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Scientific data 122건

  1. [해외논문]   The FAIR Guiding Principles for scientific data management and stewardship  

    Wilkinson, Mark D. (Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid , Madrid 28223, Spain ) , Dumontier, Michel (Stanford University , Stanford 94305-5411, USA ) , Aalbersberg, IJsbrand Jan (Elsevier, Amsterdam 1043 NX, The Netherlands ) , Appleton, Gabrielle (Elsevier, Amsterdam 1043 NX, The Netherlands ) , Axton, Myles (Nature Genetics , New York 10004-1562, USA ) , Baak, Arie (Euretos and Phortos Consultants , Rotterdam 2741 CA, The Netherlands ) , Blomberg, Niklas (ELIXIR, Wellcome Genome Campus , Hinxton CB10 1SA, UK ) , Boiten, Jan-Willem (Lygature , Eindhoven 5656 AG, The Netherlands ) , da Silva Santos, Luiz Bonino (Vrije Universiteit Amsterdam, Dutch Techcenter for Life Sciences , Amsterdam 1081 HV, The Netherlands ) , Bourne, Philip E. (Office of the Director, National Institutes of Health , Rockville 20892, USA ) , Bouwman, Jildau (TNO , Zeist 3700 AJ, The Netherlands <count) , Brookes, Anthony J. , Clark, Tim , Crosas, Mercè , , Dillo, Ingrid , Dumon, Olivier , Edmunds, Scott , Evelo, Chris T. , Finkers, Richard , Gonzalez-Beltran, Alejandra , Gray, Alasdair J.G. , Groth, Paul , Goble, Carole , Grethe, Jeffrey S. , Heringa, Jaap , 't Hoen, Peter A.C , Hooft, Rob , Kuhn, Tobias , Kok, Ruben , Kok, Joost , Lusher, Scott J. , Martone, Maryann E. , Mons, Albert , Packer, Abel L. , Persson, Bengt , Rocca-Serra, Philippe , Roos, Marco , van Schaik, Rene , Sansone, Susanna-Assunta , Schultes, Erik , Sengstag, Thierry , Slater, Ted , Strawn, George , Swertz, Morris A. , Thompson, Mark , van der Lei, Johan , van Mulligen, Erik , Velterop, Jan , Waagmeester, Andra , Wittenburg, Peter , Wolstencroft, Katherine , Zhao, Jun , Mons, Barend
    Scientific data v.3 ,pp. 160018 , 2016 ,

    초록

    There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

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  2. [해외논문]   Genome-scale DNA methylome and transcriptome profiling of human neutrophils  

    Chatterjee, Aniruddha (Department of Pathology, Dunedin School of Medicine, University of Otago , 270 Great King Street, Dunedin 9054, New Zealand ) , Stockwell, Peter A. (Department of Biochemistry, University of Otago , 710 Cumberland Street, Dunedin 9054, New Zealand ) , Rodger, Euan J. (Department of Pathology, Dunedin School of Medicine, University of Otago , 270 Great King Street, Dunedin 9054, New Zealand ) , Morison, Ian M. (Department of Pathology, Dunedin School of Medicine, University of Otago , 270 Great King Street, Dunedin 9054, New Zealand )
    Scientific data v.3 ,pp. 160019 , 2016 ,

    초록

    Methylation of DNA molecules is a key mechanism associated with human disease, altered gene expression and phenotype. Using reduced representation bisulphite sequencing (RRBS) technology we have analysed DNA methylation patterns in healthy individuals and identified genes showing significant inter-individual variation. Further, using whole genome transcriptome analysis (RNA-Seq) on the same individuals we showed a local and specific relationship of exon inclusion and variable DNA methylation pattern. For RRBS, 363 million, 100-bp reads were generated from 13 samples using Illumina GAII and HiSeq2000 platforms. Here we also present additional RRBS data for a female pair of monozygotic twins that was not described in our original publication. Further, We performed RNA-Seq on four of these individuals, generating 174 million, 51-bp high quality reads on an Illumina HiSeq2000 platform. The current data set could be exploited as a comprehensive resource for understanding the nature and mechanism of variable phenotypic traits and altered disease susceptibility due to variable DNA methylation and gene expression patterns in healthy individuals.

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  3. [해외논문]   An agricultural survey for more than 9,500 African households  

    Waha, Katharina (CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD 4067, Australia ) , Zipf, Birgit (University of Potsdam, Institute of Earth and Environmental Science, Karl-Liebknecht-Strasse 24-25, Potsdam 14476, Germany ) , Kurukulasuriya, Pradeep (Centre for Environmental Economics and Policy Analysis in Africa (CEEPA), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0001, Republic of South Africa) , Hassan, Rashid M.
    Scientific data v.3 ,pp. 160020 , 2016 ,

    초록

    Surveys for more than 9,500 households were conducted in the growing seasons 2002/2003 or 2003/2004 in eleven African countries: Burkina Faso, Cameroon, Ghana, Niger and Senegal in western Africa; Egypt in northern Africa; Ethiopia and Kenya in eastern Africa; South Africa, Zambia and Zimbabwe in southern Africa. Households were chosen randomly in districts that are representative for key agro-climatic zones and farming systems. The data set specifies farming systems characteristics that can help inform about the importance of each system for a country’s agricultural production and its ability to cope with short- and long-term climate changes or extreme weather events. Further it informs about the location of smallholders and vulnerable systems and permits benchmarking agricultural systems characteristics.

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  4. [해외논문]   X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex  

    Zhou, X. Edward (Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute , Grand Rapids, Michigan 49503, USA ) , Gao, Xiang (Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute , Grand Rapids, Michigan 49503, USA ) , Barty, Anton (Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , 22607 Hamburg, Germany ) , Kang, Yanyong (Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute , Grand Rapids, Michigan 49503, USA ) , He, Yuanzheng (Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute , Grand Rapids, Michigan 49503, USA ) , Liu, Wei (School of Molecular Sciences, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University , Tempe, Arizona 85287-1604, USA ) , Ishchenko, Andrii , White, Thomas A. , Yefanov, Oleksandr , Han, Gye Won , Xu, Qingping , de Waal, Parker W. , Suino-Powell, Kelly M. , Boutet, Sé , bastien , Williams, Garth J. , Wang, Meitian , Li, Dianfan , Caffrey, Martin , Chapman, Henry N. , Spence, John C.H. , Fromme, Petra , Weierstall, Uwe , Stevens, Raymond C. , Cherezov, Vadim , Melcher, Karsten , Xu, H. Eric
    Scientific data v.3 ,pp. 160021 , 2016 ,

    초록

    Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

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  5. [해외논문]   Global gene expression profiling of JMJD6- and JMJD4-depleted mouse NIH3T3 fibroblasts  

    Hu, Yu-Jie (Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, USA ) , Imbalzano, Anthony N. (Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, USA )
    Scientific data v.3 ,pp. 160022 , 2016 ,

    초록

    Emerging evidence suggests Jumonji domain-containing proteins are epigenetic regulators in diverse biological processes including cellular differentiation and proliferation. RNA interference-based analyses combined with gene expression profiling can effectively characterize the cellular functions of these enzymes. We found that the depletion of Jumonji domain-containing protein 6 (JMJD6) and its paralog protein Jumonji domain-containing protein 4 (JMJD4) individually by small hairpin RNAs (shRNAs) slowed cell proliferation of mouse NIH3T3 fibroblasts. We subsequently performed gene expression profiling on both JMJD6- and JMJD4-depleted mouse NIH3T3 fibroblasts using the Affymetrix GeneChip Mouse Exon 1.0 ST Array. Here we report the gene profiling datasets along with the experimental procedures. The information can be used to further investigate how JMJD6 and JMJD4 affect gene expression and cellular physiology.

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  6. [해외논문]   Reference genotype and exome data from an Australian Aboriginal population for health-based research  

    Tang, Dave (Telethon Kids Institute, The University of Western Australia ) , Anderson, Denise (Telethon Kids Institute, The University of Western Australia ) , Francis, Richard W. (Telethon Kids Institute, The University of Western Australia ) , Syn, Genevieve (Telethon Kids Institute, The University of Western Australia ) , Jamieson, Sarra E. (Telethon Kids Institute, The University of Western Australia ) , Lassmann, Timo (Telethon Kids Institute, The University of Western Australia ) , Blackwell, Jenefer M. (Telethon Kids Institute, The University of Western Australia )
    Scientific data v.3 ,pp. 160023 , 2016 ,

    초록

    Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.

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  7. [해외논문]   A multi-decade dataset of monthly beach profile surveys and inshore wave forcing at Narrabeen, Australia  

    Turner, Ian L. (Water Research Laboratory, School of Civil and Environmental Engineering, UNSW Australia, Sydney, NSW 2052, Australia ) , Harley, Mitchell D. (Water Research Laboratory, School of Civil and Environmental Engineering, UNSW Australia, Sydney, NSW 2052, Australia ) , Short, Andrew D. (School of Geosciences, University of Sydney, NSW 2006, Australia ) , Simmons, Joshua A. (Water Research Laboratory, School of Civil and Environmental Engineering, UNSW Australia, Sydney, NSW 2052, Australia ) , Bracs, Melissa A. (Water Research Laboratory, School of Civil and Environmental Engineering, UNSW Australia, Sydney, NSW 2052, Australia ) , Phillips, Matthew S. (Water Research Laboratory, School of Civil and Environmental Engineering, UNSW Australia, Sydney, NSW 2052, Australia ) , Splinter, Kristen D. (Water Research Laboratory, School of Civil and Environmental Engineering, UNSW Australia, Sydney, NSW 2052, Australia)
    Scientific data v.3 ,pp. 160024 , 2016 ,

    초록

    Long-term observational datasets that record and quantify variability, changes and trends in beach morphology at sandy coastlines together with the accompanying wave climate are rare. A monthly beach profile survey program commenced in April 1976 at Narrabeen located on Sydney’s Northern Beaches in southeast Australia is one of just a handful of sites worldwide where on-going and uninterrupted beach monitoring now spans multiple decades. With the Narrabeen survey program reaching its 40-year milestone in April 2016, it is timely that free and unrestricted use of these data be facilitated to support the next advances in beach erosion-recovery modelling. The archived dataset detailed here includes the monthly subaerial profiles, available bathymetry for each survey transect extending seawards to 20 m water depth, and time-series of ocean astronomical tide and inshore wave forcing at 10 m water depths, the latter corresponding to the location of individual survey transects. In addition, on-going access to the results of the continuing monthly survey program is described.

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  8. [해외논문]   Extensive sequencing of seven human genomes to characterize benchmark reference materials  

    Zook, Justin M. (National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA ) , Catoe, David (National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA ) , McDaniel, Jennifer (National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA ) , Vang, Lindsay (National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA ) , Spies, Noah (National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA ) , Sidow, Arend (Stanford University, Stanford, California 94305, USA ) , Weng, Ziming (Stanford University, Stanford, California 94305, USA ) , Liu, Yuling (Stanford University, Stanford, California 94305, USA ) , Mason, Christopher E. (Stanford University, Stanford, California 94305, USA ) , Alexander, Noah (Department of Physiology and Biophysics, the Feil Family Brain and Mind Research Institute, and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College, Cornell University, New York, New York 10065, USA ) , Henaff, Elizabeth (Department of Physiology and Biophysics, the Feil Family Brain and Mind Research Institute, and H) , McIntyre, Alexa B.R. , Chandramohan, Dhruva , Chen, Feng , Jaeger, Erich , Moshrefi, Ali , Pham, Khoa , Stedman, William , Liang, Tiffany , Saghbini, Michael , Dzakula, Zeljko , Hastie, Alex , Cao, Han , Deikus, Gintaras , Schadt, Eric , Sebra, Robert , Bashir, Ali , Truty, Rebecca M. , Chang, Christopher C. , Gulbahce, Natali , Zhao, Keyan , Ghosh, Srinka , Hyland, Fiona , Fu, Yutao , Chaisson, Mark , Xiao, Chunlin , Trow, Jonathan , Sherry, Stephen T. , Zaranek, Alexander W. , Ball, Madeleine , Bobe, Jason , Estep, Preston , Church, George M. , Marks, Patrick , Kyriazopoulou-Panagiotopoulou, Sofia , Zheng, Grace X.Y. , Schnall-Levin, Michael , Ordonez, Heather S. , Mudivarti, Patrice A. , Giorda, Kristina
    Scientific data v.3 ,pp. 160025 , 2016 ,

    초록

    The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. Cell lines, DNA, and data from these individuals are publicly available. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly.

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  9. [해외논문]   A curated and standardized adverse drug event resource to accelerate drug safety research  

    Banda, Juan M. (Center for Biomedical Informatics Research, Stanford University , Stanford, California 94305, USA ) , Evans, Lee (LTS Computing LLC , West Chester, Pennsylvania 19380, USA ) , Vanguri, Rami S. (Department of Biomedical Informatics, Columbia University , New York, New York 10032, USA ) , Tatonetti, Nicholas P. (Department of Biomedical Informatics, Columbia University , New York, New York 10032, USA ) , Ryan, Patrick B. (Janssen Research & Development, LLC , Titusville, New Jersey 08869, USA ) , Shah, Nigam H. (Center for Biomedical Informatics Research, Stanford University , Stanford, California 94305, USA )
    Scientific data v.3 ,pp. 160026 , 2016 ,

    초록

    Identification of adverse drug reactions (ADRs) during the post-marketing phase is one of the most important goals of drug safety surveillance. Spontaneous reporting systems (SRS) data, which are the mainstay of traditional drug safety surveillance, are used for hypothesis generation and to validate the newer approaches. The publicly available US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) data requires substantial curation before they can be used appropriately, and applying different strategies for data cleaning and normalization can have material impact on analysis results. We provide a curated and standardized version of FAERS removing duplicate case records, applying standardized vocabularies with drug names mapped to RxNorm concepts and outcomes mapped to SNOMED-CT concepts, and pre-computed summary statistics about drug-outcome relationships for general consumption. This publicly available resource, along with the source code, will accelerate drug safety research by reducing the amount of time spent performing data management on the source FAERS reports, improving the quality of the underlying data, and enabling standardized analyses using common vocabularies.

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    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  10. [해외논문]   A patient-level data meta-analysis of standard-of-care treatments from eight prostate cancer clinical trials  

    Geifman, N. (Institute for Computational Health Sciences, University of California San Francisco , Mission Hall, 550 16th Street, San Francisco, CA 94158-2549, USA ) , Butte, A.J (Institute for Computational Health Sciences, University of California San Francisco , Mission Hall, 550 16th Street, San Francisco, CA 94158-2549, USA )
    Scientific data v.3 ,pp. 160027 , 2016 ,

    초록

    Open clinical trial data offer many opportunities for the scientific community to independently verify published results, evaluate new hypotheses and conduct meta-analyses. These data provide valuable opportunities for scientific advances in medical research. Herein we present the comparative meta-analysis of different standard of care treatments from newly available comparator arm data from several prostate cancer clinical trials. Comparison of survival rates following treatment with mitoxantrone or docetaxel in combination with prednisone as well as prednisone alone, validated the previously demonstrated superiority of treatment with docetaxel. Additionally, comparison of four testosterone suppression treatments in hormone-refractory prostate cancer revealed that subjects who had undergone surgical castration had significantly lower survival rates than those treated with LHRH, anti-androgen or LHRH plus anti-androgen, suggesting that this treatment option is less optimal. This study illustrates how the use of patient-level clinical trial data enables meta-analyses that can provide new insights into clinical outcomes of standard of care treatments and thus, once validated, has the potential to help optimize healthcare delivery.

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