiral organic acids.

Kounis syndrome due to antibiotics: A global overview from pharmacovigilance databases.

PubMed

Renda, Francesca; Marotta, Elena; Landoni, Giovanni; Belletti, Alessandro; Cuconato, Virginia; Pani, Luca

2016-12-01

Kounis syndrome (KS) is characterized by concurrent presence of anaphylactic and cardiac components. Available evidence suggests that antibiotics are frequently associated to KS. We therefore analyzed KS cases associated with antibiotics use from the two largest pharmacovigilance databases. Two pharmacovigilance databases, EudraVigilance and VigiLyze, were searched for cases reporting the adverse reaction "Kounis Syndrome" with antibiotics as suspected active substance. We analyzed the period from December 1st, 2001 to February 16th, 2016. For the most reported active substance, proportional reporting ratio (PRR) was calculated. A total of 10 cases of KS associated with antibiotic use were retrieved from EudraVigilance database. Mean patients' age was 58.2years and 70% were male. The most frequently reported suspected antibiotic was the combination amoxicillin/clavulanic acid (four cases). VigiLyze database reported 13 KS cases associated to antibiotics. Mean age was 56years and 61% of patients were male. The most frequently reported antibiotic was again the combination amoxicillin/clavulanic acid (five cases). Seven duplicate cases were identified, leaving a total of 16 cases of KS, with six of them associated to amoxicillin/clavulanic acid use. The PRR value for amoxicillin/clavulanic acid against other kinds of antibiotics was 2.62 considering EudraVigilance data and 1.61 considering VigiLyze data. This analysis provided a complete picture of the cases of KS associated with antibiotic use and identified a possible association between amoxicillin/clavulanic acid and KS. Since the number of cases is low, especially considering its wide use, further analyses are needed to confirm the association. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The Better Mousetrap...Can Be Built by Engineers.

ERIC Educational Resources Information Center

McBride, Matthew

2003-01-01

Describes the growth of the INSPEC database developed by the Institution of Electrical Engineers. Highlights include an historical background of its growth from "Science Abstracts"; production methods, including computerization; indexing, including controlled (thesaurus-based), uncontrolled, chemical, and numerical indexing; and the…

Der Zitier-Index (Science-Citation-Index): Eine Datenbank fur das Ermitteln von neuen Ideen und Konzepten (The Science Citation Index: A Database for the Discovery of New Ideas and Concepts).

ERIC Educational Resources Information Center

Simon, Hans-Reiner; Thormann, K.-D.

This report discusses the use of the Science Citation Index produced by the Institute for Scientific Information (ISI) as a given "expert system" in the experimental study of different search levels. The inquiry has two objectives: (1) to test whether a "traditional" information system will also produce the rudiments of a…

Addressing the Heterogeneity of Subject Indexing in the ADS Databases

NASA Astrophysics Data System (ADS)

Dubin, David S.

A drawback of the current document representation scheme in the ADS abstract service is its heterogeneous subject indexing. Several related but inconsistent indexing languages are represented in ADS. A method of reconciling some indexing inconsistencies is described. Using lexical similarity alone, one out of six ADS descriptors can be automatically mapped to some other descriptor. Analysis of postings data can direct administrators to those mergings it is most important to check for errors.

[Public scientific knowledge distribution in health information, communication and information technology indexed in MEDLINE and LILACS databases].

PubMed

Packer, Abel Laerte; Tardelli, Adalberto Otranto; Castro, Regina Célia Figueiredo

2007-01-01

This study explores the distribution of international, regional and national scientific output in health information and communication, indexed in the MEDLINE and LILACS databases, between 1996 and 2005. A selection of articles was based on the hierarchical structure of Information Science in MeSH vocabulary. Four specific domains were determined: health information, medical informatics, scientific communications on healthcare and healthcare communications. The variables analyzed were: most-covered subjects and journals, author affiliation and publication countries and languages, in both databases. The Information Science category is represented in nearly 5% of MEDLINE and LILACS articles. The four domains under analysis showed a relative annual increase in MEDLINE. The Medical Informatics domain showed the highest number of records in MEDLINE, representing about half of all indexed articles. The importance of Information Science as a whole is more visible in publications from developed countries and the findings indicate the predominance of the United States, with significant growth in scientific output from China and South Korea and, to a lesser extent, Brazil.

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.

PubMed

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie; Zhang, Gong

2018-01-04

Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comparison of gene expression and fatty acid profiles in concentrate and forage finished beef.

PubMed

Buchanan, J W; Garmyn, A J; Hilton, G G; VanOverbeke, D L; Duan, Q; Beitz, D C; Mateescu, R G

2013-01-01

Fatty acid profiles and intramuscular expression of genes involved in fatty acid metabolism were characterized in concentrate- (CO) and forage- (FO) based finishing systems. Intramuscular samples from the adductor were taken at slaughter from 99 heifers finished on a CO diet and 58 heifers finished on a FO diet. Strip loins were obtained at fabrication to evaluate fatty acid profiles of LM muscle for all 157 heifers by using gas chromatography fatty acid methyl ester analysis. Composition was analyzed for differences by using the General Linear Model (GLM) procedure in SAS. Differences in fatty acid profile included a greater atherogenic index, greater percentage total MUFA, decreased omega-3 to omega-6 ratio, decreased percentage total PUFA, and decreased percentage omega-3 fatty acids in CO- compared with FO-finished heifers (P<0.05). Fatty acid profiles from intramuscular samples were ranked by the atherogenic index, and 20 heifers with either a high (HAI; n=10) or low (LAI; n=10) atherogenic index were selected for gene expression analysis using real-time PCR (RT-PCR). Gene expression data for the 20 individuals were analyzed as a 2 by 2 factorial arrangement of treatments using the GLM procedure in SAS. There was no significant diet × atherogenic index interaction identified for any gene (P>0.05). Upregulation was observed for PPARγ, fatty acid synthase (FASN), and fatty acid binding protein 4 (FABP4) in FO-finished compared with CO-finished heifers in both atherogenic index categories (P<0.05). Upregulation of diglyceride acyl transferase 2 (DGAT2) was observed in FO-finished heifers with a HAI (P<0.05). Expression of steroyl Co-A desaturase (SCD) was upregulated in CO-finished heifers with a LAI, and downregulated in FO-finished heifers with a HAI (P<0.05). Expression of adiponectin (ADIPOQ) was significantly downregulated in CO-finished heifers with a HAI compared with all other categories (P<0.05). The genes identified in this study which exhibit differential regulation in response to diet or in animals with extreme fatty acid profiles may provide genetic markers for selecting desirable fatty acid profiles in future selection programs.

Image query and indexing for digital x rays

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Thoma, George R.

1998-12-01

The web-based medical information retrieval system (WebMIRS) allows interned access to databases containing 17,000 digitized x-ray spine images and associated text data from National Health and Nutrition Examination Surveys (NHANES). WebMIRS allows SQL query of the text, and viewing of the returned text records and images using a standard browser. We are now working (1) to determine utility of data directly derived from the images in our databases, and (2) to investigate the feasibility of computer-assisted or automated indexing of the images to support image retrieval of images of interest to biomedical researchers in the field of osteoarthritis. To build an initial database based on image data, we are manually segmenting a subset of the vertebrae, using techniques from vertebral morphometry. From this, we will derive and add to the database vertebral features. This image-derived data will enhance the user's data access capability by enabling the creation of combined SQL/image-content queries.

Designing a multi-petabyte database for LSST

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

Becla, J; Hanushevsky, A

2005-12-21

The 3.2 giga-pixel LSST camera will produce over half a petabyte of raw images every month. This data needs to be reduced in under a minute to produce real-time transient alerts, and then cataloged and indexed to allow efficient access and simplify further analysis. The indexed catalogs alone are expected to grow at a speed of about 600 terabytes per year. The sheer volume of data, the real-time transient alerting requirements of the LSST, and its spatio-temporal aspects require cutting-edge techniques to build an efficient data access system at reasonable cost. As currently envisioned, the system will rely on amore » database for catalogs and metadata. Several database systems are being evaluated to understand how they will scale and perform at these data volumes in anticipated LSST access patterns. This paper describes the LSST requirements, the challenges they impose, the data access philosophy, and the database architecture that is expected to be adopted in order to meet the data challenges.« less

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes

PubMed Central

Rigden, Daniel J

2017-01-01

Abstract This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR. As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein–protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as ‘breakthrough’ contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the ‘golden set’ of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/. PMID:28053160

Significance of urinary hippuric acid determination as an index of toluene exposure

PubMed Central

Ikeda, Masayuki; Ohtsuji, Hatsue

1969-01-01

Ikeda, Masayuki, and Ohtsuji, Hatsue (1969).Brit. J. industr. Med.,26, 244-246. Significance of urinary hippuric acid determination as an index of toluene exposure. Urine samples from 118 male workers in photogravure printing factories were analysed for hippuric acid. The urinary levels of hippuric acid were proportional to the environmental concentrations of toluene, although within wide variations. The urinary concentration of hippuric acid corresponding to 200 p.p.m. of toluene was 3·5 g./litre (specific gravity 1·016) or 4·3 g./g. creatinine. PMID:5794951

Mapping the literature of nurse practitioners.

PubMed

Shams, Marie-Lise Antoun

2006-04-01

This study was designed to identify core journals for the nurse practitioner specialty and to determine the extent of their indexing in bibliographic databases. As part of a larger project for mapping the literature of nursing, this study followed a common methodology based on citation analysis. Four journals designated by nurse practitioners as sources for their practice information were selected. All cited references were analyzed to determine format types and publication years. Bradford's Law of Scattering was applied to identify core journals. Nine bibliographic databases were searched to estimate the index coverage of the core titles. The findings indicate that nurse practitioners rely primarily on journals (72.0%) followed by books (20.4%) for their professional knowledge. The majority of the identified core journals belong to non-nursing disciplines. This is reflected in the indexing coverage results: PubMed/MEDLINE more comprehensively indexes the core titles than CINAHL does. Nurse practitioners, as primary care providers, consult medical as well as nursing sources for their information. The implications of the citation analysis findings are significant for collection development librarians and indexing services.

DBGC: A Database of Human Gastric Cancer

PubMed Central

Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

2015-01-01

The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do PMID:26566288

DEFINING THE CHEMICAL SPACE OF PUBLIC GENOMIC DATA (S)

EPA Science Inventory

The current project aims to chemically index the genomics content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. By defining the chemical space of public genomic data, it is possibl...

The rate of growth in scientific publication and the decline in coverage provided by Science Citation Index.

PubMed

Larsen, Peder Olesen; von Ins, Markus

2010-09-01

The growth rate of scientific publication has been studied from 1907 to 2007 using available data from a number of literature databases, including Science Citation Index (SCI) and Social Sciences Citation Index (SSCI). Traditional scientific publishing, that is publication in peer-reviewed journals, is still increasing although there are big differences between fields. There are no indications that the growth rate has decreased in the last 50 years. At the same time publication using new channels, for example conference proceedings, open archives and home pages, is growing fast. The growth rate for SCI up to 2007 is smaller than for comparable databases. This means that SCI was covering a decreasing part of the traditional scientific literature. There are also clear indications that the coverage by SCI is especially low in some of the scientific areas with the highest growth rate, including computer science and engineering sciences. The role of conference proceedings, open access archives and publications published on the net is increasing, especially in scientific fields with high growth rates, but this has only partially been reflected in the databases. The new publication channels challenge the use of the big databases in measurements of scientific productivity or output and of the growth rate of science. Because of the declining coverage and this challenge it is problematic that SCI has been used and is used as the dominant source for science indicators based on publication and citation numbers. The limited data available for social sciences show that the growth rate in SSCI was remarkably low and indicate that the coverage by SSCI was declining over time. National Science Indicators from Thomson Reuters is based solely on SCI, SSCI and Arts and Humanities Citation Index (AHCI). Therefore the declining coverage of the citation databases problematizes the use of this source.

A Comparison of Global Indexing Schemes to Facilitate Earth Science Data Management

NASA Astrophysics Data System (ADS)

Griessbaum, N.; Frew, J.; Rilee, M. L.; Kuo, K. S.

2017-12-01

Recent advances in database technology have led to systems optimized for managing petabyte-scale multidimensional arrays. These array databases are a good fit for subsets of the Earth's surface that can be projected into a rectangular coordinate system with acceptable geometric fidelity. However, for global analyses, array databases must address the same distortions and discontinuities that apply to map projections in general. The array database SciDB supports enormous databases spread across thousands of computing nodes. Additionally, the following SciDB characteristics are particularly germane to the coordinate system problem: SciDB efficiently stores and manipulates sparse (i.e. mostly empty) arrays. SciDB arrays have 64-bit indexes. SciDB supports user-defined data types, functions, and operators. We have implemented two geospatial indexing schemes in SciDB. The simplest uses two array dimensions to represent longitude and latitude. For representation as 64-bit integers, the coordinates are multiplied by a scale factor large enough to yield an appropriate Earth surface resolution (e.g., a scale factor of 100,000 yields a resolution of approximately 1m at the equator). Aside from the longitudinal discontinuity, the principal disadvantage of this scheme is its fixed scale factor. The second scheme uses a single array dimension to represent the bit-codes for locations in a hierarchical triangular mesh (HTM) coordinate system. A HTM maps the Earth's surface onto an octahedron, and then recursively subdivides each triangular face to the desired resolution. Earth surface locations are represented as the concatenation of an octahedron face code and a quadtree code within the face. Unlike our integerized lat-lon scheme, the HTM allow for objects of different size (e.g., pixels with differing resolutions) to be represented in the same indexing scheme. We present an evaluation of the relative utility of these two schemes for managing and analyzing MODIS swath data.

The rate of growth in scientific publication and the decline in coverage provided by Science Citation Index

PubMed Central

von Ins, Markus

2010-01-01

The growth rate of scientific publication has been studied from 1907 to 2007 using available data from a number of literature databases, including Science Citation Index (SCI) and Social Sciences Citation Index (SSCI). Traditional scientific publishing, that is publication in peer-reviewed journals, is still increasing although there are big differences between fields. There are no indications that the growth rate has decreased in the last 50 years. At the same time publication using new channels, for example conference proceedings, open archives and home pages, is growing fast. The growth rate for SCI up to 2007 is smaller than for comparable databases. This means that SCI was covering a decreasing part of the traditional scientific literature. There are also clear indications that the coverage by SCI is especially low in some of the scientific areas with the highest growth rate, including computer science and engineering sciences. The role of conference proceedings, open access archives and publications published on the net is increasing, especially in scientific fields with high growth rates, but this has only partially been reflected in the databases. The new publication channels challenge the use of the big databases in measurements of scientific productivity or output and of the growth rate of science. Because of the declining coverage and this challenge it is problematic that SCI has been used and is used as the dominant source for science indicators based on publication and citation numbers. The limited data available for social sciences show that the growth rate in SSCI was remarkably low and indicate that the coverage by SSCI was declining over time. National Science Indicators from Thomson Reuters is based solely on SCI, SSCI and Arts and Humanities Citation Index (AHCI). Therefore the declining coverage of the citation databases problematizes the use of this source. PMID:20700371

Biochemical and dietary factors of uric acid stone formation.

PubMed

Trinchieri, Alberto; Montanari, Emanuele

2018-04-01

The aim of this study was to compare the clinical characteristics of "pure" uric acid renal stone formers (UA-RSFs) with that of mixed uric acid/calcium oxalate stone formers (UC-RSFs) and to identify which urinary and dietary risk factors predispose to their formation. A total of 136 UA-RSFs and 115 UC-RSFs were extracted from our database of renal stone formers. A control group of 60 subjects without history of renal stones was considered for comparison. Data from serum chemistries, 24-h urine collections and 24-h dietary recalls were considered. UA-RSFs had a significantly (p = 0.001) higher body mass index (26.3 ± 3.6 kg/m 2 ) than UC-RSFs, whereas body mass index of UA-RSFs was higher but not significantly than in controls (24.6 ± 4.7) (p = 0.108). The mean urinary pH was significantly lower in UA-RSFs (5.57 ± 0.58) and UC-RSFs (5.71 ± 0.56) compared with controls (5.83 ± 0.29) (p = 0.007). No difference of daily urinary uric acid excretion was observed in the three groups (p = 0.902). Daily urinary calcium excretion was significantly (p = 0.018) higher in UC-RSFs (224 ± 149 mg/day) than UA-RSFs (179 ± 115) whereas no significant difference was observed with controls (181 ± 89). UA-RSFs tend to have a lower uric acid fractional excretion (0.083 ± 0.045% vs 0.107+/-0.165; p = 0.120) and had significantly higher serum uric acid (5.33 ± 1.66 vs 4.78 ± 1.44 mg/dl; p = 0.007) than UC-RSFs. The mean energy, carbohydrate and vitamin C intakes were higher in UA-SFs (1987 ± 683 kcal, 272 ± 91 g, 112 ± 72 mg) and UC-SFs (1836 ± 74 kcal, 265 ± 117, 140 ± 118) with respect to controls (1474 ± 601, 188 ± 84, 76 ± 53) (p = 0.000). UA-RSFs should be differentiated from UC-RSFs as they present lower urinary pH, lower uric acid fractional excretion and higher serum uric acid. On the contrary, patients with UC-RSFs show urinary risk factors more similar to those for calcium oxalate stones. The dietary approach in patients forming uric acid stones should be reconsidered with more attention to the quantity and quality of carbohydrate intake.

Research on keyword retrieval method of HBase database based on index structure

NASA Astrophysics Data System (ADS)

Gong, Pijin; Lv, Congmin; Gong, Yongsheng; Ma, Haozhi; Sun, Yang; Wang, Lu

2017-10-01

With the rapid development of manned spaceflight engineering, the scientific experimental data in space application system is increasing rapidly. How to efficiently query the specific data in the mass data volume has become a problem. In this paper, a method of retrieving the object data based on the object attribute as the keyword is proposed. The HBase database is used to store the object data and object attributes, and the secondary index is constructed. The research shows that this method is a good way to retrieve specified data based on object attributes.

Salmon diet in patients with active ulcerative colitis reduced the simple clinical colitis activity index and increased the anti-inflammatory fatty acid index--a pilot study.

PubMed

Grimstad, Tore; Berge, Rolf K; Bohov, Pavol; Skorve, Jon; Gøransson, Lasse; Omdal, Roald; Aasprong, Ole G; Haugen, Margaretha; Meltzer, Helle M; Hausken, Trygve

2011-02-01

Data concerning the anti-inflammatory effect of dietary n-3 polyunsaturated fatty acids (PUFAs) in patients with ulcerative colitis (UC) are inconsistent. Salmon fillet contains n-3 PUFAs and bioactive peptides that may improve its effects compared to fish oil alone. We assessed the efficacy of a salmon-rich diet in patients with mild ulcerative colitis. An 8-week intervention pilot study was designed to assess the effects of 600 grams Atlantic salmon consumption weekly in 12 UC patients. Simple clinical colitis activity index (SCCAI), a dietary questionnaire, sigmoidoscopy, selected serum inflammatory markers, fecal calprotectin, and plasma and rectal biopsy fatty acid profiles were assessed before and after intervention. The levels of C20:4n-6 arachidonic acid in biopsies after dietary intervention were correlated with histology and endoscopy scores. The concentrations of n-3 PUFAs, C20:5n-3 eicosapentaenoic acid, C22:6n-3 docosahexaenoic acid, and the n-3/n-6 ratio increased in plasma and rectal biopsies. The anti-inflammatory fatty acid index (AIFAI) increased both in biopsies and plasma accompanied with a significantly reduced SCCAI. Based on evidence of SCCAI and AIFAI and a tendency of decreased levels of CRP and homocysteine, intake of Atlantic salmon may have beneficial effects on disease activity in patients with mild ulcerative colitis.

Proximate composition, amino acid and fatty acid composition of fish maws.

PubMed

Wen, Jing; Zeng, Ling; Xu, Youhou; Sun, Yulin; Chen, Ziming; Fan, Sigang

2016-01-01

Fish maws are commonly recommended and consumed in Asia over many centuries because it is believed to have some traditional medical properties. This study highlights and provides new information on the proximate composition, amino acid and fatty acid composition of fish maws of Cynoscion acoupa, Congresox talabonoides and Sciades proops. The results indicated that fish maws were excellent protein sources and low in fat content. The proteins in fish maws were rich in functional amino acids (FAAs) and the ratio of FAAs and total amino acids in fish maws ranged from 0.68 to 0.69. Among species, croaker C. acoupa contained the most polyunsaturated fatty acids, arachidonic acid, docosahexaenoic acid and eicosapntemacnioc acid, showing the lowest value of index of atherogenicity and index of thrombogenicity, showing the highest value of hypocholesterolemic/hypercholesterolemic ratio, which is the most desirable.

Human Retroviruses and AIDS. A compilation and analysis of nucleic acid and amino acid sequences: I--II; III--V

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

Myers, G.; Korber, B.; Wain-Hobson, S.

1993-12-31

This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (I) HIV and SIV Nucleotide Sequences; (II) Amino Acid Sequences; (III) Analyses; (IV) Related Sequences; and (V) Database Communications. Information within all the parts is updated at least twice in each year, which accounts for the modes of binding and pagination in the compendium.

Fatty acid and cholesterol profiles, hypocholesterolemic, atherogenic, and thrombogenic indices of broiler meat in the retail market.

PubMed

Attia, Youssef A; Al-Harthi, Mohammed A; Korish, Mohamed A; Shiboob, Mohamed M

2017-02-16

Broiler meat is an essential source of food due to its favourable effects on human health derived from its protein, fats, minerals, vitamins and its bioactive components. A total of 90 carcasses were collected from the retail market in Jeddah city, Saudi Arabia during April, May and June 2014 to determine the effects of meat type (frozen vs. fresh) and sources within fresh types (A, B, C) vs. frozen types (D, E and F) on their fatty acid profiles, cholesterol, their hypocholesterolemic, atherogenic and thrombogenic indices, and on their antioxidants' status. The sources of meat had a significant effect on the hypocholesterolemic and atherogenic indices, with the D source of fresh meat having the best indices. Total saturated fatty acids (SFA), unsaturated fatty acids (UFA), the UFA/SAF ratio, and the monounsaturated (MUFA), Omega-6 and Omega-7 fatty acids were significantly affected by the source of meat. The results revealed that the D source of fresh meat showed favourable fatty acid profiles with significant health benefits for human. Correlation analyses showed a significant negative relationship between the SFA and hypocholesterolemic indices, and significant positive relationships with the atherogenic index, the thrombotgenic index and the total antioxidant capacity. In addition, the relationship between UFA and the hypocholesterolemic index was strongly significantly positive, but was highly negative between the atherogenic and thrombotic indices. The correlations between omega-6 and total cholesterol and the atherogenic index was moderately negative, but was moderately positive with the hypocholesterolemic index. Fatty acids profiles and the hypocholesterolemic and atherogenic indices of broiler meat in the retail market in Jeddah city, Saudi Arabia during April-May-June showed significant differences, with the potential for favourable fatty acids to be boosted. Such variability indicates the needs for a feeding strategy to enhance the favourable fatty acids that may positively impact the health of the consumer, lowering the risk of hypercholesterolemia, atherosclerosis, and thrombogenesis although further studies are needed.

Vision science literature of Nepal in the database "Web of Science".

PubMed

Risal, S; Prasad, H N

2012-01-01

Vision Science is considered to be a quite developed discipline in Nepal, with much research currently in progress. Though the results of these endeavors are published in scientific journals, formal citation analyses have not been performed on works contributed by Nepalese vision scientists. To study Nepal's contribution to vision science literature in the database "Web of Science". The primary data source of this paper was Web of Science, a citation database of Thomas Reuters. All bibliometric analyses were performed with the help of Web of Science analysis service. In the current database of vision science literature, Nepalese authors contributed 112 publications to Web of Science, 95 of which were original articles. Pokharel GP had the highest number of citations among contributing authors of Nepal. Hennig A contributed the highest number of article as a first author. The Nepal Eye Hospital contributed the highest number of articles as an institution to the field of Vision Science. Currently, only two journals from Nepal including Journal of Nepal Medical Association (JAMA) are indexed in the Web of Science database (Sieving, 2012). To evaluate the total productivity of vision science literature from Nepal, total publication counts from national journals and articles indexed in other databases such as PubMed and Scopus must also be considered. © NEPjOPH.

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)

DSSTox EPA Integrated Risk Information System Structure-Index Locator File: SDF File and Documentation

EPA Science Inventory

EPA's Integrated Risk Information System (IRIS) database was developed and is maintained by EPA's Office of Research and Developement, National Center for Environmental Assessment. IRIS is a database of human health effects that may result from exposure to various substances fou...

Impact of Biological Feedback and Incentives on Blood Fatty Acid Concentrations, Including Omega-3 Index, in an Employer-Based Wellness Program.

PubMed

McBurney, Michael I; Bird, Julia K

2017-08-05

Eicosapentaenoic acid (EPA, C20:5n-3) and docosahexaenoic acid (DHA, C22:6n-3) are important fatty acids for the retina and brain. More than 95% of Americans have suboptimal EPA + DHA blood concentrations. This cross-sectional employer-based study assessed whole blood fatty acid levels of volunteers participating in an onsite wellness biometric screening program and was designed to determine if an incentive, a $5 coupon for a 90-day supply of fish oil supplement typically costing $18-30, stimulated incremental dietary behavior change relative to nutritional status assessment alone to increase EPA + DHA concentrations. Volunteers completed a dietary survey and finger stick blood samples were collected to be analyzed for fatty acid composition. In addition, 636 individuals participated in the initial onsite biometric screening. Three months later, and without prior knowledge, all employees were invited to a second screening. At the second screening, 198 employees volunteered for the first time and 149 employees had a second test (17.9%). At baseline, the average age ( n = 834) was 45 year and omega-3 index was 5.0% with 41% female. EPA + DHA concentration, i.e., omega-3 index, was significantly lower in men (4.8%) than women (5.2%), as were DHA and linoleic acid (LA) concentrations ( p < 0.05). Baseline omega-3 index was positively and linearly associated with omega-3 intake. Only 4% of volunteers had an omega-3 index >8% on initial screening. Among the 149 individuals with two measurements, omega-3 intake from supplements, but not food, increased significantly from 258 to 445 mg/d ( p < 0.01) at the second test as did the omega-3 index (+0.21, p < 0.02). In this employed population, only 1% redeemed a coupon for an omega-3 supplement.

Reference Clinical Database for Fixation Stability Metrics in Normal Subjects Measured with the MAIA Microperimeter.

PubMed

Morales, Marco U; Saker, Saker; Wilde, Craig; Pellizzari, Carlo; Pallikaris, Aristophanes; Notaroberto, Neil; Rubinstein, Martin; Rui, Chiara; Limoli, Paolo; Smolek, Michael K; Amoaku, Winfried M

2016-11-01

The purpose of this study was to establish a normal reference database for fixation stability measured with the bivariate contour ellipse area (BCEA) in the Macular Integrity Assessment (MAIA) microperimeter. Subjects were 358 healthy volunteers who had the MAIA examination. Fixation stability was assessed using two BCEA fixation indices (63% and 95% proportional values) and the percentage of fixation points within 1° and 2° from the fovea (P1 and P2). Statistical analysis was performed with linear regression and Pearson's product moment correlation coefficient. Average areas of 0.80 deg 2 (min = 0.03, max = 3.90, SD = 0.68) for the index BCEA@63% and 2.40 deg 2 (min = 0.20, max = 11.70, SD = 2.04) for the index BCEA@95% were found. The average values of P1 and P2 were 95% (min = 76, max = 100, SD = 5.31) and 99% (min = 91, max = 100, SD = 1.42), respectively. The Pearson's product moment test showed an almost perfect correlation index, r = 0.999, between BCEA@63% and BCEA@95%. Index P1 showed a very strong correlation with BCEA@63%, r = -0.924, as well as with BCEA@95%, r = -0.925. Index P2 demonstrated a slightly lower correlation with both BCEA@63% and BCEA@95%, r = -0.874 and -0.875, respectively. The single parameter of the BCEA@95% may be taken as accurately reporting fixation stability and serves as a reference database of normal subjects with a cutoff area of 2.40 ± 2.04 deg 2 in MAIA microperimeter. Fixation stability can be measured with different indices. This study originates reference fixation values for the MAIA using a single fixation index.

Search and Graph Database Technologies for Biomedical Semantic Indexing: Experimental Analysis.

PubMed

Segura Bedmar, Isabel; Martínez, Paloma; Carruana Martín, Adrián

2017-12-01

Biomedical semantic indexing is a very useful support tool for human curators in their efforts for indexing and cataloging the biomedical literature. The aim of this study was to describe a system to automatically assign Medical Subject Headings (MeSH) to biomedical articles from MEDLINE. Our approach relies on the assumption that similar documents should be classified by similar MeSH terms. Although previous work has already exploited the document similarity by using a k-nearest neighbors algorithm, we represent documents as document vectors by search engine indexing and then compute the similarity between documents using cosine similarity. Once the most similar documents for a given input document are retrieved, we rank their MeSH terms to choose the most suitable set for the input document. To do this, we define a scoring function that takes into account the frequency of the term into the set of retrieved documents and the similarity between the input document and each retrieved document. In addition, we implement guidelines proposed by human curators to annotate MEDLINE articles; in particular, the heuristic that says if 3 MeSH terms are proposed to classify an article and they share the same ancestor, they should be replaced by this ancestor. The representation of the MeSH thesaurus as a graph database allows us to employ graph search algorithms to quickly and easily capture hierarchical relationships such as the lowest common ancestor between terms. Our experiments show promising results with an F1 of 69% on the test dataset. To the best of our knowledge, this is the first work that combines search and graph database technologies for the task of biomedical semantic indexing. Due to its horizontal scalability, ElasticSearch becomes a real solution to index large collections of documents (such as the bibliographic database MEDLINE). Moreover, the use of graph search algorithms for accessing MeSH information could provide a support tool for cataloging MEDLINE abstracts in real time. ©Isabel Segura Bedmar, Paloma Martínez, Adrián Carruana Martín. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 01.12.2017.

25 Years of GenBank

MedlinePlus

... this page please turn Javascript on. Unique DNA database has helped advance scientific discoveries worldwide Since its origin 25 years ago, the database of nucleic acid sequences known as GenBank has ...

RPG: the Ribosomal Protein Gene database.

PubMed

Nakao, Akihiro; Yoshihama, Maki; Kenmochi, Naoya

2004-01-01

RPG (http://ribosome.miyazaki-med.ac.jp/) is a new database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms, including Drosophila melanogaster, Caenorhabditis elegans, Saccharo myces cerevisiae, Methanococcus jannaschii and Escherichia coli. Users can search the database by gene name and organism. Each record includes sequences (genomic, cDNA and amino acid sequences), intron/exon structures, genomic locations and information about orthologs. In addition, users can view and compare the gene structures of the above organisms and make multiple amino acid sequence alignments. RPG also provides information on small nucleolar RNAs (snoRNAs) that are encoded in the introns of RP genes.

RPG: the Ribosomal Protein Gene database

PubMed Central

Nakao, Akihiro; Yoshihama, Maki; Kenmochi, Naoya

2004-01-01

RPG (http://ribosome.miyazaki-med.ac.jp/) is a new database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms, including Drosophila melanogaster, Caenorhabditis elegans, Saccharo myces cerevisiae, Methanococcus jannaschii and Escherichia coli. Users can search the database by gene name and organism. Each record includes sequences (genomic, cDNA and amino acid sequences), intron/exon structures, genomic locations and information about orthologs. In addition, users can view and compare the gene structures of the above organisms and make multiple amino acid sequence alignments. RPG also provides information on small nucleolar RNAs (snoRNAs) that are encoded in the introns of RP genes. PMID:14681386

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.

PubMed

Chen, Peng; Li, Jinyan; Wong, Limsoon; Kuwahara, Hiroyuki; Huang, Jianhua Z; Gao, Xin

2013-08-01

Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K-nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state-of-the-art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx. Copyright © 2013 Wiley Periodicals, Inc.

Mapping the literature of maternal-child/gynecologic nursing.

PubMed

Jacobs, Susan Kaplan

2006-04-01

As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited in maternal-child/gynecologic nursing and the indexing services that access the cited journals. Three source journals were selected and subjected to a citation analysis of articles from 1996 to 1998. Journals were the most frequently cited format (74.1%), followed by books (19.7%), miscellaneous (4.2%), and government documents (1.9%). Bradford's Law of Scattering was applied to the results, ranking cited journal references in descending order. One-third of the citations were found in a core of 14 journal titles; one-third were dispersed among a middle zone of 100 titles; and the remaining third were scattered in a larger zone of 1,194 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by Science Citation Index and CINAHL. The core of journals cited in this nursing specialty revealed a large number of medical titles, thus, the biomedical databases provide the best access. The interdisciplinary nature of maternal-child/ gynecologic nursing topics dictates that social sciences databases are an important adjunct. The study results will assist librarians in collection development, provide end users with guidelines for selecting databases, and influence database producers to consider extending coverage to identified titles.

Mapping the literature of maternal-child/gynecologic nursing

PubMed Central

Jacobs, Susan Kaplan

2006-01-01

Objectives: As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited in maternal-child/gynecologic nursing and the indexing services that access the cited journals. Methods: Three source journals were selected and subjected to a citation analysis of articles from 1996 to 1998. Results: Journals were the most frequently cited format (74.1%), followed by books (19.7%), miscellaneous (4.2%), and government documents (1.9%). Bradford's Law of Scattering was applied to the results, ranking cited journal references in descending order. One-third of the citations were found in a core of 14 journal titles; one-third were dispersed among a middle zone of 100 titles; and the remaining third were scattered in a larger zone of 1,194 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by Science Citation Index and CINAHL. Conclusion: The core of journals cited in this nursing specialty revealed a large number of medical titles, thus, the biomedical databases provide the best access. The interdisciplinary nature of maternal-child/ gynecologic nursing topics dictates that social sciences databases are an important adjunct. The study results will assist librarians in collection development, provide end users with guidelines for selecting databases, and influence database producers to consider extending coverage to identified titles. PMID:16710464

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

Berra, P.B.; Chung, S.M.; Hachem, N.I.

This article presents techniques for managing a very large data/knowledge base to support multiple inference-mechanisms for logic programming. Because evaluation of goals can require accessing data from the extensional database, or EDB, in very general ways, one must often resort to indexing on all fields of the extensional database facts. This presents a formidable management problem in that the index data may be larger than the EDB itself. This problem becomes even more serious in this case of very large data/knowledge bases (hundreds of gigabytes), since considerably more hardware will be required to process and store the index data. Inmore » order to reduce the amount of index data considerably without losing generality, the authors form a surrogate file, which is a hashing transformation of the facts. Superimposed code words (SCW), concatenated code words (CCW), and transformed inverted lists (TIL) are possible structures for the surrogate file. since these transformations are quite regular and compact, the authors consider possible computer architecture for the processing of the surrogate file.« less

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

A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

PubMed

Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

2012-07-01

The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

FEMA Database Requirements Assessment and Resource Directory Model.

DTIC Science & Technology

1982-05-01

File (NRCM) -- WContains information on organizations that are information resources on virtually any subject. * NEW YORK TIMES ONLINE -- Full text...version of the New York Times. * Newsearch: The Daily Index (Newsearch) -- Daily indexing of the periodicals in Magazine Index, newspapers in National...a NEXIS -- Full text of all general and business news covered in a variety of news - papers, magazines and wire services. 0 Oceanic Abstracts

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

Alekhin, S.I.; Ezhela, V.V.; Filimonov, B.B.

We present an indexed guide to the literature experimental particle physics for the years 1988--1992. About 4,000 papers are indexed by Beam/Target/Momentum, Reaction Momentum (including the final state), Final State Particle, and Accelerator/Detector/Experiment. All indices are cross-referenced to the paper`s title and reference in the ID/Reference/Title Index. The information in this guide is also publicly available from a regularly updated computer database.

Invisible Authorship: Women's Names, Databases, and Technology.

ERIC Educational Resources Information Center

Tescione, Susan M.

Bibliographic databases act as search tools to locate relevant literature and information, but they also disseminate information about the works indexed in the records. Articles and authors that cannot be found cannot be cited, and the ability to disseminate data for that particular work is diminished. This study found no significant differences…

The Missing Link: Context Loss in Online Databases

ERIC Educational Resources Information Center

Mi, Jia; Nesta, Frederick

2005-01-01

Full-text databases do not allow for the complexity of the interaction of the human eye and brain with printed matter. As a result, both content and context may be lost. The authors propose additional indexing fields that would maintain the content and context of print in electronic formats.

Recent Developments in Cultural Heritage Image Databases: Directions for User-Centered Design.

ERIC Educational Resources Information Center

Stephenson, Christie

1999-01-01

Examines the Museum Educational Site Licensing (MESL) Project--a cooperative project between seven cultural heritage repositories and seven universities--as well as other developments of cultural heritage image databases for academic use. Reviews recent literature on image indexing and retrieval, interface design, and tool development, urging a…

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.…

The Efficacy of Multidimensional Constraint Keys in Database Query Performance

ERIC Educational Resources Information Center

Cardwell, Leslie K.

2012-01-01

This work is intended to introduce a database design method to resolve the two-dimensional complexities inherent in the relational data model and its resulting performance challenges through abstract multidimensional constructs. A multidimensional constraint is derived and utilized to implement an indexed Multidimensional Key (MK) to abstract a…

SLIMMER--A UNIX System-Based Information Retrieval System.

ERIC Educational Resources Information Center

Waldstein, Robert K.

1988-01-01

Describes an information retrieval system developed at Bell Laboratories to create and maintain a variety of different but interrelated databases, and to provide controlled access to these databases. The components discussed include the interfaces, indexing rules, display languages, response time, and updating procedures of the system. (6 notes…

Creating databases for biological information: an introduction.

PubMed

Stein, Lincoln

2013-06-01

The essence of bioinformatics is dealing with large quantities of information. Whether it be sequencing data, microarray data files, mass spectrometric data (e.g., fingerprints), the catalog of strains arising from an insertional mutagenesis project, or even large numbers of PDF files, there inevitably comes a time when the information can simply no longer be managed with files and directories. This is where databases come into play. This unit briefly reviews the characteristics of several database management systems, including flat file, indexed file, relational databases, and NoSQL databases. It compares their strengths and weaknesses and offers some general guidelines for selecting an appropriate database management system. Copyright 2013 by JohnWiley & Sons, Inc.

Starbase Data Tables: An ASCII Relational Database for Unix

NASA Astrophysics Data System (ADS)

Roll, John

2011-11-01

Database management is an increasingly important part of astronomical data analysis. Astronomers need easy and convenient ways of storing, editing, filtering, and retrieving data about data. Commercial databases do not provide good solutions for many of the everyday and informal types of database access astronomers need. The Starbase database system with simple data file formatting rules and command line data operators has been created to answer this need. The system includes a complete set of relational and set operators, fast search/index and sorting operators, and many formatting and I/O operators. Special features are included to enhance the usefulness of the database when manipulating astronomical data. The software runs under UNIX, MSDOS and IRAF.

Derivation of Pitzer Interaction Parameters for an Aqueous Species Pair of Sodium and Iron(II)-Citrate Complex

NASA Astrophysics Data System (ADS)

Jang, J. H.; Nemer, M.

2015-12-01

The U.S. DOE Waste Isolation Pilot Plant (WIPP) is a deep underground repository for the permanent disposal of transuranic (TRU) radioactive waste. The WIPP is located in the Permian Delaware Basin near Carlsbad, New Mexico, U.S.A. The TRU waste includes, but is not limited to, iron-based alloys and the complexing agent, citric acid. Iron is also present from the steel used in the waste containers. The objective of this analysis is to derive the Pitzer activity coefficients for the pair of Na+ and FeCit- complex to expand current WIPP thermodynamic database. An aqueous model for the dissolution of Fe(OH)2(s) in a Na3Cit solution was fitted to the experimentally measured solubility data. The aqueous model consists of several chemical reactions and related Pitzer interaction parameters. Specifically, Pitzer interaction parameters for the Na+ and FeCit- pair (β(0), β(1), and Cφ) plus the stability constant for species of FeCit- were fitted to the experimental data. Anoxic gloveboxes were used to keep the oxygen level low (<1 ppm) throughout the experiments due to redox sensitivity. EQ3NR, a computer program for geochemical aqueous speciation-solubility calculations, packaged in EQ3/6 v.8.0a, calculates the aqueous speciation and saturation index using an aqueous model addressed in EQ3/6's database. The saturation index indicates how far the system is from equilibrium with respect to the solid of interest. Thus, the smaller the sum of squared saturation indices that the aqueous model calculates for the given number of experiments, the more closely the model attributes equilibrium to each individual experiment with respect to the solid of interest. The calculation of aqueous speciation and saturation indices was repeated by adjusting stability constant of FeCit-, β(0), β(1), and Cφ in the database until the values are found that make the sum of squared saturation indices the smallest for the given number of experiments. Results will be presented at the time of conference.

Access to DNA and protein databases on the Internet.

PubMed

Harper, R

1994-02-01

During the past year, the number of biological databases that can be queried via Internet has dramatically increased. This increase has resulted from the introduction of networking tools, such as Gopher and WAIS, that make it easy for research workers to index databases and make them available for on-line browsing. Biocomputing in the nineties will see the advent of more client/server options for the solution of problems in bioinformatics.

Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

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

Myers, G.; Foley, B.; Korber, B.

1997-04-01

This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. While this publication could take the form of a review or sequence monograph, it is not so conceived.more » Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.« less

Bioavailability of Dietary Omega-3 Fatty Acids Added to a Variety of Sausages in Healthy Individuals

PubMed Central

Köhler, Anton; Heinrich, Johanna; von Schacky, Clemens

2017-01-01

A low Omega-3 Index (eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in erythrocytes) is associated with cardiac, cerebral, and other health issues. Intake of EPA and DHA, but not of alpha-linolenic acid (ALA), increases the Omega-3 Index. We investigated bioavailability, safety, palatability and tolerability of EPA and DHA in a novel source: a variety of sausages. We screened 96 healthy volunteers, and recruited 44 with an Omega-3 Index <5%. Participants were randomly assigned to receive a variety of sausages enriched with approximately 250 mg EPA and DHA per 80 g (n = 22) daily for 8 weeks, or matching placebo sausages (n = 22). All sausages contained approximately 250 mg ALA/80 g. In the verum group, the mean Omega-3 Index increased from 4.18 ± 0.54 to 5.72 ± 0.66% (p < 0.001), while it remained unchanged in the placebo group. While ALA levels increased only in the placebo group, DPA levels increased in both groups. Inter-individual variability in the response was large. The mean increase of the Omega-3 Index per intake of EPA and DHA we observed was higher than for other sources previously studied, indicating superior bioavailability. As increasing production of EPA and DHA is difficult, improvements of bioavailability can facilitate reaching the target range for the Omega-3 Index (8–11%). PMID:28629180

Bioavailability of Dietary Omega-3 Fatty Acids Added to a Variety of Sausages in Healthy Individuals.

PubMed

Köhler, Anton; Heinrich, Johanna; von Schacky, Clemens

2017-06-19

A low Omega-3 Index (eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in erythrocytes) is associated with cardiac, cerebral, and other health issues. Intake of EPA and DHA, but not of alpha-linolenic acid (ALA), increases the Omega-3 Index. We investigated bioavailability, safety, palatability and tolerability of EPA and DHA in a novel source: a variety of sausages. We screened 96 healthy volunteers, and recruited 44 with an Omega-3 Index <5%. Participants were randomly assigned to receive a variety of sausages enriched with approximately 250 mg EPA and DHA per 80 g ( n = 22) daily for 8 weeks, or matching placebo sausages ( n = 22). All sausages contained approximately 250 mg ALA/80 g. In the verum group, the mean Omega-3 Index increased from 4.18 ± 0.54 to 5.72 ± 0.66% ( p < 0.001), while it remained unchanged in the placebo group. While ALA levels increased only in the placebo group, DPA levels increased in both groups. Inter-individual variability in the response was large. The mean increase of the Omega-3 Index per intake of EPA and DHA we observed was higher than for other sources previously studied, indicating superior bioavailability. As increasing production of EPA and DHA is difficult, improvements of bioavailability can facilitate reaching the target range for the Omega-3 Index (8-11%).

ONLINE Interviews Delores Meglio of Information Access Company.

ERIC Educational Resources Information Center

Pemberton, Jeffery K.

1987-01-01

The vice president of a computerized information center discusses her career history, the development of information services and the database industry, current information technologies and the role of artificial intelligence, characteristics of indexers and abstractors employed, the kind of training needed by abstractors and indexers, and…

Newspapers and Electronic Databases: Present Technology.

ERIC Educational Resources Information Center

Newcombe, Barbara; Trivedi, Harish

1984-01-01

Discusses technology used to preserve, control, index, and retrieve information in newspapers, highlighting ways to record analyses of news stories, storage/indexing systems based on computers, information as salable commodity, preparation of news for electronic storage, answering in-house queries, questions of copyright and invasion of privacy,…

Google Scholar Search Performance: Comparative Recall and Precision

ERIC Educational Resources Information Center

Walters, William H.

2009-01-01

This paper presents a comparative evaluation of Google Scholar and 11 other bibliographic databases (Academic Search Elite, AgeLine, ArticleFirst, EconLit, GEOBASE, MEDLINE, PAIS International, POPLINE, Social Sciences Abstracts, Social Sciences Citation Index, and SocINDEX), focusing on search performance within the multidisciplinary field of…

Toward a public toxicogenomics capability for supporting predictive toxicology: survey of current resources and chemical indexing of experiments in GEO and ArrayExpress.

PubMed

Williams-Devane, ClarLynda R; Wolf, Maritja A; Richard, Ann M

2009-06-01

A publicly available toxicogenomics capability for supporting predictive toxicology and meta-analysis depends on availability of gene expression data for chemical treatment scenarios, the ability to locate and aggregate such information by chemical, and broad data coverage within chemical, genomics, and toxicological information domains. This capability also depends on common genomics standards, protocol description, and functional linkages of diverse public Internet data resources. We present a survey of public genomics resources from these vantage points and conclude that, despite progress in many areas, the current state of the majority of public microarray databases is inadequate for supporting these objectives, particularly with regard to chemical indexing. To begin to address these inadequacies, we focus chemical annotation efforts on experimental content contained in the two primary public genomic resources: ArrayExpress and Gene Expression Omnibus. Automated scripts and extensive manual review were employed to transform free-text experiment descriptions into a standardized, chemically indexed inventory of experiments in both resources. These files, which include top-level summary annotations, allow for identification of current chemical-associated experimental content, as well as chemical-exposure-related (or "Treatment") content of greatest potential value to toxicogenomics investigation. With these chemical-index files, it is possible for the first time to assess the breadth and overlap of chemical study space represented in these databases, and to begin to assess the sufficiency of data with shared protocols for chemical similarity inferences. Chemical indexing of public genomics databases is a first important step toward integrating chemical, toxicological and genomics data into predictive toxicology.

A kinetics database and scripts for PHREEQC

NASA Astrophysics Data System (ADS)

Hu, B.; Zhang, Y.; Teng, Y.; Zhu, C.

2017-12-01

Kinetics of geochemical reactions has been increasingly used in numerical models to simulate coupled flow, mass transport, and chemical reactions. However, the kinetic data are scattered in the literature. To assemble a kinetic dataset for a modeling project is an intimidating task for most. In order to facilitate the application of kinetics in geochemical modeling, we assembled kinetics parameters into a database for the geochemical simulation program, PHREEQC (version 3.0). Kinetics data were collected from the literature. Our database includes kinetic data for over 70 minerals. The rate equations are also programmed into scripts with the Basic language. Using the new kinetic database, we simulated reaction path during the albite dissolution process using various rate equations in the literature. The simulation results with three different rate equations gave difference reaction paths at different time scale. Another application involves a coupled reactive transport model simulating the advancement of an acid plume in an acid mine drainage site associated with Bear Creek Uranium tailings pond. Geochemical reactions including calcite, gypsum, and illite were simulated with PHREEQC using the new kinetic database. The simulation results successfully demonstrated the utility of new kinetic database.

The effect of propionic acid and valeric acid on the cell cycle in root meristems of Pisum sativum

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

Tramontano, W.A.; Yang, Shauyu; Delillo, A.R.

1990-01-01

Propionic acid and valeric acid at 1mM reduced the mitotic index of root meristem cells of Pisum sativum to < 1% after 12 hr in aerated White's medium. This effect varied with different acid concentrations. After a 12 hr exposure to either acid, seedlings transferred to fresh medium without either acid, resumed their normal mitotic index after 12 hr, with a burst of mitosis 8 hr post-transfer. Exposure of root meristem cells to either acid also inhibited ({sup 3}H)-TdR incorporation. Neither acid significantly altered the distribution of meristematic cells in G1 and G2 after 12 hr. The incorporation of ({supmore » 3}H) - uridine was also unaltered by the addition of either acid. This information suggests that propionic acid and valeric acid, limit progression through the cell cycle by inhibiting DNA synthesis and arresting cells in G1 and G2. These results were consistent with previous data which utilized butyric acid.« less

From Paper to Practice; Indexing Systems and Ethical Standards.

PubMed

Astaneh, Behrooz; Masoumi, Sarah

2018-04-01

Currently one of the main goals of editors is to attain a higher visibility for their journals. On the other hand, authors strive to publish their research in journals indexed in eminent databases such as Scopus, Thompson Reuters' Web of Science (ISI), Medline, etc. Therefore, clarifying the standards of indexing is of great importance. One of the most important issues in publication is the ethical considerations, which are mainly described by organizations, such as the International Committee of Medical Journal Editors and the Committee on Publication Ethics. In this study, we examined the ethical requirements of high impact databases for indexing journals to investigate whether they mention or mandate journals to adhere to publication ethics. We found that only Scopus mandated journals to state clear ethical policies on their website as a criterion for being indexed while Medline and Directory of Open Access Journals advised journals to adhere to ethics, not mandated, and Web of Science (ISI) and PubMed Central made no mention of ethics as a required criterion for indexing. Based on this short review, there seems to be a gap between the requirements of indexing systems and international guidelines for publication ethics. Currently, most indexing systems have only partially recommended journals to consider ethical issues. In such an atmosphere, we cannot expect journals or as a result, authors to professionally, completely, and whole heartedly implement ethical guidelines as a mandatory rule in their journals and research, when the indexing systems that most editors want to be indexed in and most authors want to be cited in do not mandate such guidelines.

[Construction and application of special analysis database of geoherbs based on 3S technology].

PubMed

Guo, Lan-ping; Huang, Lu-qi; Lv, Dong-mei; Shao, Ai-juan; Wang, Jian

2007-09-01

In this paper,the structures, data sources, data codes of "the spacial analysis database of geoherbs" based 3S technology are introduced, and the essential functions of the database, such as data management, remote sensing, spacial interpolation, spacial statistics, spacial analysis and developing are described. At last, two examples for database usage are given, the one is classification and calculating of NDVI index of remote sensing image in geoherbal area of Atractylodes lancea, the other one is adaptation analysis of A. lancea. These indicate that "the spacial analysis database of geoherbs" has bright prospect in spacial analysis of geoherbs.

Creating databases for biological information: an introduction.

PubMed

Stein, Lincoln

2002-08-01

The essence of bioinformatics is dealing with large quantities of information. Whether it be sequencing data, microarray data files, mass spectrometric data (e.g., fingerprints), the catalog of strains arising from an insertional mutagenesis project, or even large numbers of PDF files, there inevitably comes a time when the information can simply no longer be managed with files and directories. This is where databases come into play. This unit briefly reviews the characteristics of several database management systems, including flat file, indexed file, and relational databases, as well as ACeDB. It compares their strengths and weaknesses and offers some general guidelines for selecting an appropriate database management system.

A generic method for improving the spatial interoperability of medical and ecological databases.

PubMed

Ghenassia, A; Beuscart, J B; Ficheur, G; Occelli, F; Babykina, E; Chazard, E; Genin, M

2017-10-03

The availability of big data in healthcare and the intensive development of data reuse and georeferencing have opened up perspectives for health spatial analysis. However, fine-scale spatial studies of ecological and medical databases are limited by the change of support problem and thus a lack of spatial unit interoperability. The use of spatial disaggregation methods to solve this problem introduces errors into the spatial estimations. Here, we present a generic, two-step method for merging medical and ecological databases that avoids the use of spatial disaggregation methods, while maximizing the spatial resolution. Firstly, a mapping table is created after one or more transition matrices have been defined. The latter link the spatial units of the original databases to the spatial units of the final database. Secondly, the mapping table is validated by (1) comparing the covariates contained in the two original databases, and (2) checking the spatial validity with a spatial continuity criterion and a spatial resolution index. We used our novel method to merge a medical database (the French national diagnosis-related group database, containing 5644 spatial units) with an ecological database (produced by the French National Institute of Statistics and Economic Studies, and containing with 36,594 spatial units). The mapping table yielded 5632 final spatial units. The mapping table's validity was evaluated by comparing the number of births in the medical database and the ecological databases in each final spatial unit. The median [interquartile range] relative difference was 2.3% [0; 5.7]. The spatial continuity criterion was low (2.4%), and the spatial resolution index was greater than for most French administrative areas. Our innovative approach improves interoperability between medical and ecological databases and facilitates fine-scale spatial analyses. We have shown that disaggregation models and large aggregation techniques are not necessarily the best ways to tackle the change of support problem.

Red blood cell membrane omega-3 fatty acid levels and physical performance: Cross-sectional data from the MAPT study.

PubMed

Fougère, Bertrand; de Souto Barreto, Philipe; Goisser, Sabine; Soriano, Gaëlle; Guyonnet, Sophie; Andrieu, Sandrine; Vellas, Bruno

2018-08-01

Studies have shown that omega-3 polyunsaturated fatty acids (PUFAs) are associated with brain, cardiovascular and immune function, as well as physical performance and bone health in older adults. So far, few studies have highlighted the associations between PUFA status and performance-based tests of physical function. To study the associations between the omega-3 index (red blood cell (RBC) membrane content of omega-3 PUFAs, such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)) and physical performance measured with the Short Physical Performance Battery (SPPB) in a sample of community-dwelling older adults. Cross-sectional study using the baseline data of the Multidomain Alzheimer's Disease Trial (MAPT), a randomized, placebo-controlled trial. 1449 participants with available data on PUFAs were included. Omega-3 index and Short Physical Performance Battery (SPPB) scores were measured at enrollment and the omega-3 index expressed as the percentage of total fatty acid content was calculated. We also dichotomized the omega-3 index as low (lowest quartile) vs. high (three upper quartiles). Participants were 75.2 (±4.4) years old, 64.5% were female. Bivariate analyses found that participants who were in the lowest omega-3 index quartile (Q1) had a SPPB score significantly lower than participants in the three other quartiles (Q2-Q4). However, adjusted (for age, gender, cognitive function, depressive status, Body Mass Index and grip strength) multiple linear regression showed that the omega-3 index-SPPB score association did not reach statistical significance [β = -0.166; (-0.346; 0.013); p = 0.07] in our sample. This cross-sectional study found that participants with a low omega-3 index had worse performance-based test results of physical function than people with a high omega-3 index, but this association did not reach statistical significance once confounders were controlled for. Studies looking at the over-time associations between PUFA status and physical performance changes may shed more light on this topic. Copyright © 2017 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.

PubMed

Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll

2016-01-04

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Study on Commercial Specification of Lonicerae Japonicae Flos].

PubMed

Zhou, Jie; Zou, Lin; Liu, Wei; Bian, Li-hua; Wang, Xiao; Zhang, Yong-qing; Dan, Staerk

2015-04-01

To provide the basis data for the institute of commercial specification standard of Lonicerae Japonicae Flos. 39 samples of Lonicerae Japonicae Flos commercial of different grades in market were collected, and vernier caliper and electronic balance were used to measure the numbers of flower bud and blooming rate per 0. 5 g, contamination content, browning degree, milden and rot, length, upside diameter, middle diameter and bottom diameter of Lonicerae Japonicae Flos. The content of neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, rutin, galuteolin,3,5-icaffeoylquinic acid and 4,5-dicaffeoylquinic acid were detected by HPLC. Correlation analysis, principal component analysis and cluster analysis were used by SPSS to analyze all index data,and the correlation of appearance characteristics and intrinsic active constituents was discussed. The numbers of flower bud and blooming rate per 0. 5 g, contamination content and browning degree were principal component indexes. The length of flower bud showed a significant correlation with galuteolin content, and the browning degree and upside diameter showed a significant correlation with chlorogenic acid content. Lonicerae Japonicae Flos commercial should be divided into four specification grades by sieved indexes.

Cinnamic acid derivatives in cosmetics - current use and future prospects.

PubMed

Gunia-Krzyżak, Agnieszka; Słoczyńska, Karolina; Popiół, Justyna; Koczurkiewicz, Paulina; Marona, Henryk; Pękala, Elżbieta

2018-06-05

Cinnamic acid derivatives are widely used in cosmetics and possess various functions. This group of compounds includes both naturally occurring as well as synthetic substances. On the basis of the Cosmetic Ingredient Database (CosIng) and available literature, this review summarizes their functions in cosmetics, including their physicochemical and biological properties as well as reported adverse effects. A perfuming function is typical of many derivatives of cinnamaldehyde, cinnamyl alcohol, dihydrocinnamyl alcohol, and cinnamic acid itself; these substances are commonly used in cosmetics all over the world. Some of them show allergic and photoallergic potential, resulting in restrictions in maximum concentrations and/or a requirement to indicate the presence of some substances in the list of ingredients when their concentrations exceed certain fixed values in a cosmetic product. Another important function of cinnamic acid derivatives in cosmetics is UV protection. Ester derivatives such as ethylhexyl methoxycinnamate (octinoxate), isoamyl p-methoxycinnamte (amiloxiate), octocrylene, and cinoxate are used in cosmetics all over the world as UV filters. However, their maximum concentrations in cosmetic products are restricted due to their adverse effects, which include contact and a photocontact allergies, phototoxic contact dermatitis, contact dermatitis, estrogenic modulation, and generation of reactive oxygen species. Other rarely utilized functions of cinnamic acid derivatives are as an antioxidant, in skin conditioning, hair conditioning, as a tonic, and in antimicrobial activities. Moreover, some currently investigated natural and synthetic derivatives of cinnamic acid have shown skin lightening and anti-aging properties. Some of them may become new cosmetic ingredients in the future. In particular, 4-hydroxycinnamic acid, which is currently indexed as a skin-conditioning cosmetics ingredient, has been widely tested in vitro and in vivo as a new drug candidate for the treatment of hyperpigmentation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Computational assessment of hemodynamics-based diagnostic tools using a database of virtual subjects: Application to three case studies.

PubMed

Willemet, Marie; Vennin, Samuel; Alastruey, Jordi

2016-12-08

Many physiological indexes and algorithms based on pulse wave analysis have been suggested in order to better assess cardiovascular function. Because these tools are often computed from in-vivo hemodynamic measurements, their validation is time-consuming, challenging, and biased by measurement errors. Recently, a new methodology has been suggested to assess theoretically these computed tools: a database of virtual subjects generated using numerical 1D-0D modeling of arterial hemodynamics. The generated set of simulations encloses a wide selection of healthy cases that could be encountered in a clinical study. We applied this new methodology to three different case studies that demonstrate the potential of our new tool, and illustrated each of them with a clinically relevant example: (i) we assessed the accuracy of indexes estimating pulse wave velocity; (ii) we validated and refined an algorithm that computes central blood pressure; and (iii) we investigated theoretical mechanisms behind the augmentation index. Our database of virtual subjects is a new tool to assist the clinician: it provides insight into the physical mechanisms underlying the correlations observed in clinical practice. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Identification of multidrug resistant protein 1 of mouse leukemia P388 cells on a PVDF membrane using 6-aminoquinolyl-carbamyl (AQC)-amino acid analysis and World Wide Web (WWW)-accessible tools.

PubMed

Shindo, N; Fujimura, T; Nojima-Kazuno, S; Mineki, R; Furusawa, S; Sasaki, K; Murayama, K

1998-11-15

Multidrug resistant protein 1 (MDR1) in a doxorubicin-resistant mouse leukemia cell line (P388/DOX) was identified using its amino acid composition combined with protein database searching (ExPASy and EMBL PROPSEARCH) via the World Wide Web. The proteins were separated by one-dimensional SDS-polyacrylamide gel electrophoresis, blotted onto a polyvinylidene fluoride membrane, and stained with Coomassie brilliant blue. A 160-kDa protein band was acid-hydrolyzed in the vapor phase (6 N HC1) and converted to 6-aminoquinolyl-carbamyl (AQC)-amino acids without extraction of the amino acids from the membrane. The amino acid composition of the protein was determined using the sensitive AQC-amino acid analysis method, improving our previously described method. The improved method involved using a Cosmosil 5C8-MS column instead of a Pegasil C8; replacement of the mobile phase A, constituent, 75 mM ammonium phosphate (pH 7.5), with 30 mM sodium phosphate buffer (pH 7.2); and slight modification of the separation program (9). All manipulations for protein hydrolysis and AQC derivatization were carried out in a hood using clean tools. This minimized contamination of amino acids at the low femtomolar level. A database search was carried out with bovine serum albumin as a calibration protein. MDR1 in P388/DOX was ranked first by both databases with high reliability (score 14 for ExPASy, distance 1.34 for EMBL).

G-Bean: an ontology-graph based web tool for biomedical literature retrieval

PubMed Central

2014-01-01

Background Currently, most people use NCBI's PubMed to search the MEDLINE database, an important bibliographical information source for life science and biomedical information. However, PubMed has some drawbacks that make it difficult to find relevant publications pertaining to users' individual intentions, especially for non-expert users. To ameliorate the disadvantages of PubMed, we developed G-Bean, a graph based biomedical search engine, to search biomedical articles in MEDLINE database more efficiently. Methods G-Bean addresses PubMed's limitations with three innovations: (1) Parallel document index creation: a multithreaded index creation strategy is employed to generate the document index for G-Bean in parallel; (2) Ontology-graph based query expansion: an ontology graph is constructed by merging four major UMLS (Version 2013AA) vocabularies, MeSH, SNOMEDCT, CSP and AOD, to cover all concepts in National Library of Medicine (NLM) database; a Personalized PageRank algorithm is used to compute concept relevance in this ontology graph and the Term Frequency - Inverse Document Frequency (TF-IDF) weighting scheme is used to re-rank the concepts. The top 500 ranked concepts are selected for expanding the initial query to retrieve more accurate and relevant information; (3) Retrieval and re-ranking of documents based on user's search intention: after the user selects any article from the existing search results, G-Bean analyzes user's selections to determine his/her true search intention and then uses more relevant and more specific terms to retrieve additional related articles. The new articles are presented to the user in the order of their relevance to the already selected articles. Results Performance evaluation with 106 OHSUMED benchmark queries shows that G-Bean returns more relevant results than PubMed does when using these queries to search the MEDLINE database. PubMed could not even return any search result for some OHSUMED queries because it failed to form the appropriate Boolean query statement automatically from the natural language query strings. G-Bean is available at http://bioinformatics.clemson.edu/G-Bean/index.php. Conclusions G-Bean addresses PubMed's limitations with ontology-graph based query expansion, automatic document indexing, and user search intention discovery. It shows significant advantages in finding relevant articles from the MEDLINE database to meet the information need of the user. PMID:25474588

G-Bean: an ontology-graph based web tool for biomedical literature retrieval.

PubMed

Wang, James Z; Zhang, Yuanyuan; Dong, Liang; Li, Lin; Srimani, Pradip K; Yu, Philip S

2014-01-01

Currently, most people use NCBI's PubMed to search the MEDLINE database, an important bibliographical information source for life science and biomedical information. However, PubMed has some drawbacks that make it difficult to find relevant publications pertaining to users' individual intentions, especially for non-expert users. To ameliorate the disadvantages of PubMed, we developed G-Bean, a graph based biomedical search engine, to search biomedical articles in MEDLINE database more efficiently. G-Bean addresses PubMed's limitations with three innovations: (1) Parallel document index creation: a multithreaded index creation strategy is employed to generate the document index for G-Bean in parallel; (2) Ontology-graph based query expansion: an ontology graph is constructed by merging four major UMLS (Version 2013AA) vocabularies, MeSH, SNOMEDCT, CSP and AOD, to cover all concepts in National Library of Medicine (NLM) database; a Personalized PageRank algorithm is used to compute concept relevance in this ontology graph and the Term Frequency - Inverse Document Frequency (TF-IDF) weighting scheme is used to re-rank the concepts. The top 500 ranked concepts are selected for expanding the initial query to retrieve more accurate and relevant information; (3) Retrieval and re-ranking of documents based on user's search intention: after the user selects any article from the existing search results, G-Bean analyzes user's selections to determine his/her true search intention and then uses more relevant and more specific terms to retrieve additional related articles. The new articles are presented to the user in the order of their relevance to the already selected articles. Performance evaluation with 106 OHSUMED benchmark queries shows that G-Bean returns more relevant results than PubMed does when using these queries to search the MEDLINE database. PubMed could not even return any search result for some OHSUMED queries because it failed to form the appropriate Boolean query statement automatically from the natural language query strings. G-Bean is available at http://bioinformatics.clemson.edu/G-Bean/index.php. G-Bean addresses PubMed's limitations with ontology-graph based query expansion, automatic document indexing, and user search intention discovery. It shows significant advantages in finding relevant articles from the MEDLINE database to meet the information need of the user.

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.

Continuing the Epidemiological Function of the Addicts Index--Evidence from Matching the Home Office Addicts Index with the National Drug Treatment Monitoring System

ERIC Educational Resources Information Center

Hickman, Matthew; Griffin, Maria; Mott, Joy; Corkery, John; Madden, Peter; Sondhi, Arun; Stimson, Gerry

2004-01-01

Aims: We discuss the Addicts Index (AI) and examine whether the epidemiological trends of the AI can be continued by the regional drug misuse databases (DMDs, now known as National Drug Treatment Monitoring System (NDTMS). Methods: (i) Matching individuals recorded as addicted to opiates and/or cocaine in the AI with those reported to the North…

Toxic substances registry system: Index of material safety data sheets

NASA Technical Reports Server (NTRS)

1991-01-01

The Material Safety Data Sheets (MSDSs) listed in this index reflect product inventories and associated MSDSs which have been submitted to the Toxic Substance Registry database maintained by the Base Operations Contractor at the Kennedy Space Center. The purpose of this index is to provide a means to access information on the hazards associated with the toxic and otherwise hazardous chemicals stored and used at the Kennedy Space Center.

Bottom-Up Evaluation of Twig Join Pattern Queries in XML Document Databases

NASA Astrophysics Data System (ADS)

Chen, Yangjun

Since the extensible markup language XML emerged as a new standard for information representation and exchange on the Internet, the problem of storing, indexing, and querying XML documents has been among the major issues of database research. In this paper, we study the twig pattern matching and discuss a new algorithm for processing ordered twig pattern queries. The time complexity of the algorithmis bounded by O(|D|·|Q| + |T|·leaf Q ) and its space overhead is by O(leaf T ·leaf Q ), where T stands for a document tree, Q for a twig pattern and D is a largest data stream associated with a node q of Q, which contains the database nodes that match the node predicate at q. leaf T (leaf Q ) represents the number of the leaf nodes of T (resp. Q). In addition, the algorithm can be adapted to an indexing environment with XB-trees being used.

Searching the Social Sciences Citation Index on BRS.

ERIC Educational Resources Information Center

Janke, Richard V.

1980-01-01

Concentrates on describing and illustrating by example the unique BRS features of the online Social Sciences Citation Index. Appendices provide a key to the BRS/SSCI citation elements, BRS standardized language codes, publication type codes, author's classification of BRS/SSCI subject category codes, search examples, and database specifications.…

Converting the H. W. Wilson Company Indexes to an Automated System: A Functional Analysis.

ERIC Educational Resources Information Center

Regazzi, John J.

1984-01-01

Description of the computerized information system that supports the editorial and manufacturing processes involved in creation of Wilson's subject indexes and catalogs includes the major subsystems--online data entry, batch input processing, validation and release, file generation and database management, online and offline retrieval, publication…

The New Southern FIA Data Compilation System

Treesearch

V. Clark Baldwin; Larry Royer

2001-01-01

In general, the major national Forest Inventory and Analysis annual inventory emphasis has been on data-base design and not on data processing and calculation of various new attributes. Two key programming techniques required for efficient data processing are indexing and modularization. The Southern Research Station Compilation System utilizes modular and indexing...

Mining and Indexing Graph Databases

ERIC Educational Resources Information Center

Yuan, Dayu

2013-01-01

Graphs are widely used to model structures and relationships of objects in various scientific and commercial fields. Chemical molecules, proteins, malware system-call dependencies and three-dimensional mechanical parts are all modeled as graphs. In this dissertation, we propose to mine and index those graph data to enable fast and scalable search.…

BioWarehouse: a bioinformatics database warehouse toolkit

PubMed Central

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David WJ; Tenenbaum, Jessica D; Karp, Peter D

2006-01-01

Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the database integration problem for bioinformatics. PMID:16556315

BioWarehouse: a bioinformatics database warehouse toolkit.

PubMed

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

2006-03-23

This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

Database on veterinary clinical research in homeopathy.

PubMed

Clausen, Jürgen; Albrecht, Henning

2010-07-01

The aim of the present report is to provide an overview of the first database on clinical research in veterinary homeopathy. Detailed searches in the database 'Veterinary Clinical Research-Database in Homeopathy' (http://www.carstens-stiftung.de/clinresvet/index.php). The database contains about 200 entries of randomised clinical trials, non-randomised clinical trials, observational studies, drug provings, case reports and case series. Twenty-two clinical fields are covered and eight different groups of species are included. The database is free of charge and open to all interested veterinarians and researchers. The database enables researchers and veterinarians, sceptics and supporters to get a quick overview of the status of veterinary clinical research in homeopathy and alleviates the preparation of systematical reviews or may stimulate reproductions or even new studies. 2010 Elsevier Ltd. All rights reserved.

Students' Attitudes toward ABI/INFORM on CD-ROM: A Factor Analysis.

ERIC Educational Resources Information Center

Wang, Vicky; Lau, Shuk-fong

Two years after the introduction of CD-ROM bibliographic database searching in the Memphis State University libraries (Tennessee), a survey was conducted to examine students' attitudes toward the business database, ABI/INFORM. ABI/INFORM contains indexes and abstracts of articles from over 800 journals on management, accounting, banking, human…

Graduate Student Research Instruction: Testing an Interactive Web-Based Library Tutorial for a Health Sciences Database

ERIC Educational Resources Information Center

Lechner, David L.

2005-01-01

Interactive electronic tutorials offer flexibility in delivering library instruction; however, questions linger regarding their effectiveness compared to traditional librarian-led classroom lectures. This study examines a tutorial introducing health science students to the Cumulative Index to Nursing and Allied Health Literature database. Half the…

Annual patents review, January-December 2004

Treesearch

Roland Gleisner; Karen Scallon; Michael Fleischmann; Julie Blankenburg; Marguerite Sykes

2005-01-01

This review summarizes patents related to paper recycling that first appeared in patent databases during the 2004. Two on-line databases, Claims/U.S. Patents Abstracts and Derwent World Patents Index, were searched for this review. This feature is intended to inform readers about recent developments in equipment design, chemicals, and process technologies for recycling...

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)

New Directions in Library and Information Science Education. Final Report. Volume 2.5: Database Producer Professional Competencies.

ERIC Educational Resources Information Center

Griffiths, Jose-Marie; And Others

This document contains validated activities and competencies needed by librarians working in a database producer organization. The activities and competencies are organized according to the functions which these librarians perform: acquisitions; thesaurus development and control; indexing/abstracting; and publications and product management.…

An Evaluation of h-Index as a Measure of Research Productivity Among Canadian Academic Plastic Surgeons.

PubMed

Hu, Jiayi; Gholami, Arian; Stone, Nicholas; Bartoszko, Justyna; Thoma, Achilleas

2018-02-01

Evaluation of research productivity among plastic surgeons can be complex. The Hirsch index (h-index) was recently introduced to evaluate both the quality and quantity of one's research activity. It has been proposed to be valuable in assessing promotions and grant funding within academic medicine, including plastic surgery. Our objective is to evaluate research productivity among Canadian academic plastic surgeons using the h-index. A list of Canadian academic plastic surgeons was obtained from websites of academic training programs. The h-index was retrieved using the Scopus database. Relevant demographic and academic factors were collected and their effects on the h-index were analyzed using the t test and Wilcoxon Mann-Whitney U test. Nominal and categorical variables were analyzed using χ 2 test and 1-way analysis of variance. Univariate and multivariate models were built a priori. All P values were 2 sided, and P < .05 was considered to be significant. Our study on Canadian plastic surgeons involved 175 surgeons with an average h-index of 7.6. Over 80% of the surgeons were male. Both univariable and multivariable analysis showed that graduate degree ( P < .0001), academic rank ( P = .03), and years in practice ( P < .0001) were positively correlated with h-index. Limitations of the study include that the Scopus database and the websites of training programs were not always up-to-date. The h-index is a novel tool for evaluating research productivity in academic medicine, and this study shows that the h-index can also serve as a useful metric for measuring research productivity in the Canadian plastic surgery community. Plastic surgeons would be wise to familiarize themselves with the h-index concept and should consider using it as an adjunct to existing metrics such as total publication number.

Alternation of plasma fatty acids composition and desaturase activities in children with liver steatosis

PubMed Central

Su, Hui-Min; Yao, Tsung-Chieh; Kuo, Ming-Ling; Lai, Ming-Wei; Tsai, Ming-Han; Huang, Jing-Long

2017-01-01

Objective The aim of this study was to investigate changes in plasma fatty acids proportions and estimated desaturase activities for variable grading of liver steatosis in children. Methods In total, 111 schoolchildren (aged 8–18 years) were included in the analysis from March 2015 to August 2016. Anthropometric evaluation, liver ultrasound examination and scoring for nonalcoholic fatty liver disease (NAFLD score = 0–6), and biochemical and plasma fatty acids analysis were performed. We compared the composition ratio of fatty acids between children with high-grade liver steatosis (NAFLD score = 4–6), low-grade liver steatosis (NAFLD score = 1–3), and healthy controls (NAFLD score = 0). In addition, correlation coefficients (r) between NAFLD score, metabolic variables, and estimated activity of desaturase indices (stearoyl-coenzyme A desaturase-1 (SCD1), delta-5 and delta-6 desaturase) were calculated. Results Compared with healthy controls, children with liver steatosis showed a higher proportion of monounsaturated fatty acids (21.16 ± 2.81% vs. 19.68 ± 2.71%, p = 0.024). In addition, children with high- grade liver steatosis exhibited higher proportions of palmitic acid (C16:0), palmitoleic acid (C16:1n-7), dihomo-γ-linolenic acid (C20:3n-6), adrenic acid (C22:4n-6), and docosapentaenoic acid (C22:5n-6); and lower proportions of eicosapentaenoic acid (C20:5n-3) (P< 0.05). In all subjects, the NAFLD score was positively correlated with body mass index (BMI) (kg/m2) (r = 0.696), homeostasis model of assessment ratio–index (HOMA-IR) (r = 0.510), SCD1(16) (r = 0.273), and the delta-6 index (r = 0.494); and inversely associated with the delta-5 index (r = -0.443). Conclusion Our current data suggested that children with liver steatosis was highly associated with obesity, and insulin resistance. In addition, increased endogenous lipogenesis through altered desaturase activity may contribute to the progression of liver steatosis in children. PMID:28759573

Handwriting Identification, Matching, and Indexing in Noisy Document Images

DTIC Science & Technology

2006-01-01

algorithm to detect all parallel lines simultaneously. Our method can detect 96.8% of the severely broken rule lines in the Arabic database we collected...in the database to guide later processing. It is widely used in banks, post offices, and tax offices where the types of forms are most often pre...be used for different fields), and output the recognition results to a database . Although special anchors may be avail- able to facilitate form

Supporting Social Data Observatory with Customizable Index Structures on HBase - Architecture and Performance

DTIC Science & Technology

2013-01-01

commercial NoSQL database system. The results show that In-dexedHBase provides a data loading speed that is 6 times faster than Riak, and is...compare it with Riak, a widely adopted commercial NoSQL database system. The results show that In- dexedHBase provides a data loading speed that is 6...events. This chapter describes our research towards building an efficient and scalable storage platform for Truthy. Many existing NoSQL databases

A Unified Approach to Joint Regional/Teleseismic Calibration and Event Location with a 3D Earth Model

DTIC Science & Technology

2010-09-01

raytracing and travel-time calculation in 3D Earth models, such as the finite-difference eikonal method (e.g., Podvin and Lecomte, 1991), fast...by Reiter and Rodi (2009) in constructing JWM. Two teleseismic data sets were considered, both extracted from the EHB database (Engdahl et al...extracted from the updated EHB database distributed by the International Seismological Centre (http://www.isc.ac.uk/EHB/index.html). The new database

The Association between Databases for Indexing Studies Intended for an Exercise Meta-Analysis of Arthritis Randomized Controlled Trials

PubMed Central

Kelley, George A.; Kelley, Kristi S.

2012-01-01

Objective. The purpose of this study was to determine the database indexing of randomized controlled trials (RCTs) for a meta-analysis addressing the effects of exercise on pain and physical function in adults with arthritis and other rheumatic diseases (AORD). Methods. The number, percentage, and 95% confidence intervals (CIs) for included articles at initial and follow-up periods were calculated from PubMed, EMBASE, CENTRAL, CINAHL, SPORTDiscus, and DAO databases. The number needed to review (NNR) was also calculated along with the number of articles retrieved by expert review. Cross-referencing from reviews and included articles also occurred. Results. Thirty-four of 36 articles (94.4%, 95% CI, 81.3–99.3) were located by database searching. PubMed and CENTRAL yielded 32 of 36 articles (88.9%, 73.9–96.9). Two articles not identified in any of the other databases were found in either CINAHL or SPORTDicsus. Two other articles were located by scanning the reference lists of review articles. The NNR ranged from 2 (CINAHL) to 118 (SPORTDiscus). More articles were identified in EMBASE at follow-up (36%, 12.1–42.2 versus 86.1%, 70.5–95.3). Conclusions. Searching multiple databases and cross-referencing from reviews was important for identifying RCTs addressing the effects of exercise on pain and physical function in adults with AORD. PMID:22924128

The Association between Databases for Indexing Studies Intended for an Exercise Meta-Analysis of Arthritis Randomized Controlled Trials.

PubMed

Kelley, George A; Kelley, Kristi S

2012-01-01

Objective. The purpose of this study was to determine the database indexing of randomized controlled trials (RCTs) for a meta-analysis addressing the effects of exercise on pain and physical function in adults with arthritis and other rheumatic diseases (AORD). Methods. The number, percentage, and 95% confidence intervals (CIs) for included articles at initial and follow-up periods were calculated from PubMed, EMBASE, CENTRAL, CINAHL, SPORTDiscus, and DAO databases. The number needed to review (NNR) was also calculated along with the number of articles retrieved by expert review. Cross-referencing from reviews and included articles also occurred. Results. Thirty-four of 36 articles (94.4%, 95% CI, 81.3-99.3) were located by database searching. PubMed and CENTRAL yielded 32 of 36 articles (88.9%, 73.9-96.9). Two articles not identified in any of the other databases were found in either CINAHL or SPORTDicsus. Two other articles were located by scanning the reference lists of review articles. The NNR ranged from 2 (CINAHL) to 118 (SPORTDiscus). More articles were identified in EMBASE at follow-up (36%, 12.1-42.2 versus 86.1%, 70.5-95.3). Conclusions. Searching multiple databases and cross-referencing from reviews was important for identifying RCTs addressing the effects of exercise on pain and physical function in adults with AORD.

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

PubMed

Toofanny, Rudesh D; Simms, Andrew M; Beck, David A C; Daggett, Valerie

2011-08-10

Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation and visualization of contacts and rapid cross simulation analysis for knowledge discovery. Using page compression for the atomic coordinate tables and indexes saves ~36% of disk space without any significant decrease in calculation time and should be considered for other non-transactional databases in MS SQL SERVER 2008.

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

PubMed Central

2011-01-01

Background Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Results Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. Conclusions The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation and visualization of contacts and rapid cross simulation analysis for knowledge discovery. Using page compression for the atomic coordinate tables and indexes saves ~36% of disk space without any significant decrease in calculation time and should be considered for other non-transactional databases in MS SQL SERVER 2008. PMID:21831299

Cardiovascular Effects of Stress During Acutely Increased Free Fatty Acids in a Randomized, Double-Blind, Cross-Over Study in Humans.

PubMed

Rezaei, Safoura Sheikh; Litschauer, Brigitte; Gouya, Gazaleh; Baumgartner-Parzer, Sabina; Stulnig, Thomas; Wolzt, Michael

2018-06-01

Increased free fatty acids stimulate sympathetic nervous system activity, impair endothelium-dependent vasodilation, and increase regional blood flow. The aim of this study was to assess if fatty acids acutely elevated by infusion of intralipid/heparin affect cardiovascular reactivity employing two stressors eliciting either a cardiac (Stroop test) or vascular (Cold Face test) dominated pressor response. Two stress tasks were performed in 20 healthy subjects (10 women, 10 men) before and during a 180-min intralipid/heparin or saline infusion as placebo on alternate trial days in a randomized crossover study design. Blood pressure, heart rate, cardiac index, and total peripheral resistance index were measured. At baseline, the Stroop test did not affect hemodynamic parameters, and the Cold Face test had an impact on hemodynamic parameters except for heart rate. Plasma fatty acids concentrations increased to 810% (t=11.0, p<0.001) of baseline and C-peptide increased by 17% (t=4.66, p<0.001) during intralipid/heparin infusion. This was paralleled by increased cardiac index (F=9.98; p<0.005 vs. saline) and reduced total peripheral resistance index (F=4.46; p<0.05 vs saline). There was no effect of intralipid/heparin or saline infusion on Stroop test or Cold Face test reactivity of hemodynamic parameters. An acute increase in free fatty acids does not affect the magnitude or pattern of stress response in healthy volunteers, but primarily alter the underlying cardiovascular tone by decreasing total peripheral resistance index and increasing cardiac index to maintain a constant blood pressure. © Georg Thieme Verlag KG Stuttgart · New York.

Aspergillus flavus Blast2GO gene ontology database: elevated growth temperature alters amino acid metabolism

USDA-ARS?s Scientific Manuscript database

The availability of a representative gene ontology (GO) database is a prerequisite for a successful functional genomics study. Using online Blast2GO resources we constructed a GO database of Aspergillus flavus. Of the predicted total 13,485 A. flavus genes 8,987 were annotated with GO terms. The mea...

Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis

PubMed Central

Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

2009-01-01

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed. PMID:19015126

Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis.

PubMed

Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

2009-01-01

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed.

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.

Omega-3 Index and Obstructive Sleep Apnea: A Cross-Sectional Study.

PubMed

Tittus, Janine; Huber, Marie Theres; Storck, Klaus; Köhler, Anton; Köhler, Jan M; von Arnim, Thomas; von Schacky, Clemens

2017-10-15

Erythrocyte levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) (Omega-3 Index) were previously found to be associated with obstructive sleep apnea (OSA) at very low levels (< 5.0%) in only one epidemiologic study. OSA has comorbidities, such as arterial hypertension, heart failure, or major depression, also associated with a low Omega-3 Index. These comorbidities can be improved by increasing intake of EPA and DHA, and thus the Omega-3 Index, preferably to its target range of 8% to 11%. Symptoms of OSA might improve by increasing the Omega-3 Index, but more research is needed. In our sleep laboratory, 357 participants with OSA were recruited, and data from 315 participants were evaluated. Three categories of OSA (none/ mild, moderate, severe) were defined based on apnea-hypopnea index. Anthropometrics and lifestyle characteristics (smoking, alcohol, fish intake, omega-3 supplementation) were recorded. Erythrocyte fatty acid compositions were assessed with the HS-Omega-3 Index methodology. The mean Omega-3 Index in all 3 categories of OSA was 5.7%, and no association with OSA was found. There were more male participants with severe OSA (79.7%, P = .042) than females, and participants with severe OSA had a significantly higher body mass index (32.11 ± 6.39 kg/m 2 , P = .009) than participants with mild or moderate OSA. Lifestyle characteristics were not significantly different. In contrast to our hypothesis, an Omega-3 Index of 5.7% was not associated with OSA severity. Previously, an Omega-3 Index < 5.0% was associated. Although our results suggest aiming for an Omega-3 Index > 5.7% in an intervention trial with EPA and DHA in OSA, comorbidities of OSA suggest a target range of 8% to 11%. © 2017 American Academy of Sleep Medicine

Deriving leaf mass per area (LMA) from foliar reflectance across a variety of plant species using continuous wavelet analysis

NASA Astrophysics Data System (ADS)

Cheng, Tao; Rivard, Benoit; Sánchez-Azofeifa, Arturo G.; Féret, Jean-Baptiste; Jacquemoud, Stéphane; Ustin, Susan L.

2014-01-01

Leaf mass per area (LMA), the ratio of leaf dry mass to leaf area, is a trait of central importance to the understanding of plant light capture and carbon gain. It can be estimated from leaf reflectance spectroscopy in the infrared region, by making use of information about the absorption features of dry matter. This study reports on the application of continuous wavelet analysis (CWA) to the estimation of LMA across a wide range of plant species. We compiled a large database of leaf reflectance spectra acquired within the framework of three independent measurement campaigns (ANGERS, LOPEX and PANAMA) and generated a simulated database using the PROSPECT leaf optical properties model. CWA was applied to the measured and simulated databases to extract wavelet features that correlate with LMA. These features were assessed in terms of predictive capability and robustness while transferring predictive models from the simulated database to the measured database. The assessment was also conducted with two existing spectral indices, namely the Normalized Dry Matter Index (NDMI) and the Normalized Difference index for LMA (NDLMA). Five common wavelet features were determined from the two databases, which showed significant correlations with LMA (R2: 0.51-0.82, p < 0.0001). The best robustness (R2 = 0.74, RMSE = 18.97 g/m2 and Bias = 0.12 g/m2) was obtained using a combination of two low-scale features (1639 nm, scale 4) and (2133 nm, scale 5), the first being predominantly important. The transferability of the wavelet-based predictive model to the whole measured database was either better than or comparable to those based on spectral indices. Additionally, only the wavelet-based model showed consistent predictive capabilities among the three measured data sets. In comparison, the models based on spectral indices were sensitive to site-specific data sets. Integrating the NDLMA spectral index and the two robust wavelet features improved the LMA prediction. One of the bands used by this spectral index, 1368 nm, was located in a strong atmospheric water absorption region and replacing it with the next available band (1340 nm) led to lower predictive accuracies. However, the two wavelet features were not affected by data quality in the atmospheric absorption regions and therefore showed potential for canopy-level investigations. The wavelet approach provides a different perspective into spectral responses to LMA variation than the traditional spectral indices and holds greater promise for implementation with airborne or spaceborne imaging spectroscopy data for mapping canopy foliar dry biomass.

Application of refractometry to quality assurance monitoring of parenteral nutrition solutions.

PubMed

Chang, Wei-Kuo; Chao, You-Chen; Yeh, Ming-Kung

2008-01-01

Parenteral nutrition (PN) solution contains various concentrations of dextrose, amino acids, lipids, vitamins, electrolytes, and trace elements. Incorrect preparation of PN solution could lead to patient death. In this study we used the refractive index as a quality assurance tool to monitor the preparation of PN solution. Refractive indices of single nutrient components and PN solutions consisting of various concentrations of dextrose, amino acids, electrolytes, and lipids were measured. A mathematical equation and its linear plot were generated then used to predict the refractive index of the PN solution. The best-fit refractive index for PN solution (i.e., the predicted refractive index)=0.9798x(% dextrose)+1.2889x(% amino acids)+1.1017x(% lipids)+0.9440x(% sum of the electrolytes)+0.5367 (r2=0.99). This equation was validated by comparing the measured refractive indices of 500 clinical PN solutions to their predicted refractive indices. We found that 2 of the 500 prepared samples (0.4%) had less than the predicted refractive index (<95%). Refractive index can be used as a reliable quality assurance tool for monitoring PN preparation. Such information can be obtained at the bedside and used to confirm the accuracy of the PN solution composition.

Biomedical science journals in the Arab world.

PubMed

Tadmouri, Ghazi O

2004-10-01

Medieval Arab scientists established the basis of medical practice and gave important attention to the publication of scientific results. At present, modern scientific publishing in the Arab world is in its developmental stage. Arab biomedical journals are less than 300, most of which are published in Egypt, Lebanon, and the Kingdom of Saudi Arabia. Yet, many of these journals do not have on-line access or are indexed in major bibliographic databases. The majority of indexed journals, however, do not have a stable presence in the popular PubMed database and their indexes are discontinued since 2001. The exposure of Arab biomedical journals in international indices undoubtedly plays an important role in improving the scientific quality of these journals. The successful examples discussed in this review encourage us to call for the formation of a consortium of Arab biomedical journal publishers to assist in redressing the balance of the region from biomedical data consumption to data production.

Ultrafast fingerprint indexing for embedded systems

NASA Astrophysics Data System (ADS)

Zhou, Ru; Sin, Sang Woo; Li, Dongju; Isshiki, Tsuyoshi; Kunieda, Hiroaki

2011-10-01

A novel core-based fingerprint indexing scheme for embedded systems is presented in this paper. Our approach is enabled by our new precise and fast core-detection algorithm with the direction map. It introduces the feature of CMP (core minutiae pair), which describes the coordinates of minutiae and the direction of ridges associated with the minutiae based on the uniquely defined core coordinates. Since each CMP is identical against the shift and rotation of the fingerprint image, the CMP comparison between a template and an input image can be performed without any alignment. The proposed indexing algorithm based on CMP is suitable for embedded systems because the tremendous speed up and the memory reduction are achieved. In fact, the experiments with the fingerprint database FVC2002 show that its speed for the identifications becomes about 40 times faster than conventional approaches, even though the database includes fingerprints with no core.

DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts.

PubMed

Paraskevopoulou, Maria D; Vlachos, Ioannis S; Karagkouni, Dimitra; Georgakilas, Georgios; Kanellos, Ilias; Vergoulis, Thanasis; Zagganas, Konstantinos; Tsanakas, Panayiotis; Floros, Evangelos; Dalamagas, Theodore; Hatzigeorgiou, Artemis G

2016-01-04

microRNAs (miRNAs) are short non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of coding gene expression. Long non-coding RNAs (lncRNAs) have been recently reported to interact with miRNAs. The sponge-like function of lncRNAs introduces an extra layer of complexity in the miRNA interactome. DIANA-LncBase v1 provided a database of experimentally supported and in silico predicted miRNA Recognition Elements (MREs) on lncRNAs. The second version of LncBase (www.microrna.gr/LncBase) presents an extensive collection of miRNA:lncRNA interactions. The significantly enhanced database includes more than 70 000 low and high-throughput, (in)direct miRNA:lncRNA experimentally supported interactions, derived from manually curated publications and the analysis of 153 AGO CLIP-Seq libraries. The new experimental module presents a 14-fold increase compared to the previous release. LncBase v2 hosts in silico predicted miRNA targets on lncRNAs, identified with the DIANA-microT algorithm. The relevant module provides millions of predicted miRNA binding sites, accompanied with detailed metadata and MRE conservation metrics. LncBase v2 caters information regarding cell type specific miRNA:lncRNA regulation and enables users to easily identify interactions in 66 different cell types, spanning 36 tissues for human and mouse. Database entries are also supported by accurate lncRNA expression information, derived from the analysis of more than 6 billion RNA-Seq reads. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Aggregated Indexing of Biomedical Time Series Data

PubMed Central

Woodbridge, Jonathan; Mortazavi, Bobak; Sarrafzadeh, Majid; Bui, Alex A.T.

2016-01-01

Remote and wearable medical sensing has the potential to create very large and high dimensional datasets. Medical time series databases must be able to efficiently store, index, and mine these datasets to enable medical professionals to effectively analyze data collected from their patients. Conventional high dimensional indexing methods are a two stage process. First, a superset of the true matches is efficiently extracted from the database. Second, supersets are pruned by comparing each of their objects to the query object and rejecting any objects falling outside a predetermined radius. This pruning stage heavily dominates the computational complexity of most conventional search algorithms. Therefore, indexing algorithms can be significantly improved by reducing the amount of pruning. This paper presents an online algorithm to aggregate biomedical times series data to significantly reduce the search space (index size) without compromising the quality of search results. This algorithm is built on the observation that biomedical time series signals are composed of cyclical and often similar patterns. This algorithm takes in a stream of segments and groups them to highly concentrated collections. Locality Sensitive Hashing (LSH) is used to reduce the overall complexity of the algorithm, allowing it to run online. The output of this aggregation is used to populate an index. The proposed algorithm yields logarithmic growth of the index (with respect to the total number of objects) while keeping sensitivity and specificity simultaneously above 98%. Both memory and runtime complexities of time series search are improved when using aggregated indexes. In addition, data mining tasks, such as clustering, exhibit runtimes that are orders of magnitudes faster when run on aggregated indexes. PMID:27617298

Antimicrobial Activity of 8-Quinolinols, Salicylic Acids, Hydroxynaphthoic Acids, and Salts of Selected Quinolinols with Selected Hydroxy-Acids

PubMed Central

Gershon, Herman; Parmegiani, Raulo

1962-01-01

Seventy-seven compounds were screened by the disc-plate method against strains of five bacteria and five fungi. A new constant was proposed to describe the antimicrobial activity of a compound in a defined system of organisms. This constant includes not only the inhibitory level of activity of the material but also the number of organisms inhibited. This constant, the antimicrobial spectrum index, was compared with the antimicrobial index of Albert. PMID:13898066

Towards Fieldable Rapid Bioagent Detection: advanced Resonant Optical Waveguide and Biolayer Structures for Integrated Biosensing

DTIC Science & Technology

2007-11-01

waveguide approach in which a right-angled gadolinium gallium garnet (GGG) glass prism of index 1.965 at 633 nm is used to couple light from a HeNe laser of...SPARROW sensor consists of two planar, single mode aluminum oxide waveguides separated vertically by a lower refractive index silicon dioxide layer...and high stability could be formed on aluminum oxide, the binding of an alkyl carboxylic acid, stearic acid (n-octadecanoic acid), was investigated

Plagiarism Allegations Account for Most Retractions in Major Latin American/Caribbean Databases.

PubMed

Almeida, Renan Moritz V R; de Albuquerque Rocha, Karina; Catelani, Fernanda; Fontes-Pereira, Aldo José; Vasconcelos, Sonia M R

2016-10-01

This study focuses on retraction notices from two major Latin American/Caribbean indexing databases: SciELO and LILACS. SciELO includes open scientific journals published mostly in Latin America/the Caribbean, from which 10 % are also indexed by Thomson Reuters Web of Knowledge Journal of Citation Reports (JCR). LILACS has a similar geographical coverage and includes dissertations and conference/symposia proceedings, but it is limited to publications in the health sciences. A search for retraction notices was performed in these two databases using the keywords "retracted", "retraction" "withdrawal", "withdrawn", "removed" and "redress". Documents were manually checked to identify those that actually referred to retractions, which were then analyzed and categorized according to the reasons alleged in the notices. Dates of publication/retraction and time to retraction were also recorded. Searching procedures were performed between June and December 2014. Thirty-one retraction notices were identified, fifteen of which were in JCR-indexed journals. "Plagiarism" was alleged in six retractions of this group. Among the non-JCR journals, retraction reasons were alleged in fourteen cases, twelve of which were attributed to "plagiarism". The proportion of retracted articles for the SciELO database was approximately 0.005 %. The reasons alleged in retraction notices may be used as signposts to inform discussions in Latin America on plagiarism and research integrity. At the international level, these results suggest that the correction of the literature is becoming global and is not limited to mainstream international publications.

Nucleic acid indexing

DOEpatents

Guilfoyle, Richard A.; Guo, Zhen

2001-01-01

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

Nucleic acid indexing

DOEpatents

Guilfoyle, Richard A.; Guo, Zhen

1999-01-01

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

Relationship between the omega-3 index and specialized pro-resolving lipid mediators in patients with peripheral arterial disease taking fish oil supplements.

PubMed

Schaller, Melinda S; Zahner, Greg J; Gasper, Warren J; Harris, William S; Conte, Michael S; Hills, Nancy K; Grenon, S Marlene

Oral supplementation with n-3 polyunsaturated fatty acids (PUFA) increases the omega-3 index, a biomarker of red blood cell eicosapentaenoic acid and docosahexaenoic acid, and plasma levels of biosynthesis pathway markers and potent lipid mediators involved in the resolution of inflammation among patients with peripheral arterial disease (PAD). We aimed to quantify the association between an upstream change in the omega-3 index and downstream changes in lipid mediator production. We conducted a secondary analysis of the OMEGA-PAD I Trial, a randomized, placebo controlled trial investigating high-dose n-3 PUFA oral supplementation in PAD patients. Eighty subjects were randomized to either 4.4 g of fish oil or placebo for 1 month. Regression analyses using generalized estimating equation techniques were used to investigate the relationship between changes in the omega-3 index and changes in lipid mediators, pre- and post-intervention. In the fish oil group, there was a significant increase in the omega-3 index (5 ± 1% to 9 ± 2%, P < .001) as well as in the plasma levels of several downstream lipid mediator pathway markers of resolution, which are involved with the regulation of leukocyte effector function and host defense. A doubling of the omega-3 index correlated with increases of 2.3-fold in 18-hydroxy-eicosapentaenoic acid (HEPE; P < .0001), 1.7-fold in 15-HEPE (P = .03), 1.9-fold in 5-HEPE (P = .04), and 3.6-fold in 4-hydroxy-docosahexaenoic acid (P < .001). Among subjects with symptomatic PAD who took oral fish oil supplements for 1 month, observed changes in the omega-3 index were strongly associated with increases in downstream mediators in the biochemical pathways of resolution. Copyright © 2017 National Lipid Association. All rights reserved.

Atherogenicity index and health-related fatty acids in different stages of lactation from Friesian, Jersey and Friesian×Jersey cross cow milk under a pasture-based dairy system.

PubMed

Nantapo, C T W; Muchenje, V; Hugo, A

2014-03-01

The objective of the study was to investigate the effect of stage of lactation on the fatty acid profiles of milk from Friesian, Jersey and Friesian×Jersey cows. Linoleic acid in pastures was highest in the second phase which coincided with mid-lactation days (p<0.05). Highest milk moisture content and lowest fat free dry matter content was seen in early lactation (p<0.05). Higher fat content was observed in late lactation than early lactation. Highest butyric, caproic, linoleic, omega-6 and polyunsaturated fatty acids were observed for milk from Friesian cows. Highest conjugated fatty acids, α-linolenic acid, linoleic acid, saturated fatty acids, polyunsaturated fatty acids, omega-6, and omega-3 were observed in early lactation. Atherogenicity index and desaturase activity indices were highest in late lactation. In conclusion, stage of lactation and genotype affected milk health-related fatty acid profiles. Copyright © 2013 Elsevier Ltd. All rights reserved.

The research questions and methodological adequacy of clinical studies of the voice and larynx published in Brazilian and international journals.

PubMed

Vieira, Vanessa Pedrosa; De Biase, Noemi; Peccin, Maria Stella; Atallah, Alvaro Nagib

2009-06-01

To evaluate the methodological adequacy of voice and laryngeal study designs published in speech-language pathology and otorhinolaryngology journals indexed for the ISI Web of Knowledge (ISI Web) and the MEDLINE database. A cross-sectional study conducted at the Universidade Federal de São Paulo (Federal University of São Paulo). Two Brazilian speech-language pathology and otorhinolaryngology journals (Pró-Fono and Revista Brasileira de Otorrinolaringologia) and two international speech-language pathology and otorhinolaryngology journals (Journal of Voice, Laryngoscope), all dated between 2000 and 2004, were hand-searched by specialists. Subsequently, voice and larynx publications were separated, and a speech-language pathologist and otorhinolaryngologist classified 374 articles from the four journals according to objective and study design. The predominant objective contained in the articles was that of primary diagnostic evaluation (27%), and the most frequent study design was case series (33.7%). A mere 7.8% of the studies were designed adequately with respect to the stated objectives. There was no statistical difference in the methodological quality of studies indexed for the ISI Web and the MEDLINE database. The studies published in both national journals, indexed for the MEDLINE database, and international journals, indexed for the ISI Web, demonstrate weak methodology, with research poorly designed to meet the proposed objectives. There is much scientific work to be done in order to decrease uncertainty in the field analysed.

A new casemix adjustment index for hospital mortality among patients with congestive heart failure.

PubMed

Polanczyk, C A; Rohde, L E; Philbin, E A; Di Salvo, T G

1998-10-01

Comparative analysis of hospital outcomes requires reliable adjustment for casemix. Although congestive heart failure is one of the most common indications for hospitalization, congestive heart failure casemix adjustment has not been widely studied. The purposes of this study were (1) to describe and validate a new congestive heart failure-specific casemix adjustment index to predict in-hospital mortality and (2) to compare its performance to the Charlson comorbidity index. Data from all 4,608 admissions to the Massachusetts General Hospital from January 1990 to July 1996 with a principal ICD-9-CM discharge diagnosis of congestive heart failure were evaluated. Massachusetts General Hospital patients were randomly divided in a derivation and a validation set. By logistic regression, odds ratios for in-hospital death were computed and weights were assigned to construct a new predictive index in the derivation set. The performance of the index was tested in an internal Massachusetts General Hospital validation set and in a non-Massachusetts General Hospital external validation set incorporating data from all 1995 New York state hospital discharges with a primary discharge diagnosis of congestive heart failure. Overall in-hospital mortality was 6.4%. Based on the new index, patients were assigned to six categories with incrementally increasing hospital mortality rates ranging from 0.5% to 31%. By logistic regression, "c" statistics of the congestive heart failure-specific index (0.83 and 0.78, derivation and validation set) were significantly superior to the Charlson index (0.66). Similar incrementally increasing hospital mortality rates were observed in the New York database with the congestive heart failure-specific index ("c" statistics 0.75). In an administrative database, this congestive heart failure-specific index may be a more adequate casemix adjustment tool to predict hospital mortality in patients hospitalized for congestive heart failure.

Object-oriented structures supporting remote sensing databases

NASA Technical Reports Server (NTRS)

Wichmann, Keith; Cromp, Robert F.

1995-01-01

Object-oriented databases show promise for modeling the complex interrelationships pervasive in scientific domains. To examine the utility of this approach, we have developed an Intelligent Information Fusion System based on this technology, and applied it to the problem of managing an active repository of remotely-sensed satellite scenes. The design and implementation of the system is compared and contrasted with conventional relational database techniques, followed by a presentation of the underlying object-oriented data structures used to enable fast indexing into the data holdings.

Measuring "Equity" and "Equitability" in School Effectiveness Research

ERIC Educational Resources Information Center

Kelly, Anthony

2012-01-01

This paper introduces a Gini-type index for measuring "attainment equity" in schools; that is to say, how far a school (or group of schools) is from having a "fair" proportion of its examination success attributable to a fair proportion of its student population. Using data from the National Pupil Database, the Index is applied…

Enriched Title-Based Keyword Index Generation Using dBase II.

ERIC Educational Resources Information Center

Rajendran, P. P.

1986-01-01

Describes the use of a database management system (DBMS)--dBaseII--to create an enriched title-based keyword index for a collection of news items at the Renewable Energy Resources Information Center of the Asian Institute of Technology. The use of DBMSs in libraries in developing countries is emphasized. (Author/LRW)

Australian Education Index Data Base (AUSINET). Users Manual.

ERIC Educational Resources Information Center

Findlay, Margaret A., Comp.

This manual describes the contents, purpose, and use of the Australian Education Index Database (AEII), which is produced by the Library and Information Services Unit of the Australian Council for Educational Research to provide access to Australian generated information both in published and unpublished forms. An overview of AEII is followed by…

The Distribution of Information: The Role for Online Public Access Catalogs.

ERIC Educational Resources Information Center

Matthews, Joseph R.

1994-01-01

Describes the Online Public Access Catalog (OPAC) and the inclusion of abstracting and indexing industry databases in OPACs. Topics addressed include the implications of including abstracting and indexing tape and CD-ROM products in OPACs; the need for standards allowing library systems to communicate with dissimilar CD-ROM products; and computer,…

Hirsch's index: a case study conducted atthe Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo.

PubMed

Torro-Alves, N; Herculano, R D; Terçariol, C A S; Kinouchi Filho, O; Graeff, C F O

2007-11-01

An analysis of scientific bibliographic productivity using the Hirsch h-index, information from the Institute of Scientific Information database and the Curriculum Lattes (CNPq, Brazil) was performed at the Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (FFCLRP-USP) that has four departments in natural, biological and social sciences. Bibliometric evaluations of undergraduate programs showed a better performance of the departments of Chemistry (P < 0.001) and Biology (P < 0.001) when compared to the departments of Physics and Mathematics and Psychology and Education. We also analyzed the scientific output of the six graduate programs of FFCLRP: Psychology, Psychobiology, Chemistry, Physics Applied to Medicine and Biology, Comparative Biology, and Entomology. The graduate program in Psychology presented a lower h-index (P < 0.001) and had fewer papers indexed by the ISI web of science (P < 0.001) when compared to the other graduate programs. The poorer performance of the Psychology program may be associated with the limited coverage by the Thompson Institute of Scientific Information database.

Quantitative structure-activity relationship study of antioxidative peptide by using different sets of amino acids descriptors

NASA Astrophysics Data System (ADS)

Li, Yao-Wang; Li, Bo; He, Jiguo; Qian, Ping

2011-07-01

A database consisting of 214 tripeptides which contain either His or Tyr residue was applied to study quantitative structure-activity relationships (QSAR) of antioxidative tripeptides. Partial Least-Squares Regression analysis (PLSR) was conducted using parameters individually of each amino acid descriptor, including Divided Physico-chemical Property Scores (DPPS), Hydrophobic, Electronic, Steric, and Hydrogen (HESH), Vectors of Hydrophobic, Steric, and Electronic properties (VHSE), Molecular Surface-Weighted Holistic Invariant Molecular (MS-WHIM), isotropic surface area-electronic charge index (ISA-ECI) and Z-scale, to describe antioxidative tripeptides as X-variables and antioxidant activities measured with ferric thiocyanate methods were as Y-variable. After elimination of outliers by Hotelling's T 2 method and residual analysis, six significant models were obtained describing the entire data set. According to cumulative squared multiple correlation coefficients ( R2), cumulative cross-validation coefficients ( Q2) and relative standard deviation for calibration set (RSD c), the qualities of models using DPPS, HESH, ISA-ECI, and VHSE descriptors are better ( R2 > 0.6, Q2 > 0.5, RSD c < 0.39) than that of models using MS-WHIM and Z-scale descriptors ( R2 < 0.6, Q2 < 0.5, RSD c > 0.44). Furthermore, the predictive ability of models using DPPS descriptor is best among the six descriptors systems (cumulative multiple correlation coefficient for predict set ( Rext2) > 0.7). It was concluded that the DPPS is better to describe the amino acid of antioxidative tripeptides. The results of DPPS descriptor reveal that the importance of the center amino acid and the N-terminal amino acid are far more than the importance of the C-terminal amino acid for antioxidative tripeptides. The hydrophobic (positively to activity) and electronic (negatively to activity) properties of the N-terminal amino acid are suggested to play the most important significance to activity, followed by the hydrogen bond (positively to activity) of the center amino acid. The N-terminal amino acid should be a high hydrophobic and low electronic amino acid (such as Ala, Gly, Val, and Leu); the center amino acid would be an amino acid that possesses high hydrogen bond property (such as base amino acid Arg, Lys, and His). The structural characteristics of antioxidative peptide be found in this paper may contribute to the further research of antioxidative mechanism.

Bosnian and Herzegovinian medical scientists in PubMed database.

PubMed

Masic, Izet

2013-01-01

In this paper it is shortly presented PubMed as one of the most important on-line databases of the scientific biomedical literature. Also, the author has analyzed the most cited authors, professors of the medical faculties in Bosnia and Herzegovina, from the published papers in the biomedical journals abstracted and indexed in PubMed.

SERS internship fall 1995 abstracts and research papers

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

Davis, Beverly

1996-05-01

This report is a compilation of twenty abstracts and their corresponding full papers of research projects done under the US Department of Energy Science and Engineering Research Semester (SERS) program. Papers cover a broad range of topics, for example, environmental transport, supercomputers, databases, biology. Selected papers were indexed separately for inclusion the the Energy Science and Technology Database.

Using a Relational Database to Index Infectious Disease Information

PubMed Central

Brown, Jay A.

2010-01-01

Mapping medical knowledge into a relational database became possible with the availability of personal computers and user-friendly database software in the early 1990s. To create a database of medical knowledge, the domain expert works like a mapmaker to first outline the domain and then add the details, starting with the most prominent features. The resulting “intelligent database” can support the decisions of healthcare professionals. The intelligent database described in this article contains profiles of 275 infectious diseases. Users can query the database for all diseases matching one or more specific criteria (symptom, endemic region of the world, or epidemiological factor). Epidemiological factors include sources (patients, water, soil, or animals), routes of entry, and insect vectors. Medical and public health professionals could use such a database as a decision-support software tool. PMID:20623018

Database resources of the National Center for Biotechnology Information.

PubMed

2016-01-04

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Database resources of the National Center for Biotechnology Information.

PubMed

2015-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Importance of databases of nucleic acids for bioinformatic analysis focused to genomics

NASA Astrophysics Data System (ADS)

Jimenez-Gutierrez, L. R.; Barrios-Hernández, C. J.; Pedraza-Ferreira, G. R.; Vera-Cala, L.; Martinez-Perez, F.

2016-08-01

Recently, bioinformatics has become a new field of science, indispensable in the analysis of millions of nucleic acids sequences, which are currently deposited in international databases (public or private); these databases contain information of genes, RNA, ORF, proteins, intergenic regions, including entire genomes from some species. The analysis of this information requires computer programs; which were renewed in the use of new mathematical methods, and the introduction of the use of artificial intelligence. In addition to the constant creation of supercomputing units trained to withstand the heavy workload of sequence analysis. However, it is still necessary the innovation on platforms that allow genomic analyses, faster and more effectively, with a technological understanding of all biological processes.

Mapping the literature of nursing administration.

PubMed

Galganski, Carol J

2006-04-01

As part of Phase I of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies the core literature cited in nursing administration and the indexing services that provide access to the core journals. The results of this study will assist librarians and end users searching for information related to this nursing discipline, as well as database producers who might consider adding specific titles to their indexing services. Using the common methodology described in the overview article, five source journals for nursing administration were identified and selected for citation analysis over a three-year period, 1996 to 1998, to identify the most frequently cited titles according to Bradford's Law of Scattering. From this core of most productive journal titles, the bibliographic databases that provide the best access to these titles were identified. Results reveal that nursing administration literature relies most heavily on journal articles and on those titles identified as core nursing administrative titles. When the indexing coverage of nine services is compared, PubMed/MEDLINE and CINAHL provide the most comprehensive coverage of this nursing discipline. No one indexing service adequately covers this nursing discipline. Researchers needing comprehensive coverage in this area must search more than one database to effectively research their projects. While PubMed/MEDLINE and CINAHL provide more coverage for this discipline than the other indexing services, none is sufficiently broad in scope to provide indexing of nursing, health care management, and medical literature in a single file. Nurse administrators using the literature to research current work issues need to review not only the nursing titles covered by CINAHL but should also include the major weekly medical titles, core titles in health care administration, and general business sources if they wish to adequately cover the many aspects of nursing administration.

[The composition of nonesterified fatty acids in patients with metabolic syndrome].

PubMed

Novgorodtseva, T P; Ivanov, E M; Antoniuk, M V; Karaman, Iu K; Zhukova, N V; Iurenko, A V

2008-10-01

The blood composition of non-etherized fatty acids (NEFA) was studied in 22 patients with metabolic syndrome (MS) and 11 healthy individuals. The qualitative NEFA composition presented by 31 components of individual fatty acids was analyzed, by taking into account of glucose-insulin homeostatic changes in MS patients: those without insulin resistance (IR) (Group 1) and those with diagnosed IR (Group 2). MS patients with normal insulinemia were ascertained to have lower levels of lauric, myristic, palmitic, C24:0, C16:0i acids. With a decrease in the relative quantity of saturated NEFA, the levels of polyunsaturated fatty acids (FA) increased. The proportions of linoleic (C18:2 omega 6) and linolenic (C18:3 omega 3) acids doubled (p < 0.01), arachidonic acid (C20:4 omega 6) was observed to tend to rise. The cumulative FA index sigma omega 6 increased twofold. In Group 1, the integrated index of changes in the FA series (unsaturation index) was 41% higher than that in the control group (p < 0.05). In Group 2, the vector of changes in the relative quantity of NEFA was similar, but impairments were less marked than that in Group 1. The findings suggest that the development of insulin resistance is preceded by impaired blood cell transfer and absorption of NEFA.

Levels of eicosapentaenoic acid in obese schoolchildren with and without insulin resistance.

PubMed

Sánchez Meza, Karmina; Tene Pérez, Carlos Enrique; Sánchez Ramírez, Carmen Alicia; Muñiz Valencia, Roberto; Del Toro Equihua, Mario

2014-09-12

Obesity in children is now an increasing health risk worldwide in which the insulin-resistance can be present. Studies have linked a diet rich in n-3 fatty acids with a lower prevalence of insulin-resistance. To compare the levels of eicosapentaenoic acid among obese children with and without insulin-resistance. In 56 randomly school-age children with obesity, insulin-resistance was determined by the homeostasis model assessment for insulin-resistance index and the serum levels of eicosapentaenoic acid were determined by gas chromatography. Insulin-resistance was established when the index was >6.0, non- insulin- resistance when that index was within the range of 1.4-5.9. The serum levels of eicosapentaenoic acid were compared with the Kruskal-Wallis and Mann-Whitney U tests, as needed. No differences in age or sex were identified among the groups studied. The anthropometric parameters were significantly higher in the group of children with insulin-resistance than in the other two groups. The children with insulin- resistance had significantly lower levels of eicosapentaenoic acid than the non- insulin-resistance group [12.4% area under the curve vs. 37.4%, p = 0.031], respectively. Obese primary school-aged children with insulin-resistance had lower plasma levels of eicosapentaenoic acid. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

User assumptions about information retrieval systems: Ethical concerns

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

Froehlich, T.J.

Information professionals, whether designers, intermediaries, database producers or vendors, bear some responsibility for the information that they make available to users of information systems. The users of such systems may tend to make many assumptions about the information that a system provides, such as believing: that the data are comprehensive, current and accurate, that the information resources or databases have same degree of quality and consistency of indexing; that the abstracts, if they exist, correctly and adequate reflect the content of the article; that there is consistency informs of author names or journal titles or indexing within and across databases;more » that there is standardization in and across databases; that once errors are detected, they are corrected; that appropriate choices of databases or information resources are a relatively easy matter, etc. The truth is that few of these assumptions are valid in commercia or corporate or organizational databases. However, given these beliefs and assumptions by many users, often promoted by information providers, information professionals, impossible, should intervene to warn users about the limitations and constraints of the databases they are using. With the growth of the Internet and end-user products (e.g., CD-ROMs), such interventions have significantly declined. In such cases, information should be provided on start-up or through interface screens, indicating to users, the constraints and orientation of the system they are using. The principle of {open_quotes}caveat emptor{close_quotes} is naive and socially irresponsible: information professionals or systems have an obligation to provide some framework or context for the information that users are accessing.« less

Delay in indexing articles published in major pharmacy practice journals.

PubMed

Rodriguez, Ryan W

2014-02-15

The delay in time from entry in the PubMed database to indexing with medical subject heading (MeSH) terms for articles published in three major pharmacy practice journals was evaluated. In April 2013, MEDLINE data were retrieved for articles published in the American Journal of Health-System Pharmacy (AJHP), the Annals of Pharmacotherapy, and Pharmacotherapy between January 1, 2010, and December 31, 2011. Data collected for each article included the PubMed entry date, MeSH indexing date, and publication type. The PubMed entry date was defined as the Entrez date, the date the citation was added to the PubMed database. Medians and interquartile ranges (IQRs) were calculated for the time to indexing of articles and for the age of unindexed articles. The proportion of unindexed articles was also calculated. A total of 1626 publications were reviewed. Overall, the median time to indexing with MeSH terms was 114 days (IQR, 98-141 days): 107 days (IQR, 94-129 days) for AJHP, 131 days (IQR, 104-157 days) for Annals of Pharmacotherapy, and 114 days (IQR, 99-128 days) for Pharmacotherapy. The median age of unindexed articles was 807 days (IQR, 671-807 days). An analysis of three major pharmacy practice journals showed that the median time to indexing articles published in 2010 and 2011 was 114 days. While all articles from AJHP and Pharmacotherapy were indexed, 40 articles from Annals of Pharmacotherapy remained unindexed.

Acid sulfate soils are an environmental hazard in Finland

NASA Astrophysics Data System (ADS)

Pihlaja, Jouni

2016-04-01

Acid sulfate soils (ASS) create significant threats to the environment on coastal regions of the Baltic Sea in Finland. The sediments were deposited during the ancient Litorina Sea phase of the Baltic Sea about 7500-4500 years ago. Finland has larger spatial extent of the ASS than any other European country. Mostly based on anthropogenic reasons (cultivation, trenching etc.) ASS deposits are currently being exposed to oxygen which leads to chemical reaction creating sulfuric acid. The acidic waters then dissolve metals form the soil. Acidic surface run off including the metals are then leached into the water bodies weakening the water quality and killing fish or vegetation. In constructed areas acidic waters may corrode building materials. Geological Survey of Finland (GTK) is mapping ASS deposits in Finland. The goal is to map a total of 5 million hectares of the potentially ASS affected region. It has been estimated that the problematic Litorina Sea deposits, which are situated 0-100 m above the recent Baltic Sea shoreline, cover 500 000 hectares area. There are several phases in mapping. The work begins at the office with gathering the existing data, interpreting airborne geophysical data and compiling a field working plan. In the field, quality of the soil is studied and in uncertain cases samples are taken to laboratory analyses. Also electrical conductivity and pH of soil and water are measured in the field. Laboratory methods include multielemental determinations with ICP-OES, analyses of grain size and humus content (LOI), and incubation. So far, approximately 60 % of the potential ASS affected regions in Finland are mapped. Over 15 000 sites have been studied in the field and 4000 laboratory analyses are done. The spatial database presented in the scale of 1: 250 000 can be viewed at the GTK's web pages (http://gtkdata.gtk.fi/hasu/index.html).

Query Refinement: Negation Detection and Proximity Learning Georgetown at TREC 2014 Clinical Decision Support Track

DTIC Science & Technology

2014-11-01

created to serve as idealized representations of actual medical records, and include information such as medical history , current symptoms, diagnosis...NLM Medical Text Indexer (MTI).3 MeSH, or Medical Subject Headings, are terminology used by the NLM to index articles, catalog books, and searching...MeSH- indexed databases such as PubMed. However, since many medical conditions may be expressed in varying terminology , a single representation of a

SNPdbe: constructing an nsSNP functional impacts database.

PubMed

Schaefer, Christian; Meier, Alice; Rost, Burkhard; Bromberg, Yana

2012-02-15

Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe-SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from >2600 organisms; 'human' being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs. http://www.rostlab.org/services/snpdbe.

A Hybrid Spatio-Temporal Data Indexing Method for Trajectory Databases

PubMed Central

Ke, Shengnan; Gong, Jun; Li, Songnian; Zhu, Qing; Liu, Xintao; Zhang, Yeting

2014-01-01

In recent years, there has been tremendous growth in the field of indoor and outdoor positioning sensors continuously producing huge volumes of trajectory data that has been used in many fields such as location-based services or location intelligence. Trajectory data is massively increased and semantically complicated, which poses a great challenge on spatio-temporal data indexing. This paper proposes a spatio-temporal data indexing method, named HBSTR-tree, which is a hybrid index structure comprising spatio-temporal R-tree, B*-tree and Hash table. To improve the index generation efficiency, rather than directly inserting trajectory points, we group consecutive trajectory points as nodes according to their spatio-temporal semantics and then insert them into spatio-temporal R-tree as leaf nodes. Hash table is used to manage the latest leaf nodes to reduce the frequency of insertion. A new spatio-temporal interval criterion and a new node-choosing sub-algorithm are also proposed to optimize spatio-temporal R-tree structures. In addition, a B*-tree sub-index of leaf nodes is built to query the trajectories of targeted objects efficiently. Furthermore, a database storage scheme based on a NoSQL-type DBMS is also proposed for the purpose of cloud storage. Experimental results prove that HBSTR-tree outperforms TB*-tree in some aspects such as generation efficiency, query performance and query type. PMID:25051028

A hybrid spatio-temporal data indexing method for trajectory databases.

PubMed

Ke, Shengnan; Gong, Jun; Li, Songnian; Zhu, Qing; Liu, Xintao; Zhang, Yeting

2014-07-21

In recent years, there has been tremendous growth in the field of indoor and outdoor positioning sensors continuously producing huge volumes of trajectory data that has been used in many fields such as location-based services or location intelligence. Trajectory data is massively increased and semantically complicated, which poses a great challenge on spatio-temporal data indexing. This paper proposes a spatio-temporal data indexing method, named HBSTR-tree, which is a hybrid index structure comprising spatio-temporal R-tree, B*-tree and Hash table. To improve the index generation efficiency, rather than directly inserting trajectory points, we group consecutive trajectory points as nodes according to their spatio-temporal semantics and then insert them into spatio-temporal R-tree as leaf nodes. Hash table is used to manage the latest leaf nodes to reduce the frequency of insertion. A new spatio-temporal interval criterion and a new node-choosing sub-algorithm are also proposed to optimize spatio-temporal R-tree structures. In addition, a B*-tree sub-index of leaf nodes is built to query the trajectories of targeted objects efficiently. Furthermore, a database storage scheme based on a NoSQL-type DBMS is also proposed for the purpose of cloud storage. Experimental results prove that HBSTR-tree outperforms TB*-tree in some aspects such as generation efficiency, query performance and query type.

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.

Multidimensional indexing structure for use with linear optimization queries

NASA Technical Reports Server (NTRS)

Bergman, Lawrence David (Inventor); Castelli, Vittorio (Inventor); Chang, Yuan-Chi (Inventor); Li, Chung-Sheng (Inventor); Smith, John Richard (Inventor)

2002-01-01

Linear optimization queries, which usually arise in various decision support and resource planning applications, are queries that retrieve top N data records (where N is an integer greater than zero) which satisfy a specific optimization criterion. The optimization criterion is to either maximize or minimize a linear equation. The coefficients of the linear equation are given at query time. Methods and apparatus are disclosed for constructing, maintaining and utilizing a multidimensional indexing structure of database records to improve the execution speed of linear optimization queries. Database records with numerical attributes are organized into a number of layers and each layer represents a geometric structure called convex hull. Such linear optimization queries are processed by searching from the outer-most layer of this multi-layer indexing structure inwards. At least one record per layer will satisfy the query criterion and the number of layers needed to be searched depends on the spatial distribution of records, the query-issued linear coefficients, and N, the number of records to be returned. When N is small compared to the total size of the database, answering the query typically requires searching only a small fraction of all relevant records, resulting in a tremendous speedup as compared to linearly scanning the entire dataset.

Risk model of valve surgery in Japan using the Japan Adult Cardiovascular Surgery Database.

PubMed

Motomura, Noboru; Miyata, Hiroaki; Tsukihara, Hiroyuki; Takamoto, Shinichi

2010-11-01

Risk models of cardiac valve surgery using a large database are useful for improving surgical quality. In order to obtain accurate, high-quality assessments of surgical outcome, each geographic area should maintain its own database. The study aim was to collect Japanese data and to prepare a risk stratification of cardiac valve procedures, using the Japan Adult Cardiovascular Surgery Database (JACVSD). A total of 6562 valve procedure records from 97 participating sites throughout Japan was analyzed, using a data entry form with 255 variables that was sent to the JACVSD office from a web-based data collection system. The statistical model was constructed using multiple logistic regression. Model discrimination was tested using the area under the receiver operating characteristic curve (C-index). The model calibration was tested using the Hosmer-Lemeshow (H-L) test. Among 6562 operated cases, 15% had diabetes mellitus, 5% were urgent, and 12% involved preoperative renal failure. The observed 30-day and operative mortality rates were 2.9% and 4.0%, respectively. Significant variables with high odds ratios included emergent or salvage status (3.83), reoperation (3.43), and left ventricular dysfunction (3.01). The H-L test and C-index values for 30-day mortality were satisfactory (0.44 and 0.80, respectively). The results obtained in Japan were at least as good as those reported elsewhere. The performance of this risk model also matched that of the STS National Adult Cardiac Database and the European Society Database.

Physicochemical Quality, Fatty Acid Composition, and Sensory Analysis of Nellore Steers Meat Fed with Inclusion of Condensed Tannin in the Diet.

PubMed

Gesteira, Susana M; Oliveira, Ronaldo L; Silva, Thadeu M; Ribeiro, Rebeca D X; Ribeiro, Cláudio V D M; Pereira, Elzania S; Lanna, Dante P D; Pinto, Luis F B; Rocha, Tiago C; Vieira, Jusaline F; Bezerra, Leilson R

2018-05-01

This study was conducted to test the effect of dietary tannin on the fatty acid profile and sensory attributes of meat from Nellore steers. Thirty-two Nellore bull male were distributed in a completely randomized design and fed diets with condensed tannin extract as follows: 0, 10, 30, and 50 g/kg total DM basis. The physicochemical composition of the meat, lipid oxidation, fatty acid profile, flavor, tenderness, and overall acceptance were evaluated. There was a linear decrease (P ≤ 0.05) on lipid content, tenderness, cooking weight loss, myristic, palmitic, and oleic acids in meat as tannin increased in the diets. The total saturated and monounsaturated fatty acids, the atherogenicity index decreased. However, a linear increase (P ≤ 0.05) was observed for linoleic, linolenic, arachidonic, eicosapentaenoic, and docosapentaenoic acids. The physicochemical characteristic of the meat, such as moisture, ash, and protein contents, water retention capacity, final pH, Warner-Bratzler shear force, collagen, and color indexes (lightness, redness, yellowness, and chrome) did not change with dietary tannin. Also, CLA, n-6:n-3 ratio, Δ 9 -desaturase, and elongase activity were not different among diets. In conclusion, condensed tannin linearly increases unsaturated fatty acids and decreases the atherogenicity index of meat; thus, it can be recommended at the highest level (50 g/kg DM) in the diet of Nellore steers. Agriculture byproducts plays an important part in the diet of ruminant animals and consequently on food chain and has implications for the composition and quality of the livestock products (milk, meat, and eggs) that people consume. Feeding tannin to steers increases the amount of unsaturated fatty acids and meat tenderness, with a concomitant reduction on saturated fatty acids and the atherogenicity index in meat. Thus, we recommend adding tannin to steer diets to reduce the risk factors for cardiovascular diseases in red meat for human consumption. © 2018 Institute of Food Technologists®.

Esophageal chemical clearance and baseline impedance values in patients with chronic autoimmune atrophic gastritis and gastro-esophageal reflux disease.

PubMed

Tenca, Andrea; de Bortoli, Nicola; Mauro, Aurelio; Frazzoni, Marzio; Savarino, Edoardo; Massironi, Sara; Russo, Salvatore; Bertani, Lorenzo; Marchi, Santino; Penagini, Roberto

2017-09-01

The factors influencing new markers of gastro-esophageal reflux disease detected by impedance-pH monitoring - mean nocturnal baseline impedance (MNBI) and post-reflux swallow-induced peristaltic wave (PSPW) index - need to be evaluated. To compare endoscopy-negative heartburn with chronic autoimmune atrophic gastritis (CAAG). 24 patients with CAAG, 25 with non-erosive reflux disease (NERD) and 25 with functional heartburn (FH) were included. In all patients the main impedance-pH monitoring parameters were calculated. CAAG and NERD patients had a number of reflux events (non-acid ones being more common among the former group) which was higher than that found in FH (p<0.001). MNBI decreased progressively in FH (>3000Ohm), CAAG (>2000Ohm) and NERD (<1000Ohm) patients (p=0.0046). The PSPW index was similar between CAAG and NERD patients but significantly lower in comparison to FH (p<0.0001). Patients with CAAG have evidence of non-acid reflux based on the high number of reflux events and confirmed by low values of MNBI and PSPW index. MNBI is a strong marker of acid/non-acid reflux-induced mucosal damage, whereas the PSPW index can reliably discriminate patients with reflux from those with FH, independently of the acidity of refluxate. Copyright © 2017 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

The Aerospace Database data element dictionary with issues and recommendations from the meetings of July 24-25, August 13-14, and September 24-25, 1991

NASA Technical Reports Server (NTRS)

1991-01-01

The present volume contains descriptions of the individual fields (data elements) which comprise the bibliographic records of the Aerospace Database. Indexes by field name and field mnemonic are provided. In addition, the issues and recommendations defined by the NASA STI Database Upgrade Working Group are included as annotations to the individual field descriptions and are listed at the end of the volume. The activities of the Working Group were initiated by the NASA STI Program Coordinating Council as part of an effort to improve overall database quality.

Bibliometric trend and patent analysis in nano-alloys research for period 2000-2013.

PubMed

Živković, Dragana; Niculović, Milica; Manasijević, Dragan; Minić, Duško; Ćosović, Vladan; Sibinović, Maja

2015-05-04

This paper presents an overview of current situation in nano-alloys investigations based on bibliometric and patent analysis. Bibliometric analysis data, for period from 2000 to September 2013, were obtained using Scopus database as selected index database, whereas analyzed parameters were: number of scientific papers per years, authors, countries, affiliations, subject areas and document types. Analysis of nano-alloys patents was done with specific database, using the International Patent Classification and Patent Scope for the period from 2003 to 2013 year. Information found in this database was the number of patents, patent classification by country, patent applicators, main inventors and pub date.

Bibliometric trend and patent analysis in nano-alloys research for period 2000-2013.

PubMed

Živković, Dragana; Niculović, Milica; Manasijević, Dragan; Minić, Duško; Ćosović, Vladan; Sibinović, Maja

2015-01-01

This paper presents an overview of current situation in nano-alloys investigations based on bibliometric and patent analysis. Bibliometric analysis data, for the period 2000 to 2013, were obtained using Scopus database as selected index database, whereas analyzed parameters were: number of scientific papers per year, authors, countries, affiliations, subject areas and document types. Analysis of nano-alloys patents was done with specific database, using the International Patent Classification and Patent Scope for the period 2003 to 2013. Information found in this database was the number of patents, patent classification by country, patent applicators, main inventors and publication date.

The Index to Marine and Lacustrine Geological Samples (IMLGS): Linking Digital Data to Physical Samples for the Marine Community

NASA Astrophysics Data System (ADS)

Stroker, K. J.; Jencks, J. H.; Eakins, B.

2016-12-01

The Index to Marine and Lacustrine Geological Samples (IMLGS) is a community designed and maintained resource enabling researchers to locate and request seafloor and lakebed geologic samples curated by partner institutions. The Index was conceived in the dawn of the digital age by representatives from U.S. academic and government marine core repositories and the NOAA National Geophysical Data Center, now the National Centers for Environmental Information (NCEI), at a 1977 meeting convened by the National Science Foundation (NSF). The Index is based on core concepts of community oversight, common vocabularies, consistent metadata and a shared interface. The Curators Consortium, international in scope, meets biennially to share ideas and discuss best practices. NCEI serves the group by providing database access and maintenance, a list server, digitizing support and long-term archival of sample metadata, data and imagery. Over three decades, participating curators have performed the laborious task of creating and contributing metadata for over 205,000 sea floor and lake-bed cores, grabs, and dredges archived in their collections. Some partners use the Index for primary web access to their collections while others use it to increase exposure of more in-depth institutional systems. The IMLGS has a persistent URL/Digital Object Identifier (DOI), as well as DOIs assigned to partner collections for citation and to provide a persistent link to curator collections. The Index is currently a geospatially-enabled relational database, publicly accessible via Web Feature and Web Map Services, and text- and ArcGIS map-based web interfaces. To provide as much knowledge as possible about each sample, the Index includes curatorial contact information and links to related data, information and images : 1) at participating institutions, 2) in the NCEI archive, and 3) through a Linked Data interface maintained by the Rolling Deck to Repository R2R. Over 43,000 International GeoSample Numbers (IGSNs) linking to the System for Earth Sample Registration (SESAR) are included in anticipation of opportunities for interconnectivity with Integrated Earth Data Applications (IEDA) systems. The paper will discuss the database with a goal to increase the connections and links to related data at partner institutions.

PASCAL Data Base File Description and Indexing Rules in Chemistry, Biology and Medicine.

ERIC Educational Resources Information Center

Gaillardin, R.; And Others

This report on the multidisciplinary PASCAL database describes the files and the indexing rules for chemistry, biology, and medicine. PASCAL deals with all aspects of chemistry within two subfiles whose combined yearly growth is about 100,000 references. The Biopascal file, organized in the two subfiles of Plant Science and Biology and Medicine,…

Trends of E-Learning Research from 2000 to 2008: Use of Text Mining and Bibliometrics

ERIC Educational Resources Information Center

Hung, Jui-long

2012-01-01

This study investigated the longitudinal trends of e-learning research using text mining techniques. Six hundred and eighty-nine (689) refereed journal articles and proceedings were retrieved from the Science Citation Index/Social Science Citation Index database in the period from 2000 to 2008. All e-learning publications were grouped into two…

Indexing and Retrieval in ERIC: The 20th Year.

ERIC Educational Resources Information Center

Barnett, Lynn

This brief review of the Educational Resources Information Center (ERIC) system is intended to make users more aware of (1) the system as a whole, (2) the process of indexing educational literature for the database, and (3) the role of the Thesaurus of ERIC Descriptors in the overall information dissemination process. An overview of the ERIC…

Mind Maps: Hot New Tools Proposed for Cyberspace Librarians.

ERIC Educational Resources Information Center

Humphreys, Nancy K.

1999-01-01

Describes how online searchers can use a software tool based on back-of-the-book indexes to assist in dealing with search engine databases compiled by spiders that crawl across the entire Internet or through large Web sites. Discusses human versus machine knowledge, conversion of indexes to mind maps or mini-thesauri, middleware, eXtensible Markup…

Indexing and retrieving motions of characters in close contact.

PubMed

Ho, Edmond S L; Komura, Taku

2009-01-01

Human motion indexing and retrieval are important for animators due to the need to search for motions in the database which can be blended and concatenated. Most of the previous researches of human motion indexing and retrieval compute the Euclidean distance of joint angles or joint positions. Such approaches are difficult to apply for cases in which multiple characters are closely interacting with each other, as the relationships of the characters are not encoded in the representation. In this research, we propose a topology-based approach to index the motions of two human characters in close contact. We compute and encode how the two bodies are tangled based on the concept of rational tangles. The encoded relationships, which we define as TangleList, are used to determine the similarity of the pairs of postures. Using our method, we can index and retrieve motions such as one person piggy-backing another, one person assisting another in walking, and two persons dancing / wrestling. Our method is useful to manage a motion database of multiple characters. We can also produce motion graph structures of two characters closely interacting with each other by interpolating and concatenating topologically similar postures and motion clips, which are applicable to 3D computer games and computer animation.

Compressed-domain video indexing techniques using DCT and motion vector information in MPEG video

NASA Astrophysics Data System (ADS)

Kobla, Vikrant; Doermann, David S.; Lin, King-Ip; Faloutsos, Christos

1997-01-01

Development of various multimedia applications hinges on the availability of fast and efficient storage, browsing, indexing, and retrieval techniques. Given that video is typically stored efficiently in a compressed format, if we can analyze the compressed representation directly, we can avoid the costly overhead of decompressing and operating at the pixel level. Compressed domain parsing of video has been presented in earlier work where a video clip is divided into shots, subshots, and scenes. In this paper, we describe key frame selection, feature extraction, and indexing and retrieval techniques that are directly applicable to MPEG compressed video. We develop a frame-type independent representation of the various types of frames present in an MPEG video in which al frames can be considered equivalent. Features are derived from the available DCT, macroblock, and motion vector information and mapped to a low-dimensional space where they can be accessed with standard database techniques. The spatial information is used as primary index while the temporal information is used to enhance the robustness of the system during the retrieval process. The techniques presented enable fast archiving, indexing, and retrieval of video. Our operational prototype typically takes a fraction of a second to retrieve similar video scenes from our database, with over 95% success.

Electronic and Optical Sources of Information for the Humanities: A Survey of Library Users, Products and Projects in Italy.

ERIC Educational Resources Information Center

Paci, Augusta Maria; And Others

1990-01-01

Discussion of electronic information products for the humanities focuses on users in Italy. Databases are discussed; a user survey of La Sapienza University Arts Faculty is described; an example of research using two databases, FRANCIS and Philosopher's Index, is given; and Italian products and projects for the humanities are reviewed. (15…

Specific character of citations in historiography (using the example of Polish history).

PubMed

Kolasa, Władysław Marek

2012-03-01

The first part of the paper deals with the assessment of international databases in relation to the number of historical publications (representation and relevance in comparison with the model database). The second part is focused on providing answer to the question whether historiography is governed by similar bibliometric rules as exact sciences or whether it has its own specific character. Empirical database for this part of the research constituted the database prepared ad hoc: The Citation Index of the History of Polish Media (CIHPM). Among numerous typically historical features the main focus was put on: linguistic localism, specific character of publishing forms, differences in citing of various sources (contributions and syntheses) and specific character of the authorship (the Lorenz Curve and the Lotka's Law). Slightly more attention was devoted to the half-life indicator and its role in a diachronic study of a scientific field; also, a new indicator (HL14), depicting distribution of citations younger then half-life was introduced. Additionally, the comparison and correlation of selected parameters for the body of historical science (citations, HL14, the Hirsch Index, number of publications, volume and other) were also conducted.

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

PubMed Central

Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D.; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll.

2016-01-01

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. PMID:26612862

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.

Method for the reduction of image content redundancy in large image databases

DOEpatents

Tobin, Kenneth William; Karnowski, Thomas P.

2010-03-02

A method of increasing information content for content-based image retrieval (CBIR) systems includes the steps of providing a CBIR database, the database having an index for a plurality of stored digital images using a plurality of feature vectors, the feature vectors corresponding to distinct descriptive characteristics of the images. A visual similarity parameter value is calculated based on a degree of visual similarity between features vectors of an incoming image being considered for entry into the database and feature vectors associated with a most similar of the stored images. Based on said visual similarity parameter value it is determined whether to store or how long to store the feature vectors associated with the incoming image in the database.

Methodology for adding glycemic index and glycemic load values to 24-hour dietary recall database.

PubMed

Olendzki, Barbara C; Ma, Yunsheng; Culver, Annie L; Ockene, Ira S; Griffith, Jennifer A; Hafner, Andrea R; Hebert, James R

2006-01-01

We describe a method of adding the glycemic index (GI) and glycemic load (GL) values to the nutrient database of the 24-hour dietary recall interview (24HR), a widely used dietary assessment. We also calculated daily GI and GL values from the 24HR. Subjects were 641 healthy adults from central Massachusetts who completed 9067 24HRs. The 24HR-derived food data were matched to the International Table of Glycemic Index and Glycemic Load Values. The GI values for specific foods not in the table were estimated against similar foods according to physical and chemical factors that determine GI. Mixed foods were disaggregated into individual ingredients. Of 1261 carbohydrate-containing foods in the database, GI values of 602 foods were obtained from a direct match (47.7%), accounting for 22.36% of dietary carbohydrate. GI values from 656 foods (52.1%) were estimated, contributing to 77.64% of dietary carbohydrate. The GI values from three unknown foods (0.2%) could not be assigned. The average daily GI was 84 (SD 5.1, white bread as referent) and the average GL was 196 (SD 63). Using this methodology for adding GI and GL values to nutrient databases, it is possible to assess associations between GI and/or GL and body weight and chronic disease outcomes (diabetes, cancer, heart disease). This method can be used in clinical and survey research settings where 24HRs are a practical means for assessing diet. The implications for using this methodology compel a broader evaluation of diet with disease outcomes.

New database for improving virtual system “body-dress”

NASA Astrophysics Data System (ADS)

Yan, J. Q.; Zhang, S. C.; Kuzmichev, V. E.; Adolphe, D. C.

2017-10-01

The aim of this exploration is to develop a new database of solid algorithms and relations between the dress fit and the fabric mechanical properties, the pattern block construction for improving the reality of virtual system “body-dress”. In virtual simulation, the system “body-clothing” sometimes shown distinct results with reality, especially when important changes in pattern block and fabrics were involved. In this research, to enhance the simulation process, diverse fit parameters were proposed: bottom height of dress, angle of front center contours, air volume and its distribution between dress and dummy. Measurements were done and optimized by ruler, camera, 3D body scanner image processing software and 3D modeling software. In the meantime, pattern block indexes were measured and fabric properties were tested by KES. Finally, the correlation and linear regression equations between indexes of fabric properties, pattern blocks and fit parameters were investigated. In this manner, new database could be extended in programming modules of virtual design for more realistic results.

Concept-oriented indexing of video databases: toward semantic sensitive retrieval and browsing.

PubMed

Fan, Jianping; Luo, Hangzai; Elmagarmid, Ahmed K

2004-07-01

Digital video now plays an important role in medical education, health care, telemedicine and other medical applications. Several content-based video retrieval (CBVR) systems have been proposed in the past, but they still suffer from the following challenging problems: semantic gap, semantic video concept modeling, semantic video classification, and concept-oriented video database indexing and access. In this paper, we propose a novel framework to make some advances toward the final goal to solve these problems. Specifically, the framework includes: 1) a semantic-sensitive video content representation framework by using principal video shots to enhance the quality of features; 2) semantic video concept interpretation by using flexible mixture model to bridge the semantic gap; 3) a novel semantic video-classifier training framework by integrating feature selection, parameter estimation, and model selection seamlessly in a single algorithm; and 4) a concept-oriented video database organization technique through a certain domain-dependent concept hierarchy to enable semantic-sensitive video retrieval and browsing.

Our journey to digital curation of the Jeghers Medical Index.

PubMed

Gawdyda, Lori; Carter, Kimbroe; Willson, Mark; Bedford, Denise

2017-07-01

Harold Jeghers, a well-known medical educator of the twentieth century, maintained a print collection of about one million medical articles from the late 1800s to the 1990s. This case study discusses how a print collection of these articles was transformed to a digital database. Staff in the Jeghers Medical Index, St. Elizabeth Youngstown Hospital, converted paper articles to Adobe portable document format (PDF)/A-1a files. Optical character recognition was used to obtain searchable text. The data were then incorporated into a specialized database. Lastly, articles were matched to PubMed bibliographic metadata through automation and human review. An online database of the collection was ultimately created. The collection was made part of a discovery search service, and semantic technologies have been explored as a method of creating access points. This case study shows how a small medical library made medical writings of the nineteenth and twentieth centuries available in electronic format for historic or semantic research, highlighting the efficiencies of contemporary information technology.

Comparison of leucine and dispensable amino acid kinetics between Indian women with low or normal body mass indexes during pregnancy

USDA-ARS?s Scientific Manuscript database

Evidence suggests that in women with a normal to high body mass index (BMI; in kg/m(2)), the extra amino acids needed during pregnancy are met through reduced oxidation. It is not known whether a woman with a low BMI can make this adaptation successfully. The objective was to measure and compare leu...

[Faba bean fusarium wilt (Fusarium oxysporum )control and its mechanism in different wheat varieties and faba bean intercropping system].

PubMed

Dong, Yan; Dong, Kun; Zheng, Yi; Tang, Li; Yang, Zhi-Xian

2014-07-01

Field experiment and hydroponic culture were conducted to investigate effects of three wheat varieties (Yunmai 42, Yunmai 47 and Mianyang 29) and faba bean intercropping on the shoot biomass, disease index of fusarium wilt, functional diversity of microbial community and the amount of Fusarium oxysporum in rhizosphere of faba bean. Contents and components of the soluble sugars, free amino acids and organic acids in the root exudates were also examined. Results showed that, compared with monocropped faba bean, shoot biomass of faba bean significantly increased by 16.6% and 13.4%, disease index of faba bean fusarium wilt significantly decreased by 47.6% and 23.3% as intercropped with Yunmai 42 and Yunmai 47, but no significant differences of both shoot biomass and disease index were found as intercropped with Mianyang 29. Compared with monocropped faba bean, the average well color development (AWCD value) and total utilization ability of carbon sources of faba bean significantly increased, the amount of Fusarium oxysporum of faba bean rhizosphere significantly decreased, and the microbial community structures of faba bean rhizosphere changed as intercropped with YM42 and YM47, while no significant effects as intercropped with MY29. Total contents of soluble sugar, free amino acids and organic acids in root exudates were in the trend of MY29>YM47>YM42. Contents of serine, glutamic, glycine, valine, methionine, phenylalanine, lysine in root exudates of MY29 were significantly higher than that in YM42 and YM47. The arginine was detected only in the root exudates of YM42 and YM47, and leucine was detected only in the root exudates of MY29. Six organic acids of tartaric acid, malic acid, citric acid, succinic acid, fumaric acid, t-aconitic acid were detected in root exudates of MY29 and YM47, and four organic acids of tartaric acid, malic acid, citric acid, fumaric acid were detected in root exudates of YM42. Malic acid content in root exudates of YM47 and MY29 was significantly higher than that of YM42. In conclusion, intercropping influenced the microbial activity and substrate utilization of soil microorganisms, altered the microbial community diversity in rhizosphere of faba bean, reduced the amount of F. oxysporum and disease index of faba bean fusarium wilt, and promoted faba bean growth. Effects of intercropping on disease control were influenced by the intercropped wheat variety, suggesting that the differences of root exudates of wheat were important factors that affected soil-borne diseases control in intercropping.

IRIS Toxicological Review of Trichloroacetic Acid (TCA) ...

EPA Pesticide Factsheets

EPA is conducting a peer review and public comment of the scientific basis supporting the human health hazard and dose-response assessment of Trichloroacetic acid (TCA) that when finalized will appear on the Integrated Risk Information System (IRIS) database. The draft Toxicological Review of trichloroacetic acid provides scientific support and rationale for the hazard and dose-response assessment pertaining to chronic exposure to trichloroacetic acid.

Dichloroacetic acid

Integrated Risk Information System (IRIS)

Dichloroacetic acid ; CASRN 79 - 43 - 6 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogeni

Phosphoric acid

Integrated Risk Information System (IRIS)

Phosphoric acid ; CASRN 7664 - 38 - 2 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic

The physical and empirical basis for a specific clear-air turbulence risk index

NASA Technical Reports Server (NTRS)

Keller, J. L.

1985-01-01

An improved operational CAT detection and forecasting technique is developed and detailed. This technique is the specific clear air turbulence risk (SCATR) index. This index shows some promising results. The improvements seen using hand analyzed data, as a result of the more realistic representation of the vertical shear of the horizontal wind, are also realized in the data analysis used in the PROFS/CWP application. The SCATR index should improve as database enhancements such as profiler and VAS satellite data, which increase the resolution in space and time, are brought into even more sophisticated objective analysis schemes.

Effects of Fish Oil Supplementation on Gestational Diabetes Mellitus (GDM): A Systematic Review

PubMed Central

Ostadrahimi, Alireza; Mohammad-Alizadeh, Sakineh; Mirgafourvand, Mozhgan; Yaghoubi, Sina; Shahrisa, Elham; Farshbaf-Khalili, Azizeh

2016-01-01

Context One of the most common complications of pregnancy is gestational diabetes mellitus (GDM), which is increasing worldwide. Experimental and epidemiological studies have shown that higher intake of n-3 long-chain polyunsaturated fatty acids may decrease the risk of various diseases such as diabetes. The objective of this study was to assess the effect of fish oil supplementation on the prevention and treatment of GDM. Evidence Acquisition This systematic review was performed by searching several databases, including PubMed, Scopus, Google Scholar, the Cochrane Library, ProQuest, Science Direct SID, Magiran and IranMedex since 1983. The researchers also searched for references in reviewed clinical trial articles in which fish oil supplementation was compared with placebo or no supplementation. Results Only two published and in-press articles are included in this review. Based on these studies, docosahexaenoic acid (DHA)-enriched fish oil (800 mg/d) had no effect on prevention of GDM [0.97 (95% CI: 0.74, 1.27)]. Furthermore, omega-3 fatty acid supplementation containing 180 mg of eicosapentaenoic acid (EPA) and 120 mg DHA had beneficial effects on insulin resistance in women with GDM (change from baseline: 1.5 ± 7.5 vs ‏3.5 ± 8.5 mIU/mL, P = 0.02) but did not influence fasting plasma glucose, homeostatic model assessment-Beta cell function (HOMA-B), the quantitative insulin sensitivity check index (QUICKI), or lipid profiles (P > 0.05). Conclusions There is not enough evidence to support or refute the routine use of fish oil supplements during pregnancy for the prevention or treatment of diabetes. It is suggested that further randomized controlled trials be conducted to evaluate the role of fish oil supplementation in pregnancy. PMID:28191333

A guide to experimental particle physics literature, 1991-1996

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

Ezhela, V.V.; Filimonov, B.B.; Lugovsky, S.B.

1996-10-01

We present an indexed guide to experimental particle physics literature for the years 1991 - 1996. Approximately 4200 papers are indexed by (1) Beam/Target/Momentum (2) Reaction/Momentum/Data-Descriptor (including the final state) (3) Particle/Decay (4) Accelerator/Experiment/Detector. All indices are cross-referenced to the paper`s title and references in the ID/Reference/Title index. The information presented in this guide is also publicly available on a regularly-updated DATAGUIDE database from the World Wide Web.

SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

PubMed

Ramu, Chenna

2003-07-01

SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

Red blood cell oleic acid levels reflect olive oil intake while omega-3 levels reflect fish intake and the use of omega-3 acid ethyl esters: The Gruppo Italiano per lo Studio della Sopravvivenza nell'Infarto Miocardico-Heart Failure trial.

PubMed

Harris, William S; Masson, Serge; Barlera, Simona; Milani, Valentina; Pileggi, Silvana; Franzosi, Maria Grazia; Marchioli, Roberto; Tognoni, Gianni; Tavazzi, Luigi; Latini, Roberto

2016-09-01

The Gruppo Italiano per lo Studio della Sopravvivenza nell'Infarto Miocardico-Heart Failure (GISSI-HF) study reported benefits of n-3 fatty acid (FA) treatment on cardiovascular (CV) events, but the effects of treatment on a putative CV disease risk factor, the red blood cell (RBC) n-3 FA level (the omega-3 index), have not been examined in this context. We hypothesized that treatment with prescription omega-3 acid ethyl esters (O3AEE) would increase the omega-3 index to the proposed cardioprotective value of 8%. RBCs were collected from a subset of patients participating in the GISSI-HF study (n=461 out of 6975 randomized), at baseline and after 3 months of treatment with either an olive oil placebo or O3AEE (1 g/d). RBC FA levels were expressed as a percentage of total FA. Patients also reported their typical olive oil and fish intakes. RBC oleic acid levels were directly correlated with reported frequency of olive oil consumption, and the omega-3 index was correlated with reported fish intake (P for trends <0.001 for both). After treatment, the omega-3 index increased from 4.8±1.7% to 6.7±1.9% but was unchanged in the placebo group (4.7±1.7 to 4.8±1.5%) (P<.0001 for changes between groups). At 3 months, more patients reached the proposed target omega-3 index level of 8%-12% in the treated vs placebo group (22.6% vs. 1.3%, P<.0001), however, what omega-3 index levels were ultimately achieved after four years in this trial are unknown. Copyright © 2016 Elsevier Inc. All rights reserved.

Definitions of database files and fields of the Personal Computer-Based Water Data Sources Directory

USGS Publications Warehouse

Green, J. Wayne

1991-01-01

This report describes the data-base files and fields of the personal computer-based Water Data Sources Directory (WDSD). The personal computer-based WDSD was derived from the U.S. Geological Survey (USGS) mainframe computer version. The mainframe version of the WDSD is a hierarchical data-base design. The personal computer-based WDSD is a relational data- base design. This report describes the data-base files and fields of the relational data-base design in dBASE IV (the use of brand names in this abstract is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey) for the personal computer. The WDSD contains information on (1) the type of organization, (2) the major orientation of water-data activities conducted by each organization, (3) the names, addresses, and telephone numbers of offices within each organization from which water data may be obtained, (4) the types of data held by each organization and the geographic locations within which these data have been collected, (5) alternative sources of an organization's data, (6) the designation of liaison personnel in matters related to water-data acquisition and indexing, (7) the volume of water data indexed for the organization, and (8) information about other types of data and services available from the organization that are pertinent to water-resources activities.

Document image database indexing with pictorial dictionary

NASA Astrophysics Data System (ADS)

Akbari, Mohammad; Azimi, Reza

2010-02-01

In this paper we introduce a new approach for information retrieval from Persian document image database without using Optical Character Recognition (OCR).At first an attribute called subword upper contour label is defined then, a pictorial dictionary is constructed based on this attribute for the subwords. By this approach we address two issues in document image retrieval: keyword spotting and retrieval according to the document similarities. The proposed methods have been evaluated on a Persian document image database. The results have proved the ability of this approach in document image information retrieval.

Bioisostere Identification by Determining the Amino Acid Binding Preferences of Common Chemical Fragments.

PubMed

Sato, Tomohiro; Hashimoto, Noriaki; Honma, Teruki

2017-12-26

To assist in the structural optimization of hit/lead compounds during drug discovery, various computational approaches to identify potentially useful bioisosteric conversions have been reported. Here, the preference of chemical fragments to hydrogen bonds with specific amino acid residues was used to identify potential bioisosteric conversions. We first compiled a data set of chemical fragments frequently occurring in complex structures contained in the Protein Data Bank. We then used a computational approach to determine the amino acids to which these chemical fragments most frequently hydrogen bonded. The results of the frequency analysis were used to hierarchically cluster chemical fragments according to their amino acid preferences. The Euclid distance between amino acid preferences of chemical fragments for hydrogen bonding was then compared to MMP information in the ChEMBL database. To demonstrate the applicability of the approach for compound optimization, the similarity of amino acid preferences was used to identify known bioisosteric conversions of the epidermal growth factor receptor inhibitor gefitinib. The amino acid preference distance successfully detected bioisosteric fragments corresponding to the morpholine ring in gefitinib with a higher ROC score compared to those based on topological similarity of substituents and frequency of MMP in the ChEMBL database.

Indexation of cardiac output to biometric parameters in critically ill patients: A systematic analysis of a transpulmonary thermodilution-derived database.

PubMed

Saugel, Bernd; Mair, Sebastian; Götz, Simon Q; Tschirdewahn, Julia; Frank, Johanna; Höllthaler, Josef; Schmid, Roland M; Huber, Wolfgang

2015-10-01

Cardiac output (CO) (liters per minute) is usually normalized (ie, indexed) to the patient's body surface area (BSA) resulting in the hemodynamic variable cardiac index (CI) (liters per minute per square meter). We aimed (1) to evaluate the impact of different body weight-based CO indexations on the resulting CI values and (2) to identify biometric parameters independently associated with CO in critically ill patients. The study is an analysis of a database containing transpulmonary thermodilution-derived hemodynamic variables of 234 medical intensive care unit patients. Cardiac index indexed to actual BSA was statistically significantly lower compared with CI indexed to predicted BSA in the totality of patients and in the subgroups of patients with body mass index greater than or equal to 25 kg/m(2) but less than 30 kg/m(2) and body mass index greater than or equal to 30 kg/m(2) (with a statistically significant difference in the proportion of low and high CI measurements). Multivariate analysis of the first CO measurement of each patient demonstrated that CO was independently associated with age (P < .001), height (P = .001), and actual body weight (BWact) (P = .030). Multivariate analysis of the mean of the patients' CO measurements confirmed age (P < .001), height (P = .001), and BWact (P < .001) as biometric factors independently associated with CO. Age was identified as the most important factor with each year of age decreasing CO by 66 mL/min (95% confidence interval, 47-86 mL/min). The indexation of CO to BSA is highly dependent on the body weight estimation formula used to calculate BSA. Cardiac output is independently associated with the biometric factors age, height, and BWact. These factors might be considered for indexation of CO. Copyright © 2015 Elsevier Inc. All rights reserved.

Smart Location Mapping

EPA Pesticide Factsheets

The Smart Location Database, Access to Jobs and Workers via Transit, and National Walkability Index tools can help assess indicators related to the built environment, transit accessibility, and walkability.

EHME: a new word database for research in Basque language.

PubMed

Acha, Joana; Laka, Itziar; Landa, Josu; Salaburu, Pello

2014-11-14

This article presents EHME, the frequency dictionary of Basque structure, an online program that enables researchers in psycholinguistics to extract word and nonword stimuli, based on a broad range of statistics concerning the properties of Basque words. The database consists of 22.7 million tokens, and properties available include morphological structure frequency and word-similarity measures, apart from classical indexes: word frequency, orthographic structure, orthographic similarity, bigram and biphone frequency, and syllable-based measures. Measures are indexed at the lemma, morpheme and word level. We include reliability and validation analysis. The application is freely available, and enables the user to extract words based on concrete statistical criteria 1 , as well as to obtain statistical characteristics from a list of words

Technology transfer at NASA - A librarian's view

NASA Technical Reports Server (NTRS)

Buchan, Ronald L.

1991-01-01

The NASA programs, publications, and services promoting the transfer and utilization of aerospace technology developed by and for NASA are briefly surveyed. Topics addressed include the corporate sources of NASA technical information and its interest for corporate users of information services; the IAA and STAR abstract journals; NASA/RECON, NTIS, and the AIAA Aerospace Database; the RECON Space Commercialization file; the Computer Software Management and Information Center file; company information in the RECON database; and services to small businesses. Also discussed are the NASA publications Tech Briefs and Spinoff, the Industrial Applications Centers, NASA continuing bibliographies on management and patent abstracts (indexed using the NASA Thesaurus), the Index to NASA News Releases and Speeches, and the Aerospace Research Information Network (ARIN).

The Optimization of In-Memory Space Partitioning Trees for Cache Utilization

NASA Astrophysics Data System (ADS)

Yeo, Myung Ho; Min, Young Soo; Bok, Kyoung Soo; Yoo, Jae Soo

In this paper, a novel cache conscious indexing technique based on space partitioning trees is proposed. Many researchers investigated efficient cache conscious indexing techniques which improve retrieval performance of in-memory database management system recently. However, most studies considered data partitioning and targeted fast information retrieval. Existing data partitioning-based index structures significantly degrade performance due to the redundant accesses of overlapped spaces. Specially, R-tree-based index structures suffer from the propagation of MBR (Minimum Bounding Rectangle) information by updating data frequently. In this paper, we propose an in-memory space partitioning index structure for optimal cache utilization. The proposed index structure is compared with the existing index structures in terms of update performance, insertion performance and cache-utilization rate in a variety of environments. The results demonstrate that the proposed index structure offers better performance than existing index structures.

Automatic inference of indexing rules for MEDLINE

PubMed Central

Névéol, Aurélie; Shooshan, Sonya E; Claveau, Vincent

2008-01-01

Background: Indexing is a crucial step in any information retrieval system. In MEDLINE, a widely used database of the biomedical literature, the indexing process involves the selection of Medical Subject Headings in order to describe the subject matter of articles. The need for automatic tools to assist MEDLINE indexers in this task is growing with the increasing number of publications being added to MEDLINE. Methods: In this paper, we describe the use and the customization of Inductive Logic Programming (ILP) to infer indexing rules that may be used to produce automatic indexing recommendations for MEDLINE indexers. Results: Our results show that this original ILP-based approach outperforms manual rules when they exist. In addition, the use of ILP rules also improves the overall performance of the Medical Text Indexer (MTI), a system producing automatic indexing recommendations for MEDLINE. Conclusion: We expect the sets of ILP rules obtained in this experiment to be integrated into MTI. PMID:19025687

Automatic inference of indexing rules for MEDLINE.

PubMed

Névéol, Aurélie; Shooshan, Sonya E; Claveau, Vincent

2008-11-19

Indexing is a crucial step in any information retrieval system. In MEDLINE, a widely used database of the biomedical literature, the indexing process involves the selection of Medical Subject Headings in order to describe the subject matter of articles. The need for automatic tools to assist MEDLINE indexers in this task is growing with the increasing number of publications being added to MEDLINE. In this paper, we describe the use and the customization of Inductive Logic Programming (ILP) to infer indexing rules that may be used to produce automatic indexing recommendations for MEDLINE indexers. Our results show that this original ILP-based approach outperforms manual rules when they exist. In addition, the use of ILP rules also improves the overall performance of the Medical Text Indexer (MTI), a system producing automatic indexing recommendations for MEDLINE. We expect the sets of ILP rules obtained in this experiment to be integrated into MTI.

Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.

PubMed

Karpinka, J Brad; Fortriede, Joshua D; Burns, Kevin A; James-Zorn, Christina; Ponferrada, Virgilio G; Lee, Jacqueline; Karimi, Kamran; Zorn, Aaron M; Vize, Peter D

2015-01-01

Xenbase (http://www.xenbase.org), the Xenopus frog model organism database, integrates a wide variety of data from this biomedical model genus. Two closely related species are represented: the allotetraploid Xenopus laevis that is widely used for microinjection and tissue explant-based protocols, and the diploid Xenopus tropicalis which is used for genetics and gene targeting. The two species are extremely similar and protocols, reagents and results from each species are often interchangeable. Xenbase imports, indexes, curates and manages data from both species; all of which are mapped via unique IDs and can be queried in either a species-specific or species agnostic manner. All our services have now migrated to a private cloud to achieve better performance and reliability. We have added new content, including providing full support for morpholino reagents, used to inhibit mRNA translation or splicing and binding to regulatory microRNAs. New genomes assembled by the JGI for both species and are displayed in Gbrowse and are also available for searches using BLAST. Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks. Xenbase has also greatly expanded image content for figures published in papers describing Xenopus research via PubMedCentral. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Review article: cinnamon- and benzoate-free diet as a primary treatment for orofacial granulomatosis.

PubMed

Campbell, H E; Escudier, M P; Patel, P; Challacombe, S J; Sanderson, J D; Lomer, M C E

2011-10-01

Orofacial granulomatosis is a rare chronic granulomatous inflammatory disease of the lips, face and mouth. The aetiology remains unclear but may involve an allergic component. Improvements have been reported with cinnamon- and benzoate-free diets. To explore the prevalence of compound and food sensitivity and examine the dietary treatments used in orofacial granulomatosis. A comprehensive literature search was carried out and relevant studies from January 1933 to January 2010 were identified using the electronic database search engines; AGRIS 1991-2008, AMED 1985-2008, British Nursing and Index archive 1985-2008, EMBASE 1980-2008, evidence based medicine review databases (e.g. Cochrane DSR), International Pharmaceutical and Medline 1950-2008. Common sensitivities identified, predominantly through patch testing, were to benzoic acid (36%) food additives (33%), perfumes and flavourings (28%), cinnamaldehyde (27%), cinnamon (17%), benzoates (17%) and chocolate (11%). The cinnamon- and benzoate-free diet has been shown to provide benefit in 54-78% of patients with 23% requiring no adjunctive therapies. A negative or positive patch test result to cinnamaldehyde, and benzoates did not predict dietary outcome. The most concentrated source of benzoate exposure is from food preservatives. Use of liquid enteral formulas can offer a further dietary therapy, particularly in children with orofacial granulomatosis. Management of orofacial granulomatosis is challenging but cinnamon- and benzoate-free diets appear to have a definite role to play. © 2011 Blackwell Publishing Ltd.

Detection of gastro-oesophageal reflux in the neonatal unit.

PubMed

Rossor, Thomas; Lingam, Ingran; Douiri, Abdel; Bhat, Ravindra; Greenough, Anne

2018-03-13

To determine whether a pH probe or multichannel intraluminal impedance (MII) more frequently detected gastro-oesophageal reflux and test the hypothesis that acid reflux was associated with lower baseline impedance. A prospective study of infants in whom reflux was suspected and evaluated using combined pH and multichannel impedance. Studies were considered abnormal if the acid index was >10% or there were >79MII reflux events in 24 hours. The acid index was the percentage of total study time with a pH

Classification of malignant and benign lung nodules using taxonomic diversity index and phylogenetic distance.

PubMed

de Sousa Costa, Robherson Wector; da Silva, Giovanni Lucca França; de Carvalho Filho, Antonio Oseas; Silva, Aristófanes Corrêa; de Paiva, Anselmo Cardoso; Gattass, Marcelo

2018-05-23

Lung cancer presents the highest cause of death among patients around the world, in addition of being one of the smallest survival rates after diagnosis. Therefore, this study proposes a methodology for diagnosis of lung nodules in benign and malignant tumors based on image processing and pattern recognition techniques. Mean phylogenetic distance (MPD) and taxonomic diversity index (Δ) were used as texture descriptors. Finally, the genetic algorithm in conjunction with the support vector machine were applied to select the best training model. The proposed methodology was tested on computed tomography (CT) images from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), with the best sensitivity of 93.42%, specificity of 91.21%, accuracy of 91.81%, and area under the ROC curve of 0.94. The results demonstrate the promising performance of texture extraction techniques using mean phylogenetic distance and taxonomic diversity index combined with phylogenetic trees. Graphical Abstract Stages of the proposed methodology.

Applications of Sentinel-2 data for agriculture and forest monitoring using the absolute difference (ZABUD) index derived from the AgroEye software (ESA)

NASA Astrophysics Data System (ADS)

de Kok, R.; WeŻyk, P.; PapieŻ, M.; Migo, L.

2017-10-01

To convince new users of the advantages of the Sentinel_2 sensor, a simplification of classic remote sensing tools allows to create a platform of communication among domain specialists of agricultural analysis, visual image interpreters and remote sensing programmers. An index value, known in the remote sensing user domain as "Zabud" was selected to represent, in color, the essentials of a time series analysis. The color index used in a color atlas offers a working platform for an agricultural field control. This creates a database of test and training areas that enables rapid anomaly detection in the agricultural domain. The use cases and simplifications now function as an introduction to Sentinel_2 based remote sensing, in an area that before relies on VHR imagery and aerial data, to serve mainly the visual interpretation. The database extension with detected anomalies allows developers of open source software to design solutions for further agricultural control with remote sensing.

AQUAdexIM: highly efficient in-memory indexing and querying of astronomy time series images

NASA Astrophysics Data System (ADS)

Hong, Zhi; Yu, Ce; Wang, Jie; Xiao, Jian; Cui, Chenzhou; Sun, Jizhou

2016-12-01

Astronomy has always been, and will continue to be, a data-based science, and astronomers nowadays are faced with increasingly massive datasets, one key problem of which is to efficiently retrieve the desired cup of data from the ocean. AQUAdexIM, an innovative spatial indexing and querying method, performs highly efficient on-the-fly queries under users' request to search for Time Series Images from existing observation data on the server side and only return the desired FITS images to users, so users no longer need to download entire datasets to their local machines, which will only become more and more impractical as the data size keeps increasing. Moreover, AQUAdexIM manages to keep a very low storage space overhead and its specially designed in-memory index structure enables it to search for Time Series Images of a given area of the sky 10 times faster than using Redis, a state-of-the-art in-memory database.

Characterization of the amino acid contribution to the folding degree of proteins.

PubMed

Estrada, Ernesto

2004-03-01

The folding degree index (Estrada, Bioinformatics 2002;18:697-704) is extended to account for the contribution of amino acids to folding. First, the mathematical formalism for extending the folding degree index is presented. Then, the amino acid contributions to folding degree of several proteins are used to analyze its relation to secondary structure. The possibilities of using these contributions in helping or checking the assignation of secondary structure to amino acids are also introduced. The influence of external factors to the amino acids contribution to folding degree is studied through the temperature effect on ribonuclease A. Finally, the analysis of 3D protein similarity through the use of amino acid contributions to folding degree is studied by selecting a series of lysozymes. These results are compared to that obtained by sequence alignment (2D similarity) and 3D superposition of the structures, showing the uniqueness of the current approach. Copyright 2004 Wiley-Liss, Inc.

Lipolysis, lipid peroxidation, and color characteristics of Serrano Hams from Duroc and large white pigs during dry-curing.

PubMed

del Olmo, Ana; Calzada, Javier; Nuñez, Manuel

2013-11-01

Lipolysis, lipid peroxidation, and colorimetric characteristics of Serrano hams from Duroc and Large White pigs along a 15-mo curing period were investigated. Physicochemical parameters of both types of hams evolved similarly during curing. Twelve of 13 free fatty acids (FFAs) increased during curing, eicosatrienoic acid being the only exception. Linoleic, stearic, and arachidonic acids and the minor heptadecanoic acid reached lower concentrations, and the rest of minor FFAs higher concentrations, in Duroc hams than in Large White hams. The index measuring the early stage of lipid peroxidation declined from month 5 onwards, indicating that the phenomenon had been completed by month 5, while the index of the secondary stage of lipid peroxidation increased with curing time. Higher values were found for the 1st index in Duroc hams. Curing affected color parameters. Lightness decreased and redness increased in both types of hams, while yellowness decreased only in Duroc hams. Lower redness values were found for Duroc hams. Major differences in color parameters were found between muscles. Principal components analysis of FFAs yielded 2 main principal components. The 1st factor, correlated with all FFAs excepting eicosatrienoic acid, allowed discrimination between curing times. The 2nd factor, correlated with eicosatrienoic acid, permitted discrimination between breeds. © 2013 Institute of Food Technologists®

Physicochemical properties, nutritional value and techno-functional properties of goldenberry (Physalis peruviana) waste powder concise title: Composition of goldenberry juice waste.

PubMed

Mokhtar, Sayed M; Swailam, Hesham M; Embaby, Hassan El-Sayed

2018-05-15

Goldenberry waste powder, contained 5.87% moisture, 15.89% protein, 13.72% fat, 3.52% ash, 16.74% dietary fiber and 61% carbohydrates. Potassium (560 mg/100 g) was the predominant element followed by sodium (170 mg/100 g) and phosphorus (130 mg/100 g). Amino acid analysis gave high levels of cystine/methionine, histidine and tyrosine/phenylalanine. Goldenberry waste powder had good levels of the techno-functional properties including water absorption index, swelling index, foaming capacity and stability (3.38 g/g, 5.24 ml/g, 4.09 and 72.0%, respectively). Fatty acids profile showed that linoleic acid was the predominant fatty acid followed by oleic, palmitic and stearic acids. Iodine value (109.5 g/100 g of oil), acid value (2.36 mg KOH/g of oil), saponification value (183.8 mg KOH/g of oil), peroxide value (8.2 meq/kg of oil) and refractive index (1.4735) were comparable to those of soybean and sunflower oils. Goldenberry waste oil exhibited absorbance in the UV range at 100-400 nm. Copyright © 2017 Elsevier Ltd. All rights reserved.

Collecting, archiving and processing DNA from wildlife samples using FTA® databasing paper

PubMed Central

Smith, LM; Burgoyne, LA

2004-01-01

Background Methods involving the analysis of nucleic acids have become widespread in the fields of traditional biology and ecology, however the storage and transport of samples collected in the field to the laboratory in such a manner to allow purification of intact nucleic acids can prove problematical. Results FTA® databasing paper is widely used in human forensic analysis for the storage of biological samples and for purification of nucleic acids. The possible uses of FTA® databasing paper in the purification of DNA from samples of wildlife origin were examined, with particular reference to problems expected due to the nature of samples of wildlife origin. The processing of blood and tissue samples, the possibility of excess DNA in blood samples due to nucleated erythrocytes, and the analysis of degraded samples were all examined, as was the question of long term storage of blood samples on FTA® paper. Examples of the end use of the purified DNA are given for all protocols and the rationale behind the processing procedures is also explained to allow the end user to adjust the protocols as required. Conclusions FTA® paper is eminently suitable for collection of, and purification of nucleic acids from, biological samples from a wide range of wildlife species. This technology makes the collection and storage of such samples much simpler. PMID:15072582

Formic acid

Integrated Risk Information System (IRIS)

Formic acid ; CASRN 64 - 18 - 6 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effect

Acrylic acid

Integrated Risk Information System (IRIS)

Acrylic acid ( CASRN 79 - 10 - 7 ) Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Eff

Benzoic acid

Integrated Risk Information System (IRIS)

Benzoic acid ; CASRN 65 - 85 - 0 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effec

Cacodylic acid

Integrated Risk Information System (IRIS)

Cacodylic acid ; CASRN 75 - 60 - 5 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Eff

Selenious acid

Integrated Risk Information System (IRIS)

Selenious acid ; CASRN 7783 - 00 - 8 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic E

The Computer Bulletin Board. Modified Gran Plots of Very Weak Acids on a Spreadsheet.

ERIC Educational Resources Information Center

Chau, F. T.; And Others

1990-01-01

Presented are two applications of computer technology to chemistry instruction: the use of a spreadsheet program to analyze acid-base titration curves and the use of database software to catalog stockroom inventories. (CW)

Systematic review of dietary trans-fat reduction interventions

PubMed Central

Bromley, Helen; Kypridemos, Chris; O’Flaherty, Martin; Lloyd-Williams, Ffion; Guzman-Castillo, Maria; Pearson-Stuttard, Jonathan; Capewell, Simon

2017-01-01

Abstract Objective To systematically review published studies of interventions to reduce people’s intake of dietary trans-fatty acids (TFAs). Methods We searched online databases (CINAHL, the CRD Wider Public Health database, Cochrane Database of Systematic Reviews, Ovid®, MEDLINE®, Science Citation Index and Scopus) for studies evaluating TFA interventions between 1986 and 2017. Absolute decrease in TFA consumption (g/day) was the main outcome measure. We excluded studies reporting only on the TFA content in food products without a link to intake. We included trials, observational studies, meta-analyses and modelling studies. We conducted a narrative synthesis to interpret the data, grouping studies on a continuum ranging from interventions targeting individuals to population-wide, structural changes. Results After screening 1084 candidate papers, we included 23 papers: 12 empirical and 11 modelling studies. Multiple interventions in Denmark achieved a reduction in TFA consumption from 4.5 g/day in 1976 to 1.5 g/day in 1995 and then virtual elimination after legislation banning TFAs in manufactured food in 2004. Elsewhere, regulations mandating reformulation of food reduced TFA content by about 2.4 g/day. Worksite interventions achieved reductions averaging 1.2 g/day. Food labelling and individual dietary counselling both showed reductions of around 0.8 g/day. Conclusion Multicomponent interventions including legislation to eliminate TFAs from food products were the most effective strategy. Reformulation of food products and other multicomponent interventions also achieved useful reductions in TFA intake. By contrast, interventions targeted at individuals consistently achieved smaller reductions. Future prevention strategies should consider this effectiveness hierarchy to achieve the largest reductions in TFA consumption. PMID:29200523

DNA Profiling of Convicted Offender Samples for the Combined DNA Index System

ERIC Educational Resources Information Center

Millard, Julie T

2011-01-01

The cornerstone of forensic chemistry is that a perpetrator inevitably leaves trace evidence at a crime scene. One important type of evidence is DNA, which has been instrumental in both the implication and exoneration of thousands of suspects in a wide range of crimes. The Combined DNA Index System (CODIS), a network of DNA databases, provides…

LiDAR-derived site index in the U.S. Pacihic Northwest--challenges and opportunities

Treesearch

Demetrios Gatziolis

2007-01-01

Site Index (SI), a key inventory parameter, is traditionally estimated by using costly and laborious field assessments of tree height and age. The increasing availability of reliable information on stand initiation timing and extent of planted, even-aged stands maintained in digital databases suggests that information on the height of dominant trees suffices for...

IFLA General Conference, 1992. Division of Bibliographic Control: Section on Classification and Indexing; Section on Cataloguing. Papers.

ERIC Educational Resources Information Center

International Federation of Library Associations and Institutions, London (England).

Five papers from the sessions of the International Federation of Library Associations and Institutions 1992 conference on classification, indexing, and cataloging are presented. Three papers deal with knowledge classification as it relates to database design, as it is practiced in India, and in a worldwide context. The remaining two papers focus…

Visual feature discrimination versus compression ratio for polygonal shape descriptors

NASA Astrophysics Data System (ADS)

Heuer, Joerg; Sanahuja, Francesc; Kaup, Andre

2000-10-01

In the last decade several methods for low level indexing of visual features appeared. Most often these were evaluated with respect to their discrimination power using measures like precision and recall. Accordingly, the targeted application was indexing of visual data within databases. During the standardization process of MPEG-7 the view on indexing of visual data changed, taking also communication aspects into account where coding efficiency is important. Even if the descriptors used for indexing are small compared to the size of images, it is recognized that there can be several descriptors linked to an image, characterizing different features and regions. Beside the importance of a small memory footprint for the transmission of the descriptor and the memory footprint in a database, eventually the search and filtering can be sped up by reducing the dimensionality of the descriptor if the metric of the matching can be adjusted. Based on a polygon shape descriptor presented for MPEG-7 this paper compares the discrimination power versus memory consumption of the descriptor. Different methods based on quantization are presented and their effect on the retrieval performance are measured. Finally an optimized computation of the descriptor is presented.

Indexing molecules with chemical graph identifiers.

PubMed

Gregori-Puigjané, Elisabet; Garriga-Sust, Rut; Mestres, Jordi

2011-09-01

Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used. Copyright © 2011 Wiley Periodicals, Inc.

MPEG-7 audio-visual indexing test-bed for video retrieval

NASA Astrophysics Data System (ADS)

Gagnon, Langis; Foucher, Samuel; Gouaillier, Valerie; Brun, Christelle; Brousseau, Julie; Boulianne, Gilles; Osterrath, Frederic; Chapdelaine, Claude; Dutrisac, Julie; St-Onge, Francis; Champagne, Benoit; Lu, Xiaojian

2003-12-01

This paper reports on the development status of a Multimedia Asset Management (MAM) test-bed for content-based indexing and retrieval of audio-visual documents within the MPEG-7 standard. The project, called "MPEG-7 Audio-Visual Document Indexing System" (MADIS), specifically targets the indexing and retrieval of video shots and key frames from documentary film archives, based on audio-visual content like face recognition, motion activity, speech recognition and semantic clustering. The MPEG-7/XML encoding of the film database is done off-line. The description decomposition is based on a temporal decomposition into visual segments (shots), key frames and audio/speech sub-segments. The visible outcome will be a web site that allows video retrieval using a proprietary XQuery-based search engine and accessible to members at the Canadian National Film Board (NFB) Cineroute site. For example, end-user will be able to ask to point on movie shots in the database that have been produced in a specific year, that contain the face of a specific actor who tells a specific word and in which there is no motion activity. Video streaming is performed over the high bandwidth CA*net network deployed by CANARIE, a public Canadian Internet development organization.

APPLICATION OF A FUNCTIONAL MATHEMATICAL QUALITY INDEX TO ASPARAGINE, FREE SUGAR AND PHENOLIC ACID CONTENT OF 20 COMMERCIAL POTATO VARIETIES

USDA-ARS?s Scientific Manuscript database

In this article, we apply a functional mathematical index (FMI), introduced in a previous publication, to 20 commercial potato varieties. The index allows evaluation of nutritional, safety and processing “quality parameters” of different potato cultivars. The main goal of the index is to link the q...

Non-coding, mRNA-like RNAs database Y2K.

PubMed

Erdmann, V A; Szymanski, M; Hochberg, A; Groot, N; Barciszewski, J

2000-01-01

In last few years much data has accumulated on various non-translatable RNA transcripts that are synthesised in different cells. They are lacking in protein coding capacity and it seems that they work mainly or exclusively at the RNA level. All known non-coding RNA transcripts are collected in the database: http://www. man.poznan.pl/5SData/ncRNA/index.html

Non-coding, mRNA-like RNAs database Y2K

PubMed Central

Erdmann, Volker A.; Szymanski, Maciej; Hochberg, Abraham; Groot, Nathan de; Barciszewski, Jan

2000-01-01

In last few years much data has accumulated on various non-translatable RNA transcripts that are synthesised in different cells. They are lacking in protein coding capacity and it seems that they work mainly or exclusively at the RNA level. All known non-coding RNA transcripts are collected in the database: http://www.man.poznan.pl/5SData/ncRNA/index.html PMID:10592224

In Praise of Mr. S. Platter and His Marvelous, Magnificent CD ROM Laser Disc Index for ERIC and PSYCHLIT.

ERIC Educational Resources Information Center

Huffman, Robert F.

These instructions are designed to help patrons of the University of Missouri-Columbia library perform searches on PSYCHLIT, a CD-ROM (compact disc, read only memory) version of the Psych Abstracts database, and a CD-ROM version of the ERIC database, both produced by SilverPlatter Information Services. Basic information is provided about the disk…

The Circumpolar Arctic Vegetation Map: A tool for analysis of change in permafrost regions

NASA Astrophysics Data System (ADS)

Walker, D. A.; Raynolds, M. K.; Maier, H. A.

2003-12-01

Arctic vegetation occurs beyond the northern limit of trees, in areas that have an Arctic climate and Arctic flora. Here we present an overview of the recently published Circumpolar Arctic Vegetation Map (CAVM), an area analysis of the vegetation map, and a discussion of its potential for analysis of change in the Arctic. Six countries have Arctic tundra vegetation, Canada, Greenland, Iceland, Russia, Norway (Svalbard), and the US (Total Arctic area = 7.1 million km2). Some treeless areas, such as most of Iceland and the Aluetian Islands are excluded from the map because they lack an Arctic climate. The CAVM divides the Arctic into five bioclimate subzones, A thru E (Subzone A is the coldest and Subzone E is the warmest), based on a combination of summer temperature and vegetation. Fifteen vegetation types are mapped based on the dominant plant growth forms. More detailed, plant-community-level, information is contained in the database used to construct the map. The reverse side of the vegetation map has a false-color infrared image constructed from Advanced Very-High Resolution (AVHRR) satellite-derived raster data, and maps of bioclimate subzones, elevation, landscape types, lake cover, substrate chemistry, floristic provinces, the maximum normalized difference vegetation index (NDVI), and aboveground phytomass. The vegetation map was analyzed by vegetation type and biomass for each county, bioclimate subzone, and floristic province. Biomass distribution was analyzed by means of a correlation between aboveground phytomass and the normalized difference vegetation index (NDVI), a remote-sensing index of surface greenness. Biomass on zonal surfaces roughly doubles within each successively warmer subzone, from about 50 g m-2 in Subzone A to 800 g m-2- in Subzone E. But the pattern of vegetation increase is highly variable, and depends on a number of other factors. The most important appears to be the glacial history of the landscape. Areas that were glaciated during the late-Pleistocene, such as Canada, Svalbard, and Greenland, do not show such strong increases in NDVI with temperature as do areas that were not glaciated. Abundant lakes and rocky surfaces limit the greenness of these recently glaciated surfaces. The highest NDVI and phytomass are found in non-glaciated regions of Alaska and Russia. Soil acidity also affects NDVI patterns. In Subzone D, where the NDVI/ soil acidity relationship has been studied most closely, NDVI is lower on nonacidic surfaces. This has been attributed to fewer shrubs and higher proportion of graminoids (more standing dead sedge leaves) in nonacidic areas. This trend is probably caused by generally drier soils, with less production, on limestone-derived soils. The trend is less clear in Subzone E because of fewer nonacidic surfaces, and the abundance of glacial lakes with low NDVI on the acidic shield areas of Canada. Time series analysis of trends in NDVI in Subzones C, D, and E in Alaska have shown a 17% increase in the NDVI over the 21-year record. The increases have been greatest in moist nonacidic tundra. Future analyses of the circumpolar database will be directed at examining which geographic regions and vegetation types have shown the strongest increases, and how these are correlated with temperature changes.

[Relationship between previous severity of illness and outcome of in-hospital cardiac arrest].

PubMed

Serrano, M; Rodríguez, J; Espejo, A; del Olmo, R; Llanos, S; Del Castillo, J; López-Herce, J

2014-07-01

To analyze the relationship between previous severity of illness, lactic acid, creatinine and inotropic index with mortality of in-hospital cardiac arrest (CA) in children, and the value of a prognostic index designed for adults. The study included total of 44 children aged from 1 month to 18 years old who suffered a cardiac arrest while in hospital. The relationship between previous severity of illness scores (PRIMS and PELOD), lactic acid, creatinine, treatment with vasoactive drugs, inotropic index with return of spontaneous circulation and survival at hospital discharge was analyzed. The large majority (90.3%) of patients had a return of spontaneous circulation, and 59% survived at hospital discharge. More than two-thirds (68.2%) were treated with inotropic drugs at the time of the CA. The patients who died had a higher lactic acid before the CA (3.4 mmol/L) than survivors (1.4 mmol/L), P=.04. There were no significant differences in PRIMS, PELOD, creatinine, inotropic drugs, and inotropic index before CA between patients who died and survivors. A high lactic acid previous to cardiac arrest could be a prognostic factor of in-hospital cardiac arrest in children. Copyright © 2013 Asociación Española de Pediatría. Published by Elsevier Espana. All rights reserved.

Nutritional evaluation of caseins and whey proteins and their hydrolysates from Protamex*

PubMed Central

Sindayikengera, Séverin; Xia, Wen-shui

2006-01-01

Whey protein concentrate (WPC 80) and sodium caseinate were hydrolyzed by Protamex to 5%, 10%, 15%, and 20% degree of hydrolysis (DH). WPC 80, sodium caseinate and their hydrolysates were then analyzed, compared and evaluated for their nutritional qualities. Their chemical composition, protein solubility, amino acid composition, essential amino acid index (EAA index), biological value (BV), nutritional index (NI), chemical score, enzymic protein efficiency ratio (E-PER) and in vitro protein digestibility (IVPD) were determined. The results indicated that the enzymatic hydrolysis of WPC 80 and sodium caseinate by Protamex improved the solubility and IVPD of their hydrolysates. WPC 80, sodium caseinate and their hydrolysates were high-quality proteins and had a surplus of essential amino acids compared with the FAO/WHO/UNU (1985) reference standard. The nutritive value of WPC 80 and its hydrolysates was superior to that of sodium caseinate and its hydrolysates as indicated by some nutritional parameters such as the amino acid composition, chemical score, EAA index and predicted BV. However, the E-PER was lower for the WPC hydrolysates as compared to unhydrolyzed WPC 80 but sodium caseinate and its hydrolysates did not differ significantly. The nutritional qualities of WPC 80, sodium caseinate and their hydrolysates were good and make them appropriate for food formulations or as nutritional supplements. PMID:16421963

A comparative study of the origin, structure, and indexing language of the Persian and English keywords of articles indexed in the IranMedex database and their compliance with the Persian medical thesaurus and Medical Subject Headings

PubMed Central

Parsaei-Mohammadi, Parastoo; Ghasemi, Ali Hossein; Hassanzadeh-Beheshtabad, Raziyeh

2017-01-01

Introduction: In the present era, thesauri as tools in indexing play an effective role in integrating retrieval preventing fragmentation as well as a multiplicity of terminologies and also in providing information content of documents. Goals: This study aimed to investigate the keywords of articles indexed in IranMedex in terms of origin, structure and indexing situation and their Compliance with the Persian Medical Thesaurus and Medical Subject Headings (MeSH). Materials and Methods: This study is an applied research, and a survey has been conducted. Statistical population includes 32,850 Persian articles which are indexed in the IranMedex during the years 1385–1391. 379 cases were selected as sample of the study. Data collection was done using a checklist. In analyzing the findings, the SPSS Software were used. Findings: Although there was no significant difference in terms of indexing origin between the proportion of different types of the Persian and English keywords of articles indexed in the IranMedex, the compliance rates of the Persian and English keywords with the Persian medical thesaurus and MeSH were different in different years. In the meantime, the structure of keywords is leaning more towards phrase structure, and a single word structure and the majority of keywords are selected from the titles and abstracts. Conclusion: The authors’ familiarity with the thesauri and controlled tools causes homogeneity in assigning keywords and also provides more precise, faster, and easier retrieval of the keywords. It's suggested that a mixture of natural and control languages to be used in this database in order to reach more comprehensive results. PMID:28546967

A comparative study of the origin, structure, and indexing language of the Persian and English keywords of articles indexed in the IranMedex database and their compliance with the Persian medical thesaurus and Medical Subject Headings.

PubMed

Parsaei-Mohammadi, Parastoo; Ghasemi, Ali Hossein; Hassanzadeh-Beheshtabad, Raziyeh

2017-01-01

In the present era, thesauri as tools in indexing play an effective role in integrating retrieval preventing fragmentation as well as a multiplicity of terminologies and also in providing information content of documents. This study aimed to investigate the keywords of articles indexed in IranMedex in terms of origin, structure and indexing situation and their Compliance with the Persian Medical Thesaurus and Medical Subject Headings (MeSH). This study is an applied research, and a survey has been conducted. Statistical population includes 32,850 Persian articles which are indexed in the IranMedex during the years 1385-1391. 379 cases were selected as sample of the study. Data collection was done using a checklist. In analyzing the findings, the SPSS Software were used. Although there was no significant difference in terms of indexing origin between the proportion of different types of the Persian and English keywords of articles indexed in the IranMedex, the compliance rates of the Persian and English keywords with the Persian medical thesaurus and MeSH were different in different years. In the meantime, the structure of keywords is leaning more towards phrase structure, and a single word structure and the majority of keywords are selected from the titles and abstracts. The authors' familiarity with the thesauri and controlled tools causes homogeneity in assigning keywords and also provides more precise, faster, and easier retrieval of the keywords. It's suggested that a mixture of natural and control languages to be used in this database in order to reach more comprehensive results.

Alpha linolenic acid in maternal diet halts the lipid disarray due to saturated fatty acids in the liver of mice offspring at weaning.

PubMed

Shomonov-Wagner, Limor; Raz, Amiram; Leikin-Frenkel, Alicia

2015-02-26

Alpha linolenic acid (ALA, 18:3) in maternal diets has been shown to attenuate obesity associated insulin resistance (IR) in adult offspring in mice. The objective in the present study was to detect the early effects of maternal dietary saturated fatty acids (SFA) and their partial substitution with ω-3 ALA, docosa hexenoic acid (DHA,22:6) and eicosapentenoic acid 20:5 (EPA,20:5) on the HOMA index, liver lipids and fatty acid desaturases in the offspring at weaning. 3 month old C57Bl6/J female mice were fed diets containing normal amount of calories but rich in SFA alone or partially replaced with ALA, DHA or EPA before mating, during pregnancy and lactation. Pregnant mice fed SFA produced offspring with the highest HOMA index, liver lipids and desaturase activities. ALA prevented SFA induced lipid increase but DHA and EPA only reduced it by 42% and 31% respectively. ALA, DHA and EPA decreased HOMA index by 84%, 75% and 83% respectively. ALA, DHA and EPA decreased Δ6 and SCD1 desaturase activities about 30%. SFA feeding to mothers predisposes their offspring to develop IR and liver lipid accumulation already at weaning. ω3 fatty acids reduce IR, ALA halts lipid accumulation whereas DHA and EPA only blunt it.ALA and DHA restore the increased SCD1 to normal. These studies suggest that ω-3 fatty acids have different potencies to preclude lipid accumulation in the offspring partially by affecting pathways associated to SCD1 modulation.

Omega-3 Fatty Acids for Autistic Spectrum Disorder: A Systematic Review

ERIC Educational Resources Information Center

Bent, Stephen; Bertoglio, Kiah; Hendren, Robert L.

2009-01-01

We conducted a systematic review to determine the safety and efficacy of omega-3 fatty acids for autistic spectrum disorder (ASD). Articles were identified by a search of MEDLINE, EMBASE, and the Cochrane Database using the terms autism or autistic and omega-3 fatty acids. The search identified 143 potential articles and six satisfied all…

PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes.

PubMed

Damiano, F; Gallerani, R; Liuni, S; Licciulli, F; Ceci, L R

2001-01-01

The PLMItRNA database for mitochondrial tRNA molecules and genes in VIRIDIPLANTAE: (green plants) [Volpetti,V., Gallerani,R., DeBenedetto,C., Liuni,S., Licciulli,F. and Ceci,L.R. (2000) Nucleic Acids Res., 28, 159-162] has been enlarged to include algae. The database now contains 436 genes and 16 tRNA entries relative to 25 higher plants, eight green algae, four red algae (RHODOPHYTAE:) and two STRAMENOPILES: The PLMItRNA database is accessible via the WWW at http://bio-www.ba.cnr.it:8000/PLMItRNA.

Metabolites Associated With Lean Mass and Adiposity in Older Black Men.

PubMed

Murphy, Rachel A; Moore, Steven C; Playdon, Mary; Meirelles, Osorio; Newman, Anne B; Milijkovic, Iva; Kritchevsky, Stephen B; Schwartz, Ann; Goodpaster, Bret H; Sampson, Joshua; Cawthon, Peggy; Simonsick, Eleanor M; Gerszten, Robert E; Clish, Clary B; Harris, Tamara B

2017-10-01

To identify biomarkers of body mass index, body fat, trunk fat, and appendicular lean mass, nontargeted metabolomics was performed in plasma from 319 black men in the Health, Aging and Body Composition study (median age 72 years, median body mass index 26.8 kg/m2). Body mass index was calculated from measured height and weight; percent fat, percent trunk fat, and appendicular lean mass were measured with dual-energy x-ray absorptiometry. Pearson partial correlations between body composition measures and metabolites were adjusted for age, study site, and smoking. Out of 350 metabolites, body mass index, percent fat, percent trunk fat, and appendicular lean mass were significantly correlated with 92, 48, 96, and 43 metabolites at p less than .0014. Metabolites most strongly correlated with body composition included carnitine, a marker of fatty acid oxidation (positively correlated), triacylglycerols (positively correlated), and amino acids including branched-chain amino acids (positively correlated except for acetylglycine and serine). Gaussian Graphical Models of metabolites found that 25 lipid metabolites clustered into a single network. Groups of five amino acids, three plasmalogens, and two carnitines were also observed. Findings confirm prior reports of associations between amino acids, lean mass, and fat mass in addition to associations not previously reported. Future studies should consider whether these metabolites are relevant for metabolic disease processes. Published by Oxford University Press on behalf of The Gerontological Society of America 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

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

PubMed Central

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 PMID:15608287

Chemical composition and nutritional evaluation of the seeds of Acacia tortilis (Forssk.) Hayne ssp. raddiana.

PubMed

Embaby, Hassan E; Rayan, Ahmed M

2016-06-01

Chemical composition and nutritional evaluation as well as physicochemical and functional properties of seed flour of Acacia tortilis (Forssk.) Hayne ssp. raddiana were studied. The results indicated that seeds contained 5.30% moisture, 3.99% ash, 9.19% fat, 14.31% fiber, 27.21% protein and 45.30% carbohydrates. Potassium was the predominant element followed by calcium and then phosphorous. Phytic acid, tannins and trypsin inhibitor as antinutrients were detected. The amino acid profile compared well with FAO/WHO recommended pattern except for cystine/methionine, isoleucine, tyrosine/phenylalanine, lysine and threonine. Also, the first limiting amino acid was lysine. Fatty acid composition showed that linoleic acid was the major fatty acid, followed by palmitic, stearic, oleic and arachidic acids. The seed oil showed absorbance in the ultraviolet ranges, thus it can be used as a broad spectrum UV protectant. For physicochemical and functional properties, acacia seeds flour had excellent water holding index, swelling index, foaming capacity and foam stability. Copyright © 2016 Elsevier Ltd. All rights reserved.

Isopropyl methyl phosphonic acid (IMPA)

Integrated Risk Information System (IRIS)

Isopropyl methyl phosphonic acid ( IMPA ) ; CASRN 1832 - 54 - 8 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assess

IRIS Toxicological Review of Trichloroacetic Acid (TCA) (External Review Draft)

EPA Science Inventory

EPA is conducting a peer review and public comment of the scientific basis supporting the human health hazard and dose-response assessment of Trichloroacetic acid (TCA) that when finalized will appear on the Integrated Risk Information System (IRIS) database.

Analysis of glyoxal and related substances by means of high-performance liquid chromatography with refractive index detection.

PubMed

Zhang, Zhiyong; Zhao, Dishun; Xu, Baoyun

2013-01-01

A simple and rapid method is described for the analysis of glyoxal and related substances by high-performance liquid chromatography with a refractive index detector. The following chromatographic conditions were adopted: Aminex HPX-87H column, mobile phase consisting of 0.01N H2SO4, flow rate of 0.8 mL/min and temperature of 65°C. The application of the analytical technique developed in this study demonstrated that the aqueous reaction mixture produced by the oxidation of acetaldehyde with HNO3 was composed of glyoxal, acetaldehyde, acetic acid, formic acid, glyoxylic acid, oxalic acid, butanedione and glycolic acid. The method was validated by evaluating analytical parameters such as linearity, limits of detection and quantification, precision, recovery and robustness. The proposed methodology was successfully applied to the production of glyoxal.

Percutaneous nephrolithotomy in England: practice and outcomes described in the Hospital Episode Statistics database.

PubMed

Armitage, James N; Withington, John; van der Meulen, Jan; Cromwell, David A; Glass, Jonathan; Finch, William G; Irving, Stuart O; Burgess, Neil A

2014-05-01

To investigate the postoperative outcomes of percutaneous nephrolithotomy (PCNL) in English National Health Service (NHS) hospitals. We extracted records from the Hospital Episode Statistics (HES) database for all patients undergoing PCNL between March 2006 and January 2011 in English NHS hospitals. Outcome measures were haemorrhage, infection within the index admission, and rates of emergency readmission and in-hospital mortality within 30 days of surgery. A total of 5750 index PCNL procedures were performed in 165 hospitals. During the index admission, haemorrhage was recorded in 81 patients (1.4%), 192 patients (3.8%) had a urinary tract infection (UTI), 95 patients (1.7%) had fever, and 41 patients (0.7%) had sepsis. There were 595 emergency readmissions in 518 patients (9.0%). Reasons for readmission were varied: 70 (1.2%) with UTI, 15 (0.3%) sepsis, 73 (1.3%) haematuria, 25 (0.4%) haemorrhage, and 25 (0.4%) acute urinary retention. There were 13 (0.2%) in-hospital deaths within 30 days of surgery. Haemorrhage and infection represent relatively common and potentially severe complications of PCNL. Mortality is extremely rare after PCNL (about one in 400 procedures overall) but almost one in 10 patients have an unplanned hospital readmission within 30 days of surgery. Complications of PCNL may be under-reported in the HES database and need to be corroborated using other data sources. © 2013 The Authors. BJU International © 2013 BJU International.

Correlation analysis of omega-3 fatty acids and mortality of sepsis and sepsis-induced ARDS in adults: data from previous randomized controlled trials.

PubMed

Chen, HuaiSheng; Wang, Su; Zhao, Ying; Luo, YuTian; Tong, HuaSheng; Su, Lei

2018-05-31

This study aimed to investigate the possible effect of omega-3 fatty acids on reducing the mortality of sepsis and sepsis-induced acute respiratory distress syndrome (ARDS) in adults. Medline, Embase, Cochrane Library, China National Knowledge Infrastructure (CNKI) database, WangFang database, and Chinese BioMedical Literature Database from their inception to March 6, 2017, were searched using systematic review researching methods. Five factors were analyzed to investigate the correlation between omega-3 fatty acids (either parenteral or enteral supplementation) and mortality rate. Forty randomized controlled trials (RCTs) were initially included, but only 25 of them assessed mortality. Of these RCTs, nine used enteral nutrition (EN) and 16 used parenteral nutrition (PN). The total mortality rate in the omega-3 fatty acid group was lower than that in the control group. However, the odds ratio (OR) value was not significantly different in the EN or PN subgroup. Eighteen RCTs including 1790 patients with similar severity of sepsis and ARDS were also analyzed. The OR value was not significantly different in the EN or PN subgroup. Omega-3 fatty acids did not show positive effect on improving mortality of sepsis-induced ARDS (p = 0.39). But in EN subgroup, omega-3 fatty acids treatment seemed to have some benefits in reducing mortality rate (p = 0.04). In the RCTs including similar baseline patients, partial correlation analysis found that the concentration ratio of n-6 to n-3 fatty acids had positive correlation with reduction of mortality (RM) (γ = 0.60, P = 0.02), whereas the total number of each RCT had negative correlation with RM (γ = - 0.54, P = 0.05). This review found that omega-3 fatty acid supplementation could reduce the mortality rate of sepsis and sepsis-induced ARDS. However, further investigation based on suitable concentrations and indications is needed to support the findings.

Milk fatty acid unsaturation: genetic parameters and effects of stearoyl-CoA desaturase (SCD1) and acyl CoA: diacylglycerol acyltransferase 1 (DGAT1).

PubMed

Schennink, A; Heck, J M L; Bovenhuis, H; Visker, M H P W; van Valenberg, H J F; van Arendonk, J A M

2008-05-01

With regard to human health aspects of milk fat, increasing the amount of unsaturated fatty acids in milk is an important selection objective. The cow's diet has an influence on the degree of unsaturation, but literature suggests that genetics also plays a role. To estimate genetic variation in milk fatty acid unsaturation indices, milk fatty acid composition of 1,933 Dutch Holstein Friesian heifers was measured and unsaturation indices were calculated. An unsaturation index represents the concentration of the unsaturated product proportional to the sum of the unsaturated product and the saturated substrate. Intraherd heritabilities were moderate, ranging from 0.23 +/- 0.07 for conjugated linoleic acid (CLA) index to 0.46 +/- 0.09 for C16 index. We genotyped the cows for the SCD1 A293V and DGAT1 K232A polymorphisms, which are known to alter milk fatty acid composition. Both genes explain part of the genetic variation in unsaturation indices. The SCD1 V allele is associated with lower C10, C12, and C14 indices, and with higher C16, C18, and CLA indices in comparison to the SCD1 A allele, with no differences in total unsaturation index. In comparison to the DGAT1 K allele, the DGAT1 A allele is associated with lower C10, C12, C14, and C16 indices and with higher C18, CLA, and total indices. We conclude that selective breeding can contribute to higher unsaturation indices, and that selective breeding can capitalize on genotypic information of both the SCD1 A293V and the DGAT1 K232A polymorphism.

Untargeted metabolomic analysis using liquid chromatography quadrupole time-of-flight mass spectrometry for non-volatile profiling of wines.

PubMed

Arbulu, M; Sampedro, M C; Gómez-Caballero, A; Goicolea, M A; Barrio, R J

2015-02-09

The current study presents a method for comprehensive untargeted metabolomic fingerprinting of the non-volatile profile of the Graciano Vitis vinifera wine variety, using liquid chromatography/electrospray ionization time of flight mass spectrometry (LC-ESI-QTOF). Pre-treatment of samples, chromatographic columns, mobile phases, elution gradients and ionization sources, were evaluated for the extraction of the maximum number of metabolites in red wine. Putative compounds were extracted from the raw data using the extraction algorithm, molecular feature extractor (MFE). For the metabolite identification the WinMet database was designed based on electronic databases and literature research and includes only the putative metabolites reported to be present in oenological matrices. The results from WinMet were compared with those in the METLIN database to evaluate how much the databases overlap for performing identifications. The reproducibility of the analysis was assessed using manual processing following replicate injections of Vitis vinifera cv. Graciano wine spiked with external standards. In the present work, 411 different metabolites in Graciano Vitis vinifera red wine were identified, including primary wine metabolites such as sugars (4%), amino acids (23%), biogenic amines (4%), fatty acids (2%), and organic acids (32%) and secondary metabolites such as phenols (27%) and esters (8%). Significant differences between varieties Tempranillo and Graciano were related to the presence of fifteen specific compounds. Copyright © 2014 Elsevier B.V. All rights reserved.

Digestion of fatty acids in ruminants: a meta-analysis of flows and variation factors: 2. C18 fatty acids.

PubMed

Glasser, F; Schmidely, P; Sauvant, D; Doreau, M

2008-05-01

In ruminants, dietary lipids are extensively hydrogenated by rumen micro-organisms, and the extent of this biohydrogenation is a major determinant of long-chain fatty acid profiles of animal products (milk, meat). This paper reports on the duodenal flows of C18 fatty acids and their absorption in the small intestine, using a meta-analysis of a database of 77 experiments (294 treatments). We established equations for the prediction of duodenal flows of various 18-carbon (C18) fatty acids as a function of the intakes of their precursors and other dietary factors (source and/or technological treatment of dietary lipids). We also quantified the influence of several factors modifying rumen metabolism (pH, forage : concentrate ratio, level of intake, fish oil supplementation). We established equations for the apparent absorption of these fatty acids in the small intestine as a function of their duodenal flows. For all C18 unsaturated fatty acids, apparent absorption was a linear function of duodenal flow. For 18:0, apparent absorption levelled off for high duodenal flows. From this database, with fatty acid flows expressed in g/kg dry matter intake, we could not find any significant differences between animal categories (lactating cows, other cattle or sheep) in terms of rumen metabolism or intestinal absorption of C18 fatty acids.

The use of large databases to inform the development of an intestinal scoring system for the poultry industry.

PubMed

Kasab-Bachi, H; Arruda, A G; Roberts, T E; Wilson, J B

2017-10-01

There is increasing interest among the poultry industry to develop a comprehensive index that can be used to evaluate overall intestinal health and impact on production performance. The Intestinal Integrity (I 2 ) index is a quantitative measurement tool used to assess the intestinal health of flocks that use the Health Tracking System (HTSi), a global surveillance system developed by Elanco Animal Health that captures flock-level information on health and performance. To generate an I 2 index score for a flock, the presence of 23 intestinal health conditions is assessed and recorded, then entered into a mathematical equation. The objective of this study was to use data from the HTSi dataset to investigate the association between health conditions contained within the I 2 index and five performance outcomes: average daily gain (ADG), mortality during the first week, feed conversion ratio (FCR), European Production Efficiency Factor (EPEF), and percent livability. At the time of analysis, the HTSi dataset contained information from the years 2006-2015 on 921,646 individual bird necropsy records from over 153,576 flocks at 1,570 broiler production flows across 53 countries. Flock-level production data used for this study were available for a subset of this population, 33,212 total flocks representing 6 US and 4 UK production flows. A separate multivariable linear or logistic regression model, with farm as a random effect, was built for each of the five outcomes mentioned above. All models controlled for clustering of flocks within production flows. Significant associations were found between key performance indicators and ten intestinal conditions (gross E. acervulina, gross E. maxima, microscopic E. maxima, gizzard erosions, roundworms, excessive intestinal fluid, thin intestines, excessive intestinal mucus, feed passage, and necrotic enteritis) and two management parameters (production flow and down time). Results from this study demonstrate that large databases, such as the HTSi database, can be used to inform and evaluate changes that can optimize intestinal health, and hence welfare, productivity, and sustainability of the poultry industry. In addition, large databases can be used for monitoring and benchmarking intestinal health of poultry and informing the development of innovative indices such as the I 2 index for scoring intestinal health and providing routine data for its calculation. Copyright © 2017 Elsevier B.V. All rights reserved.

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

PubMed Central

2013-01-01

Background It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence databases because of the high computational costs of the underlying sequence-structure alignment problem. Results We present new fast index-based and online algorithms for approximate matching of RNA sequence-structure patterns supporting a full set of edit operations on single bases and base pairs. Our methods efficiently compute semi-global alignments of structural RNA patterns and substrings of the target sequence whose costs satisfy a user-defined sequence-structure edit distance threshold. For this purpose, we introduce a new computing scheme to optimally reuse the entries of the required dynamic programming matrices for all substrings and combine it with a technique for avoiding the alignment computation of non-matching substrings. Our new index-based methods exploit suffix arrays preprocessed from the target database and achieve running times that are sublinear in the size of the searched sequences. To support the description of RNA molecules that fold into complex secondary structures with multiple ordered sequence-structure patterns, we use fast algorithms for the local or global chaining of approximate sequence-structure pattern matches. The chaining step removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our improved online algorithm is faster than the best previous method by up to factor 45. Our best new index-based algorithm achieves a speedup of factor 560. Conclusions The presented methods achieve considerable speedups compared to the best previous method. This, together with the expected sublinear running time of the presented index-based algorithms, allows for the first time approximate matching of RNA sequence-structure patterns in large sequence databases. Beyond the algorithmic contributions, we provide with RaligNAtor a robust and well documented open-source software package implementing the algorithms presented in this manuscript. The RaligNAtor software is available at http://www.zbh.uni-hamburg.de/ralignator. PMID:23865810

A modified TNM staging system for non-metastatic colorectal cancer based on nomogram analysis of SEER database.

PubMed

Kong, Xiangxing; Li, Jun; Cai, Yibo; Tian, Yu; Chi, Shengqiang; Tong, Danyang; Hu, Yeting; Yang, Qi; Li, Jingsong; Poston, Graeme; Yuan, Ying; Ding, Kefeng

2018-01-08

To revise the American Joint Committee on Cancer TNM staging system for colorectal cancer (CRC) based on a nomogram analysis of Surveillance, Epidemiology, and End Results (SEER) database, and to prove the rationality of enhancing T stage's weighting in our previously proposed T-plus staging system. Total 115,377 non-metastatic CRC patients from SEER were randomly grouped as training and testing set by ratio 1:1. The Nomo-staging system was established via three nomograms based on 1-year, 2-year and 3-year disease specific survival (DSS) Logistic regression analysis of the training set. The predictive value of Nomo-staging system for the testing set was evaluated by concordance index (c-index), likelihood ratio (L.R.) and Akaike information criteria (AIC) for 1-year, 2-year, 3-year overall survival (OS) and DSS. Kaplan-Meier survival curve was used to valuate discrimination and gradient monotonicity. And an external validation was performed on database from the Second Affiliated Hospital of Zhejiang University (SAHZU). Patients with T1-2 N1 and T1N2a were classified into stage II while T4 N0 patients were classified into stage III in Nomo-staging system. Kaplan-Meier survival curves of OS and DSS in testing set showed Nomo-staging system performed better in discrimination and gradient monotonicity, and the external validation in SAHZU database also showed distinctly better discrimination. The Nomo-staging system showed higher value in L.R. and c-index, and lower value in AIC when predicting OS and DSS in testing set. The Nomo-staging system showed better performance in prognosis prediction and the weight of lymph nodes status in prognosis prediction should be cautiously reconsidered.

Survival in commercially insured multiple sclerosis patients and comparator subjects in the U.S.

PubMed

Kaufman, D W; Reshef, S; Golub, H L; Peucker, M; Corwin, M J; Goodin, D S; Knappertz, V; Pleimes, D; Cutter, G

2014-05-01

Compare survival in patients with multiple sclerosis (MS) from a U.S. commercial health insurance database with a matched cohort of non-MS subjects. 30,402 MS patients and 89,818 non-MS subjects (comparators) in the OptumInsight Research (OIR) database from 1996 to 2009 were included. An MS diagnosis required at least 3 consecutive months of database reporting, with two or more ICD-9 codes of 340 at least 30 days apart, or the combination of 1 ICD-9-340 code and at least 1 MS disease-modifying treatment (DMT) code. Comparators required the absence of ICD-9-340 and DMT codes throughout database reporting. Up to three comparators were matched to each patient for: age in the year of the first relevant code (index year - at least 3 months of reporting in that year were required); sex; region of residence in the index year. Deaths were ascertained from the National Death Index and the Social Security Administration Death Master File. Subjects not identified as deceased were assumed to be alive through the end of 2009. Annual mortality rates were 899/100,000 among MS patients and 446/100,000 among comparators. Standardized mortality ratios compared to the U.S. population were 1.70 and 0.80, respectively. Kaplan-Meier analysis yielded a median survival from birth that was 6 years lower among MS patients than among comparators. The results show, for the first time in a U.S. population, a survival disadvantage for contemporary MS patients compared to non-MS subjects from the same healthcare system. The 6-year decrement in lifespan parallels a recent report from British Columbia. Copyright © 2013 Elsevier B.V. All rights reserved.

The use of the h-index in academic otolaryngology.

PubMed

Svider, Peter F; Choudhry, Zaid A; Choudhry, Osamah J; Baredes, Soly; Liu, James K; Eloy, Jean Anderson

2013-01-01

The h-index is an objective and easily calculable measure that can be used to evaluate both the relevance and amount of scientific contributions of an individual author. Our objective was to examine how the h-index of academic otolaryngologists relates with academic rank. A descriptive and correlational design was used for analysis of academic otolaryngologists' h-indices using the Scopus database. H-indices of faculty members from 50 otolaryngology residency programs were calculated using the Scopus database, and data was organized by academic rank. Additionally, an analysis of the h-indices of departmental chairpersons among different specialties was performed. H-index values of academic otolaryngologists were higher with increased academic rank among the levels of assistant professor, associate professor, and professor. There was no significant difference between the h-indices of professors and department chairpersons within otolaryngology. H-indices of chairpersons in different academic specialties were compared and were significantly different, suggesting that the use of this metric may not be appropriate for comparing different fields. The h-index is a reliable tool for quantifying academic productivity within otolaryngology. This measure is easily calculable and may be useful when evaluating decisions regarding advancement within academic otolaryngology departments. Comparison of this metric among faculty members from different fields, however, may not be reliable. Copyright © 2012 The American Laryngological, Rhinological, and Otological Society, Inc.

Researcher and Author Impact Metrics: Variety, Value, and Context.

PubMed

Gasparyan, Armen Yuri; Yessirkepov, Marlen; Duisenova, Akmaral; Trukhachev, Vladimir I; Kostyukova, Elena I; Kitas, George D

2018-04-30

Numerous quantitative indicators are currently available for evaluating research productivity. No single metric is suitable for comprehensive evaluation of the author-level impact. The choice of particular metrics depends on the purpose and context of the evaluation. The aim of this article is to overview some of the widely employed author impact metrics and highlight perspectives of their optimal use. The h -index is one of the most popular metrics for research evaluation, which is easy to calculate and understandable for non-experts. It is automatically displayed on researcher and author profiles on citation databases such as Scopus and Web of Science. Its main advantage relates to the combined approach to the quantification of publication and citation counts. This index is increasingly cited globally. Being an appropriate indicator of publication and citation activity of highly productive and successfully promoted authors, the h -index has been criticized primarily for disadvantaging early career researchers and authors with a few indexed publications. Numerous variants of the index have been proposed to overcome its limitations. Alternative metrics have also emerged to highlight 'societal impact.' However, each of these traditional and alternative metrics has its own drawbacks, necessitating careful analyses of the context of social attention and value of publication and citation sets. Perspectives of the optimal use of researcher and author metrics is dependent on evaluation purposes and compounded by information sourced from various global, national, and specialist bibliographic databases.

2-Methyl-4-chlorophenoxyacetic acid (MCPA)

Integrated Risk Information System (IRIS)

2 - Methyl - 4 - chlorophenoxyacetic acid ( MCPA ) ; CASRN 94 - 74 - 6 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard

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

Reisman, D.J.

A variety of issues must be addressed in development of software for information resources. One is accessibility and use of information. Another is that to properly design, abstract, index, and do quality control on a database requires the effort of well-trained and knowledgeable personnel as well as substantial financial resources. Transferring data to other locations has inherent difficulties, including those related to incompatibility. The main issue in developing health risk assessment databases is the needs of the user.