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Sample records for medline references sequence

  1. Sequence Factorization with Multiple References.

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    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  2. Using the Genetics Home Reference Website | NIH MedlinePlus the Magazine

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    ... of this page please turn Javascript on. Feature: Genetics 101 Using the Genetics Home Reference Website Past Issues / Summer 2013 Table ... as the GHR website keeps growing. What Is Genetic Counseling? Genetic counseling provides information and support to ...

  3. The Release 6 reference sequence of the Drosophila melanogaster genome.

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    Hoskins, Roger A; Carlson, Joseph W; Wan, Kenneth H; Park, Soo; Mendez, Ivonne; Galle, Samuel E; Booth, Benjamin W; Pfeiffer, Barret D; George, Reed A; Svirskas, Robert; Krzywinski, Martin; Schein, Jacqueline; Accardo, Maria Carmela; Damia, Elisabetta; Messina, Giovanni; Méndez-Lago, María; de Pablos, Beatriz; Demakova, Olga V; Andreyeva, Evgeniya N; Boldyreva, Lidiya V; Marra, Marco; Carvalho, A Bernardo; Dimitri, Patrizio; Villasante, Alfredo; Zhimulev, Igor F; Rubin, Gerald M; Karpen, Gary H; Celniker, Susan E

    2015-03-01

    Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads. © 2015 Hoskins et al.; Published by Cold Spring Harbor Laboratory Press.

  4. Reference genome sequence of the model plant Setaria.

    Science.gov (United States)

    Bennetzen, Jeffrey L; Schmutz, Jeremy; Wang, Hao; Percifield, Ryan; Hawkins, Jennifer; Pontaroli, Ana C; Estep, Matt; Feng, Liang; Vaughn, Justin N; Grimwood, Jane; Jenkins, Jerry; Barry, Kerrie; Lindquist, Erika; Hellsten, Uffe; Deshpande, Shweta; Wang, Xuewen; Wu, Xiaomei; Mitros, Therese; Triplett, Jimmy; Yang, Xiaohan; Ye, Chu-Yu; Mauro-Herrera, Margarita; Wang, Lin; Li, Pinghua; Sharma, Manoj; Sharma, Rita; Ronald, Pamela C; Panaud, Olivier; Kellogg, Elizabeth A; Brutnell, Thomas P; Doust, Andrew N; Tuskan, Gerald A; Rokhsar, Daniel; Devos, Katrien M

    2012-05-13

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  5. Reference genome sequence of the model plant Setaria

    Energy Technology Data Exchange (ETDEWEB)

    Bennetzen, Jeffrey L [ORNL; Schmutz, Jeremy [Hudson Alpha Institute of Biotechnology; Wang, Hao [University of Georgia, Athens, GA; Percifield, Ryan [University of Georgia, Athens, GA; Hawkins, Jennifer [University of Georgia, Athens, GA; Pontaroli, Ana C. [University of Georgia, Athens, GA; Estep, Matt [University of Georgia, Athens, GA; Feng, Liang [University of Georgia, Athens, GA; Vaughn, Justin N [ORNL; Grimwood, Jane [Hudson Alpha Institute of Biotechnology; Jenkins, Jerry [Hudson Alpha Institute of Biotechnology; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Lindquist, Erika [U.S. Department of Energy, Joint Genome Institute; Hellsten, Uffe [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Wang, Xuewen [University of Georgia, Athens, GA; Wu, Xiaomei [University of Georgia, Athens, GA; Mitros, Therese [University of California, Berkeley; Triplett, Jimmy [University of Missouri, St. Louis; Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Mauro-Herrera, Margarita [Oklahoma State University; Wang, Lin [Cornell University; Li, Pinghua [Cornell University; Sharma, Manoj [University of California, Davis; Sharma, Rita [University of California, Davis; Ronald, Pamela [University of California, Davis; Panaud, Olivier [Universite de Perpignan, Perpignan, France; Kellogg, Elizabeth A. [University of Missouri, St. Louis; Brutnell, Thomas P. [Cornell University; Doust, Andrew N. [Oklahoma State University; Tuskan, Gerald A [ORNL; Rokhsar, Daniel [U.S. Department of Energy, Joint Genome Institute; Devos, Katrien M [ORNL

    2012-01-01

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  6. Reference genome sequence of the model plant Setaria

    Energy Technology Data Exchange (ETDEWEB)

    Bennetzen, Jeffrey L [ORNL; Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tuskan, Gerald A [ORNL

    2012-01-01

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The {approx}400-Mb assembly covers {approx}80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  7. Transcriptome sequencing of the Microarray Quality Control (MAQC RNA reference samples using next generation sequencing

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    Thierry-Mieg Danielle

    2009-06-01

    Full Text Available Abstract Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.

  8. No Reference Prediction of Quality Metrics for H.264 Compressed Infrared Image Sequences for UAV Applications

    DEFF Research Database (Denmark)

    Hossain, Kabir; Mantel, Claire; Forchhammer, Søren

    2018-01-01

    The framework for this research work is the acquisition of Infrared (IR) images from Unmanned Aerial Vehicles (UAV). In this paper we consider the No-Reference (NR) prediction of Full Reference Quality Metrics for Infrared (IR) video sequences which are compressed and thus distorted by an H.264...

  9. A STUDY ON DETERMINING THE REFERENCE SPREADING SEQUENCES FOR A DS/CDMACOMMUNICATION SYSTEM

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    Cebrail ÇİFTLİKLİ

    2002-02-01

    Full Text Available In a direct sequence/code division multiple access (DS/CDMA system, the role of the spreading sequences (codes is crucial since the multiple access interference (MAI is the main performance limitation. In this study, we propose an accurate criterion which enables the determination of the reference spreading codes which yield lower bit error rates (BER's in a given code set for a DS/CDMA system using despreading sequences weighted by stepping chip waveforms. The numerical results show that the spreading codes determined by the proposed criterion are the most suitable codes for using as references.

  10. Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.

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    Manal Helal

    Full Text Available BACKGROUND: The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. METHODS: A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. RESULTS: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52% corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578. CONCLUSION: The identification of centroids of 16S rRNA gene sequence clusters using novel distance matrix clustering enables the identification of the most representative sequences for each individual species of Nocardia and allows the quantitation of inter- and intra

  11. MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

    DEFF Research Database (Denmark)

    Petersen, Thomas Nordahl; Lukjancenko, Oksana; Thomsen, Martin Christen Frølund

    2017-01-01

    number of false positive species annotations are a problem unless thresholds or post-processing are applied to differentiate between correct and false annotations. MGmapper is a package to process raw next generation sequence data and perform reference based sequence assignment, followed by a post...... pipeline is freely available as a bitbucked package (https://bitbucket.org/genomicepidemiology/mgmapper). A web-version (https://cge.cbs.dtu.dk/services/MGmapper) provides the basic functionality for analysis of small fastq datasets....

  12. Newborn Screening: MedlinePlus Health Topic

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    ... more articles Reference Desk Glossary (National Center for Biotechnology Information) Find an Expert Eunice Kennedy Shriver National ... other than English on Newborn Screening NIH MedlinePlus Magazine Hearing Loss: Screening Newborns Screening Newborns' Hearing Now ...

  13. Liver Transplantation: MedlinePlus Health Topic

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    ... Statistics and Research The SRTR/OPTN Annual Data Report (Scientific Registry of Transplant Recipients) Clinical Trials ClinicalTrials.gov: Liver Transplantation (National Institutes of Health) Journal Articles References and abstracts from MEDLINE/PubMed (National ...

  14. Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads.

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    Jovan Rebolledo-Mendez

    Full Text Available The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight's half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects' and Twilight's genome or due to errors in the reference. EquCab2 is regarded as "The Twilight Assembly." The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies

  15. MedlinePlus

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    U.S. Department of Health & Human Services — MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, the world’s...

  16. MedlinePlus Tour

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    ... captioning, click the CC button on the lower right-hand corner of the player. Video player keyboard shortcuts Transcript Welcome to MedlinePlus, the consumer health information website from the National Library of ...

  17. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

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    Rideout, Jai Ram; He, Yan; Navas-Molina, Jose A; Walters, William A; Ursell, Luke K; Gibbons, Sean M; Chase, John; McDonald, Daniel; Gonzalez, Antonio; Robbins-Pianka, Adam; Clemente, Jose C; Gilbert, Jack A; Huse, Susan M; Zhou, Hong-Wei; Knight, Rob; Caporaso, J Gregory

    2014-01-01

    We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to "classic" open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, "classic" open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of "classic" open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by "classic" open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME's uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME's OTU picking workflows and

  18. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

    Directory of Open Access Journals (Sweden)

    Jai Ram Rideout

    2014-08-01

    Full Text Available We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity. Because more of our algorithm can be run in parallel relative to “classic” open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, “classic” open-reference OTU clustering is often faster. We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons. To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of “classic” open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by “classic” open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME’s uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced. Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in

  19. Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis.

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    Guo, Yan; Dai, Yulin; Yu, Hui; Zhao, Shilin; Samuels, David C; Shyr, Yu

    2017-03-01

    Analyses of high throughput sequencing data starts with alignment against a reference genome, which is the foundation for all re-sequencing data analyses. Each new release of the human reference genome has been augmented with improved accuracy and completeness. It is presumed that the latest release of human reference genome, GRCh38 will contribute more to high throughput sequencing data analysis by providing more accuracy. But the amount of improvement has not yet been quantified. We conducted a study to compare the genomic analysis results between the GRCh38 reference and its predecessor GRCh37. Through analyses of alignment, single nucleotide polymorphisms, small insertion/deletions, copy number and structural variants, we show that GRCh38 offers overall more accurate analysis of human sequencing data. More importantly, GRCh38 produced fewer false positive structural variants. In conclusion, GRCh38 is an improvement over GRCh37 not only from the genome assembly aspect, but also yields more reliable genomic analysis results. Copyright © 2017. Published by Elsevier Inc.

  20. Locus Reference Genomic sequences: An improved basis for describing human DNA variants

    KAUST Repository

    Dalgleish, Raymond; Flicek, Paul; Cunningham, Fiona; Astashyn, Alex; Tully, Raymond E; Proctor, Glenn; Chen, Yuan; McLaren, William M; Larsson, Pontus; Vaughan, Brendan W; Bé roud, Christophe; Dobson, Glen; Lehvä slaiho, Heikki; Taschner, Peter EM; den Dunnen, Johan T; Devereau, Andrew; Birney, Ewan; Brookes, Anthony J; Maglott, Donna R

    2010-01-01

    As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.

  1. Locus Reference Genomic sequences: An improved basis for describing human DNA variants

    KAUST Repository

    Dalgleish, Raymond

    2010-04-15

    As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.

  2. Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

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    Monson-Miller Jennifer

    2012-02-01

    Full Text Available Abstract Background The availability of low cost sequencing has spurred its application to discovery and typing of variation, including variation induced by mutagenesis. Mutation discovery is challenging as it requires a substantial amount of sequencing and analysis to detect very rare changes and distinguish them from noise. Also challenging are the cases when the organism of interest has not been sequenced or is highly divergent from the reference. Results We describe the development of a simple method for reduced representation sequencing. Input DNA was digested with a single restriction enzyme and ligated to Y adapters modified to contain a sequence barcode and to provide a compatible overhang for ligation. We demonstrated the efficiency of this method at SNP discovery using rice and arabidopsis. To test its suitability for the discovery of very rare SNP, one control and three mutagenized rice individuals (1, 5 and 10 mM sodium azide were used to prepare genomic libraries for Illumina sequencers by ligating barcoded adapters to NlaIII restriction sites. For genome-dependent discovery 15-30 million of 80 base reads per individual were aligned to the reference sequence achieving individual sequencing coverage from 7 to 15×. We identified high-confidence base changes by comparing sequences across individuals and identified instances consistent with mutations, i.e. changes that were found in a single treated individual and were solely GC to AT transitions. For genome-independent discovery 70-mers were extracted from the sequence of the control individual and single-copy sequence was identified by comparing the 70-mers across samples to evaluate copy number and variation. This de novo "genome" was used to align the reads and identify mutations as above. Covering approximately 1/5 of the 380 Mb genome of rice we detected mutation densities ranging from 0.6 to 4 per Mb of diploid DNA depending on the mutagenic treatment. Conclusions The

  3. Diversity in non-repetitive human sequences not found in the reference genome.

    Science.gov (United States)

    Kehr, Birte; Helgadottir, Anna; Melsted, Pall; Jonsson, Hakon; Helgason, Hannes; Jonasdottir, Adalbjörg; Jonasdottir, Aslaug; Sigurdsson, Asgeir; Gylfason, Arnaldur; Halldorsson, Gisli H; Kristmundsdottir, Snaedis; Thorgeirsson, Gudmundur; Olafsson, Isleifur; Holm, Hilma; Thorsteinsdottir, Unnur; Sulem, Patrick; Helgason, Agnar; Gudbjartsson, Daniel F; Halldorsson, Bjarni V; Stefansson, Kari

    2017-04-01

    Genomes usually contain some non-repetitive sequences that are missing from the reference genome and occur only in a population subset. Such non-repetitive, non-reference (NRNR) sequences have remained largely unexplored in terms of their characterization and downstream analyses. Here we describe 3,791 breakpoint-resolved NRNR sequence variants called using PopIns from whole-genome sequence data of 15,219 Icelanders. We found that over 95% of the 244 NRNR sequences that are 200 bp or longer are present in chimpanzees, indicating that they are ancestral. Furthermore, 149 variant loci are in linkage disequilibrium (r 2 > 0.8) with a genome-wide association study (GWAS) catalog marker, suggesting disease relevance. Additionally, we report an association (P = 3.8 × 10 -8 , odds ratio (OR) = 0.92) with myocardial infarction (23,360 cases, 300,771 controls) for a 766-bp NRNR sequence variant. Our results underline the importance of including variation of all complexity levels when searching for variants that associate with disease.

  4. Effector-independent motor sequence representations exist in extrinsic and intrinsic reference frames.

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    Wiestler, Tobias; Waters-Metenier, Sheena; Diedrichsen, Jörn

    2014-04-02

    Many daily activities rely on the ability to produce meaningful sequences of movements. Motor sequences can be learned in an effector-specific fashion (such that benefits of training are restricted to the trained hand) or an effector-independent manner (meaning that learning also facilitates performance with the untrained hand). Effector-independent knowledge can be represented in extrinsic/world-centered or in intrinsic/body-centered coordinates. Here, we used functional magnetic resonance imaging (fMRI) and multivoxel pattern analysis to determine the distribution of intrinsic and extrinsic finger sequence representations across the human neocortex. Participants practiced four sequences with one hand for 4 d, and then performed these sequences during fMRI with both left and right hand. Between hands, these sequences were equivalent in extrinsic or intrinsic space, or were unrelated. In dorsal premotor cortex (PMd), we found that sequence-specific activity patterns correlated higher for extrinsic than for unrelated pairs, providing evidence for an extrinsic sequence representation. In contrast, primary sensory and motor cortices showed effector-independent representations in intrinsic space, with considerable overlap of the two reference frames in caudal PMd. These results suggest that effector-independent representations exist not only in world-centered, but also in body-centered coordinates, and that PMd may be involved in transforming sequential knowledge between the two. Moreover, although effector-independent sequence representations were found bilaterally, they were stronger in the hemisphere contralateral to the trained hand. This indicates that intermanual transfer relies on motor memories that are laid down during training in both hemispheres, but preferentially draws upon sequential knowledge represented in the trained hemisphere.

  5. MedlinePlus FAQ: MedlinePlus and MEDLINE/PubMed

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    ... What is the difference between MedlinePlus and MEDLINE/PubMed? To use the sharing features on this page, ... latest health professional articles on your topic. MEDLINE/PubMed: Is a database of professional biomedical literature Is ...

  6. MedlinePlus FAQ: Can you tell me how to cite MedlinePlus pages?

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    ... MedlinePlus, the National Library of Medicine recommends the citation style below, based upon Citing Medicine . This style, like many other citation styles, requires that for online references you include the ...

  7. Reference voltage calculation method based on zero-sequence component optimisation for a regional compensation DVR

    Science.gov (United States)

    Jian, Le; Cao, Wang; Jintao, Yang; Yinge, Wang

    2018-04-01

    This paper describes the design of a dynamic voltage restorer (DVR) that can simultaneously protect several sensitive loads from voltage sags in a region of an MV distribution network. A novel reference voltage calculation method based on zero-sequence voltage optimisation is proposed for this DVR to optimise cost-effectiveness in compensation of voltage sags with different characteristics in an ungrounded neutral system. Based on a detailed analysis of the characteristics of voltage sags caused by different types of faults and the effect of the wiring mode of the transformer on these characteristics, the optimisation target of the reference voltage calculation is presented with several constraints. The reference voltages under all types of voltage sags are calculated by optimising the zero-sequence component, which can reduce the degree of swell in the phase-to-ground voltage after compensation to the maximum extent and can improve the symmetry degree of the output voltages of the DVR, thereby effectively increasing the compensation ability. The validity and effectiveness of the proposed method are verified by simulation and experimental results.

  8. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

    DEFF Research Database (Denmark)

    Maretty, Lasse; Jensen, Jacob Malte; Petersen, Bent

    2017-01-01

    Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome......-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set...... or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high...

  9. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

    DEFF Research Database (Denmark)

    Maretty, Lasse; Jensen, Jacob Malte; Petersen, Bent

    2017-01-01

    Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome...... or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high......-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set...

  10. Iterative normalization technique for reference sequence generation for zero-tail discrete fourier transform spread orthogonal frequency division multiplexing

    DEFF Research Database (Denmark)

    2017-01-01

    Systems, methods, apparatuses, and computer program products for generating sequences for zero-tail discrete fourier transform (DFT)-spread-orthogonal frequency division multiplexing (OFDM) (ZT DFT-s-OFDM) reference signals. One method includes adding a zero vector to an input sequence...... of each of the elements, converting the sequence to time domain, generating a zero-padded sequence by forcing a zero head and tail of the sequence, and repeating the steps until a final sequence with zero-tail and flat frequency response is obtained....

  11. The development of rhythmic attending in auditory sequences: attunement, referent period, focal attending.

    Science.gov (United States)

    Drake, C; Jones, M R; Baruch, C

    2000-12-15

    This paper is divided into three sections. The first section is theoretical; it extends Dynamic Attending Theory (Jones, M. R. Psychological Review 83 (1976) 323; Jones, M. R. Perception and Psychophysics 41(6) (1987) 631; Jones, M. R. Psychomusicology 9(2) (1990) 193; Jones, M. R., & Boltz, M. Psychological Review 96(3) (1989) 459) to developmental questions concerning tempo and time hierarchies. Generally Dynamic Attending Theory proposes that, when listening to a complex auditory sequence, listeners spontaneously focus on events occurring at an intermediate rate (the referent level), and they then may shift attention to events occurring over longer or shorter time spans, that is at lower (faster) or higher (slower) hierarchical levels (focal attending). The second section of the paper is experimental. It examines maturational changes of three dynamic attending activities involving referent period and level, attunement, and focal attending. Tasks involve both motor tapping (including spontaneous motor tempo and synchronization with simple sequences and music) and tempo discrimination. We compare performances by 4-, 6-, 8-, and 10-year-old children and adults, with or without musical training. Results indicate three changes with increased age and musical training: (1) a slowing of the mean spontaneous tapping rate (a reflection of the referent period) and mean synchronization rate (a reflection of the referent level), (2) enhanced ability to synchronize tapping and discriminate tempo (improved attunement), and (3) an enlarged range of tapping rates towards slower rates and higher hierarchical levels (improved focal attending). A final section considers results in light of the theory proposed here. It is suggested that growth trends can be expressed in terms of listeners' engagement of slower attending oscillators with age and experience, accompanied by the passage from the initial use of a single oscillator towards the coupling of multiple oscillators.

  12. The zebrafish reference genome sequence and its relationship to the human genome

    Science.gov (United States)

    Howe, Kerstin; Clark, Matthew D.; Torroja, Carlos F.; Torrance, James; Berthelot, Camille; Muffato, Matthieu; Collins, John E.; Humphray, Sean; McLaren, Karen; Matthews, Lucy; McLaren, Stuart; Sealy, Ian; Caccamo, Mario; Churcher, Carol; Scott, Carol; Barrett, Jeffrey C.; Koch, Romke; Rauch, Gerd-Jörg; White, Simon; Chow, William; Kilian, Britt; Quintais, Leonor T.; Guerra-Assunção, José A.; Zhou, Yi; Gu, Yong; Yen, Jennifer; Vogel, Jan-Hinnerk; Eyre, Tina; Redmond, Seth; Banerjee, Ruby; Chi, Jianxiang; Fu, Beiyuan; Langley, Elizabeth; Maguire, Sean F.; Laird, Gavin K.; Lloyd, David; Kenyon, Emma; Donaldson, Sarah; Sehra, Harminder; Almeida-King, Jeff; Loveland, Jane; Trevanion, Stephen; Jones, Matt; Quail, Mike; Willey, Dave; Hunt, Adrienne; Burton, John; Sims, Sarah; McLay, Kirsten; Plumb, Bob; Davis, Joy; Clee, Chris; Oliver, Karen; Clark, Richard; Riddle, Clare; Eliott, David; Threadgold, Glen; Harden, Glenn; Ware, Darren; Mortimer, Beverly; Kerry, Giselle; Heath, Paul; Phillimore, Benjamin; Tracey, Alan; Corby, Nicole; Dunn, Matthew; Johnson, Christopher; Wood, Jonathan; Clark, Susan; Pelan, Sarah; Griffiths, Guy; Smith, Michelle; Glithero, Rebecca; Howden, Philip; Barker, Nicholas; Stevens, Christopher; Harley, Joanna; Holt, Karen; Panagiotidis, Georgios; Lovell, Jamieson; Beasley, Helen; Henderson, Carl; Gordon, Daria; Auger, Katherine; Wright, Deborah; Collins, Joanna; Raisen, Claire; Dyer, Lauren; Leung, Kenric; Robertson, Lauren; Ambridge, Kirsty; Leongamornlert, Daniel; McGuire, Sarah; Gilderthorp, Ruth; Griffiths, Coline; Manthravadi, Deepa; Nichol, Sarah; Barker, Gary; Whitehead, Siobhan; Kay, Michael; Brown, Jacqueline; Murnane, Clare; Gray, Emma; Humphries, Matthew; Sycamore, Neil; Barker, Darren; Saunders, David; Wallis, Justene; Babbage, Anne; Hammond, Sian; Mashreghi-Mohammadi, Maryam; Barr, Lucy; Martin, Sancha; Wray, Paul; Ellington, Andrew; Matthews, Nicholas; Ellwood, Matthew; Woodmansey, Rebecca; Clark, Graham; Cooper, James; Tromans, Anthony; Grafham, Darren; Skuce, Carl; Pandian, Richard; Andrews, Robert; Harrison, Elliot; Kimberley, Andrew; Garnett, Jane; Fosker, Nigel; Hall, Rebekah; Garner, Patrick; Kelly, Daniel; Bird, Christine; Palmer, Sophie; Gehring, Ines; Berger, Andrea; Dooley, Christopher M.; Ersan-Ürün, Zübeyde; Eser, Cigdem; Geiger, Horst; Geisler, Maria; Karotki, Lena; Kirn, Anette; Konantz, Judith; Konantz, Martina; Oberländer, Martina; Rudolph-Geiger, Silke; Teucke, Mathias; Osoegawa, Kazutoyo; Zhu, Baoli; Rapp, Amanda; Widaa, Sara; Langford, Cordelia; Yang, Fengtang; Carter, Nigel P.; Harrow, Jennifer; Ning, Zemin; Herrero, Javier; Searle, Steve M. J.; Enright, Anton; Geisler, Robert; Plasterk, Ronald H. A.; Lee, Charles; Westerfield, Monte; de Jong, Pieter J.; Zon, Leonard I.; Postlethwait, John H.; Nüsslein-Volhard, Christiane; Hubbard, Tim J. P.; Crollius, Hugues Roest; Rogers, Jane; Stemple, Derek L.

    2013-01-01

    Zebrafish have become a popular organism for the study of vertebrate gene function1,2. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease3–5. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes6, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination. PMID:23594743

  13. The zebrafish reference genome sequence and its relationship to the human genome.

    Science.gov (United States)

    Howe, Kerstin; Clark, Matthew D; Torroja, Carlos F; Torrance, James; Berthelot, Camille; Muffato, Matthieu; Collins, John E; Humphray, Sean; McLaren, Karen; Matthews, Lucy; McLaren, Stuart; Sealy, Ian; Caccamo, Mario; Churcher, Carol; Scott, Carol; Barrett, Jeffrey C; Koch, Romke; Rauch, Gerd-Jörg; White, Simon; Chow, William; Kilian, Britt; Quintais, Leonor T; Guerra-Assunção, José A; Zhou, Yi; Gu, Yong; Yen, Jennifer; Vogel, Jan-Hinnerk; Eyre, Tina; Redmond, Seth; Banerjee, Ruby; Chi, Jianxiang; Fu, Beiyuan; Langley, Elizabeth; Maguire, Sean F; Laird, Gavin K; Lloyd, David; Kenyon, Emma; Donaldson, Sarah; Sehra, Harminder; Almeida-King, Jeff; Loveland, Jane; Trevanion, Stephen; Jones, Matt; Quail, Mike; Willey, Dave; Hunt, Adrienne; Burton, John; Sims, Sarah; McLay, Kirsten; Plumb, Bob; Davis, Joy; Clee, Chris; Oliver, Karen; Clark, Richard; Riddle, Clare; Elliot, David; Eliott, David; Threadgold, Glen; Harden, Glenn; Ware, Darren; Begum, Sharmin; Mortimore, Beverley; Mortimer, Beverly; Kerry, Giselle; Heath, Paul; Phillimore, Benjamin; Tracey, Alan; Corby, Nicole; Dunn, Matthew; Johnson, Christopher; Wood, Jonathan; Clark, Susan; Pelan, Sarah; Griffiths, Guy; Smith, Michelle; Glithero, Rebecca; Howden, Philip; Barker, Nicholas; Lloyd, Christine; Stevens, Christopher; Harley, Joanna; Holt, Karen; Panagiotidis, Georgios; Lovell, Jamieson; Beasley, Helen; Henderson, Carl; Gordon, Daria; Auger, Katherine; Wright, Deborah; Collins, Joanna; Raisen, Claire; Dyer, Lauren; Leung, Kenric; Robertson, Lauren; Ambridge, Kirsty; Leongamornlert, Daniel; McGuire, Sarah; Gilderthorp, Ruth; Griffiths, Coline; Manthravadi, Deepa; Nichol, Sarah; Barker, Gary; Whitehead, Siobhan; Kay, Michael; Brown, Jacqueline; Murnane, Clare; Gray, Emma; Humphries, Matthew; Sycamore, Neil; Barker, Darren; Saunders, David; Wallis, Justene; Babbage, Anne; Hammond, Sian; Mashreghi-Mohammadi, Maryam; Barr, Lucy; Martin, Sancha; Wray, Paul; Ellington, Andrew; Matthews, Nicholas; Ellwood, Matthew; Woodmansey, Rebecca; Clark, Graham; Cooper, James D; Cooper, James; Tromans, Anthony; Grafham, Darren; Skuce, Carl; Pandian, Richard; Andrews, Robert; Harrison, Elliot; Kimberley, Andrew; Garnett, Jane; Fosker, Nigel; Hall, Rebekah; Garner, Patrick; Kelly, Daniel; Bird, Christine; Palmer, Sophie; Gehring, Ines; Berger, Andrea; Dooley, Christopher M; Ersan-Ürün, Zübeyde; Eser, Cigdem; Geiger, Horst; Geisler, Maria; Karotki, Lena; Kirn, Anette; Konantz, Judith; Konantz, Martina; Oberländer, Martina; Rudolph-Geiger, Silke; Teucke, Mathias; Lanz, Christa; Raddatz, Günter; Osoegawa, Kazutoyo; Zhu, Baoli; Rapp, Amanda; Widaa, Sara; Langford, Cordelia; Yang, Fengtang; Schuster, Stephan C; Carter, Nigel P; Harrow, Jennifer; Ning, Zemin; Herrero, Javier; Searle, Steve M J; Enright, Anton; Geisler, Robert; Plasterk, Ronald H A; Lee, Charles; Westerfield, Monte; de Jong, Pieter J; Zon, Leonard I; Postlethwait, John H; Nüsslein-Volhard, Christiane; Hubbard, Tim J P; Roest Crollius, Hugues; Rogers, Jane; Stemple, Derek L

    2013-04-25

    Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.

  14. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

    Directory of Open Access Journals (Sweden)

    Martin Mascher

    Full Text Available The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS, a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new

  15. Pain Relievers: MedlinePlus Health Topic

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    ... Health) ClinicalTrials.gov: Narcotics (National Institutes of Health) Journal Articles References and abstracts from MEDLINE/PubMed (National ... Concentration Before Giving Acetaminophen to Infants (Food and Drug Administration) ... Related Health Topics Chronic Pain Medicines Opioid Abuse and Addiction Over-the-Counter Medicines Pain Other ...

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  18. Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

    NARCIS (Netherlands)

    Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; Vos, de Willem M.

    2015-01-01

    Background: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to

  19. Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses.

    Directory of Open Access Journals (Sweden)

    Arthur W Pightling

    Full Text Available The wide availability of whole-genome sequencing (WGS and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i depth of sequencing coverage, ii choice of reference-guided short-read sequence assembler, iii choice of reference genome, and iv whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT, using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming. We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers

  20. MedlinePlus FAQ: What's the difference between MedlinePlus and MedlinePlus Connect?

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    ... MedlinePlus Connect is a free service that allows electronic health record (EHR) systems to easily link users to MedlinePlus, ... updates Subscribe to RSS Follow us Disclaimers Copyright Privacy Accessibility Quality Guidelines Viewers & Players MedlinePlus Connect for ...

  1. Routine Whole-Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center

    Directory of Open Access Journals (Sweden)

    Geraldine Durand

    2018-03-01

    Full Text Available The French National Reference Center for Staphylococci currently uses DNA arrays and spa typing for the initial epidemiological characterization of Staphylococcus aureus strains. We here describe the use of whole-genome sequencing (WGS to investigate retrospectively four distinct and virulent S. aureus lineages [clonal complexes (CCs: CC1, CC5, CC8, CC30] involved in hospital and community outbreaks or sporadic infections in France. We used a WGS bioinformatics pipeline based on de novo assembly (reference-free approach, single nucleotide polymorphism analysis, and on the inclusion of epidemiological markers. We examined the phylogeographic diversity of the French dominant hospital-acquired CC8-MRSA (methicillin-resistant S. aureus Lyon clone through WGS analysis which did not demonstrate evidence of large-scale geographic clustering. We analyzed sporadic cases along with two outbreaks of a CC1-MSSA (methicillin-susceptible S. aureus clone containing the Panton–Valentine leukocidin (PVL and results showed that two sporadic cases were closely related. We investigated an outbreak of PVL-positive CC30-MSSA in a school environment and were able to reconstruct the transmission history between eight families. We explored different outbreaks among newborns due to the CC5-MRSA Geraldine clone and we found evidence of an unsuspected link between two otherwise distinct outbreaks. Here, WGS provides the resolving power to disprove transmission events indicated by conventional methods (same sequence type, spa type, toxin profile, and antibiotic resistance profile and, most importantly, WGS can reveal unsuspected transmission events. Therefore, WGS allows to better describe and understand outbreaks and (inter-national dissemination of S. aureus lineages. Our findings underscore the importance of adding WGS for (inter-national surveillance of infections caused by virulent clones of S. aureus but also substantiate the fact that technological optimization at

  2. Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

    Science.gov (United States)

    Yang, Yaping; Muzny, Donna M.; Xia, Fan; Niu, Zhiyv; Person, Richard; Ding, Yan; Ward, Patricia; Braxton, Alicia; Wang, Min; Buhay, Christian; Veeraraghavan, Narayanan; Hawes, Alicia; Chiang, Theodore; Leduc, Magalie; Beuten, Joke; Zhang, Jing; He, Weimin; Scull, Jennifer; Willis, Alecia; Landsverk, Megan; Craigen, William J.; Bekheirnia, Mir Reza; Stray-Pedersen, Asbjorg; Liu, Pengfei; Wen, Shu; Alcaraz, Wendy; Cui, Hong; Walkiewicz, Magdalena; Reid, Jeffrey; Bainbridge, Matthew; Patel, Ankita; Boerwinkle, Eric; Beaudet, Arthur L.; Lupski, James R.; Plon, Sharon E.; Gibbs, Richard A.; Eng, Christine M.

    2015-01-01

    ), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics. CONCLUSIONS AND RELEVANCE Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients. PMID:25326635

  3. A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

    Science.gov (United States)

    Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike; Khan, Arifa S

    2018-01-01

    Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have

  4. Sequence-based comparative study of classical swine fever virus genogroup 2.2 isolate with pestivirus reference strains.

    Science.gov (United States)

    Kumar, Ravi; Rajak, Kaushal Kishor; Chandra, Tribhuwan; Muthuchelvan, Dhanavelu; Saxena, Arpit; Chaudhary, Dheeraj; Kumar, Ajay; Pandey, Awadh Bihari

    2015-09-01

    This study was undertaken with the aim to compare and establish the genetic relatedness between classical swine fever virus (CSFV) genogroup 2.2 isolate and pestivirus reference strains. The available complete genome sequences of CSFV/IND/UK/LAL-290 strain and other pestivirus reference strains were retrieved from GenBank. The complete genome sequence, complete open reading frame, 5' and 3' non-coding region (NCR) sequences were analyzed and compared with reference pestiviruses strains. Clustal W model in MegAlign program of Lasergene 6.0 software was used for analysis of genetic heterogeneity. Phylogenetic analysis was carried out using MEGA 6.06 software package. The complete genome sequence alignment of CSFV/IND/UK/LAL-290 isolate and reference pestivirus strains showed 58.9-72% identities at the nucleotide level and 50.3-76.9% at amino acid level. Sequence homology of 5' and 3' NCRs was found to be 64.1-82.3% and 22.9-71.4%, respectively. In phylogenetic analysis, overall tree topology was found similar irrespective of sequences used in this study; however, whole genome phylogeny of pestivirus formed two main clusters, which further distinguished into the monophyletic clade of each pestivirus species. CSFV/IND/UK/LAL-290 isolate placed with the CSFV Eystrup strain in the same clade with close proximity to border disease virus and Aydin strains. CSFV/IND/UK/LAL-290 exhibited the analogous genomic organization to those of all reference pestivirus strains. Based on sequence identity and phylogenetic analysis, the isolate showed close homology to Aydin/04-TR virus and distantly related to Bungowannah virus.

  5. A1C: MedlinePlus Health Topic

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  12. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

    Directory of Open Access Journals (Sweden)

    Kodner Robin B

    2010-10-01

    Full Text Available Abstract Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Conclusions Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.

  13. Overview of errors in the reference sequence and annotation of Mycobacterium tuberculosis H37Rv, and variation amongst its isolates

    KAUST Repository

    Köser, Claudio U.

    2012-06-01

    Since its publication in 1998, the genome sequence of the Mycobacterium tuberculosis H37Rv laboratory strain has acted as the cornerstone for the study of tuberculosis. In this review we address some of the practical aspects that have come to light relating to the use of H37Rv throughout the past decade which are of relevance for the ongoing genomic and laboratory studies of this pathogen. These include errors in the genome reference sequence and its annotation, as well as the recently detected variation amongst isolates of H37Rv from different laboratories. © 2011 Elsevier B.V..

  14. SEQUENCING AND DE NOVO DRAFT ASSEMBLIES OF A FATHEAD MINNOW (Pimpehales promelas) reference genome

    Data.gov (United States)

    U.S. Environmental Protection Agency — The dataset provides the URLs for accessing the genome sequence data and two draft assemblies as well as fathead minnow genotyping data associated with estimating...

  15. Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.

    Science.gov (United States)

    Martin, Guillaume; Baurens, Franc-Christophe; Droc, Gaëtan; Rouard, Mathieu; Cenci, Alberto; Kilian, Andrzej; Hastie, Alex; Doležel, Jaroslav; Aury, Jean-Marc; Alberti, Adriana; Carreel, Françoise; D'Hont, Angélique

    2016-03-16

    Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata). We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of Musa acuminata. Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total Musa scaffold number from 7513 to 1532 (i.e. by 80%), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5% of the assembly was anchored to the 11 Musa chromosomes compared to the previous 70%. Unknown sites (N) were reduced from 17.3 to 10.0%. The release of the Musa acuminata reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in

  16. Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome

    Science.gov (United States)

    This study was undertaken to develop genome-scale resources for the fathead minnow (Pimphales promelas) an important model organism widely used in both aquatic ecotoxicology research and in regulatory toxicity testing. We report on the first sequencing and two draft assemblies fo...

  17. Reference-quality genome sequence of Aegilops tauschii, the source of wheat D genome, shows that recombination shapes genome structure and evolution

    Science.gov (United States)

    Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat and an important genetic resource for wheat. A reference-quality sequence for the Ae. tauschii genome was produced with a combination of ordered-clone sequencing, whole-genome shotgun sequencing, and BioNano optical geno...

  18. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

    DEFF Research Database (Denmark)

    Maretty, Lasse; Jensen, Jacob Malte; Petersen, Bent

    2017-01-01

    or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high......-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set...

  19. Beyond MEDLINE for literature searches.

    Science.gov (United States)

    Conn, Vicki S; Isaramalai, Sang-arun; Rath, Sabyasachi; Jantarakupt, Peeranuch; Wadhawan, Rohini; Dash, Yashodhara

    2003-01-01

    To describe strategies for a comprehensive literature search. MEDLINE searches result in limited numbers of studies that are often biased toward statistically significant findings. Diversified search strategies are needed. Empirical evidence about the recall and precision of diverse search strategies is presented. Challenges and strengths of each search strategy are identified. Search strategies vary in recall and precision. Often sensitivity and specificity are inversely related. Valuable search strategies include examination of multiple diverse computerized databases, ancestry searches, citation index searches, examination of research registries, journal hand searching, contact with the "invisible college," examination of abstracts, Internet searches, and contact with sources of synthesized information. Extending searches beyond MEDLINE enables researchers to conduct more systematic comprehensive searches.

  20. The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

    DEFF Research Database (Denmark)

    Gopalakrishnan, Shyam; Samaniego Castruita, Jose Alfredo; Sinding, Mikkel Holger Strander

    2017-01-01

    Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a......Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data...... that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped...

  1. Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms

    Science.gov (United States)

    Asamizu, Erika; Shirasawa, Kenta; Hirakawa, Hideki; Sato, Shusei; Tabata, Satoshi; Yano, Kentaro; Ariizumi, Tohru; Shibata, Daisuke; Ezura, Hiroshi

    2012-01-01

    A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database. PMID:23227037

  2. Analyses of Tissue Culture Adaptation of Human Herpesvirus-6A by Whole Genome Deep Sequencing Redefines the Reference Sequence and Identifies Virus Entry Complex Changes.

    Science.gov (United States)

    Tweedy, Joshua G; Escriva, Eric; Topf, Maya; Gompels, Ursula A

    2017-12-31

    Tissue-culture adaptation of viruses can modulate infection. Laboratory passage and bacterial artificial chromosome (BAC)mid cloning of human cytomegalovirus, HCMV, resulted in genomic deletions and rearrangements altering genes encoding the virus entry complex, which affected cellular tropism, virulence, and vaccine development. Here, we analyse these effects on the reference genome for related betaherpesviruses, Roseolovirus, human herpesvirus 6A (HHV-6A) strain U1102. This virus is also naturally "cloned" by germline subtelomeric chromosomal-integration in approximately 1% of human populations, and accurate references are key to understanding pathological relationships between exogenous and endogenous virus. Using whole genome next-generation deep-sequencing Illumina-based methods, we compared the original isolate to tissue-culture passaged and the BACmid-cloned virus. This re-defined the reference genome showing 32 corrections and 5 polymorphisms. Furthermore, minor variant analyses of passaged and BACmid virus identified emerging populations of a further 32 single nucleotide polymorphisms (SNPs) in 10 loci, half non-synonymous indicating cell-culture selection. Analyses of the BAC-virus genome showed deletion of the BAC cassette via loxP recombination removing green fluorescent protein (GFP)-based selection. As shown for HCMV culture effects, select HHV-6A SNPs mapped to genes encoding mediators of virus cellular entry, including virus envelope glycoprotein genes gB and the gH/gL complex. Comparative models suggest stabilisation of the post-fusion conformation. These SNPs are essential to consider in vaccine-design, antimicrobial-resistance, and pathogenesis.

  3. New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Schmutz, Jeremy

    2013-03-01

    Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on New approaches and technologies to sequence de novo plant reference genomes at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 in Walnut Creek, CA.

  4. Unraveling systematic inventory of Echinops (Asteraceae) with special reference to nrDNA ITS sequence-based molecular typing of Echinops abuzinadianus.

    Science.gov (United States)

    Ali, M A; Al-Hemaid, F M; Lee, J; Hatamleh, A A; Gyulai, G; Rahman, M O

    2015-10-02

    The present study explored the systematic inventory of Echinops L. (Asteraceae) of Saudi Arabia, with special reference to the molecular typing of Echinops abuzinadianus Chaudhary, an endemic species to Saudi Arabia, based on the internal transcribed spacer (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA. A sequence similarity search using BLAST and a phylogenetic analysis of the ITS sequence of E. abuzinadianus revealed a high level of sequence similarity with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. abuzinadianus could potentially be used for molecular genotyping.

  5. MedlinePlus Milestones: 1998-present

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    ... Connect , a service linking patients or providers in electronic health record (EHR) systems to related MedlinePlus information on conditions ... updates Subscribe to RSS Follow us Disclaimers Copyright Privacy Accessibility Quality Guidelines Viewers & Players MedlinePlus Connect for ...

  6. MedlinePlus Connect in Use

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  7. Dry Mouth: MedlinePlus Health Topic

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    ... MEDLINE/PubMed (National Library of Medicine) Article: Transcription profiling of peripheral B cells in antibody-positive primary ... our quality guidelines . About MedlinePlus Site Map FAQs Customer Support Get email updates Subscribe to RSS Follow ...

  8. Pacemakers and Implantable Defibrillators: MedlinePlus Health Topic

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    ... ClinicalTrials.gov: Pacemaker, Artificial (National Institutes of Health) Journal Articles References and abstracts from MEDLINE/PubMed (National ... Leadless Cardiac Pacemakers: The Next Evolution in Pacemaker Technology. ... on Pacemakers and Implantable Defibrillators is the National Heart, Lung, and Blood Institute Other Languages Find health information in languages other than English on Pacemakers and ...

  9. MedlinePlus XML Data Sources

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    ... on MedlinePlus health topic pages. With the Web service, software developers can build applications that leverage the authoritative, reliable health information in MedlinePlus. The MedlinePlus Web service is free of charge and does not require ...

  10. A BRCA2 mutation incorrectly mapped in the original BRCA2 reference sequence, is a common West Danish founder mutation disrupting mRNA splicing

    DEFF Research Database (Denmark)

    Thomassen, Mads; Pedersen, Inge Søkilde; Vogel, Ida

    2011-01-01

    Inherited mutations in the tumor suppressor genes BRCA1 and BRCA2 predispose carriers to breast and ovarian cancer. The authors have identified a mutation in BRCA2, 7845+1G>A (c.7617+1G>A), not previously regarded as deleterious because of incorrect mapping of the splice junction in the originally...... published genomic reference sequence. This reference sequence is generally used in many laboratories and it maps the mutation 16 base pairs inside intron 15. However, according to the recent reference sequences the mutation is located in the consensus donor splice sequence. By reverse transcriptase analysis......, loss of exon 15 in the final transcript interrupting the open reading frame was demonstrated. Furthermore, the mutation segregates with a cancer phenotype in 18 Danish families. By genetic analysis of more than 3,500 Danish breast/ovarian cancer risk families, the mutation was identified as the most...

  11. Iterative normalization technique for reference sequence generation for zero-tail discrete fourier transform spread orthogonal frequency division multiplexing

    DEFF Research Database (Denmark)

    2017-01-01

    , and performing an iterative manipulation of the input sequence. The performing of the iterative manipulation of the input sequence may include, for example: computing frequency domain response of the sequence, normalizing elements of the computed frequency domain sequence to unitary power while maintaining phase...

  12. De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

    Directory of Open Access Journals (Sweden)

    Sarah L. Westcott

    2015-12-01

    Full Text Available Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the quality of the OTU assignments, the ability of the method to properly represent the distances between the sequences, is more important.Methods. Our analysis implemented six de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and Swarm and the open and closed-reference methods. Using two previously published datasets we used the Matthew’s Correlation Coefficient (MCC to assess the stability and quality of OTU assignments.Results. The stability of OTU assignments did not reflect the quality of the assignments. Depending on the dataset being analyzed, the average linkage and the distance and abundance-based greedy clustering methods generated OTUs that were more likely to represent the actual distances between sequences than the open and closed-reference methods. We also demonstrated that for the greedy algorithms VSEARCH produced assignments that were comparable to those produced by USEARCH making VSEARCH a viable free and open source alternative to USEARCH. Further interrogation of the reference-based methods indicated that when USEARCH or VSEARCH were used to identify the closest reference, the OTU assignments were sensitive to the order of the reference sequences because the reference sequences can be identical over the region being considered. More troubling was the observation that while both USEARCH and

  13. Study of the fast inversion recovery pulse sequence. With reference to fast fluid attenuated inversion recovery and fast short TI inversion recovery pulse sequence

    International Nuclear Information System (INIS)

    Tsuchihashi, Toshio; Maki, Toshio; Suzuki, Takeshi

    1997-01-01

    The fast inversion recovery (fast IR) pulse sequence was evaluated. We compared the fast fluid attenuated inversion recovery (fast FLAIR) pulse sequence in which inversion time (TI) was established as equal to the water null point for the purpose of the water-suppressed T 2 -weighted image, with the fast short TI inversion recovery (fast STIR) pulse sequence in which TI was established as equal to the fat null point for purpose of fat suppression. In the fast FLAIR pulse sequence, the water null point was increased by making TR longer. In the FLAIR pulse sequence, the longitudinal magnetization contrast is determined by TI. If TI is increased, T 2 -weighted contrast improves in the same way as increasing TR for the SE pulse sequence. Therefore, images should be taken with long TR and long TI, which are longer than TR and longer than the water null point. On the other hand, the fat null point is not affected by TR in the fast STIR pulse sequence. However, effective TE was affected by variation of the null point. This increased in proportion to the increase in effective TE. Our evaluation indicated that the fast STIR pulse sequence can control the extensive signals from fat in a short time. (author)

  14. MedlinePlus Connect: Web Service

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  18. MedlinePlus.gov on Twitter

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    ... page please turn Javascript on. MedlinePlus.gov on Twitter Past Issues / Fall 2009 Table of Contents You can now follow MedlinePlus.gov on Twitter: twitter.com/medlineplus4you The medlineplus4you Twitter feed provides ...

  19. Finding biomedical categories in Medline®

    Directory of Open Access Journals (Sweden)

    Yeganova Lana

    2012-10-01

    Full Text Available Abstract Background There are several humanly defined ontologies relevant to Medline. However, Medline is a fast growing collection of biomedical documents which creates difficulties in updating and expanding these humanly defined ontologies. Automatically identifying meaningful categories of entities in a large text corpus is useful for information extraction, construction of machine learning features, and development of semantic representations. In this paper we describe and compare two methods for automatically learning meaningful biomedical categories in Medline. The first approach is a simple statistical method that uses part-of-speech and frequency information to extract a list of frequent nouns from Medline. The second method implements an alignment-based technique to learn frequent generic patterns that indicate a hyponymy/hypernymy relationship between a pair of noun phrases. We then apply these patterns to Medline to collect frequent hypernyms as potential biomedical categories. Results We study and compare these two alternative sets of terms to identify semantic categories in Medline. We find that both approaches produce reasonable terms as potential categories. We also find that there is a significant agreement between the two sets of terms. The overlap between the two methods improves our confidence regarding categories predicted by these independent methods. Conclusions This study is an initial attempt to extract categories that are discussed in Medline. Rather than imposing external ontologies on Medline, our methods allow categories to emerge from the text.

  20. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

    Science.gov (United States)

    Vuilleumier, Stéphane; Chistoserdova, Ludmila; Lee, Ming-Chun; Bringel, Françoise; Lajus, Aurélie; Zhou, Yang; Gourion, Benjamin; Barbe, Valérie; Chang, Jean; Cruveiller, Stéphane; Dossat, Carole; Gillett, Will; Gruffaz, Christelle; Haugen, Eric; Hourcade, Edith; Levy, Ruth; Mangenot, Sophie; Muller, Emilie; Nadalig, Thierry; Pagni, Marco; Penny, Christian; Peyraud, Rémi; Robinson, David G; Roche, David; Rouy, Zoé; Saenampechek, Channakhone; Salvignol, Grégory; Vallenet, David; Wu, Zaining; Marx, Christopher J; Vorholt, Julia A; Olson, Maynard V; Kaul, Rajinder; Weissenbach, Jean; Médigue, Claudine; Lidstrom, Mary E

    2009-01-01

    Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid). These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic

  1. Automatic inference of indexing rules for MEDLINE

    Directory of Open Access Journals (Sweden)

    Shooshan Sonya E

    2008-11-01

    Full Text Available Abstract 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.

  2. NIH Institutes and MLN MedlinePlus Advisory Board | NIH MedlinePlus the Magazine

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    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [3.1 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  3. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

    Directory of Open Access Journals (Sweden)

    Stéphane Vuilleumier

    Full Text Available Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared.The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17 that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid.These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire

  4. Antibiotic Resistance: MedlinePlus Health Topic

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    ... GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Health Topics → Antibiotic Resistance URL of this page: https://medlineplus.gov/antibioticresistance. ...

  5. MedlinePlus: Awards and Recognition

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    ... winner of the 2005 World Summit on the Information Society Awards for e-health. Winner of the Thomas Reuters/Frank Bradway Rogers Information Advancement Award in 2014 for MedlinePlus Connect and ...

  6. MedlinePlus Connect: How it Works

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  12. Pneumococcal Infections: MedlinePlus Health Topic

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  16. Diets: MedlinePlus Health Topic

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  20. Male Infertility: MedlinePlus Health Topic

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  1. Prediabetes:MedlinePlus Health Topic

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  2. Healthy Aging: MedlinePlus Health Topic

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    ... Aging National Institute on Aging Also in Spanish Topic Image MedlinePlus Email Updates Get Healthy Aging updates ... 65 Health screening - women - over 65 Related Health Topics Exercise for Seniors Nutrition for Seniors Seniors' Health ...

  3. Psoriatic Arthritis: MedlinePlus Health Topic

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    ... Handouts Psoriatic arthritis (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Psoriatic Arthritis updates ... this? GO MEDICAL ENCYCLOPEDIA Psoriatic arthritis Related Health Topics Arthritis Psoriasis National Institutes of Health The primary ...

  4. Hip Replacement: MedlinePlus Health Topic

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    ... invasive hip replacement (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Hip Replacement updates ... replacement - precautions Minimally invasive hip replacement Related Health Topics Hip Injuries and Disorders National Institutes of Health ...

  5. Diabetes: MedlinePlus Health Topic

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    ... High blood sugar (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Diabetes updates by ... ketones test Show More Show Less Related Health Topics A1C Blood Sugar Diabetes and Pregnancy Diabetes Complications ...

  6. Platelet Disorders: MedlinePlus Health Topic

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    ... Thromobocytopenia - drug-induced (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Platelet Disorders updates ... Willebrand disease Show More Show Less Related Health Topics Bleeding Disorders Blood Clots Blood Count Tests Blood ...

  7. Cardiac Rehabilitation: MedlinePlus Health Topic

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    ... in Spanish Electrocardiogram (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Cardiac Rehabilitation updates ... How to take your pulse Pulse Related Health Topics Heart Attack Heart Diseases How to Prevent Heart ...

  8. Dialysis: MedlinePlus Health Topic

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    ... access for hemodialysis (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Dialysis updates by ... for hemodialysis Show More Show Less Related Health Topics Creatinine Kidney Cysts Kidney Failure Peritoneal Disorders National ...

  9. Eye Wear: MedlinePlus Health Topic

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    ... When You Exercise (National Institute on Aging) - PDF Topic Image MedlinePlus Email Updates Get Eye Wear updates by email What's this? GO Related Health Topics Refractive Errors National Institutes of Health The primary ...

  10. Cardiac Arrest: MedlinePlus Health Topic

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    ... Handouts Cardiac arrest (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Cardiac Arrest updates ... this? GO MEDICAL ENCYCLOPEDIA Cardiac arrest Related Health Topics Arrhythmia CPR Pacemakers and Implantable Defibrillators National Institutes ...

  11. Kawasaki Disease: MedlinePlus Health Topic

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    ... Spanish Kawasaki disease (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Kawasaki Disease updates ... GO MEDICAL ENCYCLOPEDIA Electrocardiogram Kawasaki disease Related Health Topics Vasculitis National Institutes of Health The primary NIH ...

  12. Diabetic Diet: MedlinePlus Health Topic

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    ... Sweeteners - sugar substitutes (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Diabetic Diet updates ... you have diabetes Sweeteners - sugar substitutes Related Health Topics Blood Sugar Diabetes Diabetes in Children and Teens ...

  13. Infection Control: MedlinePlus Health Topic

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    ... Staph infections - hospital (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Infection Control updates ... infections when visiting Staph infections - hospital Related Health Topics Hepatitis HIV/AIDS MRSA National Institutes of Health ...

  14. Menopause: MedlinePlus Health Topic

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    ... Spanish What is Menopause? (National Institute on Aging) Topic Image MedlinePlus Email Updates Get Menopause updates by ... test Menopause Types of hormone therapy Related Health Topics Hormone Replacement Therapy Menstruation Premature Ovarian Failure National ...

  15. Vaginitis: MedlinePlus Health Topic

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    ... Spanish Vulvovaginitis - overview (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Vaginitis updates by ... Vaginitis test - wet mount Vulvovaginitis - overview Related Health Topics Trichomoniasis Vaginal Diseases Yeast Infections Other Languages Find ...

  16. Hearing Aids: MedlinePlus Health Topic

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    ... for hearing loss (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Hearing Aids updates ... MEDICAL ENCYCLOPEDIA Devices for hearing loss Related Health Topics Cochlear Implants Hearing Disorders and Deafness National Institutes ...

  17. Kidney Tests: MedlinePlus Health Topic

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    ... Spanish Total protein (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Kidney Tests updates ... hour volume Show More Show Less Related Health Topics Kidney Cancer Kidney Diseases National Institutes of Health ...

  18. Ischemic Stroke: MedlinePlus Health Topic

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    ... Spanish Thrombolytic therapy (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Ischemic Stroke updates ... cardiogenic embolism Stroke - slideshow Thrombolytic therapy Related Health Topics Hemorrhagic Stroke Stroke Stroke Rehabilitation National Institutes of ...

  19. Pulmonary Rehabilitation: MedlinePlus Health Topic

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    ... Handouts Postural drainage (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Pulmonary Rehabilitation updates ... this? GO MEDICAL ENCYCLOPEDIA Postural drainage Related Health Topics Lung Diseases National Institutes of Health The primary ...

  20. Death, dying and informatics: misrepresenting religion on MedLine.

    Science.gov (United States)

    Rodríguez Del Pozo, Pablo; Fins, Joseph J

    2005-07-01

    The globalization of medical science carries for doctors worldwide a correlative duty to deepen their understanding of patients' cultural contexts and religious backgrounds, in order to satisfy each as a unique individual. To become better informed, practitioners may turn to MedLine, but it is unclear whether the information found there is an accurate representation of culture and religion. To test MedLine's representation of this field, we chose the topic of death and dying in the three major monotheistic religions. We searched MedLine using PubMed in order to retrieve and thematically analyze full-length scholarly journal papers or case reports dealing with religious traditions and end-of-life care. Our search consisted of a string of words that included the most common denominations of the three religions, the standard heading terms used by the National Reference Center for Bioethics Literature (NRCBL), and the Medical Subject Headings (MeSH) used by the National Library of Medicine. Eligible articles were limited to English-language papers with an abstract. We found that while a bibliographic search in MedLine on this topic produced instant results and some valuable literature, the aggregate reflected a selection bias. American writers were over-represented given the global prevalence of these religious traditions. Denominationally affiliated authors predominated in representing the Christian traditions. The Islamic tradition was under-represented. MedLine's capability to identify the most current, reliable and accurate information about purely scientific topics should not be assumed to be the same case when considering the interface of religion, culture and end-of-life care.

  1. Death, dying and informatics: misrepresenting religion on MedLine

    Directory of Open Access Journals (Sweden)

    Fins Joseph J

    2005-07-01

    Full Text Available Abstract Background The globalization of medical science carries for doctors worldwide a correlative duty to deepen their understanding of patients' cultural contexts and religious backgrounds, in order to satisfy each as a unique individual. To become better informed, practitioners may turn to MedLine, but it is unclear whether the information found there is an accurate representation of culture and religion. To test MedLine's representation of this field, we chose the topic of death and dying in the three major monotheistic religions. Methods We searched MedLine using PubMed in order to retrieve and thematically analyze full-length scholarly journal papers or case reports dealing with religious traditions and end-of-life care. Our search consisted of a string of words that included the most common denominations of the three religions, the standard heading terms used by the National Reference Center for Bioethics Literature (NRCBL, and the Medical Subject Headings (MeSH used by the National Library of Medicine. Eligible articles were limited to English-language papers with an abstract. Results We found that while a bibliographic search in MedLine on this topic produced instant results and some valuable literature, the aggregate reflected a selection bias. American writers were over-represented given the global prevalence of these religious traditions. Denominationally affiliated authors predominated in representing the Christian traditions. The Islamic tradition was under-represented. Conclusion MedLine's capability to identify the most current, reliable and accurate information about purely scientific topics should not be assumed to be the same case when considering the interface of religion, culture and end-of-life care.

  2. Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.

    Science.gov (United States)

    Kuroshu, Reginaldo M; Watanabe, Junichi; Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka; Kasahara, Masahiro

    2010-05-07

    Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence approximately 800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only approximately US$3 per clone, demonstrating a significant advantage over previous approaches.

  3. Molecular Identification of Unusual Pathogenic Yeast Isolates by Large Ribosomal Subunit Gene Sequencing: 2 Years of Experience at the United Kingdom Mycology Reference Laboratory▿

    Science.gov (United States)

    Linton, Christopher J.; Borman, Andrew M.; Cheung, Grace; Holmes, Ann D.; Szekely, Adrien; Palmer, Michael D.; Bridge, Paul D.; Campbell, Colin K.; Johnson, Elizabeth M.

    2007-01-01

    Rapid identification of yeast isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. We present here an analysis of the utility of PCR amplification and sequence analysis of the hypervariable D1/D2 region of the 26S rRNA gene for the identification of yeast species submitted to the United Kingdom Mycology Reference Laboratory over a 2-year period. A total of 3,033 clinical isolates were received from 2004 to 2006 encompassing 50 different yeast species. While more than 90% of the isolates, corresponding to the most common Candida species, could be identified by using the AUXACOLOR2 yeast identification kit, 153 isolates (5%), comprised of 47 species, could not be identified by using this system and were subjected to molecular identification via 26S rRNA gene sequencing. These isolates included some common species that exhibited atypical biochemical and phenotypic profiles and also many rarer yeast species that are infrequently encountered in the clinical setting. All 47 species requiring molecular identification were unambiguously identified on the basis of D1/D2 sequences, and the molecular identities correlated well with the observed biochemical profiles of the various organisms. Together, our data underscore the utility of molecular techniques as a reference adjunct to conventional methods of yeast identification. Further, we show that PCR amplification and sequencing of the D1/D2 region reliably identifies more than 45 species of clinically significant yeasts and can also potentially identify new pathogenic yeast species. PMID:17251397

  4. The Sequence of Acquisition of Personal Pronoun Case and Person Reference among 6 Year Old Children in Two Selected Malaysian Kindergartens

    Directory of Open Access Journals (Sweden)

    Arshad Abd Samad

    2017-03-01

    Full Text Available Pronoun case and person reference refer to the position of the pronoun in the sentence and the person the pronoun refers to respectively.  Examining the acquisition of pronoun case and person reference among young children can be insightful as, besides their obvious relevance to language development, both these constructs can have implications on other aspects of child development.  Attention given by children to these various constructs may indicate the importance children place on the concept of ego and self as well as on social relations.  The sequence of acquisition of personal pronouns among these children is therefore an important phenomenon to be examined as it can reflect linguistic and socio-cognitive development.  This largely descriptive study examines the sequence of acquisition of the English pronouns among forty 6 year old Malaysian children learning ESL in two kindergartens.  The children in the study were presented with 33 drawings to assess their familiarity with case and person reference expressed through English personal pronouns.  They were required to select the correct pronoun from three pronouns that were used to describe each drawing.  This paper reports on the accuracy rates for each pronoun and assumes that high accuracy rates indicate a more complete acquisition of the pronoun.  Error forms by the children were also be identified and examined.  Data obtained were compared to acquisition sequences in the literature and general implications related to the acquisition of personal pronouns among children in an ESL setting in Malaysia will be discussed.

  5. The Medline/full-text research project.

    Science.gov (United States)

    McKinin, E J; Sievert, M; Johnson, E D; Mitchell, J A

    1991-05-01

    This project was designed to test the relative efficacy of index terms and full-text for the retrieval of documents in those MEDLINE journals for which full-text searching was also available. The full-text files used were MEDIS from Mead Data Central and CCML from BRS Information Technologies. One hundred clinical medical topics were searched in these two files as well as the MEDLINE file to accumulate the necessary data. It was found that full-text identified significantly more relevant articles than did the indexed file, MEDLINE. The full-text searches, however, lacked the precision of searches done in the indexed file. Most relevant items missed in the full-text files, but identified in MEDLINE, were missed because the searcher failed to account for some aspect of natural language, used a logical or positional operator that was too restrictive, or included a concept which was implied, but not expressed in the natural language. Very few of the unique relevant full-text citations would have been retrieved by title or abstract alone. Finally, as of July, 1990 the more current issue of a journal was just as likely to appear in MEDLINE as in one of the full-text files.

  6. The medline UK filter: development and validation of a geographic search filter to retrieve research about the UK from OVID medline.

    Science.gov (United States)

    Ayiku, Lynda; Levay, Paul; Hudson, Tom; Craven, Jenny; Barrett, Elizabeth; Finnegan, Amy; Adams, Rachel

    2017-07-13

    A validated geographic search filter for the retrieval of research about the United Kingdom (UK) from bibliographic databases had not previously been published. To develop and validate a geographic search filter to retrieve research about the UK from OVID medline with high recall and precision. Three gold standard sets of references were generated using the relative recall method. The sets contained references to studies about the UK which had informed National Institute for Health and Care Excellence (NICE) guidance. The first and second sets were used to develop and refine the medline UK filter. The third set was used to validate the filter. Recall, precision and number-needed-to-read (NNR) were calculated using a case study. The validated medline UK filter demonstrated 87.6% relative recall against the third gold standard set. In the case study, the medline UK filter demonstrated 100% recall, 11.4% precision and a NNR of nine. A validated geographic search filter to retrieve research about the UK with high recall and precision has been developed. The medline UK filter can be applied to systematic literature searches in OVID medline for topics with a UK focus. © 2017 Crown copyright. Health Information and Libraries Journal © 2017 Health Libraries GroupThis article is published with the permission of the Controller of HMSO and the Queen's Printer for Scotland.

  7. Overview of errors in the reference sequence and annotation of Mycobacterium tuberculosis H37Rv, and variation amongst its isolates

    KAUST Repository

    Kö ser, Claudio U.; Niemann, Stefan; Summers, David K.; Archer, John A.C.

    2012-01-01

    Since its publication in 1998, the genome sequence of the Mycobacterium tuberculosis H37Rv laboratory strain has acted as the cornerstone for the study of tuberculosis. In this review we address some of the practical aspects that have come to light

  8. Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species.

    Science.gov (United States)

    Yasuike, Motoshige; Nishiki, Issei; Iwasaki, Yuki; Nakamura, Yoji; Fujiwara, Atushi; Shimahara, Yoshiko; Kamaishi, Takashi; Yoshida, Terutoyo; Nagai, Satoshi; Kobayashi, Takanori; Katoh, Masaya

    2017-01-01

    Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages. The virulence factor candidates provide an essential basis for understanding their pathogenic mechanisms at the molecular level by the fish nocardiosis research community in future studies. We also found many potential antibiotic resistance genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N. cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes were present in all five Nocardia genomes (core genes) and 1,982 genes were unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a greater number of mobile elements and genes of unknown function that comprise the differences in structure and gene content from the other Nocardia genomes. In addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC transport system. Because of limited resources in ocean environments, these N. seriolae UTF1 specific ABC transporters might facilitate adaptation strategies essential for marine environment survival. Thus, the availability of the complete N. seriolae UTF1 genome sequence will provide a valuable resource for comparative genomic studies of N. seriolae isolates, as well as provide new insights into the ecological and functional diversity of

  9. Heart Surgery: MedlinePlus Health Topic

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    ... Living With Related Issues Specifics See, Play and Learn Videos and Tutorials Research Clinical Trials Journal Articles Resources ... Also in Spanish Videos and Tutorials MedlinePlus: Surgery Videos ... strategy is better to reduce postoperative stroke... Article: Ferumoxtyol-enhanced MR ...

  10. Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

    Science.gov (United States)

    Verwaaijen, Bart; Wibberg, Daniel; Nelkner, Johanna; Gordin, Miriam; Rupp, Oliver; Winkler, Anika; Bremges, Andreas; Blom, Jochen; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

    2018-02-10

    Lettuce (Lactuca sativa, L.) is an important annual plant of the family Asteraceae (Compositae). The commercial lettuce cultivar Tizian has been used in various scientific studies investigating the interaction of the plant with phytopathogens or biological control agents. Here, we present the de novo draft genome sequencing and gene prediction for this specific cultivar derived from transcriptome sequence data. The assembled scaffolds amount to a size of 2.22 Gb. Based on RNAseq data, 31,112 transcript isoforms were identified. Functional predictions for these transcripts were determined within the GenDBE annotation platform. Comparison with the cv. Salinas reference genome revealed a high degree of sequence similarity on genome and transcriptome levels, with an average amino acid identity of 99%. Furthermore, it was observed that two large regions are either missing or are highly divergent within the cv. Tizian genome compared to cv. Salinas. One of these regions covers the major resistance complex 1 region of cv. Salinas. The cv. Tizian draft genome sequence provides a valuable resource for future functional and transcriptome analyses focused on this lettuce cultivar. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. NLM MedlinePlus Magazine Team | NIH MedlinePlus the Magazine

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    ... Home Current issue contents Magazine Team Follow us Magazine Team National Library of Medicine at the National ... MLS, MA TREASURER Dennis Cryer, MD NIH MedlinePlus magazine is published by Friends of the NLM in ...

  12. MedlinePlus FAQ: Will MedlinePlus work on my mobile device?

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    ... mobile.html Question: Will MedlinePlus work on my mobile device? To use the sharing features on this page, ... Some video content might not play on your mobile device. See our FAQ on playing videos on phones ...

  13. NLM MedlinePlus Magazine Team | NIH MedlinePlus the Magazine

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    ... Robert George DIRECTOR OF OPERATIONS Carolyn Medeiros DIRECTOR, BUSINESS DEVELOPMENT Michele Tezduyar MANAGING EDITOR Emily Poe SENIOR ... MD 20814 CONNECT WITH US Follow us on Facebook Facebook MedlinePlus www.facebook.com/mplus.gov Facebook ...

  14. Consistency and reproducibility of next-generation sequencing and other multigene mutational assays: A worldwide ring trial study on quantitative cytological molecular reference specimens.

    Science.gov (United States)

    Malapelle, Umberto; Mayo-de-Las-Casas, Clara; Molina-Vila, Miguel A; Rosell, Rafael; Savic, Spasenija; Bihl, Michel; Bubendorf, Lukas; Salto-Tellez, Manuel; de Biase, Dario; Tallini, Giovanni; Hwang, David H; Sholl, Lynette M; Luthra, Rajyalakshmi; Weynand, Birgit; Vander Borght, Sara; Missiaglia, Edoardo; Bongiovanni, Massimo; Stieber, Daniel; Vielh, Philippe; Schmitt, Fernando; Rappa, Alessandra; Barberis, Massimo; Pepe, Francesco; Pisapia, Pasquale; Serra, Nicola; Vigliar, Elena; Bellevicine, Claudio; Fassan, Matteo; Rugge, Massimo; de Andrea, Carlos E; Lozano, Maria D; Basolo, Fulvio; Fontanini, Gabriella; Nikiforov, Yuri E; Kamel-Reid, Suzanne; da Cunha Santos, Gilda; Nikiforova, Marina N; Roy-Chowdhuri, Sinchita; Troncone, Giancarlo

    2017-08-01

    Molecular testing of cytological lung cancer specimens includes, beyond epidermal growth factor receptor (EGFR), emerging predictive/prognostic genomic biomarkers such as Kirsten rat sarcoma viral oncogene homolog (KRAS), neuroblastoma RAS viral [v-ras] oncogene homolog (NRAS), B-Raf proto-oncogene, serine/threonine kinase (BRAF), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA). Next-generation sequencing (NGS) and other multigene mutational assays are suitable for cytological specimens, including smears. However, the current literature reflects single-institution studies rather than multicenter experiences. Quantitative cytological molecular reference slides were produced with cell lines designed to harbor concurrent mutations in the EGFR, KRAS, NRAS, BRAF, and PIK3CA genes at various allelic ratios, including low allele frequencies (AFs; 1%). This interlaboratory ring trial study included 14 institutions across the world that performed multigene mutational assays, from tissue extraction to data analysis, on these reference slides, with each laboratory using its own mutation analysis platform and methodology. All laboratories using NGS (n = 11) successfully detected the study's set of mutations with minimal variations in the means and standard errors of variant fractions at dilution points of 10% (P = .171) and 5% (P = .063) despite the use of different sequencing platforms (Illumina, Ion Torrent/Proton, and Roche). However, when mutations at a low AF of 1% were analyzed, the concordance of the NGS results was low, and this reflected the use of different thresholds for variant calling among the institutions. In contrast, laboratories using matrix-assisted laser desorption/ionization-time of flight (n = 2) showed lower concordance in terms of mutation detection and mutant AF quantification. Quantitative molecular reference slides are a useful tool for monitoring the performance of different multigene mutational

  15. Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory

    Science.gov (United States)

    Crisan, Anamaria; McKee, Geoffrey; Munzner, Tamara

    2018-01-01

    Background Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics—including clinicians, laboratorians, epidemiologists, and researchers—is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results. Methods We used Design Study Methodology—a human centered approach drawn from the information visualization domain—to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders’ needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report. Results We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design

  16. Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory

    Directory of Open Access Journals (Sweden)

    Anamaria Crisan

    2018-01-01

    Full Text Available Background Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics—including clinicians, laboratorians, epidemiologists, and researchers—is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB genomic test results. Methods We used Design Study Methodology—a human centered approach drawn from the information visualization domain—to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders’ needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report. Results We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type. When we compared our four prototype reports against the existing design, we found that for the majority (86.7% of

  17. Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory.

    Science.gov (United States)

    Crisan, Anamaria; McKee, Geoffrey; Munzner, Tamara; Gardy, Jennifer L

    2018-01-01

    Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics-including clinicians, laboratorians, epidemiologists, and researchers-is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results. We used Design Study Methodology-a human centered approach drawn from the information visualization domain-to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders' needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report. We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design comparisons, participants preferred the

  18. RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study.

    Science.gov (United States)

    Berghoff, Bork A; Karlsson, Torgny; Källman, Thomas; Wagner, E Gerhart H; Grabherr, Manfred G

    2017-01-01

    Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). While advances in high-throughput RNA-sequencing (RNA-seq) technologies allow for inexpensive data generation, accurate post-processing and normalization across samples is required to eliminate any systematic noise introduced by the biochemical and/or technical processes. Existing methods thus either normalize on selected known reference genes that are invariant in expression across the experiment, assume that the majority of genes are invariant, or that the effects of up- and down-regulated genes cancel each other out during the normalization. Here, we present a novel method, moose 2 , which predicts invariant genes in silico through a dynamic programming (DP) scheme and applies a quadratic normalization based on this subset. The method allows for specifying a set of known or experimentally validated invariant genes, which guides the DP. We experimentally verified the predictions of this method in the bacterium Escherichia coli , and show how moose 2 is able to (i) estimate the expression value distances between RNA-seq samples, (ii) reduce the variation of expression values across all samples, and (iii) to subsequently reveal new functional groups of genes during the late stages of DNA damage. We further applied the method to three eukaryotic data sets, on which its performance compares favourably to other methods. The software is implemented in C++ and is publicly available from http://grabherr.github.io/moose2/. The proposed RNA-seq normalization method, moose 2 , is a valuable alternative to existing methods, with two major advantages: (i) in silico prediction of invariant genes provides a list of potential reference genes for downstream analyses, and (ii) non-linear artefacts in RNA-seq data

  19. Combating HIV/AIDS | NIH MedlinePlus the Magazine

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    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [3.1 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  20. Helping others hear better | NIH MedlinePlus the Magazine

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    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [2.68 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  1. Mary Tyler Moore Helps Launch NIH MedlinePlus Magazine

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    ... Issues Mary Tyler Moore Helps Launch NIH MedlinePlus Magazine Past Issues / Winter 2007 Table of Contents For ... Javascript on. Among those attending the NIH MedlinePlus magazine launch on Capitol Hill were (l-r) NIH ...

  2. Recovery and Treatment | NIH MedlinePlus the Magazine

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    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [3.1 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  3. Racing Against Lung Cancer | NIH MedlinePlus the Magazine

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  4. Exploring Graphic Medicine | NIH MedlinePlus the Magazine

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    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [1.5 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  5. The Opioid Crisis | NIH MedlinePlus the Magazine

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  6. The ABCs of GERD | NIH MedlinePlus the Magazine

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  7. A Lifelong Asthma Struggle | NIH MedlinePlus the Magazine

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  8. NIH on the web | NIH MedlinePlus the Magazine

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  9. Hope for Aphasia Patients | NIH MedlinePlus Magazine

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  10. Surgery of the Future | NIH MedlinePlus the Magazine

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  11. 10 NIH Research Highlights | NIH MedlinePlus the Magazine

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  12. NIH MedlinePlus the Magazine: Health, Medical & Wellness Articles

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    ... to the Web site for NIH MedlinePlus, the magazine. Our purpose is to present you with the ... sponsorship and other charitable donations for NIH MedlinePlus magazine's publication and distribution, many more thousands of Americans ...

  13. Remembering Mary Tyler Moore | MedlinPlus Magazine

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  14. Expanding Hearing Healthcare | NIH MedlinePlus the Magazine

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  15. NIH on the web | NIH MedlinePlus the Magazine

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  16. MedlinePlus FAQ: Disease or Condition Information

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  18. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  19. Toddler Nutrition: MedlinePlus Health Topic

    Science.gov (United States)

    ... Cardiometabolic Risk. Article: Bringing babies and breasts into workplaces: Support for breastfeeding mothers... Toddler Nutrition -- see more articles Reference Desk Toddler Nutrition and Health Resource List (Department of Agriculture) - PDF Find an ...

  20. Gas: MedlinePlus Health Topic

    Science.gov (United States)

    ... attenuation via probiotic intervention reduces flatulence in adult human:... Article: The overlap of gastroesophageal reflux disease and functional constipation in... Gas -- see more articles Reference Desk Your Digestive System and How It Works (National Institute of Diabetes ...

  1. A novel algorithm for analyzing drug-drug interactions from MEDLINE literature.

    Science.gov (United States)

    Lu, Yin; Shen, Dan; Pietsch, Maxwell; Nagar, Chetan; Fadli, Zayd; Huang, Hong; Tu, Yi-Cheng; Cheng, Feng

    2015-11-27

    Drug-drug interaction (DDI) is becoming a serious clinical safety issue as the use of multiple medications becomes more common. Searching the MEDLINE database for journal articles related to DDI produces over 330,000 results. It is impossible to read and summarize these references manually. As the volume of biomedical reference in the MEDLINE database continues to expand at a rapid pace, automatic identification of DDIs from literature is becoming increasingly important. In this article, we present a random-sampling-based statistical algorithm to identify possible DDIs and the underlying mechanism from the substances field of MEDLINE records. The substances terms are essentially carriers of compound (including protein) information in a MEDLINE record. Four case studies on warfarin, ibuprofen, furosemide and sertraline implied that our method was able to rank possible DDIs with high accuracy (90.0% for warfarin, 83.3% for ibuprofen, 70.0% for furosemide and 100% for sertraline in the top 10% of a list of compounds ranked by p-value). A social network analysis of substance terms was also performed to construct networks between proteins and drug pairs to elucidate how the two drugs could interact.

  2. The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone.

    Directory of Open Access Journals (Sweden)

    Brian M Forde

    Full Text Available Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.

  3. NIH Institutes and MLN MedlinePlus Advisory Board

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    ... main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [1.9 mb] ... nih.gov (301) 496-7301 National Institute of Mental Health (NIMH) www.nimh.nih.gov 1-866- ...

  4. MedlinePlus FAQ: Listing Your Web Site

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    ... JavaScript. Answer: MedlinePlus is a selected list of authoritative resources. MedlinePlus uses quality guidelines to evaluate Web ... ensure that the information we link to is authoritative, accurate, up-to-date, educational and available at ...

  5. MRI of the temporo-mandibular joint: which sequence is best suited to assess the cortical bone of the mandibular condyle? A cadaveric study using micro-CT as the standard of reference.

    Science.gov (United States)

    Karlo, Christoph A; Patcas, Raphael; Kau, Thomas; Watzal, Helmut; Signorelli, Luca; Müller, Lukas; Ullrich, Oliver; Luder, Hans-Ulrich; Kellenberger, Christian J

    2012-07-01

    To determine the best suited sagittal MRI sequence out of a standard temporo-mandibular joint (TMJ) imaging protocol for the assessment of the cortical bone of the mandibular condyles of cadaveric specimens using micro-CT as the standard of reference. Sixteen TMJs in 8 human cadaveric heads (mean age, 81 years) were examined by MRI. Upon all sagittal sequences, two observers measured the cortical bone thickness (CBT) of the anterior, superior and posterior portions of the mandibular condyles (i.e. objective analysis), and assessed for the presence of cortical bone thinning, erosions or surface irregularities as well as subcortical bone cysts and anterior osteophytes (i.e. subjective analysis). Micro-CT of the condyles was performed to serve as the standard of reference for statistical analysis. Inter-observer agreements for objective (r = 0.83-0.99, P < 0.01) and subjective (κ = 0.67-0.88) analyses were very good. Mean CBT measurements were most accurate, and cortical bone thinning, erosions, surface irregularities and subcortical bone cysts were best depicted on the 3D fast spoiled gradient echo recalled sequence (3D FSPGR). The most reliable MRI sequence to assess the cortical bone of the mandibular condyles on sagittal imaging planes is the 3D FSPGR sequence. MRI may be used to assess the cortical bone of the TMJ. • Depiction of cortical bone is best on 3D FSPGR sequences. • MRI can assess treatment response in patients with TMJ abnormalities.

  6. Evaluation of the Abbott realtime HCV genotype II RUO (GT II) assay with reference to 5'UTR, core and NS5B sequencing.

    Science.gov (United States)

    Mallory, Melanie A; Lucic, Danijela X; Sears, Mitchell T; Cloherty, Gavin A; Hillyard, David R

    2014-05-01

    HCV genotyping is a critical tool for guiding initiation of therapy and selecting the most appropriate treatment regimen. To evaluate the concordance between the Abbott GT II assay and genotyping by sequencing subregions of the HCV 5'UTR, core and NS5B. The Abbott assay was used to genotype 127 routine patient specimens and 35 patient specimens with unusual subtypes and mixed infection. Abbott results were compared to genotyping by 5'UTR, core and NS5B sequencing. Sequences were genotyped using the NCBI non-redundant database and the online genotyping tool COMET. Among routine specimens, core/NS5B sequencing identified 93 genotype 1s, 13 genotype 2s, 15 genotype 3s, three genotype 4s, two genotype 6s and one recombinant specimen. Genotype calls by 5'UTR, core, NS5B sequencing and the Abbott assay were 97.6% concordant. Core/NS5B sequencing identified two discrepant samples as genotype 6 (subtypes 6l and 6u) while Abbott and 5'UTR sequencing identified these samples as genotype 1 with no subtype. The Abbott assay subtyped 91.4% of genotype 1 specimens. Among the 35 rare specimens, the Abbott assay inaccurately genotyped 3k, 6e, 6o, 6q and one genotype 4 variant; gave indeterminate results for 3g, 3h, 4r, 6m, 6n, and 6q specimens; and agreed with core/NS5B sequencing for mixed specimens. The Abbott assay is an automated HCV genotyping method with improved accuracy over 5'UTR sequencing. Samples identified by the Abbott assay as genotype 1 with no subtype may be rare subtypes of other genotypes and thus require confirmation by another method. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. MRI of the temporo-mandibular joint: which sequence is best suited to assess the cortical bone of the mandibular condyle? A cadaveric study using micro-CT as the standard of reference

    International Nuclear Information System (INIS)

    Karlo, Christoph A.; Patcas, Raphael; Signorelli, Luca; Mueller, Lukas; Kau, Thomas; Watzal, Helmut; Kellenberger, Christian J.; Ullrich, Oliver; Luder, Hans-Ulrich

    2012-01-01

    To determine the best suited sagittal MRI sequence out of a standard temporo-mandibular joint (TMJ) imaging protocol for the assessment of the cortical bone of the mandibular condyles of cadaveric specimens using micro-CT as the standard of reference. Sixteen TMJs in 8 human cadaveric heads (mean age, 81 years) were examined by MRI. Upon all sagittal sequences, two observers measured the cortical bone thickness (CBT) of the anterior, superior and posterior portions of the mandibular condyles (i.e. objective analysis), and assessed for the presence of cortical bone thinning, erosions or surface irregularities as well as subcortical bone cysts and anterior osteophytes (i.e. subjective analysis). Micro-CT of the condyles was performed to serve as the standard of reference for statistical analysis. Inter-observer agreements for objective (r = 0.83-0.99, P < 0.01) and subjective (κ = 0.67-0.88) analyses were very good. Mean CBT measurements were most accurate, and cortical bone thinning, erosions, surface irregularities and subcortical bone cysts were best depicted on the 3D fast spoiled gradient echo recalled sequence (3D FSPGR). The most reliable MRI sequence to assess the cortical bone of the mandibular condyles on sagittal imaging planes is the 3D FSPGR sequence. (orig.)

  8. MRI of the temporo-mandibular joint: which sequence is best suited to assess the cortical bone of the mandibular condyle? A cadaveric study using micro-CT as the standard of reference

    Energy Technology Data Exchange (ETDEWEB)

    Karlo, Christoph A. [University Hospital Zurich, Department of Diagnostic and Interventional Radiology, Zurich (Switzerland); University Children' s Hospital Zurich, Department of Diagnostic Imaging, Zurich (Switzerland); Patcas, Raphael; Signorelli, Luca; Mueller, Lukas [University of Zurich, Clinic for Orthodontics and Pediatric Dentistry, Center of Dental Medicine, Zurich (Switzerland); Kau, Thomas; Watzal, Helmut; Kellenberger, Christian J. [University Children' s Hospital Zurich, Department of Diagnostic Imaging, Zurich (Switzerland); Ullrich, Oliver [University of Zurich, Institute of Anatomy, Faculty of Medicine, Zurich (Switzerland); Luder, Hans-Ulrich [University of Zurich, Section of Orofacial Structures and Development, Center of Dental Medicine, Zurich (Switzerland)

    2012-07-15

    To determine the best suited sagittal MRI sequence out of a standard temporo-mandibular joint (TMJ) imaging protocol for the assessment of the cortical bone of the mandibular condyles of cadaveric specimens using micro-CT as the standard of reference. Sixteen TMJs in 8 human cadaveric heads (mean age, 81 years) were examined by MRI. Upon all sagittal sequences, two observers measured the cortical bone thickness (CBT) of the anterior, superior and posterior portions of the mandibular condyles (i.e. objective analysis), and assessed for the presence of cortical bone thinning, erosions or surface irregularities as well as subcortical bone cysts and anterior osteophytes (i.e. subjective analysis). Micro-CT of the condyles was performed to serve as the standard of reference for statistical analysis. Inter-observer agreements for objective (r = 0.83-0.99, P < 0.01) and subjective ({kappa} = 0.67-0.88) analyses were very good. Mean CBT measurements were most accurate, and cortical bone thinning, erosions, surface irregularities and subcortical bone cysts were best depicted on the 3D fast spoiled gradient echo recalled sequence (3D FSPGR). The most reliable MRI sequence to assess the cortical bone of the mandibular condyles on sagittal imaging planes is the 3D FSPGR sequence. (orig.)

  9. Genetics Home Reference: arginase deficiency

    Science.gov (United States)

    ... belongs to a class of genetic diseases called urea cycle disorders. The urea cycle is a sequence of reactions ... links) Baby's First Test GeneReview: Arginase Deficiency GeneReview: Urea Cycle Disorders Overview MedlinePlus Encyclopedia: Hereditary urea cycle abnormality National ...

  10. Welcome to NIH MedlinePlus, the magazine

    Science.gov (United States)

    ... from the world's largest medical library, NIH's National Library of Medicine. MedlinePlus has extensive information from the NIH and other trusted sources on more than 700 diseases and conditions. There ...

  11. Traumatic Brain Injury: MedlinePlus Health Topic

    Science.gov (United States)

    ... injury - discharge (Medical Encyclopedia) Also in Spanish Chronic subdural hematoma (Medical Encyclopedia) Also in Spanish EEG (Medical Encyclopedia) ... Intracranial pressure monitoring (Medical Encyclopedia) Also in Spanish Subdural hematoma (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus ...

  12. Treating Cataracts | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... Claudine Klose, 63, lives on a farm in New York's Hudson Valley. She had successful cataract surgery in 2013 and shared her experience recently with NIH MedlinePlus magazine. What did you notice about your vision that ...

  13. To Your Health: NLM Update—MedlinePlus

    Science.gov (United States)

    ... illustrate health care May 7 2018 Transcript Genetic architecture of mental disorders April 30 2018 Transcript Why ... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 ...

  14. Mentoring in Medicine | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... front is Andrew Morrison, MIM vice president of marketing. Giving Students a Vision of Healthcare Careers Research ... federal tax purposes. Web site: www.fnlm.org Mobile MedlinePlus! Trusted medical information on your mobile phone. ...

  15. MedlinePlus Connect: Frequently Asked Questions (FAQs)

    Science.gov (United States)

    ... topic data in XML format. Using the Web service, software developers can build applications that utilize MedlinePlus health topic information. The service accepts keyword searches as requests and returns relevant ...

  16. Kids Create Healthy Comics | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... School Students Using Medline Plus Kids Create Healthy Comics Past Issues / Fall 2015 Table of Contents Fresh, ... use of reliable health information resources." The Four Comic Books Are: The Expert Investigator explores the impact ...

  17. Sexual Problems in Men: MedlinePlus Health Topic

    Science.gov (United States)

    ... Spanish Retrograde ejaculation (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Sexual Problems in ... Premature ejaculation Reifenstein syndrome Retrograde ejaculation Related Health Topics Erectile Dysfunction Penis Disorders Prostate Diseases Testicular Disorders ...

  18. Baby Health Checkup: MedlinePlus Health Topic

    Science.gov (United States)

    ... Know (Centers for Disease Control and Prevention) - PDF Topic Image MedlinePlus Email Updates Get Baby Health Checkup ... GO MEDICAL ENCYCLOPEDIA Well-child visits Related Health Topics Childhood Immunization Common Infant and Newborn Problems Infant ...

  19. Cancer--Living with Cancer: MedlinePlus Health Topic

    Science.gov (United States)

    ... during cancer treatment (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Cancer--Living with ... care plan Show More Show Less Related Health Topics Cancer Cancer Chemotherapy Palliative Care National Institutes of ...

  20. How to Prevent Heart Disease: MedlinePlus Health Topic

    Science.gov (United States)

    ... and your heart (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get How to Prevent ... your heart Stress and your heart Related Health Topics Blood Thinners Cholesterol Heart Diseases Heart Health Tests ...

  1. Tetanus, Diphtheria, and Pertussis Vaccines: MedlinePlus Health Topic

    Science.gov (United States)

    ... Know (Centers for Disease Control and Prevention) - PDF Topic Image MedlinePlus Email Updates Get Tetanus, Diphtheria, and ... updates by email What's this? GO Related Health Topics Childhood Immunization Diphtheria Immunization Tetanus Whooping Cough National ...

  2. Laser Eye Surgery: MedlinePlus Health Topic

    Science.gov (United States)

    ... corneal surgery - discharge (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Laser Eye Surgery ... surgery - what to ask your doctor Related Health Topics Refractive Errors National Institutes of Health The primary ...

  3. Child Mental Health: MedlinePlus Health Topic

    Science.gov (United States)

    ... events and children (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Child Mental Health ... in childhood Traumatic events and children Related Health Topics Bullying Child Behavior Disorders Mental Disorders Mental Health ...

  4. Bone Marrow Transplantation: MedlinePlus Health Topic

    Science.gov (United States)

    ... marrow transplant - discharge (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Bone Marrow Transplantation ... transplant - slideshow Graft-versus-host disease Related Health Topics Bone Marrow Diseases Stem Cells National Institutes of ...

  5. Nutrition for Seniors: MedlinePlus Health Topic

    Science.gov (United States)

    ... America) National Institute on Aging Also in Spanish Topic Image MedlinePlus Email Updates Get Nutrition for Seniors updates by email What's this? GO Related Health Topics Nutrition Seniors' Health National Institutes of Health The ...

  6. Blood Count Tests: MedlinePlus Health Topic

    Science.gov (United States)

    ... Spanish WBC count (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Blood Count Tests ... WBC count Show More Show Less Related Health Topics Bleeding Disorders Blood Laboratory Tests National Institutes of ...

  7. Hormone Replacement Therapy: MedlinePlus Health Topic

    Science.gov (United States)

    ... of hormone therapy (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Hormone Replacement Therapy ... Estrogen overdose Types of hormone therapy Related Health Topics Menopause National Institutes of Health The primary NIH ...

  8. Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes [v2; ref status: indexed, http://f1000r.es/2x3

    Directory of Open Access Journals (Sweden)

    Ted Kalbfleisch

    2014-02-01

    Full Text Available Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease.  High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals.  Comparisons between these species have provided unique insights into mammalian gene function.  However, the number of species with reference genomes is small compared to those needed for studying molecular evolutionary relationships in the tree of life.  For example, among the even-toed ungulates there are approximately 300 species whose phylogenetic relationships have been calculated in the 10k trees project.  Only six of these have reference genomes:  cattle, swine, sheep, goat, water buffalo, and bison.  Although reference sequences will eventually be developed for additional hoof stock, the resources in terms of time, money, infrastructure and expertise required to develop a quality reference genome may be unattainable for most species for at least another decade.  In this work we mapped 35 Gb of next generation sequence data of a Katahdin sheep to its own species’ reference genome (Ovis aries Oar3.1 and to that of a species that diverged 15 to 30 million years ago (Bos taurus UMD3.1.  In total, 56% of reads covered 76% of UMD3.1 to an average depth of 6.8 reads per site, 83 million variants were identified, of which 78 million were homozygous and likely represent interspecies nucleotide differences. Excluding repeat regions and sex chromosomes, nearly 3.7 million heterozygous sites were identified in this animal vs. bovine UMD3.1, representing polymorphisms occurring in sheep.  Of these, 41% could be readily mapped to orthologous positions in ovine Oar3.1 with 80% corroborated as heterozygous.  These variant sites, identified via interspecies mapping could be used for comparative genomics, disease association studies, and ultimately to understand

  9. Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines

    NARCIS (Netherlands)

    Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.; Lucas, Patrick M.

    2013-01-01

    Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which

  10. PubMed alternatives to search MEDLINE: An environmental scan

    Directory of Open Access Journals (Sweden)

    Arun Keepanasseril

    2014-01-01

    Full Text Available The prime objective of this article is to introduce the newer methods to access, search and process MEDLINE citations. It also aims to provide a brief overview of each service′s salient features. A targeted search was conducted in MEDLINE through the OVID gateway. This was followed with a search in Google Scholar as well as Google and Bing. Ninety-two web-based services that can be used to search MEDLINE were identified. The list was shortened to 24 by applying a set of relevancy criteria to select those services more relevant to general medical and dental users. Salient features of the selected services are outlined and a use case based classification of the system has been proposed to help dental practitioners and researchers select the appropriate service for a given purpose.

  11. Supplementary searches of PubMed to improve currency of MEDLINE and MEDLINE In-Process searches via Ovid.

    Science.gov (United States)

    Duffy, Steven; de Kock, Shelley; Misso, Kate; Noake, Caro; Ross, Janine; Stirk, Lisa

    2016-10-01

    The research investigated whether conducting a supplementary search of PubMed in addition to the main MEDLINE (Ovid) search for a systematic review is worthwhile and to ascertain whether this PubMed search can be conducted quickly and if it retrieves unique, recently published, and ahead-of-print studies that are subsequently considered for inclusion in the final systematic review. Searches of PubMed were conducted after MEDLINE (Ovid) and MEDLINE In-Process (Ovid) searches had been completed for seven recent reviews. The searches were limited to records not in MEDLINE or MEDLINE In-Process (Ovid). Additional unique records were identified for all of the investigated reviews. Search strategies were adapted quickly to run in PubMed, and reviewer screening of the results was not time consuming. For each of the investigated reviews, studies were ordered for full screening; in six cases, studies retrieved from the supplementary PubMed searches were included in the final systematic review. Supplementary searching of PubMed for studies unavailable elsewhere is worthwhile and improves the currency of the systematic reviews.

  12. MeSHmap: a text mining tool for MEDLINE.

    OpenAIRE

    Srinivasan, P.

    2001-01-01

    Our research goal is to explore text mining from the metadata included in MEDLINE documents. We present MeSHmap our prototype text mining system that exploits the MeSH indexing accompanying MEDLINE records. MeSHmap supports searches via PubMed followed by user driven exploration of the MeSH terms and subheadings in the retrieved set. The potential of the system goes beyond text retrieval. It may also be used to compare entities of the same type such as pairs of drugs or pairs of procedures et...

  13. Book Catalogs; Selected References.

    Science.gov (United States)

    Brandhorst, Wesley T.

    The 116 citations on book catalogs are divided into the following two main sections: (1) Selected References, in alphabetic sequence by personal or institutional author and (2) Anonymous Entries, in alphabetic sequence by title. One hundred and seven of the citations cover the years 1960 through March 1969. There are five scattered citations in…

  14. Dialysis search filters for PubMed, Ovid MEDLINE, and Embase databases.

    Science.gov (United States)

    Iansavichus, Arthur V; Haynes, R Brian; Lee, Christopher W C; Wilczynski, Nancy L; McKibbon, Ann; Shariff, Salimah Z; Blake, Peter G; Lindsay, Robert M; Garg, Amit X

    2012-10-01

    Physicians frequently search bibliographic databases, such as MEDLINE via PubMed, for best evidence for patient care. The objective of this study was to develop and test search filters to help physicians efficiently retrieve literature related to dialysis (hemodialysis or peritoneal dialysis) from all other articles indexed in PubMed, Ovid MEDLINE, and Embase. A diagnostic test assessment framework was used to develop and test robust dialysis filters. The reference standard was a manual review of the full texts of 22,992 articles from 39 journals to determine whether each article contained dialysis information. Next, 1,623,728 unique search filters were developed, and their ability to retrieve relevant articles was evaluated. The high-performance dialysis filters consisted of up to 65 search terms in combination. These terms included the words "dialy" (truncated), "uremic," "catheters," and "renal transplant wait list." These filters reached peak sensitivities of 98.6% and specificities of 98.5%. The filters' performance remained robust in an independent validation subset of articles. These empirically derived and validated high-performance search filters should enable physicians to effectively retrieve dialysis information from PubMed, Ovid MEDLINE, and Embase.

  15. Idiographic duo-trio tests using a constant-reference based on preference of each consumer: Sample presentation sequence in difference test can be customized for individual consumers to reduce error.

    Science.gov (United States)

    Kim, Min-A; Sim, Hye-Min; Lee, Hye-Seong

    2016-11-01

    As reformulations and processing changes are increasingly needed in the food industry to produce healthier, more sustainable, and cost effective products while maintaining superior quality, reliable measurements of consumers' sensory perception and discrimination are becoming more critical. Consumer discrimination methods using a preferred-reference duo-trio test design have been shown to be effective in improving the discrimination performance by customizing sample presentation sequences. However, this design can add complexity to the discrimination task for some consumers, resulting in more errors in sensory discrimination. The objective of the present study was to investigate the effects of different types of test instructions using the preference-reference duo-trio test design where a paired-preference test is followed by 6 repeated preferred-reference duo-trio tests, in comparison to the analytical method using the balanced-reference duo-trio. Analyses of d' estimates (product-related measure) and probabilistic sensory discriminators in momentary numbers of subjects showing statistical significance (subject-related measure) revealed that only preferred-reference duo-trio test using affective reference-framing, either by providing no information about the reference or information on a previously preferred sample, improved the sensory discrimination more than the analytical method. No decrease in discrimination performance was observed with any type of instruction, confirming that consumers could handle the test methods. These results suggest that when repeated tests are feasible, using the affective discrimination method would be operationally more efficient as well as ecologically more reliable for measuring consumers' sensory discrimination ability. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Welcome to MedlinePlus en español

    Science.gov (United States)

    ... para el público de la Biblioteca Nacional de Medicina, la biblioteca médica más grande del mundo. Los ... B. Lindberg, M.D. Director, Biblioteca Nacional de Medicina MedlinePlus.gov/salud Spring 2007 Issue: Volume 2 ...

  17. Comparing Medline citations using modified N-grams

    Science.gov (United States)

    Nawab, Rao Muhammad Adeel; Stevenson, Mark; Clough, Paul

    2014-01-01

    Objective We aim to identify duplicate pairs of Medline citations, particularly when the documents are not identical but contain similar information. Materials and methods Duplicate pairs of citations are identified by comparing word n-grams in pairs of documents. N-grams are modified using two approaches which take account of the fact that the document may have been altered. These are: (1) deletion, an item in the n-gram is removed; and (2) substitution, an item in the n-gram is substituted with a similar term obtained from the Unified Medical Language System  Metathesaurus. N-grams are also weighted using a score derived from a language model. Evaluation is carried out using a set of 520 Medline citation pairs, including a set of 260 manually verified duplicate pairs obtained from the Deja Vu database. Results The approach accurately detects duplicate Medline document pairs with an F1 measure score of 0.99. Allowing for word deletions and substitution improves performance. The best results are obtained by combining scores for n-grams of length 1–5 words. Discussion Results show that the detection of duplicate Medline citations can be improved by modifying n-grams and that high performance can also be obtained using only unigrams (F1=0.959), particularly when allowing for substitutions of alternative phrases. PMID:23715801

  18. The phylogenetic relationships of insectivores with special reference to the lesser hedgehog tenrec as inferred from the complete sequence of their mitochondrial genome.

    Science.gov (United States)

    Nikaido, Masato; Cao, Ying; Okada, Norihiro; Hasegawa, Masami

    2003-02-01

    The complete mitochondrial genome of a lesser hedgehog tenrec Echinops telfairi was determined in this study. It is an endemic African insectivore that is found specifically in Madagascar. The tenrec's back is covered with hedgehog-like spines. Unlike other spiny mammals, such as spiny mice, spiny rats, spiny dormice and porcupines, lesser hedgehog tenrecs look amazingly like true hedgehogs (Erinaceidae). However, they are distinguished morphologically from hedgehogs by the absence of a jugal bone. We determined the complete sequence of the mitochondrial genome of a lesser hedgehog tenrec and analyzed the results phylogenetically to determine the relationships between the tenrec and other insectivores (moles, shrews and hedgehogs), as well as the relationships between the tenrec and endemic African mammals, classified as Afrotheria, that have recently been shown by molecular analysis to be close relatives of the tenrec. Our data confirmed the afrotherian status of the tenrec, and no direct relation was recovered between the tenrec and the hedgehog. Comparing our data with those of others, we found that within-species variations in the mitochondrial DNA of lesser hedgehog tenrecs appear to be the largest recognized to date among mammals, apart from orangutans, which might be interesting from the view point of evolutionary history of tenrecs on Madagascar.

  19. A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence.

    Science.gov (United States)

    Grattapaglia, Dario; Mamani, Eva M C; Silva-Junior, Orzenil B; Faria, Danielle A

    2015-03-01

    Keystone species in their native ranges, eucalypts, are ecologically and genetically very diverse, growing naturally along extensive latitudinal and altitudinal ranges and variable environments. Besides their ecological importance, eucalypts are also the most widely planted trees for sustainable forestry in the world. We report the development of a novel collection of 535 microsatellites for species of Eucalyptus, 494 designed from ESTs and 41 from genomic libraries. A selected subset of 223 was evaluated for individual identification, parentage testing, and ancestral information content in the two most extensively studied species, Eucalyptus grandis and Eucalyptus globulus. Microsatellites showed high transferability and overlapping allele size range, suggesting they have arisen still in their common ancestor and confirming the extensive genome conservation between these two species. A consensus linkage map with 437 microsatellites, the most comprehensive microsatellite-only genetic map for Eucalyptus, was built by assembling segregation data from three mapping populations and anchored to the Eucalyptus genome. An overall colinearity between recombination-based and physical positioning of 84% of the mapped microsatellites was observed, with some ordering discrepancies and sporadic locus duplications, consistent with the recently described whole genome duplication events in Eucalyptus. The linkage map covered 95.2% of the 605.8-Mbp assembled genome sequence, placing one microsatellite every 1.55 Mbp on average, and an overall estimate of physical to recombination distance of 618 kbp/cM. The genetic parameters estimates together with linkage and physical position data for this large set of microsatellites should assist marker choice for genome-wide population genetics and comparative mapping in Eucalyptus. © 2014 John Wiley & Sons Ltd.

  20. Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface.

    Science.gov (United States)

    Simon, Michael; Hausner, Elke; Klaus, Susan F; Dunton, Nancy E

    2010-08-23

    The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized terminology (e.g. by consistent use of the

  1. Automatically identifying gene/protein terms in MEDLINE abstracts.

    Science.gov (United States)

    Yu, Hong; Hatzivassiloglou, Vasileios; Rzhetsky, Andrey; Wilbur, W John

    2002-01-01

    Natural language processing (NLP) techniques are used to extract information automatically from computer-readable literature. In biology, the identification of terms corresponding to biological substances (e.g., genes and proteins) is a necessary step that precedes the application of other NLP systems that extract biological information (e.g., protein-protein interactions, gene regulation events, and biochemical pathways). We have developed GPmarkup (for "gene/protein-full name mark up"), a software system that automatically identifies gene/protein terms (i.e., symbols or full names) in MEDLINE abstracts. As a part of marking up process, we also generated automatically a knowledge source of paired gene/protein symbols and full names (e.g., LARD for lymphocyte associated receptor of death) from MEDLINE. We found that many of the pairs in our knowledge source do not appear in the current GenBank database. Therefore our methods may also be used for automatic lexicon generation. GPmarkup has 73% recall and 93% precision in identifying and marking up gene/protein terms in MEDLINE abstracts. A random sample of gene/protein symbols and full names and a sample set of marked up abstracts can be viewed at http://www.cpmc.columbia.edu/homepages/yuh9001/GPmarkup/. Contact. hy52@columbia.edu. Voice: 212-939-7028; fax: 212-666-0140.

  2. Genetics Home Reference: ornithine transcarbamylase deficiency

    Science.gov (United States)

    ... belongs to a class of genetic diseases called urea cycle disorders. The urea cycle is a sequence of reactions ... Baby's First Test GeneReview: Ornithine Transcarbamylase Deficiency GeneReview: Urea Cycle Disorders Overview MedlinePlus Encyclopedia: Hereditary urea cycle abnormality National ...

  3. On the query reformulation technique for effective MEDLINE document retrieval.

    Science.gov (United States)

    Yoo, Sooyoung; Choi, Jinwook

    2010-10-01

    Improving the retrieval accuracy of MEDLINE documents is still a challenging issue due to low retrieval precision. Focusing on a query expansion technique based on pseudo-relevance feedback (PRF), this paper addresses the problem by systematically examining the effects of expansion term selection and adjustment of the term weights of the expanded query using a set of MEDLINE test documents called OHSUMED. Implementing a baseline information retrieval system based on the Okapi BM25 retrieval model, we compared six well-known term ranking algorithms for useful expansion term selection and then compared traditional term reweighting algorithms with our new variant of the standard Rocchio's feedback formula, which adopts a group-based weighting scheme. Our experimental results on the OHSUMED test collection showed a maximum improvement of 20.2% and 20.4% for mean average precision and recall measures over unexpanded queries when terms were expanded using a co-occurrence analysis-based term ranking algorithm in conjunction with our term reweighting algorithm (p-valueretrieval.

  4. Growth references

    NARCIS (Netherlands)

    Buuren, S. van

    2007-01-01

    A growth reference describes the variation of an anthropometric measurement within a group of individuals. A reference is a tool for grouping and analyzing data and provides a common basis for comparing populations.1 A well known type of reference is the age-conditional growth diagram. The

  5. Genetics Home Reference: isolated lissencephaly sequence

    Science.gov (United States)

    ... than normal ( microcephaly ). This underdevelopment of the brain causes severe intellectual disability, delayed development, and recurrent seizures (epilepsy) in individuals with ILS. More than 90 percent ...

  6. Genetics Home Reference: isolated Pierre Robin sequence

    Science.gov (United States)

    ... or Free article on PubMed Central Mackay DR. Controversies in the diagnosis and management of the Robin ... Site Map Subscribe Customer Support USA.gov Copyright Privacy Accessibility FOIA Viewers & Players U.S. Department of Health & ...

  7. We’re All in This Together | NIH MedlinePlus the Magazine

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    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [4.3 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  8. Achoo! Cold, Flu, or Something Else? | NIH MedlinePlus the Magazine

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  9. Psoriasis: On the Road to Discovery | NIH MedlinePlus the Magazine

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  10. Nick Jonas on Type 1 Diabetes | NIH MedlinePlus the Magazine

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  11. Asthma: What You Need to Know | NIH MedlinePlus the Magazine

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  12. Preventing Pregnancy with a Gel for Men? | NIH MedlinePlus the Magazine

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  13. Caregiving: It Takes a Village | NIH MedlinePlus the Magazine

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  14. Breathtaking: Managing a COPD Diagnosis | NIH MedlinePlus the Magazine

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  15. Understanding and preventing tick bites | NIH MedlinePlus the Magazine

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  16. Battling C. Difficile: Don’t Delay | NIH MedlinePlus the Magazine

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  17. From the lab - Exercise Key to Keeping Weight Off | NIH MedlinePlus the Magazine

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  18. From the lab - Can Potassium Help Your Heart? | NIH MedlinePlus the Magazine

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  19. Sickle Cell Disease: What You Should Know | NIH MedlinePlus the Magazine

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  20. A Journey with Mid-life Hearing Loss | NIH MedlinePlus the Magazine

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  1. Joint Replacement Surgery: What you Need to Know | NIH MedlinePlus the Magazine

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  2. The Future of Asthma Monitoring | NIH MedlinePlus the Magazine

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  3. Too ‘Stubborn’ to Give in to COPD | NIH MedlinePlus the Magazine

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  4. Cholesterol: The Good, the Bad, and the Unhealthy | NIH MedlinePlus the Magazine

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  5. Palliative Care: A Spectrum of Support | NIH MedlinePlus the Magazine

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  6. Confronting 9/11 Trauma from Childhood into Adulthood | NIH MedlinePlus the Magazine

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  7. Solving the Undiagnosed Disease Puzzle at NIH | NIH MedlinePlus the Magazine

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  8. Love and Life without Gluten | NIH MedlinePlus the Magazine

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  9. A Couple’s Caregiving Journey | NIH MedlinePlus the Magazine

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  10. Surgeon General Outlines Opioid Plan | NIH MedlinePlus the Magazine

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  11. From the lab - Testing Malaria-Resistant Mosquitoes | NIH MedlinePlus the Magazine

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  12. A Path to Hope for Sickle Cell Disease | NIH MedlinePlus the Magazine

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  13. Step Inside NIH’s Sickle Cell Branch | NIH MedlinePlus the Magazine

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  14. From the lab - Progress Against Zika | NIH MedlinePlus the Magazine

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  15. A Closer Look at Cancer Imaging Tools | NIH MedlinePlus the Magazine

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  16. Exploring the Celiac Disease Mystery | NIH MedlinePlus the Magazine

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  17. Beyond Pain Relief: Total Knee Replacement Surgery | NIH MedlinePlus the Magazine

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  18. TV Star Jim Parsons Shines Light on NIH Research | NIH MedlinePlus the Magazine

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  19. Advance Care Plan: A Checklist for the Future | NIH MedlinePlus the Magazine

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  20. Understanding Asthma from the Inside Out | NIH MedlinePlus the Magazine

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  1. Keys to Recovery after Knee Replacement Surgery | NIH MedlinePlus the Magazine

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  2. Fighting the Flu with a Universal Vaccine | NIH MedlinePlus the Magazine

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  3. Genetics Home Reference: hypochondroplasia

    Science.gov (United States)

    ... the elbows, a sway of the lower back ( lordosis ), and bowed legs. These signs are generally less ... Management Resources (2 links) GeneReview: Hypochondroplasia MedlinePlus Encyclopedia: Lordosis General Information from MedlinePlus (5 links) Diagnostic Tests ...

  4. Genetics Home Reference: hypophosphatasia

    Science.gov (United States)

    ... by a softening of the bones known as osteomalacia. In adults, recurrent fractures in the foot and ... Management Resources (2 links) GeneReview: Hypophosphatasia MedlinePlus Encyclopedia: Osteomalacia General Information from MedlinePlus (5 links) Diagnostic Tests ...

  5. Glucose in Urine Test: MedlinePlus Lab Test Information

    Science.gov (United States)

    ... glucose test to help make a diagnosis. References American Diabetes Association [Internet]. Arlington (VA): American Diabetes Association; c1995–2017. Checking Your Blood Glucose [cited 2017 ...

  6. Using incomplete citation data for MEDLINE results ranking.

    Science.gov (United States)

    Herskovic, Jorge R; Bernstam, Elmer V

    2005-01-01

    Information overload is a significant problem for modern medicine. Searching MEDLINE for common topics often retrieves more relevant documents than users can review. Therefore, we must identify documents that are not only relevant, but also important. Our system ranks articles using citation counts and the PageRank algorithm, incorporating data from the Science Citation Index. However, citation data is usually incomplete. Therefore, we explore the relationship between the quantity of citation information available to the system and the quality of the result ranking. Specifically, we test the ability of citation count and PageRank to identify "important articles" as defined by experts from large result sets with decreasing citation information. We found that PageRank performs better than simple citation counts, but both algorithms are surprisingly robust to information loss. We conclude that even an incomplete citation database is likely to be effective for importance ranking.

  7. [Reference citation].

    Science.gov (United States)

    Brkić, Silvija

    2013-01-01

    Scientific and professional papers represent the information basis for scientific research and professional work. References important for the paper should be cited within the text, and listed at the end of the paper. This paper deals with different styles of reference citation. Special emphasis was placed on the Vancouver Style for reference citation in biomedical journals established by the International Committee of Medical Journal Editors. It includes original samples for citing various types of articles, both printed and electronic, as well as recommendations related to reference citation in accordance with the methodology and ethics of scientific research and guidelines for preparing manuscripts for publication.

  8. Friends of the National Library of Medicine, Welcome to NIH MedlinePlus, the magazine | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... Contents Dear Readers, WELCOME to NIH MedlinePlus , the magazine. The purpose of NIH MedlinePlus , the magazine, is to provide you with a FREE , trusted ... medical information. Published four times a year, the magazine showcases the National Institutes of Health's (NIH) latest ...

  9. Reference Assessment

    Science.gov (United States)

    Bivens-Tatum, Wayne

    2006-01-01

    This article presents interesting articles that explore several different areas of reference assessment, including practical case studies and theoretical articles that address a range of issues such as librarian behavior, patron satisfaction, virtual reference, or evaluation design. They include: (1) "Evaluating the Quality of a Chat Service"…

  10. Recent references

    International Nuclear Information System (INIS)

    Ramavataram, S.

    1991-01-01

    In support of a continuing program of systematic evaluation of nuclear structure data, the National Nuclear Data Center maintains a complete computer file of references to the nuclear physics literature. Each reference is tagged by a keyword string, which indicates the kinds of data contained in the article. This master file of Nuclear Structure References (NSR) contains complete keyword indexes to literature published since 1969, with partial indexing of older references. Any reader who finds errors in the keyword descriptions is urged to report them to the National Nuclear Data Center so that the master NSR file can be corrected. In 1966, the first collection of Recent References was published as a separate issue of Nuclear Data Sheets. Every four months since 1970, a similar indexed bibliography to new nuclear experiments has been prepared from additions to the NSR file and published. Beginning in 1978, Recent References was cumulated annually, with the third issue completely superseding the two issues previously published during a given year. Due to publication policy changes, cumulation of Recent Reference was discontinued in 1986. The volume and issue number of all the cumulative issues published to date are given. NNDC will continue to respond to individual requests for special bibliographies on nuclear physics topics, in addition to those easily obtained from Recent References. If the required information is available from the keyword string, a reference list can be prepared automatically from the computer files. This service can be provided on request, in exchange for the timely communication of new nuclear physics results (e.g., preprints). A current copy of the NSR file may also be obtained in a standard format on magnetic tape from NNDC. Requests for special searches of the NSR file may also be directed to the National Nuclear Data Center

  11. Web-Scale Discovery Services Retrieve Relevant Results in Health Sciences Topics Including MEDLINE Content

    Directory of Open Access Journals (Sweden)

    Elizabeth Margaret Stovold

    2017-06-01

    coverage of MEDLINE, they recorded the first 50 results from each of the 6 PubMed searches in a spreadsheet. During data collection at the WSD sites, they searched for these references to discover if the WSD tool at each site indexed these known items. Authors adopted measures to control for any customisation of the product setup at each data collection site. In particular, they excluded local holdings from the results by limiting the searches to scholarly, peer-reviewed articles. Main results – Authors reported results for 5 of the 6 sites. All of the WSD tools retrieved between 50-60% relevant results. EDS retrieved the highest number of relevant records (195/360 and 216/360, while Primo retrieved the lowest (167/328 and 169/325. There was good observer agreement (k=0.725 for the relevance assessment. The duplicate detection rate was similar in EDS and Summon (between 96-97% unique articles, while the Primo searches returned 82.9-84.9% unique articles. All three tools retrieved relevant results that were not indexed in MEDLINE, and retrieved relevant material indexed in MEDLINE that was not retrieved in the PubMed searches. EDS and Summon retrieved more non-MEDLINE material than Primo. EDS performed best in the known-item searches, with 300/300 and 299/300 items retrieved, while Primo performed worst with 230/300 and 267/300 items retrieved. The Summon platform features an “automated query expansion” search function, where user-entered keywords are matched to related search terms and these are automatically searched along with the original keyword. The authors observed that this function resulted in a wholly relevant first page of results for one of the search questions tested in Summon. Conclusion – While EDS performed slightly better overall, the difference was not great enough in this small sample of test sites to recommend EDS over the other tools being tested. The automated query expansion found in Summon is a useful function that is worthy of further

  12. Spanish scientific output on Helicobacter pylori. A study through Medline.

    Science.gov (United States)

    Trapero-Marugán, M; Gisbert, J P; Pajares, J M

    2006-04-01

    to analyze scientific output from Spanish hospitals in relation to Helicobacter pylori infection. papers collected from the Medline database between January 1988 and December 2003 were selected. Our search strategy was: "Helicobacter pylori" [MeSH] AND ((Spain [AD] OR Espana [AD] OR Spanien [AD] OR Espagne [AD] OR Espanha [AD]) OR (Spanish [LA]) OR Spain). The following was analyzed: geographic area, Spanish or foreign publication, topic, and year of publication. Output and impact bibliometric markers were evaluated. in all, 691 papers were identified, of which 241 were excluded. Number of papers went from 2 in 1988 to 47 in 2002 and 13 in 2003. There were more reports in Spanish versus foreign journals (58 vs. 42%). In the first 5 years the areas with greater output were associated with diagnosis and microbiology (33 and 20%), whereas therapy was the predominating subject during the last 5 years (27%). Original papers were most common among publications (69%). Hospitals with highest output included La Princesa (24%) and Ramón y Cajal (17.6%) in Madrid, and Parc Taulí in Barcelona (6.4%). Mean impact factor progressively increased from 1.826 in 1988 to 2.142 in 2002 and 2.493 in 2003. the production and impact of documents published by Spanish scientists regarding H. pylori infection considerably increased during the past two decades.

  13. Evaluating the MEDLINE Core Clinical Journals filter: data-driven evidence assessing clinical utility.

    Science.gov (United States)

    Klein-Fedyshin, Michele; Ketchum, Andrea M; Arnold, Robert M; Fedyshin, Peter J

    2014-12-01

    MEDLINE offers the Core Clinical Journals filter to limit to clinically useful journals. To determine its effectiveness for searching and patient-centric decision making, this study compared literature used for Morning Report in Internal Medicine with journals in the filter. An EndNote library with references answering 327 patient-related questions during Morning Report from 2007 to 2012 was exported to a file listing variables including designated Core Clinical Journal, Impact Factor, date used and medical subject. Bradford's law of scattering was applied ranking the journals and reflecting their clinical utility. Recall (sensitivity) and precision of the Core Morning Report journals and non-Core set was calculated. This study applied bibliometrics to compare the 628 articles used against these criteria to determine journals impacting decision making. Analysis shows 30% of clinically used articles are from the Core Clinical Journals filter and 16% of the journals represented are Core titles. When Bradford-ranked, 55% of the top 20 journals are Core. Articles sources used. Among the 63 Morning Report subjects, 55 have <50% precision and 41 have <50% recall including 37 subjects with 0% precision and 0% recall. Low usage of publications within the Core Clinical Journals filter indicates less relevance for hospital-based care. The divergence from high-impact medicine titles suggests clinically valuable journals differ from academically important titles. With few subjects demonstrating high recall or precision, the MEDLINE Core Clinical Journals filter may require a review and update to better align with current clinical needs. © 2014 John Wiley & Sons, Ltd.

  14. Genetics Home Reference: Emanuel syndrome

    Science.gov (United States)

    ... of Emanuel syndrome include an unusually small head ( microcephaly ), distinctive facial features, and a small lower jaw ( ... MedlinePlus Encyclopedia: Cleft Lip and Palate MedlinePlus Encyclopedia: Microcephaly MedlinePlus Encyclopedia: Preauricular Tag or Pit General Information ...

  15. Genetics Home Reference: Feingold syndrome

    Science.gov (United States)

    ... Feingold syndrome include an unusually small head size ( microcephaly ), a small jaw ( micrognathia ), a narrow opening of ... Duodenal Atresia MedlinePlus Encyclopedia: Esophageal Atresia MedlinePlus Encyclopedia: Microcephaly MedlinePlus Encyclopedia: Webbing of the Fingers or Toes ...

  16. Setting reference targets

    International Nuclear Information System (INIS)

    Ruland, R.E.

    1997-04-01

    Reference Targets are used to represent virtual quantities like the magnetic axis of a magnet or the definition of a coordinate system. To explain the function of reference targets in the sequence of the alignment process, this paper will first briefly discuss the geometry of the trajectory design space and of the surveying space, then continue with an overview of a typical alignment process. This is followed by a discussion on magnet fiducialization. While the magnetic measurement methods to determine the magnetic centerline are only listed (they will be discussed in detail in a subsequent talk), emphasis is given to the optical/mechanical methods and to the task of transferring the centerline position to reference targets

  17. Development and testing of a medline search filter for identifying patient and public involvement in health research.

    Science.gov (United States)

    Rogers, Morwenna; Bethel, Alison; Boddy, Kate

    2017-06-01

    Research involving the public as partners often proves difficult to locate due to the variations in terms used to describe public involvement, and inability of medical databases to index this concept effectively. To design a search filter to identify literature where patient and public involvement (PPI) was used in health research. A reference standard of 172 PPI papers was formed. The references were divided into a development set and a test set. Search terms were identified from common words, phrases and synonyms in the development set. These terms were combined as a search strategy for medline via OvidSP, which was then tested for sensitivity against the test set. The resultant search filter was then assessed for sensitivity, specificity and precision using a previously published systematic review. The search filter was found to be highly sensitive 98.5% in initial testing. When tested against results generated by a 'real-life' systematic review, the filter had a specificity of 81%. However, sensitivity dropped to 58%. Adjustments to the population group of terms increased the sensitivity to 73%. The PPI filter designed for medline via OvidSP could aid information specialists and researchers trying to find literature specific to PPI. © 2016 Health Libraries Group.

  18. Bibliometric analysis of scientific production indexed in MEDLINE, about hospital based home care services

    Directory of Open Access Journals (Sweden)

    Javier Sanz-Valero

    2017-01-01

    Full Text Available Objective: A thematic and bibliometric analysis was done for the available scientific production about the home care services based in the hospital. Methods: Bibliometric analysis. Data was obtained from MEDLINE database using MeSH “Home Care Services, Hospital-Based” as Major Topic. Search date: July 2016. The study sample was calculated by estimating population parameters for an infinite population and the selection was a simple random without replacement. Results: A total of 386 references were analysed. The number of original articles was of 204 (52,85%, identifying 243 institutions, with an index of cooperation of 3,75±1,16 authors/article. English was the predominant language in 279 (72,28% articles. The obsolescence was of 13 years according to the Burton-Kebler Index and the Price Index was of 14,40%. Bradford nucleon was constituted by 23 journals. The thematic classification determines a relevance of 70.73%. Conclusions: There was a high obsolescence and an anglophone orientation. Also, there was a weak relation between institutions and corporation index. Over the time there was an improvement of the access to the primary source, in line with the Open Access initiative. The production was collected in a high number of journals (in a very dispersed form. The thematic classification meets the studied issue.

  19. MedlinePlus Connect: Linking Patient Portals and Electronic Health Records to Health Information

    Science.gov (United States)

    ... Here: Home → MedlinePlus Connect URL of this page: https://medlineplus.gov/connect/overview.html MedlinePlus Connect Linking ... will change.) Old URLs New URLs Web Application https://apps.nlm.nih.gov/medlineplus/services/mpconnect.cfm? ...

  20. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  1. Intelligent system for topic survey in MEDLINE by keyword recommendation and learning text characteristics.

    Science.gov (United States)

    Tanaka, M; Nakazono, S; Matsuno, H; Tsujimoto, H; Kitamura, Y; Miyano, S

    2000-01-01

    We have implemented a system for assisting experts in selecting MEDLINE records for database construction purposes. This system has two specific features: The first is a learning mechanism which extracts characteristics in the abstracts of MEDLINE records of interest as patterns. These patterns reflect selection decisions by experts and are used for screening the records. The second is a keyword recommendation system which assists and supplements experts' knowledge in unexpected cases. Combined with a conventional keyword-based information retrieval system, this system may provide an efficient and comfortable environment for MEDLINE record selection by experts. Some computational experiments are provided to prove that this idea is useful.

  2. PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm

    Directory of Open Access Journals (Sweden)

    Chuong Cheng-Ming

    2006-10-01

    Full Text Available Abstract Background Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. Results PubFocus web server automates analysis of MEDLINE/PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus also prioritizes citations and evaluates authors' impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies. Conclusion We have developed citations' prioritisation algorithm based on journal impact factor, forward referencing volume, referencing dynamics, and author's contribution level. It can be applied either to the primary set of PubMed search results or to the subsets of these results identified through key terms from controlled biomedical vocabularies and ontologies. NCI (National Cancer Institute thesaurus and MGD (Mouse Genome Database mammalian gene orthology have been implemented for key terms analytics. PubFocus provides a scalable platform for the integration of multiple available ontology databases. PubFocus analytics can be adapted for input sources of biomedical citations other than PubMed.

  3. Genetics Home Reference: N-acetylglutamate synthase deficiency

    Science.gov (United States)

    ... belongs to a class of genetic diseases called urea cycle disorders. The urea cycle is a sequence of reactions ... Other Diagnosis and Management Resources (3 links) GeneReview: Urea Cycle Disorders Overview MedlinePlus Encyclopedia: Hereditary Urea Cycle Abnormality National ...

  4. MedlinePlus® Everywhere: Access from Your Phone, Tablet or Desktop

    Science.gov (United States)

    ... responsivefull.html MedlinePlus® Everywhere: Access from Your Phone, Tablet or Desktop To use the sharing features on ... provide a consistent user experience from a desktop, tablet, or phone. All users, regardless of how they ...

  5. A Leader in Clinical Trials, Medical Data, & Electronic Health Information | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... of C. Everett Koop, the former Surgeon General; Charles Drew, the “father of the blood bank”; Rosalind ... MedlinePlus information resources about prescriptions. Soon, such information will be available through one click on the name ...

  6. For Distinguished Public Service: Medical Library Association Honors FNLM and NIH MedlinePlus Magazine | NIH ...

    Science.gov (United States)

    ... Medical Library Association Honors FNLM and NIH MedlinePlus Magazine Past Issues / Summer 2011 Table of Contents MLA ... From You We want your feedback on the magazine and ideas for future issues, as well as ...

  7. The Match of Her Life | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... answer questions for this issue of NIH MedlinePlus magazine about her breast cancer. You discovered you had ... way of healing. As this issue of the magazine went to press, Navratilova was receiving radiation therapy ...

  8. FNLM 2013 Events & Programs Announced | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... study in their field of expertise. Annual Awards Dinner In 2013, the Awards Dinner to celebrate advances ... Mobile MedlinePlus! Trusted medical information on your mobile phone. http://m.medlineplus.gov and in Spanish at ...

  9. To Your Health: NLM update transcript - NIH MedlinePlus magazine Winter 2018

    Science.gov (United States)

    ... who is a star of 'The Big Bang Theory' television show, and the producer/narrator of a ... trials, NIH MedlinePlus magazine reports the current life expectancy of a person with sickle cell disease is ...

  10. NIH Launches National COPD Action Plan | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... COPD Action Plan Follow us NIH Launches National COPD Action Plan Photo: National Heart, Lung, and Blood ... questions for NIH MedlinePlus magazine. Why was the COPD National Action Plan created? The staggering numbers associated ...

  11. Annotating patents with Medline MeSH codes via citation mapping.

    Science.gov (United States)

    Griffin, Thomas D; Boyer, Stephen K; Councill, Isaac G

    2010-01-01

    Both patents and Medline are important document collections for discovering new relationships between chemicals and biology, searching for prior art for patent applications and retrieving background knowledge for current research activities. Finding relevance to a topic within patents is often made difficult by poor categorization, badly written descriptions, and even intentional obfuscation. Unlike patents, the Medline corpus has Medical Subject Heading (MeSH) keywords manually added to their articles, giving a medically relevant taxonomy to the 18 million article abstracts. Our work attempts to accurately recognize the citations made in patents to Medline-indexed articles, linking them to their corresponding PubMed ID and exploiting the associated MeSH to enhance patent search by annotating the referencing patents with their Medline citations' MeSH codes. The techniques, system features, and benefits are explained.

  12. Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

    OpenAIRE

    Muin, Michael; Fontelo, Paul

    2006-01-01

    Abstract Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhanci...

  13. Is a Widely Available Cure for Sickle Cell Disease on the Horizon? | NIH MedlinePlus the Magazine

    Science.gov (United States)

    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [1.5 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  14. Journalist Liz Hernandez hopes to make Alzheimer’s a thing of the past | NIH MedlinePlus the Magazine

    Science.gov (United States)

    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [4.3 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  15. Finding Better and More Personalized Ways to Diagnose Cancer at NIH | NIH MedlinePlus the Magazine

    Science.gov (United States)

    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [3.1 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  16. From the lab - CancerSEEK: Blood Test Could Detect Cancer Earlier | NIH MedlinePlus the Magazine

    Science.gov (United States)

    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [3.1 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  17. From Bench to Bedside: Researchers of NIH’s Clinical Center | NIH MedlinePlus the Magazine

    Science.gov (United States)

    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [1.5 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  18. From the lab - Brain Scan Technology Extends Treatment Window for Stroke | NIH MedlinePlus the Magazine

    Science.gov (United States)

    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [3.1 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  19. Genetics Home Reference: bladder cancer

    Science.gov (United States)

    ... Testing Registry: Malignant tumor of urinary bladder Other Diagnosis and Management Resources (1 link) MedlinePlus Encyclopedia: Bladder Cancer General Information from MedlinePlus (5 links) Diagnostic Tests ...

  20. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  1. Impact of SciELO and MEDLINE indexing on submissions to Jornal de Pediatria.

    Science.gov (United States)

    Blank, Danilo; Buchweitz, Claudia; Procianoy, Renato S

    2005-01-01

    To evaluate the impact of SciELO and MEDLINE indexing on the number of articles submitted to Jornal de Pediatria. Analysis of total article submission, submission of articles from foreign countries and acceptance figures in the following periods: stage I - pre-website (Jan 2000-Mar 2001); stage II - website (Apr 2001-Jul 2002); stage III - SciELO (Aug 2002-Aug 2003); stage IV - MEDLINE (Sep 2003-Dec 2004). There was a significant trend toward linear increase in the number of submissions along the study period (p = 0.009). The number of manuscripts submitted in stages I through IV was 184, 240, 297, and 482, respectively. The number of submissions was similar in stages I and II (p = 0.148), but statistically higher in Stage III (p SciELO indexing was associated with an increase in Brazilian manuscript submissions to Jornal de Pediatria, whereas MEDLINE indexing led to an increase in both Brazilian and foreign submissions.

  2. The MedlinePlus public user interface: studies of design challenges and opportunities

    Science.gov (United States)

    Marill, Jennifer L.; Miller, Naomi; Kitendaugh, Paula

    2006-01-01

    Question: What are the challenges involved in designing, modifying, and improving a major health information portal that serves over sixty million page views a month? Setting: MedlinePlus, the National Library of Medicine's (NLM's) consumer health Website, is examined. Method: Challenges are presented as six “studies,” which describe selected design issues and how NLM staff resolved them. Main Result: Improving MedlinePlus is an iterative process. Changes in the public user interface are ongoing, reflecting Web design trends, usability testing recommendations, user survey results, new technical requirements, and the need to grow the site in an orderly way. Conclusion: Testing and analysis should accompany Website design modifications. New technologies may enhance a site but also introduce problems. Further modifications to MedlinePlus will be informed by the experiences described here. PMID:16404467

  3. High-performance information search filters for CKD content in PubMed, Ovid MEDLINE, and EMBASE.

    Science.gov (United States)

    Iansavichus, Arthur V; Hildebrand, Ainslie M; Haynes, R Brian; Wilczynski, Nancy L; Levin, Adeera; Hemmelgarn, Brenda R; Tu, Karen; Nesrallah, Gihad E; Nash, Danielle M; Garg, Amit X

    2015-01-01

    Finding relevant articles in large bibliographic databases such as PubMed, Ovid MEDLINE, and EMBASE to inform care and future research is challenging. Articles relevant to chronic kidney disease (CKD) are particularly difficult to find because they are often published under different terminology and are found across a wide range of journal types. We used computer automation within a diagnostic test assessment framework to develop and validate information search filters to identify CKD articles in large bibliographic databases. 22,992 full-text articles in PubMed, Ovid MEDLINE, or EMBASE. 1,374,148 unique search filters. We established the reference standard of article relevance to CKD by manual review of all full-text articles using prespecified criteria to determine whether each article contained CKD content or not. We then assessed filter performance by calculating sensitivity, specificity, and positive predictive value for the retrieval of CKD articles. Filters with high sensitivity and specificity for the identification of CKD articles in the development phase (two-thirds of the sample) were then retested in the validation phase (remaining one-third of the sample). We developed and validated high-performance CKD search filters for each bibliographic database. Filters optimized for sensitivity reached at least 99% sensitivity, and filters optimized for specificity reached at least 97% specificity. The filters were complex; for example, one PubMed filter included more than 89 terms used in combination, including "chronic kidney disease," "renal insufficiency," and "renal fibrosis." In proof-of-concept searches, physicians found more articles relevant to the topic of CKD with the use of these filters. As knowledge of the pathogenesis of CKD grows and definitions change, these filters will need to be updated to incorporate new terminology used to index relevant articles. PubMed, Ovid MEDLINE, and EMBASE can be filtered reliably for articles relevant to CKD. These

  4. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  5. Genetics Home Reference: focal dermal hypoplasia

    Science.gov (United States)

    ... in people with focal dermal hypoplasia is an omphalocele , which is an opening in the wall of ... Dermal Hypoplasia MedlinePlus Encyclopedia: Ectodermal dysplasia MedlinePlus Encyclopedia: Omphalocele General Information from MedlinePlus (5 links) Diagnostic Tests ...

  6. Married...with Food Allergies | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... this page please turn Javascript on. Feature: Food Allergies Married...with Food Allergies Past Issues / Spring 2011 Table of Contents Photo: ... life together and a common problem—severe food allergies. NIH MedlinePlus magazine’s Naomi Miller caught up with ...

  7. Parkinson's Disease Research at NIH | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... of this page please turn JavaScript on. Feature: Parkinson's Disease Parkinson's Disease Research at NIH Past Issues / Winter 2014 ... areas of its research: MedlinePlus . medlineplus.gov . Type "Parkinson's disease" in the Search box. NIHSeniorHealth —Parkinson's Disease ...

  8. The development of search filters for adverse effects of surgical interventions in medline and Embase.

    Science.gov (United States)

    Golder, Su; Wright, Kath; Loke, Yoon Kong

    2018-03-31

    Search filter development for adverse effects has tended to focus on retrieving studies of drug interventions. However, a different approach is required for surgical interventions. To develop and validate search filters for medline and Embase for the adverse effects of surgical interventions. Systematic reviews of surgical interventions where the primary focus was to evaluate adverse effect(s) were sought. The included studies within these reviews were divided randomly into a development set, evaluation set and validation set. Using word frequency analysis we constructed a sensitivity maximising search strategy and this was tested in the evaluation and validation set. Three hundred and fifty eight papers were included from 19 surgical intervention reviews. Three hundred and fifty two papers were available on medline and 348 were available on Embase. Generic adverse effects search strategies in medline and Embase could achieve approximately 90% relative recall. Recall could be further improved with the addition of specific adverse effects terms to the search strategies. We have derived and validated a novel search filter that has reasonable performance for identifying adverse effects of surgical interventions in medline and Embase. However, we appreciate the limitations of our methods, and recommend further research on larger sample sizes and prospective systematic reviews. © 2018 The Authors Health Information and Libraries Journal published by John Wiley & Sons Ltd on behalf of Health Libraries Group.

  9. High school peer tutors teach MedlinePlus: a model for Hispanic outreach*

    Science.gov (United States)

    Warner, Debra G.; Olney, Cynthia A.; Wood, Fred B.; Hansen, Lucille; Bowden, Virginia M.

    2005-01-01

    Objectives: The objective was to introduce the MedlinePlus Website to the predominantly Hispanic residents of the Lower Rio Grande Valley region of Texas by partnering with a health professions magnet high school (known as Med High). Methods: Community assessment was used in the planning stages and included pre-project focus groups with students and teachers. Outreach methods included peer tutor selection, train-the-trainer sessions, school and community outreach, and pre- and posttests of MedlinePlus training sessions. Evaluation methods included Web statistics; end-of-project interviews; focus groups with students, faculty, and librarians; and end-of-project surveys of students and faculty. Results: Four peer tutors reached more than 2,000 people during the project year. Students and faculty found MedlinePlus to be a useful resource. Faculty and librarians developed new or revised teaching methods incorporating MedlinePlus. The project enhanced the role of school librarians as agents of change at Med High. The project continues on a self-sustaining basis. Conclusions: Using peer tutors is an effective way to educate high school students about health information resources and, through the students, to reach families and community members. PMID:15858628

  10. Use of the critical incident technique to evaluate the impact of MEDLINE

    International Nuclear Information System (INIS)

    Wilson, S.R.; Starr-Schneidkraut, N.; Cooper, M.D.

    1989-01-01

    The NLM has an ongoing responsibility to assess the extent to which its information products and services support the requirements of its users. This enables the Library to craft ever more responsive systems that capitalize on the latest advances in information and computer technology and, when necessary, to modify existing systems whose performance may no longer be optimal or consistent with the functions intended. The importance of this requirement was underscored in the recent report of the Outreach Planning Panel to the NLM Board of regents. A fundamental concern is the need to identify the impact of MEDLINE-derived information--i.e., does the use of MEDLINE ''make a difference''? In what ways is it used, and with what effect? In particular, is information retrieved from MEDLINE used successfully by health professionals to support medical decision-making and patient care? Previous efforts to address this question have been limited to the collection of available anecdotal reports. Traditional survey methodology, with pre-defined response categories, while used effectively to determine general areas in which MEDLINE information is used, is not well suited to developing a detailed understanding of user motivation, behavior, and resulting consequences. 8 refs., 6 figs., 2 tab

  11. Usefulness of systematic review search strategies in finding child health systematic reviews in MEDLINE

    NARCIS (Netherlands)

    Boluyt, Nicole; Tjosvold, Lisa; Lefebvre, Carol; Klassen, Terry P.; Offringa, Martin

    2008-01-01

    OBJECTIVE: To determine the sensitivity and precision of existing search strategies for retrieving child health systematic reviews in MEDLINE using PubMed. DESIGN: Filter (diagnostic) accuracy study. We identified existing search strategies for systematic reviews, combined them with a filter that

  12. La producción científica española en bioética a través de MEDLINE Scientific production in bioethics in Spain through MEDLINE

    Directory of Open Access Journals (Sweden)

    José Manuel Ramos

    2007-10-01

    Full Text Available Fundamento: Describir la producción científica española en bioética entre 1966 y 2003. Métodos: Se seleccionaron los documentos publicados por autores españoles y recogidos en la base de datos MEDLINE, mediante el cruce de las palabras bioética con otras diversas del mismo ámbito. Resultados: Se estudiaron 858 documentos, de los cuales 78 (9,1% se publicaron entre 1966 y 1983, 163 (19% entre 1984 y 1993, y 617 (71,9% entre 1994 y 2003. Los principales temas publicados fueron: legislación y derechos (15,4% e investigación y comités de ética (13,1%. En el último período se ha observado un aumento significativo de las publicaciones sobre genética y clonación y un descenso sobre las de aborto. El 38,9% de los documentos se atribuyó a universidades y el 38,5% a hospitales. Conclusiones: La publicaciones científicas de bioética se incrementó durante el período de estudio, lo que demuestra un aumento progresivo de la producción científica española en bioética.Objective: To describe Spain's scientific production in the field of bioethics from 1966 to 2003. Methods: Manuscripts published by Spanish authors between 1966 and 2003 and containing key word references to bioethics, ethics, and 22 other related terms were retrieved from the Medline database. Results: 858 documents were selected: 78 (9.1% were published between 1966 and 1983, 163 (19% between 1984 and 1993, and 617 (71.9% between 1994 and 2003. The main subject areas treated were laws and rights (15.4% and research and ethics committees (13.1%. The last of these periods witnessed an increase in publications on genetics and human cloning and a decrease in those treating abortion. Institutional affiliations referred mainly to universities (38.9% and hospitals (38.5%. Conclusions: There was a progressive increase in the number of scientific publications on bioethics by Spanish authors during the study period.

  13. Developing optimal search strategies for detecting clinically sound prognostic studies in MEDLINE: an analytic survey

    Directory of Open Access Journals (Sweden)

    Haynes R Brian

    2004-06-01

    Full Text Available Abstract Background Clinical end users of MEDLINE have a difficult time retrieving articles that are both scientifically sound and directly relevant to clinical practice. Search filters have been developed to assist end users in increasing the success of their searches. Many filters have been developed for the literature on therapy and reviews but little has been done in the area of prognosis. The objective of this study is to determine how well various methodologic textwords, Medical Subject Headings, and their Boolean combinations retrieve methodologically sound literature on the prognosis of health disorders in MEDLINE. Methods An analytic survey was conducted, comparing hand searches of journals with retrievals from MEDLINE for candidate search terms and combinations. Six research assistants read all issues of 161 journals for the publishing year 2000. All articles were rated using purpose and quality indicators and categorized into clinically relevant original studies, review articles, general papers, or case reports. The original and review articles were then categorized as 'pass' or 'fail' for methodologic rigor in the areas of prognosis and other clinical topics. Candidate search strategies were developed for prognosis and run in MEDLINE – the retrievals being compared with the hand search data. The sensitivity, specificity, precision, and accuracy of the search strategies were calculated. Results 12% of studies classified as prognosis met basic criteria for scientific merit for testing clinical applications. Combinations of terms reached peak sensitivities of 90%. Compared with the best single term, multiple terms increased sensitivity for sound studies by 25.2% (absolute increase, and increased specificity, but by a much smaller amount (1.1% when sensitivity was maximized. Combining terms to optimize both sensitivity and specificity achieved sensitivities and specificities of approximately 83% for each. Conclusion Empirically derived

  14. Genetics Home Reference: citrullinemia

    Science.gov (United States)

    ... belongs to a class of genetic diseases called urea cycle disorders. Learn more about the genes associated with citrullinemia ... GeneReview: Citrin Deficiency GeneReview: Citrullinemia Type I GeneReview: Urea Cycle Disorders Overview MedlinePlus Encyclopedia: Hereditary Urea Cycle Abnormality National ...

  15. The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data.

    Directory of Open Access Journals (Sweden)

    Dragos Scarlet

    Full Text Available Vertebrate evolution is accompanied by a substantial conservation of transcriptional programs with more than a third of unique orthologous genes showing constrained levels of expression. Moreover, there are genes and exons exhibiting excellent expression stability according to RNA-seq data across a panel of eighteen tissues including the ovary (Human Body Map 2.0.We hypothesized that orthologs of these exons would also be highly uniformly expressed across neonatal ovaries of the horse, which would render them appropriate reference genes (RGs for normalization of reverse transcription quantitative PCR (RT-qPCR data in this context. The expression stability of eleven novel RGs (C1orf43, CHMP2A, EMC7, GPI, PSMB2, PSMB4, RAB7A, REEP5, SNRPD3, VCP and VPS29 was assessed by RT-qPCR in ovaries of seven neonatal fillies and compared to that of the expressed repetitive element ERE-B, two universal (OAZ1 and RPS29 and four traditional RGs (ACTB, GAPDH, UBB and B2M. Expression stability analyzed with the software tool RefFinder top ranked the normalization factor constituted of the genes SNRPD3 and VCP, a gene pair that is not co-expressed according to COEXPRESdb and GeneMANIA. The traditional RGs GAPDH, B2M, ACTB and UBB were only ranked 3rd and 12th to 14th, respectively.The functional diversity of the novel RGs likely facilitates expression studies over a wide range of physiological and pathological contexts related to the neonatal equine ovary. In addition, this study augments the potential for RT-qPCR-based profiling of human samples by introducing seven new human RG assays (C1orf43, CHMP2A, EMC7, GPI, RAB7A, VPS29 and UBB.

  16. PubMed had a higher sensitivity than Ovid-MEDLINE in the search for systematic reviews.

    Science.gov (United States)

    Katchamart, Wanruchada; Faulkner, Amy; Feldman, Brian; Tomlinson, George; Bombardier, Claire

    2011-07-01

    To compare the performance of Ovid-MEDLINE vs. PubMed for identifying randomized controlled trials of methotrexate (MTX) in patients with rheumatoid arthritis (RA). We created search strategies for Ovid-MEDLINE and PubMed for a systematic review of MTX in RA. Their performance was evaluated using sensitivity, precision, and number needed to read (NNR). Comparing searches in Ovid-MEDLINE vs. PubMed, PubMed retrieved more citations overall than Ovid-MEDLINE; however, of the 20 citations that met eligibility criteria for the review, Ovid-MEDLINE retrieved 17 and PubMed 18. The sensitivity was 85% for Ovid-MEDLINE vs. 90% for PubMed, whereas the precision and NNR were comparable (precision: 0.881% for Ovid-MEDLINE vs. 0.884% for PubMed and NNR: 114 for Ovid-MEDLINE vs. 113 for PubMed). In systematic reviews of RA, PubMed has higher sensitivity than Ovid-MEDLINE with comparable precision and NNR. This study highlights the importance of well-designed database-specific search strategies. Copyright © 2010 Elsevier Inc. All rights reserved.

  17. Genetics Home Reference: osteoglophonic dysplasia

    Science.gov (United States)

    ... 1 link) Genetic Testing Registry: Osteoglophonic dysplasia Other Diagnosis and Management Resources (1 link) Seattle Children's Hospital: Dwarfism and Bone Dysplasias General Information from MedlinePlus (5 ...

  18. Operationalizing Semantic Medline for meeting the information needs at point of care

    Science.gov (United States)

    Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

    2015-01-01

    Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible. PMID:26306259

  19. An IR-Based Approach Utilizing Query Expansion for Plagiarism Detection in MEDLINE.

    Science.gov (United States)

    Nawab, Rao Muhammad Adeel; Stevenson, Mark; Clough, Paul

    2017-01-01

    The identification of duplicated and plagiarized passages of text has become an increasingly active area of research. In this paper, we investigate methods for plagiarism detection that aim to identify potential sources of plagiarism from MEDLINE, particularly when the original text has been modified through the replacement of words or phrases. A scalable approach based on Information Retrieval is used to perform candidate document selection-the identification of a subset of potential source documents given a suspicious text-from MEDLINE. Query expansion is performed using the ULMS Metathesaurus to deal with situations in which original documents are obfuscated. Various approaches to Word Sense Disambiguation are investigated to deal with cases where there are multiple Concept Unique Identifiers (CUIs) for a given term. Results using the proposed IR-based approach outperform a state-of-the-art baseline based on Kullback-Leibler Distance.

  20. Operationalizing Semantic Medline for meeting the information needs at point of care.

    Science.gov (United States)

    Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

    2015-01-01

    Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible.

  1. A short guide to peer-reviewed, MEDLINE-indexed complementary and alternative medicine journals.

    Science.gov (United States)

    Morgan, Sherry; Littman, Lynn; Palmer, Christina; Singh, Gurneet; LaRiccia, Patrick J

    2012-01-01

    Complementary and alternative medicine (CAM) comprises a multitude of disciplines, for example, acupuncture, ayurvedic medicine, biofeedback, herbal medicine, and homeopathic medicine. While research on CAM interventions has increased and the CAM literature has proliferated since the mid-1990s, a number of our colleagues have expressed difficulties in deciding where to publish CAM articles. In response, we created a short guide to peer-reviewed MEDLINE-indexed journals that publish CAM articles. We examined numerous English-language sources to identify titles that met our criteria, whether specific to or overlapping CAM. A few of the resources in which we found the journal titles that we included are Alternative Medicine Foundation, American Holistic Nurses Association, CINAHL/Nursing Database, Journal Citation Reports database, MEDLINE, PubMed, and Research Council for Complementary Medicine. We organized the 69 selected titles for easy use by creating 2 user-friendly tables, one listing titles in alphabetical order and one listing them in topical categories. A few examples of the topical categories are Acupuncture, CAM (general), Chinese Medicine, Herbal/Plant/Phytotherapy, Neuroscience/Psychology, Nursing/Clinical Care. Our study is the first to list general CAM journals, specialty CAM journals, and overlapping mainstream journals that are peer reviewed, in English, and indexed in MEDLINE. Our goal was to assist both authors seeking publication and mainstream journal editors who receive an overabundance of publishable articles but must recommend that authors seek publication elsewhere due to space and priority issues. Publishing in journals indexed by and included in MEDLINE (or PubMed) ensures that citations to articles will be found easily. Copyright © 2012 Lippincott Williams & Wilkins.

  2. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  3. Standard Reference Tables -

    Data.gov (United States)

    Department of Transportation — The Standard Reference Tables (SRT) provide consistent reference data for the various applications that support Flight Standards Service (AFS) business processes and...

  4. Evaluation of Term Ranking Algorithms for Pseudo-Relevance Feedback in MEDLINE Retrieval.

    Science.gov (United States)

    Yoo, Sooyoung; Choi, Jinwook

    2011-06-01

    The purpose of this study was to investigate the effects of query expansion algorithms for MEDLINE retrieval within a pseudo-relevance feedback framework. A number of query expansion algorithms were tested using various term ranking formulas, focusing on query expansion based on pseudo-relevance feedback. The OHSUMED test collection, which is a subset of the MEDLINE database, was used as a test corpus. Various ranking algorithms were tested in combination with different term re-weighting algorithms. Our comprehensive evaluation showed that the local context analysis ranking algorithm, when used in combination with one of the reweighting algorithms - Rocchio, the probabilistic model, and our variants - significantly outperformed other algorithm combinations by up to 12% (paired t-test; p algorithm pairs, at least in the context of the OHSUMED corpus. Comparative experiments on term ranking algorithms were performed in the context of a subset of MEDLINE documents. With medical documents, local context analysis, which uses co-occurrence with all query terms, significantly outperformed various term ranking methods based on both frequency and distribution analyses. Furthermore, the results of the experiments demonstrated that the term rank-based re-weighting method contributed to a remarkable improvement in mean average precision.

  5. Knowledge production status of Iranian researchers in the gastric cancer area: based on the medline database.

    Science.gov (United States)

    Ghojazadeh, Morteza; Naghavi-Behzad, Mohammad; Nasrolah-Zadeh, Raheleh; Bayat-Khajeh, Parvaneh; Piri, Reza; Mirnia, Keyvan; Azami-Aghdash, Saber

    2014-01-01

    Scientometrics is a useful method for management of financial and human resources and has been applied many times in medical sciences during recent years. The aim of this study was to investigate the status of science production by Iranian scientists in the gastric cancer field based on the Medline database. In this descriptive-cross sectional study Iranian science production concerning gastric cancer during 2000-2011 was investigated based on Medline. After two stages of searching, 121 articles were found, then we reviewed publication date, authors names, journal title, impact factor (IF), and cooperation coefficient between researchers. SPSS.19 was used for statistical analysis. There was a significant increase in published articles about gastric cancer by Iranian researchers in Medline database during 2006-2011. Mean cooperation coefficient between researchers was 6.14±3.29 person per article. Articles of this field were published in 19 countries and 56 journals. Those basex in Thailand, England, and America had the most published Iranian articles. Tehran University of Medical Sciences and Mohammadreza Zali had the most outstanding role in publishing scientific articles. According to results of this study, improving cooperation of researchers in conducting research and scientometric studies about other fields may have an important role in increasing both quality and quantity of published studies.

  6. Psoriasis Doesn't Slow Down Texan Brian LaFoy | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... willing to do. I'm one of the lucky ones." Find Out More National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) MedlinePlus-Psoriasis Clinical Trials Search Psoriasis Spring 2017 Issue: Volume 12 Number 1 Page 22 MedlinePlus Subscribe Magazine Information Contact ...

  7. LPTAU, Quasi Random Sequence Generator

    International Nuclear Information System (INIS)

    Sobol, Ilya M.

    1993-01-01

    1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

  8. Genetics Home Reference: Rett syndrome

    Science.gov (United States)

    ... Genetic Testing Registry: Rett syndrome Other Diagnosis and Management Resources (4 links) Boston Children's Hospital GeneReview: MECP2-Related Disorders MedlinePlus Encyclopedia: Rett Syndrome RettSyndrome.org: Rett Syndrome Clinics General Information from MedlinePlus (5 links) Diagnostic Tests ...

  9. Do language fluency and other socioeconomic factors influence the use of PubMed and MedlinePlus?

    Science.gov (United States)

    Sheets, L; Gavino, A; Callaghan, F; Fontelo, P

    2013-01-01

    Increased usage of MedlinePlus by Spanish-speakers was observed after introduction of MedlinePlus in Spanish. This probably reflects increased usage of MEDLINE and PubMed by those with greater fluency in the language in which it is presented; but this has never been demonstrated in English speakers. Evidence that lack of English fluency deters international healthcare personnel from using PubMed could support the use of multi-language search tools like Babel-MeSH. This study aims to measure the effects of language fluency and other socioeconomic factors on PubMed MEDLINE and MedlinePlus access by international users. We retrospectively reviewed server pageviews of PubMed and MedlinePlus from various periods of time, and analyzed them against country statistics on language fluency, GDP, literacy rate, Internet usage, medical schools, and physicians per capita, to determine whether they were associated. We found fluency in English to be positively associated with pageviews of PubMed and MedlinePlus in countries with high literacy rates. Spanish was generally found to be positively associated with pageviews of MedlinePlus en Español. The other parameters also showed varying degrees of association with pageviews. After adjusting for the other factors investigated in this study, language fluency was a consistently significant predictor of the use of PubMed, MedlinePlus English and MedlinePlus en Español. This study may support the need for multi-language search tools and may increase access of health information resources from non-English speaking countries.

  10. PVWatts Version 1 Technical Reference

    Energy Technology Data Exchange (ETDEWEB)

    Dobos, A. P.

    2013-10-01

    The NREL PVWatts(TM) calculator is a web application developed by the National Renewable Energy Laboratory (NREL) that estimates the electricity production of a grid-connected photovoltaic system based on a few simple inputs. PVWatts combines a number of sub-models to predict overall system performance, and makes several hidden assumptions about performance parameters. This technical reference details the individual sub-models, documents assumptions and hidden parameters, and explains the sequence of calculations that yield the final system performance estimation.

  11. 2002 reference document; Document de reference 2002

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-07-01

    This 2002 reference document of the group Areva, provides information on the society. Organized in seven chapters, it presents the persons responsible for the reference document and for auditing the financial statements, information pertaining to the transaction, general information on the company and share capital, information on company operation, changes and future prospects, assets, financial position, financial performance, information on company management and executive board and supervisory board, recent developments and future prospects. (A.L.B.)

  12. Collaborative reference management system

    CSIR Research Space (South Africa)

    Le Roux, WH

    2009-05-01

    Full Text Available Developers free Yes, GPL License All BibTeX, BiblX, MODS XML, RIS BibTeX, Compac, ISI, BiblX, RIS, RefWorks RefWorks US$100 per year No All, web- based BibTeX and RIS BibTeX (partially), CSA, BiblX, ISI, Medline, Ovid, PubMed, RIS, Sci... fully to ensure your views are not misconstrued • Consider the five “Cs” of effective communication – Clarity, Completeness, Conciseness, Correctness and concreteness. According to Spence et al’s (2005) research, communication consists out of fifty...

  13. VBE reference framework

    NARCIS (Netherlands)

    Afsarmanesh, H.; Camarinha-Matos, L.M.; Ermilova, E.; Camarinha-Matos, L.M.; Afsarmanesh, H.; Ollus, M.

    2008-01-01

    Defining a comprehensive and generic "reference framework" for Virtual organizations Breeding Environments (VBEs), addressing all their features and characteristics, is challenging. While the definition and modeling of VBEs has become more formalized during the last five years, "reference models"

  14. CMS Statistics Reference Booklet

    Data.gov (United States)

    U.S. Department of Health & Human Services — The annual CMS Statistics reference booklet provides a quick reference for summary information about health expenditures and the Medicare and Medicaid health...

  15. Changing quantum reference frames

    OpenAIRE

    Palmer, Matthew C.; Girelli, Florian; Bartlett, Stephen D.

    2013-01-01

    We consider the process of changing reference frames in the case where the reference frames are quantum systems. We find that, as part of this process, decoherence is necessarily induced on any quantum system described relative to these frames. We explore this process with examples involving reference frames for phase and orientation. Quantifying the effect of changing quantum reference frames serves as a first step in developing a relativity principle for theories in which all objects includ...

  16. Is Genetic Testing Right for You? | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... Testing CLINSEQ®: A Large-Scale Medical Sequencing Clinical Research Pilot Study Prenatal Screening - Prenatal testing information, including ultrasound, amniocentesis, and chorionic villus sampling ( ...

  17. Welcome from Library Director Donald A.B. Lindberg, M.D. | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... turn Javascript on. Welcome to the NIH MedlinePlus Magazine. Past Issues / Spring 2013 Table of Contents Donald ... about their efforts to cure disease. Lastly, the magazine's lively graphics, fun quizzes and practical tips have ...

  18. Milestones in Medical Research, The Human Genome and ClinicalTrials.gov | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... the information in this issue of NIH MedlinePlus magazine helps you and your loved ones stay healthier! ... From You! We want your feedback on the magazine, ideas for future issues, as well as questions ...

  19. National Library of Medicine Celebrates 30 Years of Progress and Charts the Future | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... described the genesis of the National Center for Biotechnology Information (NCBI); the Visible Human Project (a digital ... expand the publication and distribution of NIH MedlinePlus magazine, thousands and thousands more people will gain valuable, ...

  20. A Review of Published Articles in the Field of Biomedical Nanotechnology in Medline Database during 2000-2010

    OpenAIRE

    Peyman Sheikhzade

    2015-01-01

    Background and objectives : Nanotechnology is a new technology which is increasingly used over the past decade. Due to its great significance, governments are tending to invest greatly on the research and development on nanotechnology in various sectors and aspects. The purpose of this study was to determine the status of biomedical nanotechnology publications over the past ten years (2010-2000) in Medline/ PubMed. Material and Methods : This was a descriptive study. The Medline database wa...

  1. Genetics Home Reference: atopic dermatitis

    Science.gov (United States)

    ... adults, the rashes typically occur on the wrists, ankles, and eyelids in addition to the bend of ... Information from MedlinePlus (5 links) Diagnostic Tests Drug Therapy Genetic ... Manual Consumer Version The University of Chicago Medicine World ...

  2. Genetics Home Reference: spondylothoracic dysostosis

    Science.gov (United States)

    ... normal-length arms and legs, called short-trunk dwarfism. The spine and rib abnormalities, which are present ... Additional Information & Resources MedlinePlus (2 links) Health Topic: Dwarfism Health Topic: Spine Injuries and Disorders Genetic and ...

  3. IAEA biological reference materials

    International Nuclear Information System (INIS)

    Parr, R.M.; Schelenz, R.; Ballestra, S.

    1988-01-01

    The Analytical Quality Control Services programme of the IAEA encompasses a wide variety of intercomparisons and reference materials. This paper reviews only those aspects of the subject having to do with biological reference materials. The 1988 programme foresees 13 new intercomparison exercises, one for major, minor and trace elements, five for radionuclides, and seven for stable isotopes. Twenty-two natural matrix biological reference materials are available: twelve for major, minor and trace elements, six for radionuclides, and four for chlorinated hydrocarbons. Seven new intercomparisons and reference materials are in preparation or under active consideration. Guidelines on the correct use of reference materials are being prepared for publication in 1989 in consultation with other major international producers and users of biological reference materials. The IAEA database on available reference materials is being updated and expanded in scope, and a new publication is planned for 1989. (orig.)

  4. Temporal Reference, Attentional Modulation, and Crossmodal Assimilation

    Directory of Open Access Journals (Sweden)

    Yingqi Wan

    2018-06-01

    Full Text Available Crossmodal assimilation effect refers to the prominent phenomenon by which ensemble mean extracted from a sequence of task-irrelevant distractor events, such as auditory intervals, assimilates/biases the perception (such as visual interval of the subsequent task-relevant target events in another sensory modality. In current experiments, using visual Ternus display, we examined the roles of temporal reference, materialized as the time information accumulated before the onset of target event, as well as the attentional modulation in crossmodal temporal interaction. Specifically, we examined how the global time interval, the mean auditory inter-intervals and the last interval in the auditory sequence assimilate and bias the subsequent percept of visual Ternus motion (element motion vs. group motion. We demonstrated that both the ensemble (geometric mean and the last interval in the auditory sequence contribute to bias the percept of visual motion. Longer mean (or last interval elicited more reports of group motion, whereas the shorter mean (or last auditory intervals gave rise to more dominant percept of element motion. Importantly, observers have shown dynamic adaptation to the temporal reference of crossmodal assimilation: when the target visual Ternus stimuli were separated by a long gap interval after the preceding sound sequence, the assimilation effect by ensemble mean was reduced. Our findings suggested that crossmodal assimilation relies on a suitable temporal reference on adaptation level, and revealed a general temporal perceptual grouping principle underlying complex audio-visual interactions in everyday dynamic situations.

  5. From the lab - Eyes May be ‘Windows to the Brain’ in Stroke Patients | NIH MedlinePlus the Magazine

    Science.gov (United States)

    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [3.1 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  6. Integrative mining of traditional Chinese medicine literature and MEDLINE for functional gene networks.

    Science.gov (United States)

    Zhou, Xuezhong; Liu, Baoyan; Wu, Zhaohui; Feng, Yi

    2007-10-01

    The amount of biomedical data in different disciplines is growing at an exponential rate. Integrating these significant knowledge sources to generate novel hypotheses for systems biology research is difficult. Traditional Chinese medicine (TCM) is a completely different discipline, and is a complementary knowledge system to modern biomedical science. This paper uses a significant TCM bibliographic literature database in China, together with MEDLINE, to help discover novel gene functional knowledge. We present an integrative mining approach to uncover the functional gene relationships from MEDLINE and TCM bibliographic literature. This paper introduces TCM literature (about 50,000 records) as one knowledge source for constructing literature-based gene networks. We use the TCM diagnosis, TCM syndrome, to automatically congregate the related genes. The syndrome-gene relationships are discovered based on the syndrome-disease relationships extracted from TCM literature and the disease-gene relationships in MEDLINE. Based on the bubble-bootstrapping and relation weight computing methods, we have developed a prototype system called MeDisco/3S, which has name entity and relation extraction, and online analytical processing (OLAP) capabilities, to perform the integrative mining process. We have got about 200,000 syndrome-gene relations, which could help generate syndrome-based gene networks, and help analyze the functional knowledge of genes from syndrome perspective. We take the gene network of Kidney-Yang Deficiency syndrome (KYD syndrome) and the functional analysis of some genes, such as CRH (corticotropin releasing hormone), PTH (parathyroid hormone), PRL (prolactin), BRCA1 (breast cancer 1, early onset) and BRCA2 (breast cancer 2, early onset), to demonstrate the preliminary results. The underlying hypothesis is that the related genes of the same syndrome will have some biological functional relationships, and will constitute a functional network. This paper presents

  7. Genetics Home Reference: hereditary diffuse gastric cancer

    Science.gov (United States)

    ... Health Conditions Hereditary diffuse gastric cancer Hereditary diffuse gastric cancer Printable PDF Open All Close All Enable Javascript ... Diffuse Gastric Cancer MedlinePlus Encyclopedia: Gastric Cancer National Cancer ... Option Overview General Information from MedlinePlus ( ...

  8. Genetics Home Reference: Manitoba oculotrichoanal syndrome

    Science.gov (United States)

    ... opening in the wall of the abdomen (an omphalocele ) that allows the abdominal organs to protrude through ... 2 links) GeneReview: Manitoba Oculotrichoanal Syndrome MedlinePlus Encyclopedia: Omphalocele Repair General Information from MedlinePlus (5 links) Diagnostic ...

  9. Genetics Home Reference: Donnai-Barrow syndrome

    Science.gov (United States)

    ... opening in the wall of the abdomen (an omphalocele ) that allows the abdominal organs to protrude through ... Hernia MedlinePlus Encyclopedia: Hearing Loss - Infants MedlinePlus Encyclopedia: Omphalocele Nemours Foundation: Hearing Evaluation in Children General Information ...

  10. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  11. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  12. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  13. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  14. Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts

    Directory of Open Access Journals (Sweden)

    Spackman K

    2005-04-01

    Full Text Available Abstract Background Text-mining can assist biomedical researchers in reducing information overload by extracting useful knowledge from large collections of text. We developed a novel text-mining method based on analyzing the network structure created by symbol co-occurrences as a way to extend the capabilities of knowledge extraction. The method was applied to the task of automatic gene and protein name synonym extraction. Results Performance was measured on a test set consisting of about 50,000 abstracts from one year of MEDLINE. Synonyms retrieved from curated genomics databases were used as a gold standard. The system obtained a maximum F-score of 22.21% (23.18% precision and 21.36% recall, with high efficiency in the use of seed pairs. Conclusion The method performs comparably with other studied methods, does not rely on sophisticated named-entity recognition, and requires little initial seed knowledge.

  15. Strategies to optimize MEDLINE and EMBASE search strategies for anesthesiology systematic reviews. An experimental study.

    Science.gov (United States)

    Volpato, Enilze de Souza Nogueira; Betini, Marluci; Puga, Maria Eduarda; Agarwal, Arnav; Cataneo, Antônio José Maria; Oliveira, Luciane Dias de; Bazan, Rodrigo; Braz, Leandro Gobbo; Pereira, José Eduardo Guimarães; El Dib, Regina

    2018-01-15

    A high-quality electronic search is essential for ensuring accuracy and comprehensiveness among the records retrieved when conducting systematic reviews. Therefore, we aimed to identify the most efficient method for searching in both MEDLINE (through PubMed) and EMBASE, covering search terms with variant spellings, direct and indirect orders, and associations with MeSH and EMTREE terms (or lack thereof). Experimental study. UNESP, Brazil. We selected and analyzed 37 search strategies that had specifically been developed for the field of anesthesiology. These search strategies were adapted in order to cover all potentially relevant search terms, with regard to variant spellings and direct and indirect orders, in the most efficient manner. When the strategies included variant spellings and direct and indirect orders, these adapted versions of the search strategies selected retrieved the same number of search results in MEDLINE (mean of 61.3%) and a higher number in EMBASE (mean of 63.9%) in the sample analyzed. The numbers of results retrieved through the searches analyzed here were not identical with and without associated use of MeSH and EMTREE terms. However, association of these terms from both controlled vocabularies retrieved a larger number of records than did the use of either one of them. In view of these results, we recommend that the search terms used should include both preferred and non-preferred terms (i.e. variant spellings and direct/indirect order of the same term) and associated MeSH and EMTREE terms, in order to develop highly-sensitive search strategies for systematic reviews.

  16. Testing search strategies for systematic reviews in the Medline literature database through PubMed.

    Science.gov (United States)

    Volpato, Enilze S N; Betini, Marluci; El Dib, Regina

    2014-04-01

    A high-quality electronic search is essential in ensuring accuracy and completeness in retrieved records for the conducting of a systematic review. We analysed the available sample of search strategies to identify the best method for searching in Medline through PubMed, considering the use or not of parenthesis, double quotation marks, truncation and use of a simple search or search history. In our cross-sectional study of search strategies, we selected and analysed the available searches performed during evidence-based medicine classes and in systematic reviews conducted in the Botucatu Medical School, UNESP, Brazil. We analysed 120 search strategies. With regard to the use of phrase searches with parenthesis, there was no difference between the results with and without parenthesis and simple searches or search history tools in 100% of the sample analysed (P = 1.0). The number of results retrieved by the searches analysed was smaller using double quotations marks and using truncation compared with the standard strategy (P = 0.04 and P = 0.08, respectively). There is no need to use phrase-searching parenthesis to retrieve studies; however, we recommend the use of double quotation marks when an investigator attempts to retrieve articles in which a term appears to be exactly the same as what was proposed in the search form. Furthermore, we do not recommend the use of truncation in search strategies in the Medline via PubMed. Although the results of simple searches or search history tools were the same, we recommend using the latter.

  17. Ontology-Driven Search and Triage: Design of a Web-Based Visual Interface for MEDLINE.

    Science.gov (United States)

    Demelo, Jonathan; Parsons, Paul; Sedig, Kamran

    2017-02-02

    Diverse users need to search health and medical literature to satisfy open-ended goals such as making evidence-based decisions and updating their knowledge. However, doing so is challenging due to at least two major difficulties: (1) articulating information needs using accurate vocabulary and (2) dealing with large document sets returned from searches. Common search interfaces such as PubMed do not provide adequate support for exploratory search tasks. Our objective was to improve support for exploratory search tasks by combining two strategies in the design of an interactive visual interface by (1) using a formal ontology to help users build domain-specific knowledge and vocabulary and (2) providing multi-stage triaging support to help mitigate the information overload problem. We developed a Web-based tool, Ontology-Driven Visual Search and Triage Interface for MEDLINE (OVERT-MED), to test our design ideas. We implemented a custom searchable index of MEDLINE, which comprises approximately 25 million document citations. We chose a popular biomedical ontology, the Human Phenotype Ontology (HPO), to test our solution to the vocabulary problem. We implemented multistage triaging support in OVERT-MED, with the aid of interactive visualization techniques, to help users deal with large document sets returned from searches. Formative evaluation suggests that the design features in OVERT-MED are helpful in addressing the two major difficulties described above. Using a formal ontology seems to help users articulate their information needs with more accurate vocabulary. In addition, multistage triaging combined with interactive visualizations shows promise in mitigating the information overload problem. Our strategies appear to be valuable in addressing the two major problems in exploratory search. Although we tested OVERT-MED with a particular ontology and document collection, we anticipate that our strategies can be transferred successfully to other contexts.

  18. The Douglas-fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae

    Science.gov (United States)

    David B. Neale; Patrick E. McGuire; Nicholas C. Wheeler; Kristian A. Stevens; Marc W. Crepeau; Charis Cardeno; Aleksey V. Zimin; Daniela Puiu; Geo M. Pertea; U. Uzay Sezen; Claudio Casola; Tomasz E. Koralewski; Robin Paul; Daniel Gonzalez-Ibeas; Sumaira Zaman; Richard Cronn; Mark Yandell; Carson Holt; Charles H. Langley; James A. Yorke; Steven L. Salzberg; Jill L. Wegrzyn

    2017-01-01

    A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50...

  19. Indoor air: Reference bibliography

    International Nuclear Information System (INIS)

    Campbell, D.; Staves, D.; McDonald, S.

    1989-07-01

    The U. S. Environmental Protection Agency initially established the indoor air Reference Bibliography in 1987 as an appendix to the Indoor Air Quality Implementation Plan. The document was submitted to Congress as required under Title IV--Radon Gas and Indoor Air Quality Research of the Superfund Amendments and Reauthorization Act of 1986. The Reference Bibliography is an extensive bibliography of reference materials on indoor air pollution. The Bibliography contains over 4500 citations and continues to increase as new articles appear

  20. Genetics Home Reference: Beckwith-Wiedemann syndrome

    Science.gov (United States)

    ... opening in the wall of the abdomen (an omphalocele ) that allows the abdominal organs to protrude through ... Beckwith-Wiedemann syndrome MedlinePlus Encyclopedia: Macroglossia MedlinePlus Encyclopedia: Omphalocele General Information from MedlinePlus (5 links) Diagnostic Tests ...

  1. Android quick APIs reference

    CERN Document Server

    Cinar, Onur

    2015-01-01

    The Android Quick APIs Reference is a condensed code and APIs reference for the new Google Android 5.0 SDK. It presents the essential Android APIs in a well-organized format that can be used as a handy reference. You won't find any technical jargon, bloated samples, drawn out history lessons, or witty stories in this book. What you will find is a software development kit and APIs reference that is concise, to the point and highly accessible. The book is packed with useful information and is a must-have for any mobile or Android app developer or programmer. In the Android Quick APIs Refe

  2. Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

    Science.gov (United States)

    Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

    2012-01-01

    The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

  3. Marketing Reference Services.

    Science.gov (United States)

    Norman, O. Gene

    1995-01-01

    Relates the marketing concept to library reference services. Highlights include a review of the literature and an overview of marketing, including research, the marketing mix, strategic plan, marketing plan, and marketing audit. Marketing principles are applied to reference services through the marketing mix elements of product, price, place, and…

  4. Reference class forecasting

    DEFF Research Database (Denmark)

    Flyvbjerg, Bent

    optimisme og misinformation. RCF bygger på teorier, som vandt Daniel Kahneman Nobelprisen i økonomi i 2002. RCF estimerer budgettet for et givet projekt på grundlag af de faktiske udfald for budgetterne i en reference-klasse af projekter. RCF udføres i tre trin: 1. Identifikation af en relevant reference...

  5. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

  6. Uranium reference materials

    International Nuclear Information System (INIS)

    Donivan, S.; Chessmore, R.

    1987-07-01

    The Technical Measurements Center has prepared uranium mill tailings reference materials for use by remedial action contractors and cognizant federal and state agencies. Four materials were prepared with varying concentrations of radionuclides, using three tailings materials and a river-bottom soil diluent. All materials were ground, dried, and blended thoroughly to ensure homogeneity. The analyses on which the recommended values for nuclides in the reference materials are based were performed, using independent methods, by the UNC Geotech (UNC) Chemistry Laboratory, Grand Junction, Colorado, and by C.W. Sill (Sill), Idaho National Engineering Laboratory, Idaho Falls, Idaho. Several statistical tests were performed on the analytical data to characterize the reference materials. Results of these tests reveal that the four reference materials are homogeneous and that no large systematic bias exists between the analytical methods used by Sill and those used by TMC. The average values for radionuclides of the two data sets, representing an unbiased estimate, were used as the recommended values for concentrations of nuclides in the reference materials. The recommended concentrations of radionuclides in the four reference materials are provided. Use of these reference materials will aid in providing uniform standardization among measurements made by remedial action contractors. 11 refs., 9 tabs

  7. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  8. STL pocket reference

    CERN Document Server

    Lischner, Ray

    2003-01-01

    The STL Pocket Reference describes the functions, classes, and templates in that part of the C++ standard library often referred to as the Standard Template Library (STL). The STL encompasses containers, iterators, algorithms, and function objects, which collectively represent one of the most important and widely used subsets of standard library functionality. The C++ standard library, even the subset known as the STL, is vast. It's next to impossible to work with the STL without some sort of reference at your side to remind you of template parameters, function invocations, return types--ind

  9. Handbook of reference electrodes

    CERN Document Server

    Inzelt, György; Scholz, Fritz

    2013-01-01

    Reference Electrodes are a crucial part of any electrochemical system, yet an up-to-date and comprehensive handbook is long overdue. Here, an experienced team of electrochemists provides an in-depth source of information and data for the proper choice and construction of reference electrodes. This includes all kinds of applications such as aqueous and non-aqueous solutions, ionic liquids, glass melts, solid electrolyte systems, and membrane electrodes. Advanced technologies such as miniaturized, conducting-polymer-based, screen-printed or disposable reference electrodes are also covered. Essen

  10. Regular Expression Pocket Reference

    CERN Document Server

    Stubblebine, Tony

    2007-01-01

    This handy little book offers programmers a complete overview of the syntax and semantics of regular expressions that are at the heart of every text-processing application. Ideal as a quick reference, Regular Expression Pocket Reference covers the regular expression APIs for Perl 5.8, Ruby (including some upcoming 1.9 features), Java, PHP, .NET and C#, Python, vi, JavaScript, and the PCRE regular expression libraries. This concise and easy-to-use reference puts a very powerful tool for manipulating text and data right at your fingertips. Composed of a mixture of symbols and text, regular exp

  11. Neptunium: a bibliographic reference

    International Nuclear Information System (INIS)

    Mosley, R.E.

    1979-06-01

    A comprehensive bibliograhy of the literature on the element neptunium published prior to January 1976 is presented. A short abstract is given for each listed reference, with a few exceptions. The references are divided into sections categorized as General, Man-Made Sources (Reactors), Man-Made Sources (Fuel Reprocessing), Chemistry (Solubility), Chemistry (Compounds), Chemistry (Isotopes), Analyses (Instrumental), Analyses (Chemical), Chemical (Animal), Biological (Effects), Biological (Animal-Metabolism-Retention), Biological (Air Movement), Biological (Human Inhalation), Measurement, and Dosimetry. The bibliography contains author and keyword indexes and was compiled to serve as a quick reference source for neptunium-related work. 184 citations

  12. CSS Pocket Reference

    CERN Document Server

    Meyer, Eric

    2011-01-01

    When you're working with CSS and need a quick answer, CSS Pocket Reference delivers. This handy, concise book provides all of the essential information you need to implement CSS on the fly. Ideal for intermediate to advanced web designers and developers, the 4th edition is revised and updated for CSS3, the latest version of the Cascading Style Sheet specification. Along with a complete alphabetical reference to CSS3 selectors and properties, you'll also find a short introduction to the key concepts of CSS. Based on Cascading Style Sheets: The Definitive Guide, this reference is an easy-to-us

  13. Biomedical Engineering Desk Reference

    CERN Document Server

    Ratner, Buddy D; Schoen, Frederick J; Lemons, Jack E; Dyro, Joseph; Martinsen, Orjan G; Kyle, Richard; Preim, Bernhard; Bartz, Dirk; Grimnes, Sverre; Vallero, Daniel; Semmlow, John; Murray, W Bosseau; Perez, Reinaldo; Bankman, Isaac; Dunn, Stanley; Ikada, Yoshito; Moghe, Prabhas V; Constantinides, Alkis

    2009-01-01

    A one-stop Desk Reference, for Biomedical Engineers involved in the ever expanding and very fast moving area; this is a book that will not gather dust on the shelf. It brings together the essential professional reference content from leading international contributors in the biomedical engineering field. Material covers a broad range of topics including: Biomechanics and Biomaterials; Tissue Engineering; and Biosignal Processing* A hard-working desk reference providing all the essential material needed by biomedical and clinical engineers on a day-to-day basis * Fundamentals, key techniques,

  14. LINQ Pocket Reference

    CERN Document Server

    Albahari, Joseph

    2008-01-01

    Ready to take advantage of LINQ with C# 3.0? This guide has the detail you need to grasp Microsoft's new querying technology, and concise explanations to help you learn it quickly. And once you begin to apply LINQ, the book serves as an on-the-job reference when you need immediate reminders. All the examples in the LINQ Pocket Reference are preloaded into LINQPad, the highly praised utility that lets you work with LINQ interactively. Created by the authors and free to download, LINQPad will not only help you learn LINQ, it will have you thinking in LINQ. This reference explains: LINQ's ke

  15. R quick syntax reference

    CERN Document Server

    Tollefson, Margot

    2014-01-01

    The R Quick Syntax Reference is a handy reference book detailing the intricacies of the R language. Not only is R a free, open-source tool, R is powerful, flexible, and has state of the art statistical techniques available. With the many details which must be correct when using any language, however, the R Quick Syntax Reference makes using R easier.Starting with the basic structure of R, the book takes you on a journey through the terminology used in R and the syntax required to make R work. You will find looking up the correct form for an expression quick and easy. With a copy of the R Quick

  16. Optimal primitive reference frames

    International Nuclear Information System (INIS)

    Jennings, David

    2011-01-01

    We consider the smallest possible directional reference frames allowed and determine the best one can ever do in preserving quantum information in various scenarios. We find that for the preservation of a single spin state, two orthogonal spins are optimal primitive reference frames; and in a product state, they do approximately 22% as well as an infinite-sized classical frame. By adding a small amount of entanglement to the reference frame, this can be raised to 2(2/3) 5 =26%. Under the different criterion of entanglement preservation, a very similar optimal reference frame is found; however, this time it is for spins aligned at an optimal angle of 87 deg. In this case 24% of the negativity is preserved. The classical limit is considered numerically, and indicates under the criterion of entanglement preservation, that 90 deg. is selected out nonmonotonically, with a peak optimal angle of 96.5 deg. for L=3 spins.

  17. Reference Climatological Stations

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Reference Climatological Stations (RCS) network represents the first effort by NOAA to create and maintain a nationwide network of stations located only in areas...

  18. Toxicity Reference Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Toxicity Reference Database (ToxRefDB) contains approximately 30 years and $2 billion worth of animal studies. ToxRefDB allows scientists and the interested...

  19. Python essential reference

    CERN Document Server

    Beazley, David M

    2009-01-01

    Python Essential Reference is the definitive reference guide to the Python programming language — the one authoritative handbook that reliably untangles and explains both the core Python language and the most essential parts of the Python library. Designed for the professional programmer, the book is concise, to the point, and highly accessible. It also includes detailed information on the Python library and many advanced subjects that is not available in either the official Python documentation or any other single reference source. Thoroughly updated to reflect the significant new programming language features and library modules that have been introduced in Python 2.6 and Python 3, the fourth edition of Python Essential Reference is the definitive guide for programmers who need to modernize existing Python code or who are planning an eventual migration to Python 3. Programmers starting a new Python project will find detailed coverage of contemporary Python programming idioms.

  20. Collaborative networks: Reference modeling

    NARCIS (Netherlands)

    Camarinha-Matos, L.M.; Afsarmanesh, H.

    2008-01-01

    Collaborative Networks: Reference Modeling works to establish a theoretical foundation for Collaborative Networks. Particular emphasis is put on modeling multiple facets of collaborative networks and establishing a comprehensive modeling framework that captures and structures diverse perspectives of

  1. Ozone Standard Reference Photometer

    Data.gov (United States)

    Federal Laboratory Consortium — The Standard Reference Photometer (SRP) Program began in the early 1980s as collaboration between NIST and the U.S. Environmental Protection Agency (EPA) to design,...

  2. A structural SVM approach for reference parsing.

    Science.gov (United States)

    Zhang, Xiaoli; Zou, Jie; Le, Daniel X; Thoma, George R

    2011-06-09

    Automated extraction of bibliographic data, such as article titles, author names, abstracts, and references is essential to the affordable creation of large citation databases. References, typically appearing at the end of journal articles, can also provide valuable information for extracting other bibliographic data. Therefore, parsing individual reference to extract author, title, journal, year, etc. is sometimes a necessary preprocessing step in building citation-indexing systems. The regular structure in references enables us to consider reference parsing a sequence learning problem and to study structural Support Vector Machine (structural SVM), a newly developed structured learning algorithm on parsing references. In this study, we implemented structural SVM and used two types of contextual features to compare structural SVM with conventional SVM. Both methods achieve above 98% token classification accuracy and above 95% overall chunk-level accuracy for reference parsing. We also compared SVM and structural SVM to Conditional Random Field (CRF). The experimental results show that structural SVM and CRF achieve similar accuracies at token- and chunk-levels. When only basic observation features are used for each token, structural SVM achieves higher performance compared to SVM since it utilizes the contextual label features. However, when the contextual observation features from neighboring tokens are combined, SVM performance improves greatly, and is close to that of structural SVM after adding the second order contextual observation features. The comparison of these two methods with CRF using the same set of binary features show that both structural SVM and CRF perform better than SVM, indicating their stronger sequence learning ability in reference parsing.

  3. Enterprise Reference Library

    Science.gov (United States)

    Bickham, Grandin; Saile, Lynn; Havelka, Jacque; Fitts, Mary

    2011-01-01

    Introduction: Johnson Space Center (JSC) offers two extensive libraries that contain journals, research literature and electronic resources. Searching capabilities are available to those individuals residing onsite or through a librarian s search. Many individuals have rich collections of references, but no mechanisms to share reference libraries across researchers, projects, or directorates exist. Likewise, information regarding which references are provided to which individuals is not available, resulting in duplicate requests, redundant labor costs and associated copying fees. In addition, this tends to limit collaboration between colleagues and promotes the establishment of individual, unshared silos of information The Integrated Medical Model (IMM) team has utilized a centralized reference management tool during the development, test, and operational phases of this project. The Enterprise Reference Library project expands the capabilities developed for IMM to address the above issues and enhance collaboration across JSC. Method: After significant market analysis for a multi-user reference management tool, no available commercial tool was found to meet this need, so a software program was built around a commercial tool, Reference Manager 12 by The Thomson Corporation. A use case approach guided the requirements development phase. The premise of the design is that individuals use their own reference management software and export to SharePoint when their library is incorporated into the Enterprise Reference Library. This results in a searchable user-specific library application. An accompanying share folder will warehouse the electronic full-text articles, which allows the global user community to access full -text articles. Discussion: An enterprise reference library solution can provide a multidisciplinary collection of full text articles. This approach improves efficiency in obtaining and storing reference material while greatly reducing labor, purchasing and

  4. Comparability of reference values

    International Nuclear Information System (INIS)

    Rossbach, M.; Stoeppler, M.

    1993-01-01

    Harmonization of certified values in Reference Materials (RMs) can be carried out by applying nuclear analytical techniques to RMs of various matrix types and concentration levels. Although RMs generally should not be used as primary standards the cross evaluation of concentrations in RMs leads to better compatibility of reference values and thus to a greater agreement between analytical results from different laboratories using these RMs for instrument calibration and quality assurance. (orig.)

  5. Electronics engineer's reference book

    CERN Document Server

    Turner, L W

    1976-01-01

    Electronics Engineer's Reference Book, 4th Edition is a reference book for electronic engineers that reviews the knowledge and techniques in electronics engineering and covers topics ranging from basics to materials and components, devices, circuits, measurements, and applications. This edition is comprised of 27 chapters; the first of which presents general information on electronics engineering, including terminology, mathematical equations, mathematical signs and symbols, and Greek alphabet and symbols. Attention then turns to the history of electronics; electromagnetic and nuclear radiatio

  6. 2002 reference document

    International Nuclear Information System (INIS)

    2002-01-01

    This 2002 reference document of the group Areva, provides information on the society. Organized in seven chapters, it presents the persons responsible for the reference document and for auditing the financial statements, information pertaining to the transaction, general information on the company and share capital, information on company operation, changes and future prospects, assets, financial position, financial performance, information on company management and executive board and supervisory board, recent developments and future prospects. (A.L.B.)

  7. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  9. The contribution of next generation sequencing to epilepsy genetics

    DEFF Research Database (Denmark)

    Møller, Rikke S.; Dahl, Hans A.; Helbig, Ingo

    2015-01-01

    During the last decade, next generation sequencing technologies such as targeted gene panels, whole exome sequencing and whole genome sequencing have led to an explosion of gene identifications in monogenic epilepsies including both familial epilepsies and severe epilepsies, often referred to as ...

  10. Building the sequence map of the human pan-genome

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Li, Yingrui; Zheng, Hancheng

    2010-01-01

    analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain approximately 19-40 Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing...

  11. Describing, Instantiating and Evaluating a Reference Architecture : A Case Study

    NARCIS (Netherlands)

    Avgeriou, Paris

    2003-01-01

    The result of a domain maturing is the emergence of reference architectures that offer numerous advantages to software architects and other stakeholders. However there is no straightforward way to describe a reference architecture and in sequence to design instances for specific systems, while at

  12. Reference Japanese man

    International Nuclear Information System (INIS)

    Tanaka, Giichiro

    1985-01-01

    To make real and accurate dose assessment method so far, it is necessitated to provide ''Reference Japanese Man'' based on anotomical, physiological and biochemical data of Japanese people instead of the Reference Man presented in ICRP Publications 23 and 30. This review describes present status of researched for the purpose of establishing of Reference Japanese Man. The Reference Japanese Man is defined as a male or female adult who lives in Japan with a Japanese life-style and food custom. His stature and body weight, and the other data was decided as mean values of male or female people of Japan. As for food custom, Japanese people take significantly smaller amount of meat and milk products than Western people, while larger intake amount of cereals and marine products such as fish or seaweeds. Weight of organs is a principal factor for internal dose assessment and mean values for living Japanese adult has been investigated and the value employable for dose assessment for organs and tissues are shown. To employ these values of Reference Japanese Man, it should be taken into account of age. Metabolic parameters should also be considered. Iodine metabolism in Japanese is quite different from that of Western people. The above-mentioned data are now tentatively employing in modification of table of MIRD method and others. (Takagi, S.)

  13. [Limiting a Medline/PubMed query to the "best" articles using the JCR relative impact factor].

    Science.gov (United States)

    Avillach, P; Kerdelhué, G; Devos, P; Maisonneuve, H; Darmoni, S J

    2014-12-01

    Medline/PubMed is the most frequently used medical bibliographic research database. The aim of this study was to propose a new generic method to limit any Medline/PubMed query based on the relative impact factor and the A & B categories of the SIGAPS score. The entire PubMed corpus was used for the feasibility study, then ten frequent diseases in terms of PubMed indexing and the citations of four Nobel prize winners. The relative impact factor (RIF) was calculated by medical specialty defined in Journal Citation Reports. The two queries, which included all the journals in category A (or A OR B), were added to any Medline/PubMed query as a central point of the feasibility study. Limitation using the SIGAPS category A was larger than the when using the Core Clinical Journals (CCJ): 15.65% of PubMed corpus vs 8.64% for CCJ. The response time of this limit applied to the entire PubMed corpus was less than two seconds. For five diseases out of ten, limiting the citations with the RIF was more effective than with the CCJ. For the four Nobel prize winners, limiting the citations with the RIF was more effective than the CCJ. The feasibility study to apply a new filter based on the relative impact factor on any Medline/PubMed query was positive. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  14. Parapsychology and the neurosciences: a computer-based content analysis of abstracts in the database "MEDLINE" from 1975 to 1995.

    Science.gov (United States)

    Fassbender, P

    1997-04-01

    A computer-based content of 109 abstracts retrieved by the subject heading "parapsychology" from the database MEDLINE for the years 1975-1995 is presented. Data were analyzed by four categories to terms denoting (1) research methods, (2) neurosciences, (3) humanities/psychodynamics, and (4) parapsychology. Results indicated a growing interest in neuroscientific and neuropsychological explanations and theories.

  15. Comparison of two schemes for automatic keyword extraction from MEDLINE for functional gene clustering.

    Science.gov (United States)

    Liu, Ying; Ciliax, Brian J; Borges, Karin; Dasigi, Venu; Ram, Ashwin; Navathe, Shamkant B; Dingledine, Ray

    2004-01-01

    One of the key challenges of microarray studies is to derive biological insights from the unprecedented quatities of data on gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the nature of the functional links among genes within the derived clusters. However, the quality of the keyword lists extracted from biomedical literature for each gene significantly affects the clustering results. We extracted keywords from MEDLINE that describes the most prominent functions of the genes, and used the resulting weights of the keywords as feature vectors for gene clustering. By analyzing the resulting cluster quality, we compared two keyword weighting schemes: normalized z-score and term frequency-inverse document frequency (TFIDF). The best combination of background comparison set, stop list and stemming algorithm was selected based on precision and recall metrics. In a test set of four known gene groups, a hierarchical algorithm correctly assigned 25 of 26 genes to the appropriate clusters based on keywords extracted by the TDFIDF weighting scheme, but only 23 og 26 with the z-score method. To evaluate the effectiveness of the weighting schemes for keyword extraction for gene clusters from microarray profiles, 44 yeast genes that are differentially expressed during the cell cycle were used as a second test set. Using established measures of cluster quality, the results produced from TFIDF-weighted keywords had higher purity, lower entropy, and higher mutual information than those produced from normalized z-score weighted keywords. The optimized algorithms should be useful for sorting genes from microarray lists into functionally discrete clusters.

  16. Reference costs of electricity

    International Nuclear Information System (INIS)

    Terraz, N.

    1997-01-01

    The calculation of electric power production reference costs is used in France, even in the present case of over-capacity, for comparing the relative interest of the various means of power generation (nuclear plants, coal plants, hydroelectricity, gas combined cycles, etc.) and as an aid for future investment decisions. Reference costs show a sharp decrease between 1993 and 1997 due to advancements in nuclear plant operating ability and fossil fuel price decrease. Actuarial rates, plant service life, fuel costs and exchange rates are important parameters. The various costs from the research stage to the waste processing stages are discussed and the reference costs of the various power generation systems are presented and compared together with their competitiveness; the future of wind energy and cogeneration and the prospective of the renewal of nuclear plants at the 2010 horizon are also addressed

  17. Genetics Home Reference: Gorlin syndrome

    Science.gov (United States)

    ... for This Condition basal cell nevus syndrome BCNS Gorlin-Goltz syndrome NBCCS nevoid basal cell carcinoma syndrome Related Information ... named? Additional Information & Resources MedlinePlus (2 links) Encyclopedia: Basal Cell Nevus Syndrome Health Topic: Skin Cancer Genetic and Rare Diseases ...

  18. Genetics Home Reference: Tourette syndrome

    Science.gov (United States)

    ... and Vocal Tic Disorder Gilles de la Tourette Syndrome Gilles de la Tourette's syndrome GTS TD Tourette Disorder Tourette's Disease TS Related ... Additional Information & Resources MedlinePlus (2 links) Encyclopedia: Gilles de la Tourette syndrome Health Topic: Tourette Syndrome Genetic and Rare Diseases ...

  19. Electrical engineer's reference book

    CERN Document Server

    Jones, G R

    2013-01-01

    A long established reference book: radical revision for the fifteenth edition includes complete rearrangement to take in chapters on new topics and regroup the subjects covered for easy access to information.The Electrical Engineer's Reference Book, first published in 1945, maintains its original aims: to reflect the state of the art in electrical science and technology and cater for the needs of practising engineers. Most chapters have been revised and many augmented so as to deal properly with both fundamental developments and new technology and applications that have come to the fore since

  20. Python pocket reference

    CERN Document Server

    Lutz, Mark

    2010-01-01

    This is the book to reach for when you're coding on the fly and need an answer now. It's an easy-to-use reference to the core language, with descriptions of commonly used modules and toolkits, and a guide to recent changes, new features, and upgraded built-ins -- all updated to cover Python 3.X as well as version 2.6. You'll also quickly find exactly what you need with the handy index. Written by Mark Lutz -- widely recognized as the world's leading Python trainer -- Python Pocket Reference, Fourth Edition, is the perfect companion to O'Reilly's classic Python tutorials, also written by Mark

  1. The Reference Return Ratio

    DEFF Research Database (Denmark)

    Nicolaisen, Jeppe; Faber Frandsen, Tove

    2008-01-01

    The paper introduces a new journal impact measure called The Reference Return Ratio (3R). Unlike the traditional Journal Impact Factor (JIF), which is based on calculations of publications and citations, the new measure is based on calculations of bibliographic investments (references) and returns...... (citations). A comparative study of the two measures shows a strong relationship between the 3R and the JIF. Yet, the 3R appears to correct for citation habits, citation dynamics, and composition of document types - problems that typically are raised against the JIF. In addition, contrary to traditional...

  2. Perl Pocket Reference

    CERN Document Server

    Vromans, Johan

    2011-01-01

    If you have a Perl programming question, you'll find the answer quickly in this handy, easy-to-use quick reference. The Perl Pocket Reference condenses and organizes stacks of documentation down to the most essential facts, so you can find what you need in a heartbeat. Updated for Perl 5.14, the 5th edition provides a summary of Perl syntax rules and a complete list of operators, built-in functions, and other features. It's the perfect companion to O'Reilly's authoritative and in-depth Perl programming books, including Learning Perl, Programming Perl, and the Perl Cookbook..

  3. HTML & XHTML Pocket Reference

    CERN Document Server

    Robbins, Jennifer

    2010-01-01

    After years of using spacer GIFs, layers of nested tables, and other improvised solutions for building your web sites, getting used to the more stringent standards-compliant design can be intimidating. HTML and XHTML Pocket Reference is the perfect little book when you need answers immediately. Jennifer Niederst-Robbins, author Web Design in a Nutshell, has revised and updated the fourth edition of this pocket guide by taking the top 20% of vital reference information from her Nutshell book, augmenting it judiciously, cross-referencing everything, and organizing it according to the most com

  4. CSS Pocket Reference

    CERN Document Server

    Meyer, Eric A

    2007-01-01

    They say that good things come in small packages, and it's certainly true for this edition of CSS Pocket Reference. Completely revised and updated to reflect the latest Cascading Style Sheet specifications in CSS 2.1, this indispensable little book covers the most essential information that web designers and developers need to implement CSS effectively across all browsers. Inside, you'll find: A short introduction to the key concepts of CSS A complete alphabetical reference to all CSS 2.1 selectors and properties A chart displaying detailed information about CSS support for every style ele

  5. JDBC Pocket Reference

    CERN Document Server

    Bales, Donald

    2003-01-01

    JDBC--the Java Database Connectivity specification--is a complex set of application programming interfaces (APIs) that developers need to understand if they want their Java applications to work with databases. JDBC is so complex that even the most experienced developers need to refresh their memories from time to time on specific methods and details. But, practically speaking, who wants to stop and thumb through a weighty tutorial volume each time a question arises? The answer is the JDBC Pocket Reference, a data-packed quick reference that is both a time-saver and a lifesaver. The JDBC P

  6. Reference values for electrooculography

    International Nuclear Information System (INIS)

    Barrientos Castanno, Alberto; Herrera Mora, Maritza; Garcia Baez, Obel

    2012-01-01

    Obtain electrooculographic reference values based on the patterns set by the Standardization Committee of the International Society for Clinical Electrophysiology of Vision (ISCEV). the lowest amplitude values of the potential ranged between 388 and 882 μv in the dark phase. The light peak was obtained between 9 and 10 minutes, and during this phase the potential reached an amplitude ranging between 808 and 1 963 μv. This amplitude variability may be related to the fact that the test was conducted without pupillary mydriasis. The reference value obtained for Arden index was 1,55 to 2,87

  7. NASCAP programmer's reference manual

    Science.gov (United States)

    Mandell, M. J.; Stannard, P. R.; Katz, I.

    1993-05-01

    The NASA Charging Analyzer Program (NASCAP) is a computer program designed to model the electrostatic charging of complicated three-dimensional objects, both in a test tank and at geosynchronous altitudes. This document is a programmer's reference manual and user's guide. It is designed as a reference to experienced users of the code, as well as an introduction to its use for beginners. All of the many capabilities of NASCAP are covered in detail, together with examples of their use. These include the definition of objects, plasma environments, potential calculations, particle emission and detection simulations, and charging analysis.

  8. The value of new genome references.

    Science.gov (United States)

    Worley, Kim C; Richards, Stephen; Rogers, Jeffrey

    2017-09-15

    Genomic information has become a ubiquitous and almost essential aspect of biological research. Over the last 10-15 years, the cost of generating sequence data from DNA or RNA samples has dramatically declined and our ability to interpret those data increased just as remarkably. Although it is still possible for biologists to conduct interesting and valuable research on species for which genomic data are not available, the impact of having access to a high quality whole genome reference assembly for a given species is nothing short of transformational. Research on a species for which we have no DNA or RNA sequence data is restricted in fundamental ways. In contrast, even access to an initial draft quality genome (see below for definitions) opens a wide range of opportunities that are simply not available without that reference genome assembly. Although a complete discussion of the impact of genome sequencing and assembly is beyond the scope of this short paper, the goal of this review is to summarize the most common and highest impact contributions that whole genome sequencing and assembly has had on comparative and evolutionary biology. Copyright © 2016. Published by Elsevier Inc.

  9. Computer-aided visualization and analysis system for sequence evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Chee, Mark S.; Wang, Chunwei; Jevons, Luis C.; Bernhart, Derek H.; Lipshutz, Robert J.

    2004-05-11

    A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

  10. ROOT Reference Documentation

    CERN Document Server

    Fuakye, Eric Gyabeng

    2017-01-01

    A ROOT Reference Documentation has been implemented to generate all the lists of libraries needed for each ROOT class. Doxygen has no option to generate or add the lists of libraries for each ROOT class. Therefore shell scripting and a basic C++ program was employed to import the lists of libraries needed by each ROOT class.

  11. Hospitality Services Reference Book.

    Science.gov (United States)

    Texas Tech Univ., Lubbock. Home Economics Curriculum Center.

    This reference book provides information needed by employees in hospitality services occupations. It includes 29 chapters that cover the following topics: the hospitality services industry; professional ethics; organization and management structures; safety practices and emergency procedures; technology; property maintenance and repair; purchasing…

  12. Quantum frames of reference

    International Nuclear Information System (INIS)

    Kaufherr, T.

    1981-01-01

    The idea that only relative variables have physical meaning came to be known as Mach's principle. Carrying over this idea to quantum theory, has led to the consideration of finite mass, macroscopic reference frames, relative to which all physical quantities are measured. During the process of measurement, a finite mass observer receives a kickback, and this reaction of the measuring device is not negligible in quantum theory because of the quantization of the action. Hence, the observer himself has to be included in the system that is being considered. Using this as the starting point, a number of thought experiments involving finite mass observers is discussed which have quantum uncertainties in their time or in their position. These thought experiments serve to elucidate in a qualitative way some of the difficulties involved, as well as pointing out a direction to take in seeking solutions to them. When the discussion is extended to include more than one observer, the question of the covariance of the theory immediately arises. Because none of the frames of reference should be preferred, the theory should be covariant. This demand expresses an equivalence principle which here is extended to include reference frames which are in quantum uncertainties relative to each other. Formulating the problem in terms of canonical variables, the ensueing free Hamiltonian contains vector and scalar potentials which represent the kick that the reference frame receives during measurement. These are essentially gravitational type potentials, resulting, as it were, from the extension of the equivalence principle into the quantum domain

  13. Pollen reference collection digitization

    NARCIS (Netherlands)

    Ercan, F.E.Z.; Donders, T.H.; Bijl, P.K.; Wagner, F.

    2016-01-01

    The extensive Utrecht University pollen reference collection holds thousands of pollen samples of many species and genera from all over the world and has been a basis for the widely-used North West European Pollen Flora. These samples are fixed on glass slides for microscopy use, but the aging

  14. Virtual Reference Services.

    Science.gov (United States)

    Brewer, Sally

    2003-01-01

    As the need to access information increases, school librarians must create virtual libraries. Linked to reliable reference resources, the virtual library extends the physical collection and library hours and lets students learn to use Web-based resources in a protected learning environment. The growing number of virtual schools increases the need…

  15. Reference-Dependent Sympathy

    Science.gov (United States)

    Small, Deborah A.

    2010-01-01

    Natural disasters and other traumatic events often draw a greater charitable response than do ongoing misfortunes, even those that may cause even more widespread misery, such as famine or malaria. Why is the response disproportionate to need? The notion of reference dependence critical to Prospect Theory (Kahneman & Tversky, 1979) maintains that…

  16. Genetics Home Reference

    Science.gov (United States)

    ... Page Search Home Health Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Share: Email Facebook Twitter Genetics Home Reference provides consumer-friendly information about the effects of genetic variation on human health. Health Conditions More than 1,200 health ...

  17. Python library reference

    NARCIS (Netherlands)

    G. van Rossum (Guido)

    1995-01-01

    textabstractPython is an extensible, interpreted, object-oriented programming language. It supports a wide range of applications, from simple text processing scripts to interactive WWW browsers. While the Python Reference Manual describes the exact syntax and semantics of the language, it does not

  18. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  19. ``Frames of Reference'' revisited

    Science.gov (United States)

    Steyn-Ross, Alistair; Ivey, Donald G.

    1992-12-01

    The PSSC teaching film, ``Frames of Reference,'' was made in 1960, and was one of the first audio-visual attempts at showing how your physical ``point of view,'' or frame of reference, necessarily alters both your perceptions and your observations of motion. The gentle humor and original demonstrations made a lasting impact on many audiences, and with its recent re-release as part of the AAPT Cinema Classics videodisc it is timely that we should review both the message and the methods of the film. An annotated script and photographs from the film are presented, followed by extension material on rotating frames which teachers may find appropriate for use in their classrooms: constructions, demonstrations, an example, and theory.

  20. Program reference schedule baseline

    International Nuclear Information System (INIS)

    1986-07-01

    This Program Reference Schedule Baseline (PRSB) provides the baseline Program-level milestones and associated schedules for the Civilian Radioactive Waste Management Program. It integrates all Program-level schedule-related activities. This schedule baseline will be used by the Director, Office of Civilian Radioactive Waste Management (OCRWM), and his staff to monitor compliance with Program objectives. Chapter 1 includes brief discussions concerning the relationship of the PRSB to the Program Reference Cost Baseline (PRCB), the Mission Plan, the Project Decision Schedule, the Total System Life Cycle Cost report, the Program Management Information System report, the Program Milestone Review, annual budget preparation, and system element plans. Chapter 2 includes the identification of all Level 0, or Program-level, milestones, while Chapter 3 presents and discusses the critical path schedules that correspond to those Level 0 milestones

  1. OSH technical reference manual

    Energy Technology Data Exchange (ETDEWEB)

    1993-11-01

    In an evaluation of the Department of Energy (DOE) Occupational Safety and Health programs for government-owned contractor-operated (GOCO) activities, the Department of Labor`s Occupational Safety and Health Administration (OSHA) recommended a technical information exchange program. The intent was to share written safety and health programs, plans, training manuals, and materials within the entire DOE community. The OSH Technical Reference (OTR) helps support the secretary`s response to the OSHA finding by providing a one-stop resource and referral for technical information that relates to safe operations and practice. It also serves as a technical information exchange tool to reference DOE-wide materials pertinent to specific safety topics and, with some modification, as a training aid. The OTR bridges the gap between general safety documents and very specific requirements documents. It is tailored to the DOE community and incorporates DOE field experience.

  2. Electrical engineer's reference book

    CERN Document Server

    Laughton, M A

    1985-01-01

    Electrical Engineer's Reference Book, Fourteenth Edition focuses on electrical engineering. The book first discusses units, mathematics, and physical quantities, including the international unit system, physical properties, and electricity. The text also looks at network and control systems analysis. The book examines materials used in electrical engineering. Topics include conducting materials, superconductors, silicon, insulating materials, electrical steels, and soft irons and relay steels. The text underscores electrical metrology and instrumentation, steam-generating plants, turbines

  3. Reference Sources in Chemistry

    OpenAIRE

    Sthapit, Dilip Man

    1995-01-01

    Information plays an important role in the development of every field. Therefore a brief knowledge regarding information sources is necessary to function in any field. There are many information sources about scientific and technical subjects. In this context there are many reference sources in Chemistry too. Chemistry is one important part of the science which deals with the study of the composition of substances and the chemical changes that they undergo. The purpose of this report is...

  4. Radioactive certified reference materials

    International Nuclear Information System (INIS)

    Watanabe, Kazuo

    2010-01-01

    Outline of radioactive certified reference materials (CRM) for the analysis of nuclear materials and radioactive nuclides were described. The nuclear fuel CRMs are supplied by the three institutes: NBL in the US, CETAMA in France and IRMM in Belgium. For the RI CRMs, the Japan Radioisotope Association is engaged in activities concerning supply. The natural-matrix CRMs for the analysis of trace levels of radio-nuclides are prepared and supplied by NIST in the US and the IAEA. (author)

  5. Reference Japanese man

    International Nuclear Information System (INIS)

    Tanaka, G.-I.; Kawamura, H.; Nakahara, Y.

    1979-01-01

    The weight of organs from autopsy cases of normal Japanese adults, children, and infants is presented for the purpose of approaching a Reference Japanese Man. The skeletal content and the daily intake of alkaline earth elements are given. A lower rate of transfer (K 2 ) to the thyroid gland of ingested radioiodine, as well as a remarkably shorter biological half-life than the data adopted by ICRP, is also proved as a result of this study. (author)

  6. Reference handbook: Level detectors

    International Nuclear Information System (INIS)

    1990-01-01

    The purpose of this handbook is to provide Rocky Flats personnel with the information necessary to understand level measurement and detection. Upon completion of this handbook you should be able to do the following: List three reasons for measuring level. Describe the basic operating principles of the sight glass. Demonstrate proper techniques for reading a sight glass. Describe the basic operating principles of a float level detector. Describe the basic operating principles of a bubbler level indicating system. Explain the differences between a wet and dry reference leg indicating system, and describe how each functions. This handbook is designed for use by experienced Rocky Flats operators to reinforce and improve their current knowledge level, and by entry-level operators to ensure that they possess a minimum level of fundamental knowledge. Level Detectors is applicable to many job classifications and can be used as a reference for classroom work or for self-study. Although this reference handbook is by no means all-encompassing, you will gain enough information about this subject area to assist you in contributing to the safe operation of Rocky Flats Plant

  7. Electroacoustical reference data

    CERN Document Server

    Eargle, John M

    2002-01-01

    The need for a general collection of electroacoustical reference and design data in graphical form has been felt by acousticians and engineers for some time. This type of data can otherwise only be found in a collection of handbooks. Therefore, it is the author's intention that this book serve as a single source for many electroacoustical reference and system design requirements. In form, the volume closely resembles Frank Massa's Acoustic Design Charts, a handy book dating from 1942 that has long been out of print. The basic format of Massa's book has been followed here: For each entry, graphical data are presented on the right page, while text, examples, and refer­ ences appear on the left page. In this manner, the user can solve a given problem without thumbing from one page to the next. All graphs and charts have been scaled for ease in data entry and reading. The book is divided into the following sections: A. General Acoustical Relationships. This section covers the behavior of sound transmis­ sion in...

  8. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  9. PubMed Informer: Monitoring MEDLINE/PubMed through E-mail Alerts, SMS, PDA downloads and RSS feeds

    Science.gov (United States)

    Muin, Michael; Fontelo, Paul; Ackerman, Michael

    2005-01-01

    Summary PubMed Informer is a Web-based monitoring tool for topics of interest from MEDLINE/PubMed primarily designed for healthcare professionals. Five tracking methods are available: Web access, e-mail, Short Message Service (SMS), PDA downloads and RSS feeds. PubMed Informer delivers focused search updates and specific information to users with varying information-seeking practices. PMID:16779344

  10. Sequencing of the Hepatitis C Virus: A Systematic Review.

    Directory of Open Access Journals (Sweden)

    Brendan Jacka

    Full Text Available Since the identification of hepatitis C virus (HCV, viral sequencing has been important in understanding HCV classification, epidemiology, evolution, transmission clustering, treatment response and natural history. The length and diversity of the HCV genome has resulted in analysis of certain regions of the virus, however there has been little standardisation of protocols. This systematic review was undertaken to map the location and frequency of sequencing on the HCV genome in peer reviewed publications, with the aim to produce a database of sequencing primers and amplicons to inform future research. Medline and Scopus databases were searched for English language publications based on keyword/MeSH terms related to sequence analysis (9 terms or HCV (3 terms, plus "primer" as a general search term. Exclusion criteria included non-HCV research, review articles, duplicate records, and incomplete description of HCV sequencing methods. The PCR primer locations of accepted publications were noted, and purpose of sequencing was determined. A total of 450 studies were accepted from the 2099 identified, with 629 HCV sequencing amplicons identified and mapped on the HCV genome. The most commonly sequenced region was the HVR-1 region, often utilised for studies of natural history, clustering/transmission, evolution and treatment response. Studies related to genotyping/classification or epidemiology of HCV genotype generally targeted the 5'UTR, Core and NS5B regions, while treatment response/resistance was assessed mainly in the NS3-NS5B region with emphasis on the Interferon sensitivity determining region (ISDR region of NS5A. While the sequencing of HCV is generally constricted to certain regions of the HCV genome there is little consistency in the positioning of sequencing primers, with the exception of a few highly referenced manuscripts. This study demonstrates the heterogeneity of HCV sequencing, providing a comprehensive database of previously

  11. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  12. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  13. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  14. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  15. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  16. The Reference Scenarios for the Swiss Emergency Planning

    International Nuclear Information System (INIS)

    Hanspeter Isaak; Navert, Stephan B.; Ralph Schulz

    2006-01-01

    For the purpose of emergency planning and preparedness, realistic reference scenarios and corresponding accident source terms have been defined on the basis of common plant features. Three types of representative reference scenarios encompass the accident sequences expected to be the most probable. Accident source terms are assumed to be identical for all Swiss nuclear power plants, although the plants differ in reactor type and power. Plant-specific probabilistic safety analyses were used to justify the reference scenarios and the postulated accident source terms. From the full spectrum of release categories available, those categories were selected which would be covered by the releases and time frames assumed in the reference scenarios. For each nuclear power plant, the cumulative frequency of accident sequences not covered by the reference scenarios was determined. It was found that the cumulative frequency for such accident sequences does not exceed about 1 x 10 -6 per year. The Swiss Federal Nuclear Safety Inspectorate concludes that the postulated accident source terms for the reference scenarios are consistent with the current international approach in emergency planning, where one should concentrate on the most probable accident sequences. (N.C.)

  17. Instrumentation reference book

    CERN Document Server

    Boyes, Walt

    2002-01-01

    Instrumentation is not a clearly defined subject, having a 'fuzzy' boundary with a number of other disciplines. Often categorized as either 'techniques' or 'applications' this book addresses the various applications that may be needed with reference to the practical techniques that are available for the instrumentation or measurement of a specific physical quantity or quality. This makes it of direct interest to anyone working in the process, control and instrumentation fields where these measurements are essential.* Comprehensive and authoritative collection of technical information* Writte

  18. XSLT 10 Pocket Reference

    CERN Document Server

    Lenz, Evan

    2008-01-01

    XSLT is an essential tool for converting XML into other kinds of documents: HTML, PDF file, and many others. It's a critical technology for XML-based platforms such as Microsoft .NET, Sun Microsystems' Sun One, as well as for most web browsers and authoring tools. As useful as XSLT is, however, most people have a difficult time getting used to its peculiar characteristics. The ability to use advanced techniques depends on a clear and exact understanding of how XSLT templates work and interact. The XSLT 1.0 Pocket Reference from O'Reilly wants to make sure you achieve that level of understan

  19. Electronics engineer's reference book

    CERN Document Server

    Mazda, F F

    1989-01-01

    Electronics Engineer's Reference Book, Sixth Edition is a five-part book that begins with a synopsis of mathematical and electrical techniques used in the analysis of electronic systems. Part II covers physical phenomena, such as electricity, light, and radiation, often met with in electronic systems. Part III contains chapters on basic electronic components and materials, the building blocks of any electronic design. Part IV highlights electronic circuit design and instrumentation. The last part shows the application areas of electronics such as radar and computers.

  20. International Geomagnetic Reference Field

    DEFF Research Database (Denmark)

    Finlay, Chris; Maus, S.; Beggan, C. D.

    2010-01-01

    The eleventh generation of the International Geomagnetic Reference Field (IGRF) was adopted in December 2009 by the International Association of Geomagnetism and Aeronomy Working Group V‐MOD. It updates the previous IGRF generation with a definitive main field model for epoch 2005.0, a main field...... model for epoch 2010.0, and a linear predictive secular variation model for 2010.0–2015.0. In this note the equations defining the IGRF model are provided along with the spherical harmonic coefficients for the eleventh generation. Maps of the magnetic declination, inclination and total intensity...

  1. Mechanical engineer's reference book

    CERN Document Server

    Parrish, A

    1973-01-01

    Mechanical Engineer's Reference Book: 11th Edition presents a comprehensive examination of the use of Systéme International d' Unités (SI) metrication. It discusses the effectiveness of such a system when used in the field of engineering. It addresses the basic concepts involved in thermodynamics and heat transfer. Some of the topics covered in the book are the metallurgy of iron and steel; screw threads and fasteners; hole basis and shaft basis fits; an introduction to geometrical tolerancing; mechanical working of steel; high strength alloy steels; advantages of making components as castings

  2. VBScript pocket reference

    CERN Document Server

    Lomax, Paul; Petrusha, Ron

    2008-01-01

    Microsoft's Visual Basic Scripting Edition (VBScript), a subset of Visual Basic for Applications, is a powerful language for Internet application development, where it can serve as a scripting language for server-side, client-side, and system scripting. Whether you're developing code for Active Server Pages, client-side scripts for Internet Explorer, code for Outlook forms, or scripts for Windows Script Host, VBScript Pocket Reference will be your constant companion. Don't let the pocket-friendly format fool you. Based on the bestsellingVBScript in a Nutshell, this small book details every V

  3. Xcode 5 developer reference

    CERN Document Server

    Wentk, Richard

    2014-01-01

    Design, code, and build amazing apps with Xcode 5 Thanks to Apple's awesome Xcode development environment, you can create the next big app for Macs, iPhones, iPads, or iPod touches. Xcode 5 contains gigabytes of great stuff to help you develop for both OS X and iOS devices - things like sample code, utilities, companion applications, documentation, and more. And with Xcode 5 Developer Reference, you now have the ultimate step-by-step guide to it all. Immerse yourself in the heady and lucrative world of Apple app development, see how to tame the latest features and functions, and find loads of

  4. NUnit Pocket Reference

    CERN Document Server

    Hamilton, Bill

    2009-01-01

    The open source NUnit framework is an excellent way to test .NET code as it is written, saving hundreds of QA hours and headaches. Unfortunately, some of those hours saved can be wasted trying to master this popular but under-documented framework. Proof that good things come in small packages, the NUnit Pocket Reference is everything you need to get NUnit up and working for you. It's the only book you'll need on this popular and practical new open source framework.

  5. Coal Data: A reference

    International Nuclear Information System (INIS)

    1991-01-01

    The purpose of Coal Data: A Reference is to provide basic information on the mining and use of coal, an important source of energy in the United States. The report is written for a general audience. The goal is to cover basic material and strike a reasonable compromise between overly generalized statements and detailed analyses. The section ''Coal Terminology and Related Information'' provides additional information about terms mentioned in the text and introduces new terms. Topics covered are US coal deposits, resources and reserves, mining, production, employment and productivity, health and safety, preparation, transportation, supply and stocks, use, coal, the environment, and more. (VC)

  6. Draft Genome Sequence of Lactobacillus rhamnosus 2166.

    OpenAIRE

    Karlyshev, Andrey V.; Melnikov, Vyacheslav G.; Kosarev, Igor V.; Abramov, Vyacheslav M.

    2014-01-01

    In this report, we present a draft sequence of the genome of Lactobacillus rhamnosus strain 2166, a potential novel probiotic. Genome annotation and read mapping onto a reference genome of L. rhamnosus strain GG allowed for the identification of the differences and similarities in the genomic contents and gene arrangements of these strains.

  7. Roaming Reference: Reinvigorating Reference through Point of Need Service

    Directory of Open Access Journals (Sweden)

    Kealin M. McCabe

    2011-11-01

    Full Text Available Roaming reference service was pursued as a way to address declining reference statistics. The service was staffed by librarians armed with iPads over a period of six months during the 2010-2011 academic year. Transactional statistics were collected in relation to query type (Research, Facilitative or Technology, location and approach (librarian to patron, patron to librarian or via chat widget. Overall, roaming reference resulted in an additional 228 reference questions, 67% (n=153 of which were research related. Two iterations of the service were implemented, roaming reference as a standalone service (Fall 2010 and roaming reference integrated with traditional reference desk duties (Winter 2011. The results demonstrate that although the Weller Library’s reference transactions are declining annually, they are not disappearing. For a roaming reference service to succeed, it must be a standalone service provided in addition to traditional reference services. The integration of the two reference models (roaming reference and reference desk resulted in a 56% decline in the total number of roaming reference questions from the previous term. The simple act of roaming has the potential to reinvigorate reference services as a whole, forcing librarians outside their comfort zones, allowing them to reach patrons at their point of need.

  8. AREVA - 2013 Reference document

    International Nuclear Information System (INIS)

    2014-01-01

    This Reference Document contains information on the AREVA group's objectives, prospects and development strategies, as well as estimates of the markets, market shares and competitive position of the AREVA group. Content: 1 - Person responsible for the Reference Document; 2 - Statutory auditors; 3 - Selected financial information; 4 - Description of major risks confronting the company; 5 - Information about the issuer; 6 - Business overview; 7 - Organizational structure; 8 - Property, plant and equipment; 9 - Situation and activities of the company and its subsidiaries; 10 - Capital resources; 11 - Research and development programs, patents and licenses; 12 - Trend information; 13 - Profit forecasts or estimates; 14 - Management and supervisory bodies; 15 - Compensation and benefits; 16 - Functioning of the management and supervisory bodies; 17 - Human resources information; 18 - Principal shareholders; 19 - Transactions with related parties; 20 - Financial information concerning assets, financial positions and financial performance; 21 - Additional information; 22 - Major contracts; 23 - Third party information, statements by experts and declarations of interest; 24 - Documents on display; 25 - Information on holdings; Appendix 1: report of the supervisory board chairman on the preparation and organization of the board's activities and internal control procedures; Appendix 2: statutory auditors' reports; Appendix 3: environmental report; Appendix 4: non-financial reporting methodology and independent third-party report on social, environmental and societal data; Appendix 5: ordinary and extraordinary general shareholders' meeting; Appendix 6: values charter; Appendix 7: table of concordance of the management report; glossaries

  9. Balinese Frame of Reference

    Directory of Open Access Journals (Sweden)

    I Nyoman Aryawibawa

    2016-04-01

    Full Text Available Abstract: Balinese Frame of Reference. Wassmann and Dasen (1998 did a study on the acquisition of Balinese frames of reference. They pointed out that, in addition to the dominant use of absolute system, the use of relative system was also observed. This article aims at verifying Wassmann and Dasen’ study. Employing monolingual Balinese speakers and using linguistic and non-linguistic tasks, Aryawibawa (2010, 2012, 2015 showed that Balinese subjects used an absolute system dominantly in responding the two tasks, e.g. The man is north/south/east/west of the car. Unlike Wassmann and Dasen’s results, no relative system was used by the subjects in solving the tasks. Instead of the relative system, an intrinsic system was also observed in this study, even though it was unfrequent. The article concludes that the absolute system was dominantly employed by Balinese speakers in describing spatial relations in Balinese. The use of the system seems to affect their cognitive functions.

  10. Antares Reference Telescope System

    International Nuclear Information System (INIS)

    Viswanathan, V.K.; Kaprelian, E.; Swann, T.; Parker, J.; Wolfe, P.; Woodfin, G.; Knight, D.

    1983-01-01

    Antares is a 24-beam, 40-TW carbon-dioxide laser-fusion system currently nearing completion at the Los Alamos National Laboratory. The 24 beams will be focused onto a tiny target (typically 300 to 1000 μm in diameter) located approximately at the center of a 7.3-m-diameter by 9.3-m-long vacuum (10 - 6 torr) chamber. The design goal is to position the targets to within 10 μm of a selected nominal position, which may be anywhere within a fixed spherical region 1 cm in diameter. The Antares Reference Telescope System is intended to help achieve this goal for alignment and viewing of the various targets used in the laser system. The Antares Reference Telescope System consists of two similar electro-optical systems positioned in a near orthogonal manner in the target chamber area of the laser. Each of these consists of four subsystems: (1) a fixed 9X optical imaging subsystem which produces an image of the target at the vidicon; (2) a reticle projection subsystem which superimposes an image of the reticle pattern at the vidicon; (3) an adjustable front-lighting subsystem which illuminates the target; and (4) an adjustable back-lighting subsystem which also can be used to illuminate the target. The various optical, mechanical, and vidicon design considerations and trade-offs are discussed. The final system chosen (which is being built) and its current status are described in detail

  11. Sensor employing internal reference electrode

    DEFF Research Database (Denmark)

    2013-01-01

    The present invention concerns a novel internal reference electrode as well as a novel sensing electrode for an improved internal reference oxygen sensor and the sensor employing same.......The present invention concerns a novel internal reference electrode as well as a novel sensing electrode for an improved internal reference oxygen sensor and the sensor employing same....

  12. Endogenizing Prospect Theory's Reference Point

    OpenAIRE

    Ulrich Schmidt; Horst Zank

    2010-01-01

    In previous models of (cumulative) prospect theory reference-dependence of preferences is imposed beforehand and the location of the reference point is exogenously determined. This note provides a foundation of prospect theory, where reference-dependence is derived from preference conditions and a unique reference point arises endogenously.

  13. Single-Shell Tank (SST) Retrieval Sequence Fiscal Year 2000 Update

    International Nuclear Information System (INIS)

    GARFIELD, J.S.

    2000-01-01

    This document describes the baseline single-shell tank (SST) waste retrieval sequence for the River Protection Project (RPP) updated for Fiscal Year 2000. The SST retrieval sequence identifies the proposed retrieval order (sequence), the tank selection and prioritization rationale, and planned retrieval dates for Hanford SSTs. In addition, the tank selection criteria and reference retrieval method for this sequence are discussed

  14. AREVA 2009 reference document

    International Nuclear Information System (INIS)

    2009-01-01

    This Reference Document contains information on the AREVA group's objectives, prospects and development strategies. It contains information on the markets, market shares and competitive position of the AREVA group. This information provides an adequate picture of the size of these markets and of the AREVA group's competitive position. Content: 1 - Person responsible for the Reference Document and Attestation by the person responsible for the Reference Document; 2 - Statutory and Deputy Auditors; 3 - Selected financial information; 4 - Risks: Risk management and coverage, Legal risk, Industrial and environmental risk, Operating risk, Risk related to major projects, Liquidity and market risk, Other risk; 5 - Information about the issuer: History and development, Investments; 6 - Business overview: Markets for nuclear power and renewable energies, AREVA customers and suppliers, Overview and strategy of the group, Business divisions, Discontinued operations: AREVA Transmission and Distribution; 7 - Organizational structure; 8 - Property, plant and equipment: Principal sites of the AREVA group, Environmental issues that may affect the issuer's; 9 - Analysis of and comments on the group's financial position and performance: Overview, Financial position, Cash flow, Statement of financial position, Events subsequent to year-end closing for 2009; 10 - Capital Resources; 11 - Research and development programs, patents and licenses; 12 -trend information: Current situation, Financial objectives; 13 - Profit forecasts or estimates; 14 - Administrative, management and supervisory bodies and senior management; 15 - Compensation and benefits; 16 - Functioning of corporate bodies; 17 - Employees; 18 - Principal shareholders; 19 - Transactions with related parties: French state, CEA, EDF group; 20 - Financial information concerning assets, financial positions and financial performance; 21 - Additional information: Share capital, Certificate of incorporation and by-laws; 22 - Major

  15. Areva - 2016 Reference document

    International Nuclear Information System (INIS)

    2017-01-01

    Areva supplies high added-value products and services to support the operation of the global nuclear fleet. The company is present throughout the entire nuclear cycle, from uranium mining to used fuel recycling, including nuclear reactor design and operating services. Areva is recognized by utilities around the world for its expertise, its skills in cutting-edge technologies and its dedication to the highest level of safety. Areva's 36,000 employees are helping build tomorrow's energy model: supplying ever safer, cleaner and more economical energy to the greatest number of people. This Reference Document contains information on Areva's objectives, prospects and development strategies. It contains estimates of the markets, market shares and competitive position of Areva

  16. A reference tristimulus colorimeter

    Science.gov (United States)

    Eppeldauer, George P.

    2002-06-01

    A reference tristimulus colorimeter has been developed at NIST with a transmission-type silicon trap detector (1) and four temperature-controlled filter packages to realize the Commission Internationale de l'Eclairage (CIE) x(λ), y(λ) and z(λ) color matching functions (2). Instead of lamp standards, high accuracy detector standards are used for the colorimeter calibration. A detector-based calibration procedure is being suggested for tristimulus colorimeters wehre the absolute spectral responsivity of the tristimulus channels is determined. Then, color (spectral) correct and peak (amplitude) normalization are applied to minimize uncertainties caused by the imperfect realizations of the CIE functions. As a result of the corrections, the chromaticity coordinates of stable light sources with different spectral power distributions can be measured with uncertainties less than 0.0005 (k=1).

  17. Tank characterization reference guide

    International Nuclear Information System (INIS)

    De Lorenzo, D.S.; DiCenso, A.T.; Hiller, D.B.; Johnson, K.W.; Rutherford, J.H.; Smith, D.J.; Simpson, B.C.

    1994-09-01

    Characterization of the Hanford Site high-level waste storage tanks supports safety issue resolution; operations and maintenance requirements; and retrieval, pretreatment, vitrification, and disposal technology development. Technical, historical, and programmatic information about the waste tanks is often scattered among many sources, if it is documented at all. This Tank Characterization Reference Guide, therefore, serves as a common location for much of the generic tank information that is otherwise contained in many documents. The report is intended to be an introduction to the issues and history surrounding the generation, storage, and management of the liquid process wastes, and a presentation of the sampling, analysis, and modeling activities that support the current waste characterization. This report should provide a basis upon which those unfamiliar with the Hanford Site tank farms can start their research

  18. Areva, reference document 2006

    International Nuclear Information System (INIS)

    2006-01-01

    This reference document contains information on the AREVA group's objectives, prospects and development strategies, particularly in Chapters 4 and 7. It contains information on the markets, market shares and competitive position of the AREVA group. Content: - 1 Person responsible for the reference document and persons responsible for auditing the financial statements; - 2 Information pertaining to the transaction (Not applicable); - 3 General information on the company and its share capital: Information on AREVA, on share capital and voting rights, Investment certificate trading, Dividends, Organization chart of AREVA group companies, Equity interests, Shareholders' agreements; - 4 Information on company operations, new developments and future prospects: Overview and strategy of the AREVA group, The Nuclear Power and Transmission and Distribution markets, The energy businesses of the AREVA group, Front End division, Reactors and Services division, Back End division, Transmission and Distribution division, Major contracts, The principal sites of the AREVA group, AREVA's customers and suppliers, Sustainable Development and Continuous Improvement, Capital spending programs, Research and development programs, intellectual property and trademarks, Risk and insurance; - 5 Assets - Financial position - Financial performance: Analysis of and comments on the group's financial position and performance, 2006 Human Resources Report, Environmental Report, Consolidated financial statements, Notes to the consolidated financial statements, AREVA SA financial statements, Notes to the corporate financial statements; 6 - Corporate Governance: Composition and functioning of corporate bodies, Executive compensation, Profit-sharing plans, AREVA Values Charter, Annual Combined General Meeting of Shareholders of May 3, 2007; 7 - Recent developments and future prospects: Events subsequent to year-end closing for 2006, Outlook; 8 - Glossary; 9 - Table of concordance

  19. Areva reference document 2007

    International Nuclear Information System (INIS)

    2008-01-01

    This reference document contains information on the AREVA group's objectives, prospects and development strategies, particularly in Chapters 4 and 7. It contains also information on the markets, market shares and competitive position of the AREVA group. Content: 1 - Person responsible for the reference document and persons responsible for auditing the financial statements; 2 - Information pertaining to the transaction (not applicable); 3 - General information on the company and its share capital: Information on Areva, Information on share capital and voting rights, Investment certificate trading, Dividends, Organization chart of AREVA group companies, Equity interests, Shareholders' agreements; 4 - Information on company operations, new developments and future prospects: Overview and strategy of the AREVA group, The Nuclear Power and Transmission and Distribution markets, The energy businesses of the AREVA group, Front End division, Reactors and Services division, Back End division, Transmission and Distribution division, Major contracts 140 Principal sites of the AREVA group, AREVA's customers and suppliers, Sustainable Development and Continuous Improvement, Capital spending programs, Research and Development programs, Intellectual Property and Trademarks, Risk and insurance; 5 - Assets financial position financial performance: Analysis of and comments on the group's financial position and performance, Human Resources report, Environmental report, Consolidated financial statements 2007, Notes to the consolidated financial statements, Annual financial statements 2007, Notes to the corporate financial statements; 6 - Corporate governance: Composition and functioning of corporate bodies, Executive compensation, Profit-sharing plans, AREVA Values Charter, Annual Ordinary General Meeting of Shareholders of April 17, 2008; 7 - Recent developments and future prospects: Events subsequent to year-end closing for 2007, Outlook; Glossary; table of concordance

  20. JVM: Java Visual Mapping tool for next generation sequencing read.

    Science.gov (United States)

    Yang, Ye; Liu, Juan

    2015-01-01

    We developed a program JVM (Java Visual Mapping) for mapping next generation sequencing read to reference sequence. The program is implemented in Java and is designed to deal with millions of short read generated by sequence alignment using the Illumina sequencing technology. It employs seed index strategy and octal encoding operations for sequence alignments. JVM is useful for DNA-Seq, RNA-Seq when dealing with single-end resequencing. JVM is a desktop application, which supports reads capacity from 1 MB to 10 GB.

  1. Reference free phasing and representation of complex variation

    DEFF Research Database (Denmark)

    Jensen, Jacob Malte

    2017-01-01

    High throughput sequencing has revolutionized our ability to interrogate genomes and entire human genomes are sequenced daily across the world. Mapping of short reads to a reference genome has enhanced our ability to detect genetic variation and is currently the most widely used technology....... Therefore, new methods for detecting variation that reduce reference bias are needed including ways of representing genomes that account for the variability within and between populations. The major histocompatibility complex (MHC) region is one of the most diverse and complex regions of the human genome...... to detect and call variation in humans. However, it has become evident that mapping of short reads to a single reference genome is subject to ascertainment bias (reference bias). This bias is especially pronounced in complex regions of the genome and particularly hampers detection of structural variation...

  2. Generalized locally Toeplitz sequences theory and applications

    CERN Document Server

    Garoni, Carlo

    2017-01-01

    Based on their research experience, the authors propose a reference textbook in two volumes on the theory of generalized locally Toeplitz sequences and their applications. This first volume focuses on the univariate version of the theory and the related applications in the unidimensional setting, while the second volume, which addresses the multivariate case, is mainly devoted to concrete PDE applications. This book systematically develops the theory of generalized locally Toeplitz (GLT) sequences and presents some of its main applications, with a particular focus on the numerical discretization of differential equations (DEs). It is the first book to address the relatively new field of GLT sequences, which occur in numerous scientific applications and are especially dominant in the context of DE discretizations. Written for applied mathematicians, engineers, physicists, and scientists who (perhaps unknowingly) encounter GLT sequences in their research, it is also of interest to those working in the fields of...

  3. Special Issue: Next Generation DNA Sequencing

    Directory of Open Access Journals (Sweden)

    Paul Richardson

    2010-10-01

    Full Text Available Next Generation Sequencing (NGS refers to technologies that do not rely on traditional dideoxy-nucleotide (Sanger sequencing where labeled DNA fragments are physically resolved by electrophoresis. These new technologies rely on different strategies, but essentially all of them make use of real-time data collection of a base level incorporation event across a massive number of reactions (on the order of millions versus 96 for capillary electrophoresis for instance. The major commercial NGS platforms available to researchers are the 454 Genome Sequencer (Roche, Illumina (formerly Solexa Genome analyzer, the SOLiD system (Applied Biosystems/Life Technologies and the Heliscope (Helicos Corporation. The techniques and different strategies utilized by these platforms are reviewed in a number of the papers in this special issue. These technologies are enabling new applications that take advantage of the massive data produced by this next generation of sequencing instruments. [...

  4. Locating qualitative studies in dementia on MEDLINE, EMBASE, CINAHL, and PsycINFO: A comparison of search strategies.

    Science.gov (United States)

    Rogers, Morwenna; Bethel, Alison; Abbott, Rebecca

    2017-10-28

    Qualitative research in dementia improves understanding of the experience of people affected by dementia. Searching databases for qualitative studies is problematic. Qualitative-specific search strategies might help with locating studies. To examine the effectiveness (sensitivity and precision) of 5 qualitative strategies on locating qualitative research studies in dementia in 4 major databases (MEDLINE, EMBASE, PsycINFO, and CINAHL). Qualitative dementia studies were checked for inclusion on MEDLINE, EMBASE, PsycINFO, and CINAHL. Five qualitative search strategies (subject headings, simple free-text terms, complex free-text terms, and 2 broad-based strategies) were tested for study retrieval. Specificity, precision and number needed to read were calculated. Two hundred fourteen qualitative studies in dementia were included. PsycINFO and CINAHL held the most qualitative studies out the 4 databases studied (N = 171 and 166, respectively) and both held unique records (N = 14 and 7, respectively). The controlled vocabulary strategy in CINAHL returned 96% (N = 192) of studies held; by contrast, controlled vocabulary in PsycINFO returned 7% (N = 13) of studies held. The broad-based strategies returned more studies (93-99%) than the other free-text strategies (22-82%). Precision ranged from 0.061 to 0.004 resulting in a number needed to read to obtain 1 relevant study ranging from 16 (simple free-text search in CINAHL) to 239 (broad-based search in EMBASE). Qualitative search strategies using 3 broad terms were more sensitive than long complex searches. The controlled vocabulary for qualitative research in CINAHL was particularly effective. Furthermore, results indicate that MEDLINE and EMBASE offer little benefit for locating qualitative dementia research if CINAHL and PSYCINFO are also searched. Copyright © 2017 John Wiley & Sons, Ltd.

  5. The diploid genome sequence of an Asian individual

    DEFF Research Database (Denmark)

    Wang, Jun; Wang, Wei; Li, Ruiqiang

    2008-01-01

    Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we...... used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP...... identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J...

  6. Sequencing of individual chromosomes of plant pathogenic Fusarium oxysporum.

    Science.gov (United States)

    Kashiwa, Takeshi; Kozaki, Toshinori; Ishii, Kazuo; Turgeon, B Gillian; Teraoka, Tohru; Komatsu, Ken; Arie, Tsutomu

    2017-01-01

    A small chromosome in reference isolate 4287 of F. oxysporum f. sp. lycopersici (Fol) has been designated as a 'pathogenicity chromosome' because it carries several pathogenicity related genes such as the Secreted In Xylem (SIX) genes. Sequence assembly of small chromosomes in other isolates, based on a reference genome template, is difficult because of karyotype variation among isolates and a high number of sequences associated with transposable elements. These factors often result in misassembly of sequences, making it unclear whether other isolates possess the same pathogenicity chromosome harboring SIX genes as in the reference isolate. To overcome this difficulty, single chromosome sequencing after Contour-clamped Homogeneous Electric Field (CHEF) separation of chromosomes was performed, followed by de novo assembly of sequences. The assembled sequences of individual chromosomes were consistent with results of probing gels of CHEF separated chromosomes with SIX genes. Individual chromosome sequencing revealed that several SIX genes are located on a single small chromosome in two pathogenic forms of F. oxysporum, beyond the reference isolate 4287, and in the cabbage yellows fungus F. oxysporum f. sp. conglutinans. The particular combination of SIX genes on each small chromosome varied. Moreover, not all SIX genes were found on small chromosomes; depending on the isolate, some were on big chromosomes. This suggests that recombination of chromosomes and/or translocation of SIX genes may occur frequently. Our method improves sequence comparison of small chromosomes among isolates. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. AREVA - 2012 Reference document

    International Nuclear Information System (INIS)

    2013-03-01

    After a presentation of the person responsible for this Reference Document, of statutory auditors, and of a summary of financial information, this report address the different risk factors: risk management and coverage, legal risk, industrial and environmental risk, operational risk, risk related to major projects, liquidity and market risk, and other risks (related to political and economic conditions, to Group's structure, and to human resources). The next parts propose information about the issuer, a business overview (markets for nuclear power and renewable energies, customers and suppliers, group's strategy, operations), a brief presentation of the organizational structure, a presentation of properties, plants and equipment (principal sites, environmental issues which may affect these items), analysis and comments on the group's financial position and performance, a presentation of capital resources, a presentation of research and development activities (programs, patents and licenses), a brief description of financial objectives and profit forecasts or estimates, a presentation of administration, management and supervision bodies, a description of the operation of corporate bodies, an overview of personnel, of principal shareholders, and of transactions with related parties, a more detailed presentation of financial information concerning assets, financial positions and financial performance. Addition information regarding share capital is given, as well as an indication of major contracts, third party information, available documents, and information on holdings

  8. Reference thorium fuel cycle

    International Nuclear Information System (INIS)

    Driggers, F.E.

    1978-08-01

    In the reference fuel cycle for the TFCT program, fissile U will be denatured by mixing with 238 U; the plants will be located in secure areas, with Pu being recycled within these secure areas; Th will be recycled with recovered U and Pu; the head end will handle a variety of core and blanket fuel assembly designs for LWRs and HWRs; the fuel may be a homogeneous mixture either of U and Th oxide pellets or sol-gel microspheres; the cladding will be Zircaloy; and MgO may be added to the fuel to improve Th dissolution. Th is being considered as the fertile component of fuel in order to increase proliferation resistance. Spent U recovered from Th-based fuels must be re-enriched before recycle to prevent very rapid buildup of 238 U. Stainless steel will be considered as a backup to Zircaloy cladding in case Zr is incompatible with commercial aqueous dissolution. Storage of recovered irradiated Th will be considered as a backup to its use in the recycle of recovered Pu and U. Estimates are made of the time for introducing the Th fuel cycle into the LWR power industry. Since U fuel exposures in LWRs are likely to increase from 30,000 to 50,000 MWD/MT, the Th reprocessing plant should also be designed for Th fuel with 50,000 MWD/MT exposure

  9. Sensor Characteristics Reference Guide

    Energy Technology Data Exchange (ETDEWEB)

    Cree, Johnathan V.; Dansu, A.; Fuhr, P.; Lanzisera, Steven M.; McIntyre, T.; Muehleisen, Ralph T.; Starke, M.; Banerjee, Pranab; Kuruganti, T.; Castello, C.

    2013-04-01

    The Buildings Technologies Office (BTO), within the U.S. Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy (EERE), is initiating a new program in Sensor and Controls. The vision of this program is: • Buildings operating automatically and continuously at peak energy efficiency over their lifetimes and interoperating effectively with the electric power grid. • Buildings that are self-configuring, self-commissioning, self-learning, self-diagnosing, self-healing, and self-transacting to enable continuous peak performance. • Lower overall building operating costs and higher asset valuation. The overarching goal is to capture 30% energy savings by enhanced management of energy consuming assets and systems through development of cost-effective sensors and controls. One step in achieving this vision is the publication of this Sensor Characteristics Reference Guide. The purpose of the guide is to inform building owners and operators of the current status, capabilities, and limitations of sensor technologies. It is hoped that this guide will aid in the design and procurement process and result in successful implementation of building sensor and control systems. DOE will also use this guide to identify research priorities, develop future specifications for potential market adoption, and provide market clarity through unbiased information

  10. Uranium tailings reference materials

    International Nuclear Information System (INIS)

    Smith, C.W.; Steger, H.F.; Bowman, W.S.

    1984-01-01

    Samples of uranium tailings from Bancroft and Elliot Lake, Ontario, and from Beaverlodge and Rabbit Lake, Saskatchewan, have been prepared as compositional reference materials at the request of the National Uranium Tailings Research Program. The four samples, UTS-1 to UTS-4, were ground to minus 104 μm, each mixed in one lot and bottled in 200-g units for UTS-1 to UTS-3 and in 100-g units for UTS-4. The materials were tested for homogeneity with respect to uranium by neutron activation analysis and to iron by an acid-decomposition atomic absorption procedure. In a free choice analytical program, 18 laboratories contributed results for one or more of total iron, titanium, aluminum, calcium, barium, uranium, thorium, total sulphur, and sulphate for all four samples, and for nickel and arsenic in UTS-4 only. Based on a statistical analysis of the data, recommended values were assigned to all elements/constituents, except for sulphate in UTS-3 and nickel in UTS-4. The radioactivity of thorium-230, radium-226, lead-210, and polonium-210 in UTS-1 to UTS-4 and of thorium-232, radium-228, and thorium-228 in UTS-1 and UTS-2 was determined in a radioanalytical program composed of eight laboratories. Recommended values for the radioactivities and associated parameters were calculated by a statistical treatment of the results

  11. Impacto da indexação no SciELO e MEDLINE sobre as submissões ao Jornal de Pediatria Impact of SciELO and MEDLINE indexing on submissions to Jornal de Pediatria

    Directory of Open Access Journals (Sweden)

    Danilo Blank

    2005-12-01

    Full Text Available OBJETIVO: Avaliar o impacto da indexação no SciELO e MEDLINE sobre o número de artigos submetidos ao Jornal de Pediatria. MÉTODOS: Análise do total de artigos submetidos, artigos estrangeiros submetidos e índices de aceitação, nos seguintes períodos: estágio I - pré-site (janeiro/2000-março/2001; estágio II - site (abril/2001-julho/2002; estágio III - SciELO (agosto/2002-agosto/2003; estágio IV - MEDLINE (setembro/2003-dezembro/2004. RESULTADOS: Houve uma tendência significativa de aumento linear no número de submissões, durante o período do estudo (p = 0,009. O número de originais submetidos nos estágios I a IV foi, respectivamente: 184, 240, 297 e 482. O número de submissões foi similar nos estágios I e II (p = 0,148, mas foi significativamente maior no estágio III (p OBJECTIVE: To evaluate the impact of SciELO and MEDLINE indexing on the number of articles submitted to Jornal de Pediatria. METHODS: Analysis of total article submission, submission of articles from foreign countries and acceptance figures in the following periods: stage I - pre-website (Jan 2000-Mar 2001; stage II - website (Apr 2001-Jul 2002; stage III - SciELO (Aug 2002-Aug 2003; stage IV - MEDLINE (Sep 2003-Dec 2004. RESULTS: There was a significant trend toward linear increase in the number of submissions along the study period (p = 0.009. The number of manuscripts submitted in stages I through IV was 184, 240, 297, and 482, respectively. The number of submissions was similar in stages I and II (p = 0.148, but statistically higher in Stage III (p < 0.001 vs. Stage I and p = 0.006 vs. Stage II and Stage IV (p < 0.001 vs. stages I and II, and p < 0.05 vs. stage III. The rate of article acceptance decreased during the study period. The number of original articles published has been stable since the 2001 March/April issue (n = 10, when the journal reached a printed page limit, leading to stricter judgment criteria and a relative decrease in acceptance

  12. ENRAF gauge reference level calculations

    Energy Technology Data Exchange (ETDEWEB)

    Huber, J.H., Fluor Daniel Hanford

    1997-02-06

    This document describes the method for calculating reference levels for Enraf Series 854 Level Detectors as installed in the tank farms. The reference level calculation for each installed level gauge is contained herein.

  13. Global Reference Tables Services Architecture

    Data.gov (United States)

    Social Security Administration — This database stores the reference and transactional data used to provide a data-driven service access method to certain Global Reference Table (GRT) service tables.

  14. Genetics Home Reference: PURA syndrome

    Science.gov (United States)

    ... TJ, Vreeburg M, Rouhl RPW, Stevens SJC, Stegmann APA, Schieving J, Pfundt R, van Dijk K, Smeets ... article on PubMed Central More from Genetics Home Reference Bulletins Genetics Home Reference Celebrates Its 15th Anniversary ...

  15. Areva - 2014 Reference document

    International Nuclear Information System (INIS)

    2015-01-01

    Areva supplies high added-value products and services to support the operation of the global nuclear fleet. The company is present throughout the entire nuclear cycle, from uranium mining to used fuel recycling, including nuclear reactor design and operating services. Areva is recognized by utilities around the world for its expertise, its skills in cutting-edge technologies and its dedication to the highest level of safety. Areva's 44,000 employees are helping build tomorrow's energy model: supplying ever safer, cleaner and more economical energy to the greatest number of people. This Reference Document contains information on Areva's objectives, prospects and development strategies. It contains estimates of the markets, market shares and competitive position of Areva. Contents: 1 - Person responsible; 2 - Statutory auditors; 3 - Selected financial information; 4 - Risk factors; 5 - Information about the issuer; 6 - Business overview; 7 - Organizational structure; 8 - Property, plant and equipment; 9 - Analysis of and comments on the group's financial position and performance; 10 - Capital resources; 11 - Research and development programs, patents and licenses; 12 - Trend information; 13 - Profit forecasts; 14 - Administrative, management and supervisory bodies and senior management; 15 - Compensation and benefits; 16 - Functioning of administrative, management and supervisory bodies and senior management; 17 - Employees; 18 - Principal shareholders; 19 - Transactions with related parties; 20 - Financial information concerning assets, financial positions and financial performance; 21 - Additional information; 22 - Major contracts; 23 - Third party information, statements by experts and declarations of interest; 24 - Documents on display; 25 - information on holdings; appendix: Report of the Chairman of the Board of Directors on governance, internal control procedures and risk management, Statutory Auditors' report, Corporate social

  16. Kerlinger's Criterial Referents Theory Revisited.

    Science.gov (United States)

    Zak, Itai; Birenbaum, Menucha

    1980-01-01

    Kerlinger's criterial referents theory of attitudes was tested cross-culturally by administering an education attitude referents summated-rating scale to 713 individuals in Israel. The response pattern to criterial and noncriterial referents was examined. Results indicated empirical cross-cultural validity of theory, but questioned measuring…

  17. Fundamentals of Managing Reference Collections

    Science.gov (United States)

    Singer, Carol A.

    2012-01-01

    Whether a library's reference collection is large or small, it needs constant attention. Singer's book offers information and insight on best practices for reference collection management, no matter the size, and shows why managing without a plan is a recipe for clutter and confusion. In this very practical guide, reference librarians will learn:…

  18. Knowledge Management and Reference Services

    Science.gov (United States)

    Gandhi, Smiti

    2004-01-01

    Many corporations are embracing knowledge management (KM) to capture the intellectual capital of their employees. This article focuses on KM applications for reference work in libraries. It defines key concepts of KM, establishes a need for KM for reference services, and reviews various KM initiatives for reference services.

  19. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  20. Colleagues Pay Tribute to Dr. Donald A.B. Lindberg, Retiring After Three Decades of NLM Leadership | NIH MedlinePlus ...

    Science.gov (United States)

    ... informatics and helped establish the National Center for Biotechnology Information (NCBI), a course-changing development that could ... expand the publication and distribution of NIH MedlinePlus magazine, thousands and thousands more people will gain valuable, ...

  1. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  2. Locating and parsing bibliographic references in HTML medical articles.

    Science.gov (United States)

    Zou, Jie; Le, Daniel; Thoma, George R

    2010-06-01

    The set of references that typically appear toward the end of journal articles is sometimes, though not always, a field in bibliographic (citation) databases. But even if references do not constitute such a field, they can be useful as a preprocessing step in the automated extraction of other bibliographic data from articles, as well as in computer-assisted indexing of articles. Automation in data extraction and indexing to minimize human labor is key to the affordable creation and maintenance of large bibliographic databases. Extracting the components of references, such as author names, article title, journal name, publication date and other entities, is therefore a valuable and sometimes necessary task. This paper describes a two-step process using statistical machine learning algorithms, to first locate the references in HTML medical articles and then to parse them. Reference locating identifies the reference section in an article and then decomposes it into individual references. We formulate this step as a two-class classification problem based on text and geometric features. An evaluation conducted on 500 articles drawn from 100 medical journals achieves near-perfect precision and recall rates for locating references. Reference parsing identifies the components of each reference. For this second step, we implement and compare two algorithms. One relies on sequence statistics and trains a Conditional Random Field. The other focuses on local feature statistics and trains a Support Vector Machine to classify each individual word, followed by a search algorithm that systematically corrects low confidence labels if the label sequence violates a set of predefined rules. The overall performance of these two reference-parsing algorithms is about the same: above 99% accuracy at the word level, and over 97% accuracy at the chunk level.

  3. Genetics Home Reference: spastic paraplegia type 8

    Science.gov (United States)

    ... exaggerated reflexes (hyperreflexia), a decreased ability to feel vibrations, muscle wasting (amyotrophy), and reduced bladder control. The ... and Therapies General Information from MedlinePlus (5 links) Diagnostic Tests Drug Therapy Genetic Counseling Palliative Care Surgery ...

  4. Genetics Home Reference: spastic paraplegia type 31

    Science.gov (United States)

    ... exaggerated reflexes (hyperreflexia), a decreased ability to feel vibrations, reduced bladder control, and high-arched feet ( pes ... and Therapies General Information from MedlinePlus (5 links) Diagnostic Tests Drug Therapy Genetic Counseling Palliative Care Surgery ...

  5. Genetics Home Reference: chylomicron retention disease

    Science.gov (United States)

    ... reflexes (hyporeflexia) and a decreased ability to feel vibrations. Related Information What does it mean if a ... Encyclopedia: Malabsorption General Information from MedlinePlus (5 links) Diagnostic Tests Drug Therapy Genetic Counseling Palliative Care Surgery ...

  6. Genetics Home Reference: familial paroxysmal nonkinesigenic dyskinesia

    Science.gov (United States)

    ... slow, prolonged contraction of muscles (dystonia); small, fast, "dance-like" motions (chorea); writhing movements of the limbs ( ... Information from MedlinePlus (5 links) Diagnostic Tests Drug Therapy Genetic Counseling Palliative Care Surgery and Rehabilitation Related ...

  7. Genetics Home Reference: familial paroxysmal kinesigenic dyskinesia

    Science.gov (United States)

    ... involve slow, prolonged muscle contractions (dystonia); small, fast, "dance-like" motions (chorea); writhing movements of the limbs ( ... Information from MedlinePlus (5 links) Diagnostic Tests Drug Therapy Genetic Counseling Palliative Care Surgery and Rehabilitation Related ...

  8. Genetics Home Reference: familial isolated pituitary adenoma

    Science.gov (United States)

    ... children or adolescents can lead to increased height (gigantism), because the long bones of their arms and ... Information & Resources MedlinePlus (6 links) Encyclopedia: Acromegaly Encyclopedia: Gigantism Encyclopedia: Pituitary Tumor Encyclopedia: Prolactinoma Health Topic: Endocrine ...

  9. Genetics Home Reference: isolated sulfite oxidase deficiency

    Science.gov (United States)

    ... and Management Resources (1 link) GeneReview: Isolated Sulfite Oxidase Deficiency General Information from MedlinePlus (5 links) Diagnostic Tests Drug Therapy Genetic Counseling Palliative Care Surgery and ...

  10. Diagnostic reference levels in digital mammography: a systematic review

    International Nuclear Information System (INIS)

    Suleiman, Moayyad E.; Brennan, Patrick C.; McEntee, Mark F.

    2015-01-01

    This study aims to review the literature on existing diagnostic reference levels (DRLs) in digital mammography and methodologies for establishing them. To this end, a systematic search through Medline, Cinahl, Web of Science, Scopus and Google scholar was conducted using search terms extracted from three terms: DRLs, digital mammography and breast screen. The search resulted in 1539 articles of which 22 were included after a screening process. Relevant data from the included studies were summarised and analysed. Differences were found in the methods utilised to establish DRLs including test subjects types, protocols followed, conversion factors employed, breast compressed thicknesses and percentile values adopted. These differences complicate comparison of DRLs among countries; hence, an internationally accepted protocol would be valuable so that international comparisons can be made. (authors)

  11. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  12. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  13. Genetics Home Reference: Müllerian aplasia and hyperandrogenism

    Science.gov (United States)

    ... do not begin menstruation by age 16 (primary amenorrhea) and will likely never have a menstrual period. ... Encyclopedia: Ovarian Overproduction of Androgens MedlinePlus Encyclopedia: Primary Amenorrhea General Information from MedlinePlus (5 links) Diagnostic Tests ...

  14. Genetics Home Reference: platyspondylic lethal skeletal dysplasia, Torrance type

    Science.gov (United States)

    ... and an exaggerated curvature of the lower back ( lordosis ). Infants with this condition are born with a ... Diagnosis and Management Resources (1 link) MedlinePlus Encyclopedia: Lordosis General Information from MedlinePlus (5 links) Diagnostic Tests ...

  15. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  16. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  17. Sequence to Sequence - Video to Text

    Science.gov (United States)

    2015-12-11

    by centering x and y flow values around 128 and multiplying by a scalar such that flow values fall between 0 and 255. We also calculate the flow magni...as for MPII- MD. 4.2. Evaluation Metrics Quantitative evaluation of the models are performed us- ing the METEOR [7] metric which was originally pro...candidate refer- ence sentences. METEOR compares exact token matches, stemmed tokens, paraphrase matches, as well as semanti- cally similar matches

  18. Bunches of random cross-correlated sequences

    International Nuclear Information System (INIS)

    Maystrenko, A A; Melnik, S S; Pritula, G M; Usatenko, O V

    2013-01-01

    The statistical properties of random cross-correlated sequences constructed by the convolution method (likewise referred to as the Rice or the inverse Fourier transformation) are examined. We clarify the meaning of the filtering function—the kernel of the convolution operator—and show that it is the value of the cross-correlation function which describes correlations between the initial white noise and constructed correlated sequences. The matrix generalization of this method for constructing a bunch of N cross-correlated sequences is presented. Algorithms for their generation are reduced to solving the problem of decomposition of the Fourier transform of the correlation matrix into a product of two mutually conjugate matrices. Different decompositions are considered. The limits of weak and strong correlations for the one-point probability and pair correlation functions of sequences generated by the method under consideration are studied. Special cases of heavy-tailed distributions of the generated sequences are analyzed. We show that, if the filtering function is rather smooth, the distribution function of generated variables has the Gaussian or Lévy form depending on the analytical properties of the distribution (or characteristic) functions of the initial white noise. Anisotropic properties of statistically homogeneous random sequences related to the asymmetry of a filtering function are revealed and studied. These asymmetry properties are expressed in terms of the third- or fourth-order correlation functions. Several examples of the construction of correlated chains with a predefined correlation matrix are given. (paper)

  19. Experience of targeted Usher exome sequencing as a clinical test

    Science.gov (United States)

    Besnard, Thomas; García-García, Gema; Baux, David; Vaché, Christel; Faugère, Valérie; Larrieu, Lise; Léonard, Susana; Millan, Jose M; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

    2014-01-01

    We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service. PMID:24498627

  20. Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE

    Science.gov (United States)

    Cohen, K. Bretonnel; Xia, Jingbo; Roeder, Christophe; Hunter, Lawrence E.

    2018-01-01

    There is currently a crisis in science related to highly publicized failures to reproduce large numbers of published studies. The current work proposes, by way of case studies, a methodology for moving the study of reproducibility in computational work to a full stage beyond that of earlier work. Specifically, it presents a case study in attempting to reproduce the reports of two R libraries for doing text mining of the PubMed/MEDLINE repository of scientific publications. The main findings are that a rational paradigm for reproduction of natural language processing papers can be established; the advertised functionality was difficult, but not impossible, to reproduce; and reproducibility studies can produce additional insights into the functioning of the published system. Additionally, the work on reproducibility lead to the production of novel user-centered documentation that has been accessed 260 times since its publication—an average of once a day per library. PMID:29568821

  1. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  2. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  3. High-performance information search filters for acute kidney injury content in PubMed, Ovid Medline and Embase.

    Science.gov (United States)

    Hildebrand, Ainslie M; Iansavichus, Arthur V; Haynes, R Brian; Wilczynski, Nancy L; Mehta, Ravindra L; Parikh, Chirag R; Garg, Amit X

    2014-04-01

    We frequently fail to identify articles relevant to the subject of acute kidney injury (AKI) when searching the large bibliographic databases such as PubMed, Ovid Medline or Embase. To address this issue, we used computer automation to create information search filters to better identify articles relevant to AKI in these databases. We first manually reviewed a sample of 22 992 full-text articles and used prespecified criteria to determine whether each article contained AKI content or not. In the development phase (two-thirds of the sample), we developed and tested the performance of >1.3-million unique filters. Filters with high sensitivity and high specificity for the identification of AKI articles were then retested in the validation phase (remaining third of the sample). We succeeded in developing and validating high-performance AKI search filters for each bibliographic database with sensitivities and specificities in excess of 90%. Filters optimized for sensitivity reached at least 97.2% sensitivity, and filters optimized for specificity reached at least 99.5% specificity. The filters were complex; for example one PubMed filter included >140 terms used in combination, including 'acute kidney injury', 'tubular necrosis', 'azotemia' and 'ischemic injury'. In proof-of-concept searches, physicians found more articles relevant to topics in AKI with the use of the filters. PubMed, Ovid Medline and Embase can be filtered for articles relevant to AKI in a reliable manner. These high-performance information filters are now available online and can be used to better identify AKI content in large bibliographic databases.

  4. Post-main-sequence planetary system evolution

    Science.gov (United States)

    Veras, Dimitri

    2016-01-01

    The fates of planetary systems provide unassailable insights into their formation and represent rich cross-disciplinary dynamical laboratories. Mounting observations of post-main-sequence planetary systems necessitate a complementary level of theoretical scrutiny. Here, I review the diverse dynamical processes which affect planets, asteroids, comets and pebbles as their parent stars evolve into giant branch, white dwarf and neutron stars. This reference provides a foundation for the interpretation and modelling of currently known systems and upcoming discoveries. PMID:26998326

  5. User Preferences in Reference Services: Virtual Reference and Academic Libraries

    Science.gov (United States)

    Cummings, Joel; Cummings, Lara; Frederiksen, Linda

    2007-01-01

    This study examines the use of chat in an academic library's user population and where virtual reference services might fit within the spectrum of public services offered by academic libraries. Using questionnaires, this research demonstrates that many within the academic community are open to the idea of chat-based reference or using chat for…

  6. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  7. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  8. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  9. Java for dummies quick reference

    CERN Document Server

    Lowe, Doug

    2012-01-01

    A reference that answers your questions as you move through your coding The demand for Android programming and web apps continues to grow at an unprecedented pace and Java is the preferred language for both. Java For Dummies Quick Reference keeps you moving through your coding while you solve a problem, look up a command or syntax, or search for a programming tip. Whether you're a Java newbie or a seasoned user, this fast reference offers you quick access to solutions without requiring that you wade through pages of tutorial material. Leverages the true reference format that is organized with

  10. Quark enables semi-reference-based compression of RNA-seq data.

    Science.gov (United States)

    Sarkar, Hirak; Patro, Rob

    2017-11-01

    The past decade has seen an exponential increase in biological sequencing capacity, and there has been a simultaneous effort to help organize and archive some of the vast quantities of sequencing data that are being generated. Although these developments are tremendous from the perspective of maximizing the scientific utility of available data, they come with heavy costs. The storage and transmission of such vast amounts of sequencing data is expensive. We present Quark, a semi-reference-based compression tool designed for RNA-seq data. Quark makes use of a reference sequence when encoding reads, but produces a representation that can be decoded independently, without the need for a reference. This allows Quark to achieve markedly better compression rates than existing reference-free schemes, while still relieving the burden of assuming a specific, shared reference sequence between the encoder and decoder. We demonstrate that Quark achieves state-of-the-art compression rates, and that, typically, only a small fraction of the reference sequence must be encoded along with the reads to allow reference-free decompression. Quark is implemented in C ++11, and is available under a GPLv3 license at www.github.com/COMBINE-lab/quark. rob.patro@cs.stonybrook.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  11. Geoseq: a tool for dissecting deep-sequencing datasets

    Directory of Open Access Journals (Sweden)

    Homann Robert

    2010-10-01

    Full Text Available Abstract Background Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO, Sequence Read Archive (SRA hosted by the NCBI, or the DNA Data Bank of Japan (ddbj. Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest. Results Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public sequencing data using a controlled vocabulary, allowing identification of relevant libraries by organism, tissue and type of experiment. Conclusions Analysis of small sets of sequences against deep-sequencing datasets, as well as identification of public datasets of interest, is simplified by Geoseq. We applied Geoseq to, a identify differential isoform expression in mRNA-seq datasets, b identify miRNAs (microRNAs in libraries, and identify mature and star sequences in miRNAS and c to identify potentially mis-annotated miRNAs. The ease of using Geoseq for these analyses suggests its utility and uniqueness as an analysis tool.

  12. Moving Reference to the Web.

    Science.gov (United States)

    McGlamery, Susan; Coffman, Steve

    2000-01-01

    Explores the possibility of using Web contact center software to offer reference assistance to remote users. Discusses a project by the Metropolitan Cooperative Library System/Santiago Library System consortium to test contact center software and to develop a virtual reference network. (Author/LRW)

  13. Reference vectors in economic choice

    Directory of Open Access Journals (Sweden)

    Teycir Abdelghani GOUCHA

    2013-07-01

    Full Text Available In this paper the introduction of notion of reference vector paves the way for a combination of classical and social approaches in the framework of referential preferences given by matrix groups. It is shown that individual demand issue from rational decision does not depend on that reference.

  14. "In Your Face" Reference Service.

    Science.gov (United States)

    Lipow, Anne Grodzins

    1999-01-01

    Discusses changes in library reference service that have occurred with growing Internet use. Topics include the human factor that is still needed; the nature of reference questions; the goal of user self-sufficiency; the invisible nature of much of librarians' work; and providing real-time, interactive point-of-need service to remote users. (LRW)

  15. Technostress and the Reference Librarian.

    Science.gov (United States)

    Kupersmith, John

    1992-01-01

    Defines "technostress" as the stress experienced by reference librarians who must constantly deal with the demands of new information technology and the changes they produce in the work place. Discussion includes suggested ways in which both organizations and individuals can work to reduce stress. (27 references) (LAE)

  16. Reference Services: A Handmaid's Tale.

    Science.gov (United States)

    Beck, Clare

    1991-01-01

    Discussion of problems in library reference services focuses on the influence of gender roles. A historical overview of gender roles in the development of American librarianship is presented that highlights stereotyped views of and attitudes toward women, which the author suggests still have influences on librarianship today. (17 references) (LRW)

  17. Examining the role of MEDLINE as a patient care information resource: an analysis of data from the Value of Libraries study.

    Science.gov (United States)

    Dunn, Kathel; Marshall, Joanne Gard; Wells, Amber L; Backus, Joyce E B

    2017-10-01

    This study analyzed data from a study on the value of libraries to understand the specific role that the MEDLINE database plays in relation to other information resources that are available to health care providers and its role in positively impacting patient care. A previous study on the use of health information resources for patient care obtained 16,122 responses from health care providers in 56 hospitals about how providers make decisions affecting patient care and the role of information resources in that process. Respondents indicated resources used in answering a specific clinical question from a list of 19 possible resources, including MEDLINE. Study data were examined using descriptive statistics and regression analysis to determine the number of information resources used and how they were used in combination with one another. Health care professionals used 3.5 resources, on average, to aid in patient care. The 2 most frequently used resources were journals (print and online) and the MEDLINE database. Using a higher number of information resources was significantly associated with a higher probability of making changes to patient care and avoiding adverse events. MEDLINE was the most likely to be among consulted resources compared to any other information resource other than journals. MEDLINE is a critical clinical care tool that health care professionals use to avoid adverse events, make changes to patient care, and answer clinical questions.

  18. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  19. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  20. Plans and progress for building a Great Lakes fauna DNA barcode reference library

    Science.gov (United States)

    DNA reference libraries provide researchers with an important tool for assessing regional biodiversity by allowing unknown genetic sequences to be assigned identities, while also providing a means for taxonomists to validate identifications. Expanding the representation of Great...