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  • Reproducibility of Results  (66)
  • Chemistry
  • Electronic structure and strongly correlated systems
  • Nature Publishing Group (NPG)  (68)
  • 2010-2014  (68)
  • 1985-1989
  • 1980-1984
  • 2011  (68)
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  • 2010-2014  (68)
  • 1985-1989
  • 1980-1984
Year
  • 1
    Publication Date: 2011-07-26
    Description: The conserved Polycomb repressive complex 2 (PRC2) generates trimethylation of histone 3 lysine 27 (H3K27me3), a modification associated with stable epigenetic silencing. Much is known about PRC2-induced silencing but key questions remain concerning its nucleation and stability. Vernalization, the perception and memory of winter in plants, is a classic epigenetic process that, in Arabidopsis, involves PRC2-based silencing of the floral repressor FLC. The slow dynamics of vernalization, taking place over weeks in the cold, generate a level of stable silencing of FLC in the subsequent warm that depends quantitatively on the length of the prior cold. These features make vernalization an ideal experimental system to investigate both the maintenance of epigenetic states and the switching between them. Here, using mathematical modelling, chromatin immunoprecipitation and an FLC:GUS reporter assay, we show that the quantitative nature of vernalization is generated by H3K27me3-mediated FLC silencing in the warm in a subpopulation of cells whose number depends on the length of the prior cold. During the cold, H3K27me3 levels progressively increase at a tightly localized nucleation region within FLC. At the end of the cold, numerical simulations predict that such a nucleation region is capable of switching the bistable epigenetic state of an individual locus, with the probability of overall FLC coverage by silencing H3K27me3 marks depending on the length of cold exposure. Thus, the model predicts a bistable pattern of FLC gene expression in individual cells, a prediction we verify using the FLC:GUS reporter system. Our proposed switching mechanism, involving the local nucleation of an opposing histone modification, is likely to be widely relevant in epigenetic reprogramming.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Angel, Andrew -- Song, Jie -- Dean, Caroline -- Howard, Martin -- England -- Nature. 2011 Jul 24;476(7358):105-8. doi: 10.1038/nature10241.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21785438" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*genetics/physiology ; Arabidopsis Proteins/genetics ; Chromatin Immunoprecipitation ; *Epigenesis, Genetic ; *Gene Expression Regulation, Plant ; Gene Silencing ; Histones/metabolism ; MADS Domain Proteins/genetics ; Methylation ; Models, Genetic ; Plant Roots/metabolism ; Polycomb-Group Proteins ; Repressor Proteins/*metabolism ; Reproducibility of Results ; Seasons ; Temperature
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2011-02-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Onslow, Mark -- Packman, Ann -- England -- Nature. 2011 Feb 24;470(7335):465; author reply 465. doi: 10.1038/470465b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350470" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conditioning, Operant ; Humans ; Randomized Controlled Trials as Topic ; Reproducibility of Results ; Stuttering/epidemiology/*therapy ; Treatment Outcome
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  • 3
    Publication Date: 2011-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Legg, David A -- Ma, Xiaoya -- Wolfe, Joanna M -- Ortega-Hernandez, Javier -- Edgecombe, Gregory D -- Sutton, Mark D -- England -- Nature. 2011 Aug 10;476(7359):E2-3; discussion E3-4. doi: 10.1038/nature10267.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Science and Engineering, Imperial College London, London SW7 2AZ UK. d.legg10@imperial.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21833046" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthropods/anatomy & histology/*classification ; Fossils ; *Phylogeny ; Pseudopodia/*classification ; Reproducibility of Results
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  • 4
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    Nature Publishing Group (NPG)
    Publication Date: 2011-10-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lehn, Jean-Marie -- England -- Nature. 2011 Oct 12;478(7368):S8-9. doi: 10.1038/478S8a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993827" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry ; Exobiology ; Hippocratic Oath ; Knowledge ; Motivation ; *Nobel Prize ; *Research Personnel/ethics/psychology/standards
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  • 5
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    Nature Publishing Group (NPG)
    Publication Date: 2011-01-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmidhuber, Jurgen -- England -- Nature. 2011 Jan 6;469(7328):34. doi: 10.1038/469034b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21209647" target="_blank"〉PubMed〈/a〉
    Keywords: *Bibliometrics ; Economic Development/statistics & numerical data ; Europe ; Reproducibility of Results ; Research/economics/*standards ; United States ; Universities/economics/standards
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  • 6
    Publication Date: 2011-03-25
    Description: Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179250/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179250/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Negre, Nicolas -- Brown, Christopher D -- Ma, Lijia -- Bristow, Christopher Aaron -- Miller, Steven W -- Wagner, Ulrich -- Kheradpour, Pouya -- Eaton, Matthew L -- Loriaux, Paul -- Sealfon, Rachel -- Li, Zirong -- Ishii, Haruhiko -- Spokony, Rebecca F -- Chen, Jia -- Hwang, Lindsay -- Cheng, Chao -- Auburn, Richard P -- Davis, Melissa B -- Domanus, Marc -- Shah, Parantu K -- Morrison, Carolyn A -- Zieba, Jennifer -- Suchy, Sarah -- Senderowicz, Lionel -- Victorsen, Alec -- Bild, Nicholas A -- Grundstad, A Jason -- Hanley, David -- MacAlpine, David M -- Mannervik, Mattias -- Venken, Koen -- Bellen, Hugo -- White, Robert -- Gerstein, Mark -- Russell, Steven -- Grossman, Robert L -- Ren, Bing -- Posakony, James W -- Kellis, Manolis -- White, Kevin P -- F32 GM074364/GM/NIGMS NIH HHS/ -- F32 GM074364-01/GM/NIGMS NIH HHS/ -- F32 GM074364-02/GM/NIGMS NIH HHS/ -- P50 GM081892/GM/NIGMS NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01 HG004037-04/HG/NHGRI NIH HHS/ -- RC2 HG005639/HG/NHGRI NIH HHS/ -- RC2 HG005639-02/HG/NHGRI NIH HHS/ -- U01 HG004264/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004264/HG/NHGRI NIH HHS/ -- England -- Nature. 2011 Mar 24;471(7339):527-31. doi: 10.1038/nature09990.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430782" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; Chromatin Immunoprecipitation ; Drosophila melanogaster/*genetics ; Enhancer Elements, Genetic/genetics ; Genome, Insect/*genetics ; Histone Deacetylases/metabolism ; Insulator Elements/genetics ; *Molecular Sequence Annotation ; Promoter Regions, Genetic/genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Reproducibility of Results ; Silencer Elements, Transcriptional/genetics ; Transcription Factors/metabolism
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  • 7
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    Nature Publishing Group (NPG)
    Publication Date: 2011-03-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jonietz, Erika -- England -- Nature. 2011 Mar 24;471(7339):S20-1. doi: 10.1038/471S20a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430717" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Azasteroids/pharmacology ; Biomarkers, Tumor/analysis/blood ; Clinical Trials as Topic/adverse effects/*methods ; Disease Models, Animal ; Drug Approval/legislation & jurisprudence ; Dutasteride ; Health ; Humans ; Male ; Neoplasms/blood/diagnosis/*prevention & control ; Prostatic Neoplasms/prevention & control ; Reproducibility of Results ; Risk Assessment ; United States ; United States Food and Drug Administration/legislation & jurisprudence
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  • 8
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    Nature Publishing Group (NPG)
    Publication Date: 2011-02-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schooler, Jonathan -- England -- Nature. 2011 Feb 24;470(7335):437. doi: 10.1038/470437a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, Santa Barbara, USA. schooler@psych.ucsb.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350443" target="_blank"〉PubMed〈/a〉
    Keywords: Databases, Factual/trends ; Information Dissemination/methods ; Publication Bias/*statistics & numerical data ; Reproducibility of Results ; *Research/standards ; Time Factors
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  • 9
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    Nature Publishing Group (NPG)
    Publication Date: 2011-04-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Van Noorden, Richard -- England -- Nature. 2011 Apr 21;472(7343):270-1. doi: 10.1038/472270a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512544" target="_blank"〉PubMed〈/a〉
    Keywords: *Accidents ; Chemistry ; *Laboratories ; Occupational Health/*statistics & numerical data ; Research Personnel ; Students ; Universities
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  • 10
    Publication Date: 2011-01-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, Neil -- Lux, Thomas -- England -- Nature. 2011 Jan 20;469(7330):302-3. doi: 10.1038/469302a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21248829" target="_blank"〉PubMed〈/a〉
    Keywords: Commerce/economics ; Communicable Diseases/epidemiology/transmission ; Economic Recession/statistics & numerical data ; *Ecosystem ; Financial Management/economics/*methods ; *Models, Biological ; *Models, Economic ; Reproducibility of Results ; Risk Factors ; Risk Management/legislation & jurisprudence/*methods
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  • 11
    Publication Date: 2011-11-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shelton, James -- England -- Nature. 2011 Nov 2;479(7371):7. doi: 10.1038/479007a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bureau for Global Health, US Agency for International Development, Washington DC, USA. jshelton@usaid.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22051636" target="_blank"〉PubMed〈/a〉
    Keywords: Bias (Epidemiology) ; Condoms/utilization ; Contraceptive Agents, Female/administration & dosage/*adverse effects ; Contraceptives, Oral, Hormonal/adverse effects ; Female ; HIV Infections/*epidemiology/*etiology/transmission ; Humans ; Injections ; Male ; Newspapers as Topic/standards ; Periodicals as Topic/*standards ; Reproducibility of Results ; Research Personnel/*standards ; Risk Assessment ; Uncertainty ; Virus Shedding
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  • 12
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    Nature Publishing Group (NPG)
    Publication Date: 2011-02-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maxmen, Amy -- England -- Nature. 2011 Feb 10;470(7333):161-2. doi: 10.1038/470161a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21307912" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Classification ; Genomics/trends ; MicroRNAs/analysis ; *Phylogeny ; Reproducibility of Results
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  • 13
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    Nature Publishing Group (NPG)
    Publication Date: 2011-01-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poste, George -- England -- Nature. 2011 Jan 13;469(7329):156-7. doi: 10.1038/469156a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Complex Adaptive Systems Initiative, Arizona State University, Scottsdale, Arizona 85257, USA. george.poste@asu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21228852" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Specimen Banks/supply & distribution ; Biomarkers/*analysis ; Biomedical Research/economics/standards/trends ; Cell Line ; Female ; Gene Expression Profiling ; Genetics, Medical/economics/*methods/standards/*trends ; Health Care Costs/trends ; Humans ; Male ; Oligonucleotide Array Sequence Analysis ; Pharmacogenetics/economics/standards/trends ; Precision Medicine/economics/standards/*trends ; Proteomics ; Reproducibility of Results ; Sample Size ; Specimen Handling/methods/standards
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  • 14
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    Nature Publishing Group (NPG)
    Publication Date: 2011-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2011 Feb 17;470(7334):305-6. doi: 10.1038/470305b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21330998" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology/*methods/*standards ; *Disclosure ; Documentation/*standards ; Genomics/methods/standards ; Reproducibility of Results ; Research Personnel ; Sequence Analysis, DNA/methods/standards ; Software
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  • 15
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    Nature Publishing Group (NPG)
    Publication Date: 2011-06-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2011 Jun 22;474(7352):419. doi: 10.1038/474419a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21697903" target="_blank"〉PubMed〈/a〉
    Keywords: Bias (Epidemiology) ; Famous Persons ; Reproducibility of Results ; Research/*standards ; Research Personnel/*standards ; Time Factors
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  • 16
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    Nature Publishing Group (NPG)
    Publication Date: 2011-03-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kutschera, U -- England -- Nature. 2011 Mar 3;471(7336):37. doi: 10.1038/471037c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21368813" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Extinction, Biological ; *Phylogeny ; Reproducibility of Results
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  • 17
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    Publication Date: 2011-05-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kwok, Roberta -- England -- Nature. 2011 May 26;473(7348):436-8. doi: 10.1038/473436a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21614053" target="_blank"〉PubMed〈/a〉
    Keywords: Adverse Drug Reaction Reporting Systems ; Animals ; Chickens ; Child ; *Drug-Related Side Effects and Adverse Reactions ; Humans ; Influenza Vaccines/adverse effects ; Narcolepsy/epidemiology/etiology ; Poliovirus Vaccine, Inactivated ; Poliovirus Vaccine, Oral/adverse effects ; *Population Surveillance/methods ; Reproducibility of Results ; Risk Assessment ; Safety/*standards/*statistics & numerical data ; Vaccines/*adverse effects/biosynthesis/*standards
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  • 18
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    Nature Publishing Group (NPG)
    Publication Date: 2011-03-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2011 Mar 17;471(7338):266. doi: 10.1038/471266a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21412289" target="_blank"〉PubMed〈/a〉
    Keywords: Artifacts ; Fatigue Syndrome, Chronic/*etiology/*virology ; Humans ; Patients/psychology ; Reproducibility of Results ; *Xenotropic murine leukemia virus-related virus/isolation & ; purification/pathogenicity
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  • 19
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Nowak et al. argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbot, Patrick -- Abe, Jun -- Alcock, John -- Alizon, Samuel -- Alpedrinha, Joao A C -- Andersson, Malte -- Andre, Jean-Baptiste -- van Baalen, Minus -- Balloux, Francois -- Balshine, Sigal -- Barton, Nick -- Beukeboom, Leo W -- Biernaskie, Jay M -- Bilde, Trine -- Borgia, Gerald -- Breed, Michael -- Brown, Sam -- Bshary, Redouan -- Buckling, Angus -- Burley, Nancy T -- Burton-Chellew, Max N -- Cant, Michael A -- Chapuisat, Michel -- Charnov, Eric L -- Clutton-Brock, Tim -- Cockburn, Andrew -- Cole, Blaine J -- Colegrave, Nick -- Cosmides, Leda -- Couzin, Iain D -- Coyne, Jerry A -- Creel, Scott -- Crespi, Bernard -- Curry, Robert L -- Dall, Sasha R X -- Day, Troy -- Dickinson, Janis L -- Dugatkin, Lee Alan -- El Mouden, Claire -- Emlen, Stephen T -- Evans, Jay -- Ferriere, Regis -- Field, Jeremy -- Foitzik, Susanne -- Foster, Kevin -- Foster, William A -- Fox, Charles W -- Gadau, Juergen -- Gandon, Sylvain -- Gardner, Andy -- Gardner, Michael G -- Getty, Thomas -- Goodisman, Michael A D -- Grafen, Alan -- Grosberg, Rick -- Grozinger, Christina M -- Gouyon, Pierre-Henri -- Gwynne, Darryl -- Harvey, Paul H -- Hatchwell, Ben J -- Heinze, Jurgen -- Helantera, Heikki -- Helms, Ken R -- Hill, Kim -- Jiricny, Natalie -- Johnstone, Rufus A -- Kacelnik, Alex -- Kiers, E Toby -- Kokko, Hanna -- Komdeur, Jan -- Korb, Judith -- Kronauer, Daniel -- Kummerli, Rolf -- Lehmann, Laurent -- Linksvayer, Timothy A -- Lion, Sebastien -- Lyon, Bruce -- Marshall, James A R -- McElreath, Richard -- Michalakis, Yannis -- Michod, Richard E -- Mock, Douglas -- Monnin, Thibaud -- Montgomerie, Robert -- Moore, Allen J -- Mueller, Ulrich G -- Noe, Ronald -- Okasha, Samir -- Pamilo, Pekka -- Parker, Geoff A -- Pedersen, Jes S -- Pen, Ido -- Pfennig, David -- Queller, David C -- Rankin, Daniel J -- Reece, Sarah E -- Reeve, Hudson K -- Reuter, Max -- Roberts, Gilbert -- Robson, Simon K A -- Roze, Denis -- Rousset, Francois -- Rueppell, Olav -- Sachs, Joel L -- Santorelli, Lorenzo -- Schmid-Hempel, Paul -- Schwarz, Michael P -- Scott-Phillips, Tom -- Shellmann-Sherman, Janet -- Sherman, Paul W -- Shuker, David M -- Smith, Jeff -- Spagna, Joseph C -- Strassmann, Beverly -- Suarez, Andrew V -- Sundstrom, Liselotte -- Taborsky, Michael -- Taylor, Peter -- Thompson, Graham -- Tooby, John -- Tsutsui, Neil D -- Tsuji, Kazuki -- Turillazzi, Stefano -- Ubeda, Francisco -- Vargo, Edward L -- Voelkl, Bernard -- Wenseleers, Tom -- West, Stuart A -- West-Eberhard, Mary Jane -- Westneat, David F -- Wiernasz, Diane C -- Wild, Geoff -- Wrangham, Richard -- Young, Andrew J -- Zeh, David W -- Zeh, Jeanne A -- Zink, Andrew -- BB/H022716/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2011 Mar 24;471(7339):E1-4; author reply E9-10. doi: 10.1038/nature09831.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430721" target="_blank"〉PubMed〈/a〉
    Keywords: *Altruism ; Animals ; *Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; *Genetic Fitness ; Genetics, Population ; Heredity ; Humans ; Male ; *Models, Biological ; Phenotype ; Reproducibility of Results ; *Selection, Genetic ; Sex Ratio
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  • 20
    Publication Date: 2011-03-29
    Description: Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088773/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088773/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ernst, Jason -- Kheradpour, Pouya -- Mikkelsen, Tarjei S -- Shoresh, Noam -- Ward, Lucas D -- Epstein, Charles B -- Zhang, Xiaolan -- Wang, Li -- Issner, Robbyn -- Coyne, Michael -- Ku, Manching -- Durham, Timothy -- Kellis, Manolis -- Bernstein, Bradley E -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01HG004037/HG/NHGRI NIH HHS/ -- RC1HG005334/HG/NHGRI NIH HHS/ -- U54 HG004570/HG/NHGRI NIH HHS/ -- U54 HG004570-01/HG/NHGRI NIH HHS/ -- U54 HG004570-02/HG/NHGRI NIH HHS/ -- U54 HG004570-02S1/HG/NHGRI NIH HHS/ -- U54 HG004570-03/HG/NHGRI NIH HHS/ -- U54 HG004570-03S1/HG/NHGRI NIH HHS/ -- U54 HG004570-04/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 May 5;473(7345):43-9. doi: 10.1038/nature09906. Epub 2011 Mar 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21441907" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Line ; Cell Line, Tumor ; *Cell Physiological Phenomena ; Cells, Cultured ; Chromatin/*genetics/*metabolism ; *Chromosome Mapping ; Gene Expression Regulation ; Genome, Human/genetics ; Hep G2 Cells ; Humans ; Promoter Regions, Genetic/genetics ; Reproducibility of Results ; Transcription Factors/genetics
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  • 21
    Publication Date: 2011-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mounce, Ross C P -- Wills, Matthew A -- England -- Nature. 2011 Aug 10;476(7359):E1; discussion E3-4. doi: 10.1038/nature10266.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK. rcpm20@bath.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21833044" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthropods/*classification ; Fossils ; *Phylogeny ; Pseudopodia/classification ; Reproducibility of Results
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  • 22
    Publication Date: 2011-04-02
    Description: Arising from W. Wiltschko et al. 419, 467-470 (2002); Wiltschko et al. replyThe magnetic compass of migratory birds is embedded in the visual system and it has been reported by Wiltschko et al. that European Robins, Erithacus rubecula, cannot show magnetic compass orientation using their left eye only. This has led to the notion that the magnetic compass should be located only in the right eye of birds. However, a complete right lateralization of the magnetic compass would be very surprising, and functional neuroanatomical data have questioned this notion. Here we show that the results of Wiltschko et al. could not be independently confirmed using double-blind protocols. European Robins can perform magnetic compass orientation with both eyes open, with the left eye open only, and with the right eye open only. No clear lateralization is observed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hein, Christine Maira -- Engels, Svenja -- Kishkinev, Dmitry -- Mouritsen, Henrik -- England -- Nature. 2011 Mar 31;471(7340):E11-2; discussion E12-3. doi: 10.1038/nature09875.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉AG Neurosensorik/Animal Navigation, IBU, University of Oldenburg, D-26111 Oldenburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21455128" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Migration/*physiology/radiation effects ; Animals ; *Eye/radiation effects ; Functional Laterality/physiology ; *Magnetics ; Models, Biological ; *Ocular Physiological Phenomena/radiation effects ; Orientation/*physiology/radiation effects ; Photic Stimulation ; Reproducibility of Results ; Seasons ; Songbirds/anatomy & histology/*physiology
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  • 23
    Publication Date: 2011-12-23
    Description: Human immunodeficiency virus (HIV) has a small genome and therefore relies heavily on the host cellular machinery to replicate. Identifying which host proteins and complexes come into physical contact with the viral proteins is crucial for a comprehensive understanding of how HIV rewires the host's cellular machinery during the course of infection. Here we report the use of affinity tagging and purification mass spectrometry to determine systematically the physical interactions of all 18 HIV-1 proteins and polyproteins with host proteins in two different human cell lines (HEK293 and Jurkat). Using a quantitative scoring system that we call MiST, we identified with high confidence 497 HIV-human protein-protein interactions involving 435 individual human proteins, with approximately 40% of the interactions being identified in both cell types. We found that the host proteins hijacked by HIV, especially those found interacting in both cell types, are highly conserved across primates. We uncovered a number of host complexes targeted by viral proteins, including the finding that HIV protease cleaves eIF3d, a subunit of eukaryotic translation initiation factor 3. This host protein is one of eleven identified in this analysis that act to inhibit HIV replication. This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310911/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310911/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jager, Stefanie -- Cimermancic, Peter -- Gulbahce, Natali -- Johnson, Jeffrey R -- McGovern, Kathryn E -- Clarke, Starlynn C -- Shales, Michael -- Mercenne, Gaelle -- Pache, Lars -- Li, Kathy -- Hernandez, Hilda -- Jang, Gwendolyn M -- Roth, Shoshannah L -- Akiva, Eyal -- Marlett, John -- Stephens, Melanie -- D'Orso, Ivan -- Fernandes, Jason -- Fahey, Marie -- Mahon, Cathal -- O'Donoghue, Anthony J -- Todorovic, Aleksandar -- Morris, John H -- Maltby, David A -- Alber, Tom -- Cagney, Gerard -- Bushman, Frederic D -- Young, John A -- Chanda, Sumit K -- Sundquist, Wesley I -- Kortemme, Tanja -- Hernandez, Ryan D -- Craik, Charles S -- Burlingame, Alma -- Sali, Andrej -- Frankel, Alan D -- Krogan, Nevan J -- P01 AI090935/AI/NIAID NIH HHS/ -- P01 AI090935-02/AI/NIAID NIH HHS/ -- P01 GM073732-05/GM/NIGMS NIH HHS/ -- P41 GM103481/GM/NIGMS NIH HHS/ -- P41 RR001081/RR/NCRR NIH HHS/ -- P41RR001614/RR/NCRR NIH HHS/ -- P50 GM081879/GM/NIGMS NIH HHS/ -- P50 GM081879-02/GM/NIGMS NIH HHS/ -- P50 GM082250/GM/NIGMS NIH HHS/ -- P50 GM082250-05/GM/NIGMS NIH HHS/ -- P50GM081879/GM/NIGMS NIH HHS/ -- P50GM082545/GM/NIGMS NIH HHS/ -- U54 RR022220/RR/NCRR NIH HHS/ -- England -- Nature. 2011 Dec 21;481(7381):365-70. doi: 10.1038/nature10719.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22190034" target="_blank"〉PubMed〈/a〉
    Keywords: Affinity Labels ; Amino Acid Sequence ; Conserved Sequence ; Eukaryotic Initiation Factor-3/chemistry/metabolism ; HEK293 Cells ; HIV Infections/metabolism/virology ; HIV Protease/metabolism ; HIV-1/*chemistry/*metabolism/physiology ; *Host-Pathogen Interactions ; Human Immunodeficiency Virus Proteins/analysis/chemistry/isolation & ; purification/*metabolism ; Humans ; Immunoprecipitation ; Jurkat Cells ; Mass Spectrometry ; Protein Binding ; Protein Interaction Mapping/*methods ; Protein Interaction Maps/*physiology ; Reproducibility of Results ; Virus Replication
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  • 24
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    Nature Publishing Group (NPG)
    Publication Date: 2011-05-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Altschuler, Eric L -- England -- Nature. 2011 May 26;473(7348):452. doi: 10.1038/473452a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21614062" target="_blank"〉PubMed〈/a〉
    Keywords: Peer Review, Research/*methods/*standards ; Reproducibility of Results ; Research Personnel/economics/psychology
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  • 25
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    Nature Publishing Group (NPG)
    Publication Date: 2011-10-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2011 Sep 27;477(7366):517-8. doi: 10.1038/477517a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21956304" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/analysis ; Climate Change/*statistics & numerical data ; Congresses as Topic ; *Conservation of Natural Resources ; India ; *International Cooperation ; Reproducibility of Results ; South Africa
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  • 26
    Publication Date: 2011-04-05
    Description: Methylation at the 5' position of cytosine in DNA has important roles in genome function and is dynamically reprogrammed during early embryonic and germ cell development. The mammalian genome also contains 5-hydroxymethylcytosine (5hmC), which seems to be generated by oxidation of 5-methylcytosine (5mC) by the TET family of enzymes that are highly expressed in embryonic stem (ES) cells. Here we use antibodies against 5hmC and 5mC together with high throughput sequencing to determine genome-wide patterns of methylation and hydroxymethylation in mouse wild-type and mutant ES cells and differentiating embryoid bodies. We find that 5hmC is mostly associated with euchromatin and that whereas 5mC is under-represented at gene promoters and CpG islands, 5hmC is enriched and is associated with increased transcriptional levels. Most, if not all, 5hmC in the genome depends on pre-existing 5mC and the balance between these two modifications is different between genomic regions. Knockdown of Tet1 and Tet2 causes downregulation of a group of genes that includes pluripotency-related genes (including Esrrb, Prdm14, Dppa3, Klf2, Tcl1 and Zfp42) and a concomitant increase in methylation of their promoters, together with an increased propensity of ES cells for extraembryonic lineage differentiation. Declining levels of TETs during differentiation are associated with decreased hydroxymethylation levels at the promoters of ES cell-specific genes together with increased methylation and gene silencing. We propose that the balance between hydroxymethylation and methylation in the genome is inextricably linked with the balance between pluripotency and lineage commitment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ficz, Gabriella -- Branco, Miguel R -- Seisenberger, Stefanie -- Santos, Fatima -- Krueger, Felix -- Hore, Timothy A -- Marques, C Joana -- Andrews, Simon -- Reik, Wolf -- G0801156/Medical Research Council/United Kingdom -- G0801727/Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2011 May 19;473(7347):398-402. doi: 10.1038/nature10008. Epub 2011 Apr 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21460836" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies/immunology ; Cell Differentiation/*genetics ; Cell Line ; Cell Lineage/genetics ; CpG Islands/genetics ; Cytosine/*analogs & derivatives/analysis/immunology/metabolism ; *DNA Methylation ; DNA-Binding Proteins/deficiency ; Down-Regulation ; Embryoid Bodies/cytology/metabolism ; Embryonic Stem Cells/*cytology/*metabolism ; Euchromatin/genetics/metabolism ; Exons/genetics ; *Gene Expression Regulation, Developmental ; Gene Silencing ; Genome/genetics ; Mice ; Pluripotent Stem Cells/cytology/metabolism ; Promoter Regions, Genetic/genetics ; Proto-Oncogene Proteins/deficiency ; Reproducibility of Results ; Sequence Analysis, DNA ; Transcription, Genetic
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  • 27
    Publication Date: 2011-05-20
    Description: Gene expression is a multistep process that involves the transcription, translation and turnover of messenger RNAs and proteins. Although it is one of the most fundamental processes of life, the entire cascade has never been quantified on a genome-wide scale. Here we simultaneously measured absolute mRNA and protein abundance and turnover by parallel metabolic pulse labelling for more than 5,000 genes in mammalian cells. Whereas mRNA and protein levels correlated better than previously thought, corresponding half-lives showed no correlation. Using a quantitative model we have obtained the first genome-scale prediction of synthesis rates of mRNAs and proteins. We find that the cellular abundance of proteins is predominantly controlled at the level of translation. Genes with similar combinations of mRNA and protein stability shared functional properties, indicating that half-lives evolved under energetic and dynamic constraints. Quantitative information about all stages of gene expression provides a rich resource and helps to provide a greater understanding of the underlying design principles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schwanhausser, Bjorn -- Busse, Dorothea -- Li, Na -- Dittmar, Gunnar -- Schuchhardt, Johannes -- Wolf, Jana -- Chen, Wei -- Selbach, Matthias -- England -- Nature. 2011 May 19;473(7347):337-42. doi: 10.1038/nature10098.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Delbruck Center for Molecular Medicine, Robert-Rossle-Str. 10, D-13092 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21593866" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Gene Expression Profiling/*methods ; *Gene Expression Regulation ; Half-Life ; Mammals/genetics ; Mice ; Models, Genetic ; NIH 3T3 Cells ; Protein Biosynthesis/genetics ; Proteins/*analysis/genetics/metabolism ; RNA, Messenger/*analysis/biosynthesis/genetics/metabolism ; Reproducibility of Results ; Staining and Labeling
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  • 28
    Publication Date: 2011-07-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Losos, Jonathan B -- Pringle, Robert M -- England -- Nature. 2011 Jul 13;475(7355):E1-2; discussion E3. doi: 10.1038/nature10140.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. jlosos@oeb.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21753806" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/physiology ; Competitive Behavior/*physiology ; *Geography ; Lizards/*physiology ; Population Density ; Predatory Behavior/*physiology ; Reproducibility of Results ; Research Design ; *Selection, Genetic ; Snakes/physiology ; Survival Analysis
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  • 29
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    Publication Date: 2011-10-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2011 Oct 26;478(7370):428. doi: 10.1038/478428a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22031398" target="_blank"〉PubMed〈/a〉
    Keywords: Climate Change/*statistics & numerical data ; *Peer Review, Research/methods/standards ; Periodicals as Topic/standards ; Reproducibility of Results
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  • 30
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    Nature Publishing Group (NPG)
    Publication Date: 2011-07-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seitz, Russell -- England -- Nature. 2011 Jul 6;475(7354):37. doi: 10.1038/475037b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21734694" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollution/adverse effects/analysis ; *Cold Temperature ; Models, Theoretical ; *Nuclear Warfare ; Reproducibility of Results ; *Smoke/analysis ; Sunlight
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  • 31
    Publication Date: 2011-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mackas, David L -- England -- Nature. 2011 Apr 14;472(7342):E4-5; discussion E8-9. doi: 10.1038/nature09951.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Ocean Sciences, Fisheries and Oceans Canada, PO Box 6000, Sidney, British Columbia, V8L 4B2, Canada. Dave.Mackas@dfo-mpo.gc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21490623" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/growth & development/isolation & purification/metabolism ; Bias (Epidemiology) ; Biomass ; Chlorophyll/analysis/*metabolism ; Data Collection/methods ; Phytoplankton/growth & development/isolation & purification/metabolism ; Reproducibility of Results ; Time Factors
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  • 32
    Publication Date: 2011-11-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brassard, Gilles -- England -- Nature. 2011 Nov 16;479(7373):307-8. doi: 10.1038/479307a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departement d'informatique et de recherche operationnelle, Universite de Montreal, Montreal, Quebec H3C 3J7, Canada. brassard@iro.umontreal.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22094688" target="_blank"〉PubMed〈/a〉
    Keywords: *Geographic Information Systems ; Quantum Theory ; Reproducibility of Results ; Time Factors ; Trust ; *Uncertainty
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  • 33
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    Nature Publishing Group (NPG)
    Publication Date: 2011-07-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maxmen, Amy -- England -- Nature. 2011 Jul 6;475(7354):23-5. doi: 10.1038/475023a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21734684" target="_blank"〉PubMed〈/a〉
    Keywords: Bone and Bones/metabolism/physiology ; Calcium/metabolism ; Dietary Supplements/utilization ; Evidence-Based Medicine/methods/standards ; Guidelines as Topic/standards ; Health Surveys/standards ; Humans ; Institute of Medicine (U.S.) ; *Meta-Analysis as Topic ; *Nutritional Requirements ; *Nutritional Sciences/standards ; Public Health/methods/standards ; Reproducibility of Results ; United States ; Vitamin D/blood/metabolism/*physiology ; Vitamin D Deficiency/blood/epidemiology
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  • 34
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    Nature Publishing Group (NPG)
    Publication Date: 2011-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gupta, Nitin -- Stopfer, Mark -- England -- Nature. 2011 Feb 3;470(7332):39. doi: 10.1038/470039a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21293361" target="_blank"〉PubMed〈/a〉
    Keywords: Meta-Analysis as Topic ; *Models, Biological ; Reproducibility of Results ; *Research Report
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  • 35
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    Nature Publishing Group (NPG)
    Publication Date: 2011-06-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brooks, T M -- England -- Nature. 2011 Jun 15;474(7351):284. doi: 10.1038/474284b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21677730" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Ecosystem ; Endangered Species/*statistics & numerical data ; *Extinction, Biological ; *Models, Biological ; Reproducibility of Results ; Species Specificity
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  • 36
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    Nature Publishing Group (NPG)
    Publication Date: 2011-03-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeWeerdt, Sarah -- England -- Nature. 2011 Mar 24;471(7339):S22-4. doi: 10.1038/471S22a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430718" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brassica/chemistry ; Breeding ; Cooking ; Curcumin/pharmacology ; *Diet/statistics & numerical data ; Fruit/chemistry ; Genetic Variation/genetics ; Genistein/pharmacology ; Genome, Human/genetics ; Humans ; Isothiocyanates ; Metagenome ; Mice ; Neoplasms/chemically induced/*diet therapy/*prevention & control ; Phytotherapy ; Rats ; Reproducibility of Results ; Risk Management ; Stilbenes/pharmacology ; Thiocyanates/pharmacology ; Time Factors ; Vegetables/chemistry
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  • 37
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. The paper by Nowak et al. has the evolution of eusociality as its title, but it is mostly about something else. It argues against inclusive fitness theory and offers an alternative modelling approach that is claimed to be more fundamental and general, but which, we believe, has no practical biological meaning for the evolution of eusociality. Nowak et al. overlook the robust empirical observation that eusociality has only arisen in clades where mothers are associated with their full-sibling offspring; that is, in families where the average relatedness of offspring to siblings is as high as to their own offspring, independent of population structure or ploidy. We believe that this omission makes the paper largely irrelevant for understanding the evolution of eusociality.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boomsma, Jacobus J -- Beekman, Madeleine -- Cornwallis, Charlie K -- Griffin, Ashleigh S -- Holman, Luke -- Hughes, William O H -- Keller, Laurent -- Oldroyd, Benjamin P -- Ratnieks, Francis L W -- England -- Nature. 2011 Mar 24;471(7339):E4-5; author reply E9-10. doi: 10.1038/nature09832.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430722" target="_blank"〉PubMed〈/a〉
    Keywords: *Altruism ; Animals ; *Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; Genetic Fitness ; Genetics, Population ; Male ; *Models, Biological ; Reproducibility of Results ; Reproduction/physiology ; Selection, Genetic ; Sex Ratio ; *Siblings
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  • 38
    Publication Date: 2011-02-05
    Description: Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077050/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077050/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mills, Ryan E -- Walter, Klaudia -- Stewart, Chip -- Handsaker, Robert E -- Chen, Ken -- Alkan, Can -- Abyzov, Alexej -- Yoon, Seungtai Chris -- Ye, Kai -- Cheetham, R Keira -- Chinwalla, Asif -- Conrad, Donald F -- Fu, Yutao -- Grubert, Fabian -- Hajirasouliha, Iman -- Hormozdiari, Fereydoun -- Iakoucheva, Lilia M -- Iqbal, Zamin -- Kang, Shuli -- Kidd, Jeffrey M -- Konkel, Miriam K -- Korn, Joshua -- Khurana, Ekta -- Kural, Deniz -- Lam, Hugo Y K -- Leng, Jing -- Li, Ruiqiang -- Li, Yingrui -- Lin, Chang-Yun -- Luo, Ruibang -- Mu, Xinmeng Jasmine -- Nemesh, James -- Peckham, Heather E -- Rausch, Tobias -- Scally, Aylwyn -- Shi, Xinghua -- Stromberg, Michael P -- Stutz, Adrian M -- Urban, Alexander Eckehart -- Walker, Jerilyn A -- Wu, Jiantao -- Zhang, Yujun -- Zhang, Zhengdong D -- Batzer, Mark A -- Ding, Li -- Marth, Gabor T -- McVean, Gil -- Sebat, Jonathan -- Snyder, Michael -- Wang, Jun -- Ye, Kenny -- Eichler, Evan E -- Gerstein, Mark B -- Hurles, Matthew E -- Lee, Charles -- McCarroll, Steven A -- Korbel, Jan O -- 1000 Genomes Project -- 062023/Wellcome Trust/United Kingdom -- 077009/Wellcome Trust/United Kingdom -- 077014/Wellcome Trust/United Kingdom -- 077192/Wellcome Trust/United Kingdom -- 085532/Wellcome Trust/United Kingdom -- G0701805/Medical Research Council/United Kingdom -- G1000758/Medical Research Council/United Kingdom -- P01 HG004120/HG/NHGRI NIH HHS/ -- P41 HG004221/HG/NHGRI NIH HHS/ -- P41 HG004221-01/HG/NHGRI NIH HHS/ -- P41 HG004221-02/HG/NHGRI NIH HHS/ -- P41 HG004221-03/HG/NHGRI NIH HHS/ -- P41 HG004221-03S1/HG/NHGRI NIH HHS/ -- P41 HG004221-03S2/HG/NHGRI NIH HHS/ -- P41 HG004221-03S3/HG/NHGRI NIH HHS/ -- R01 GM059290/GM/NIGMS NIH HHS/ -- R01 GM081533/GM/NIGMS NIH HHS/ -- R01 GM081533-01A1/GM/NIGMS NIH HHS/ -- R01 GM081533-02/GM/NIGMS NIH HHS/ -- R01 GM081533-03/GM/NIGMS NIH HHS/ -- R01 GM081533-04/GM/NIGMS NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG004719/HG/NHGRI NIH HHS/ -- R01 HG004719-01/HG/NHGRI NIH HHS/ -- R01 HG004719-02/HG/NHGRI NIH HHS/ -- R01 HG004719-02S1/HG/NHGRI NIH HHS/ -- R01 HG004719-03/HG/NHGRI NIH HHS/ -- R01 HG004719-04/HG/NHGRI NIH HHS/ -- R01 MH091350/MH/NIMH NIH HHS/ -- RC2 HG005552/HG/NHGRI NIH HHS/ -- RC2 HG005552-01/HG/NHGRI NIH HHS/ -- RC2 HG005552-02/HG/NHGRI NIH HHS/ -- U01 HG005209/HG/NHGRI NIH HHS/ -- U01 HG005209-01/HG/NHGRI NIH HHS/ -- U01 HG005209-02/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21293372" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Copy Number Variations/*genetics ; Gene Duplication/genetics ; Genetic Predisposition to Disease/genetics ; *Genetics, Population ; Genome, Human/*genetics ; *Genomics ; Genotype ; Humans ; Mutagenesis, Insertional/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Sequence Deletion/genetics
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  • 39
    Publication Date: 2011-08-05
    Description: Dust has the potential to modify global climate by influencing the radiative balance of the atmosphere and by supplying iron and other essential limiting micronutrients to the ocean. Indeed, dust supply to the Southern Ocean increases during ice ages, and 'iron fertilization' of the subantarctic zone may have contributed up to 40 parts per million by volume (p.p.m.v.) of the decrease (80-100 p.p.m.v.) in atmospheric carbon dioxide observed during late Pleistocene glacial cycles. So far, however, the magnitude of Southern Ocean dust deposition in earlier times and its role in the development and evolution of Pleistocene glacial cycles have remained unclear. Here we report a high-resolution record of dust and iron supply to the Southern Ocean over the past four million years, derived from the analysis of marine sediments from ODP Site 1090, located in the Atlantic sector of the subantarctic zone. The close correspondence of our dust and iron deposition records with Antarctic ice core reconstructions of dust flux covering the past 800,000 years (refs 8, 9) indicates that both of these archives record large-scale deposition changes that should apply to most of the Southern Ocean, validating previous interpretations of the ice core data. The extension of the record beyond the interval covered by the Antarctic ice cores reveals that, in contrast to the relatively gradual intensification of glacial cycles over the past three million years, Southern Ocean dust and iron flux rose sharply at the Mid-Pleistocene climatic transition around 1.25 million years ago. This finding complements previous observations over late Pleistocene glacial cycles, providing new evidence of a tight connection between high dust input to the Southern Ocean and the emergence of the deep glaciations that characterize the past one million years of Earth history.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martinez-Garcia, Alfredo -- Rosell-Mele, Antoni -- Jaccard, Samuel L -- Geibert, Walter -- Sigman, Daniel M -- Haug, Gerald H -- England -- Nature. 2011 Aug 3;476(7360):312-5. doi: 10.1038/nature10310.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Geological Institute, ETH Zurich, Zurich 8092, Switzerland. alfredo.martinez-garcia@erdw.ethz.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21814203" target="_blank"〉PubMed〈/a〉
    Keywords: Alkanes/analysis ; Atlantic Ocean ; Atmosphere/chemistry ; Carbon Cycle ; Carbon Dioxide/analysis ; *Climate ; Diatoms/metabolism ; Dust/*analysis ; Ecosystem ; Geologic Sediments/chemistry ; History, Ancient ; Ice/analysis ; Iron/analysis ; Nitrates/analysis ; Oceans and Seas ; Reproducibility of Results ; Seawater/*chemistry ; Uncertainty ; Wind
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  • 40
    Publication Date: 2011-11-25
    Description: Arctic sea ice extent is now more than two million square kilometres less than it was in the late twentieth century, with important consequences for the climate, the ocean and traditional lifestyles in the Arctic. Although observations show a more or less continuous decline for the past four or five decades, there are few long-term records with which to assess natural sea ice variability. Until now, the question of whether or not current trends are potentially anomalous has therefore remained unanswerable. Here we use a network of high-resolution terrestrial proxies from the circum-Arctic region to reconstruct past extents of summer sea ice, and show that-although extensive uncertainties remain, especially before the sixteenth century-both the duration and magnitude of the current decline in sea ice seem to be unprecedented for the past 1,450 years. Enhanced advection of warm Atlantic water to the Arctic seems to be the main factor driving the decline of sea ice extent on multidecadal timescales, and may result from nonlinear feedbacks between sea ice and the Atlantic meridional overturning circulation. These results reinforce the assertion that sea ice is an active component of Arctic climate variability and that the recent decrease in summer Arctic sea ice is consistent with anthropogenically forced warming.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kinnard, Christophe -- Zdanowicz, Christian M -- Fisher, David A -- Isaksson, Elisabeth -- de Vernal, Anne -- Thompson, Lonnie G -- England -- Nature. 2011 Nov 23;479(7374):509-12. doi: 10.1038/nature10581.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centro de Estudios Avanzados en Zonas Aridas, Benavente 980, Casilla 554, La Serena, 1720170, Chile. christophe.kinnard@ceaza.cl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22113692" target="_blank"〉PubMed〈/a〉
    Keywords: Arctic Regions ; Atmosphere ; Geologic Sediments/chemistry ; Global Warming/*statistics & numerical data ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Human Activities ; *Ice Cover ; Reproducibility of Results ; Seasons ; Seawater
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  • 41
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    Nature Publishing Group (NPG)
    Publication Date: 2011-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dolgin, Elie -- England -- Nature. 2011 Feb 3;470(7332):13. doi: 10.1038/470013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21293343" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cellular Reprogramming/genetics ; DNA Methylation/genetics ; Embryonic Stem Cells/cytology/*metabolism ; Epigenesis, Genetic/*genetics ; Humans ; Induced Pluripotent Stem Cells/cytology/*metabolism ; Mice ; Models, Biological ; Reproducibility of Results
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  • 42
    Publication Date: 2011-08-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Motluk, Alison -- England -- Nature. 2011 Aug 23;476(7361):382-3. doi: 10.1038/476382a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21866132" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Cryopreservation/economics/methods/*statistics & numerical data/trends ; Female ; *Human Experimentation/statistics & numerical data ; Humans ; Infant, Newborn ; Maternal Age ; Oocyte Retrieval/statistics & numerical data ; *Oocytes ; Pregnancy ; Pregnancy Outcome ; Reproducibility of Results ; Reproductive Medicine/economics/methods/standards/*statistics & numerical data ; Vitrification
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  • 43
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    Nature Publishing Group (NPG)
    Publication Date: 2011-03-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stirling, Andy -- England -- Nature. 2011 Mar 17;471(7338):305. doi: 10.1038/471305a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21412323" target="_blank"〉PubMed〈/a〉
    Keywords: Great Britain ; *Policy Making ; Public Opinion ; Reproducibility of Results ; *Science
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  • 44
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Hamilton described a selective process in which individuals affect kin (kin selection), developed a novel modelling strategy for it (inclusive fitness), and derived a rule to describe it (Hamilton's rule). Nowak et al. assert that inclusive fitness is not the best modelling strategy, and also that its production has been "meagre". The former may be debated by theoreticians, but the latter is simply incorrect. There is abundant evidence to demonstrate that inclusive fitness, kin selection and Hamilton's rule have been extraordinarily productive for understanding the evolution of sociality.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strassmann, Joan E -- Page, Robert E Jr -- Robinson, Gene E -- Seeley, Thomas D -- England -- Nature. 2011 Mar 24;471(7339):E5-6; author reply E9-10. doi: 10.1038/nature09833.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430723" target="_blank"〉PubMed〈/a〉
    Keywords: *Altruism ; Animals ; Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; Genetic Fitness ; Genetics, Population ; Genomic Imprinting ; *Heredity ; Humans ; Male ; *Models, Biological ; Reproducibility of Results ; *Selection, Genetic ; Sex Ratio
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  • 45
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    Publication Date: 2011-10-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2011 Oct 26;478(7370):439-40. doi: 10.1038/478439a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22031413" target="_blank"〉PubMed〈/a〉
    Keywords: Clinical Trials, Phase III as Topic ; Controlled Clinical Trials as Topic ; Humans ; Infant ; Malaria Vaccines/adverse effects/*immunology ; Malaria, Falciparum/epidemiology/mortality/parasitology/prevention & control ; *Mass Media ; Plasmodium falciparum/immunology ; Reproducibility of Results ; Time Factors ; World Health Organization
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  • 46
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    Nature Publishing Group (NPG)
    Publication Date: 2011-10-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Callaway, Ewen -- England -- Nature. 2011 Oct 25;478(7370):444-6. doi: 10.1038/478444a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22031418" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA Contamination ; Disease Outbreaks ; Evolution, Molecular ; Genome, Bacterial/*genetics ; History, 19th Century ; History, Ancient ; History, Medieval ; Humans ; Insect Vectors/microbiology ; London/epidemiology ; Phylogeny ; Plague/epidemiology/history/*microbiology/transmission ; Polymerase Chain Reaction ; Rats ; Reproducibility of Results ; Yersinia pestis/classification/*genetics/isolation & purification
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  • 47
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. For over fifty years, the evolution of social behaviour has been guided by the concept of inclusive fitness as a measure of evolutionary success. Nowak et al. argue that inclusive fitness should be abandoned. In so doing, however, they misrepresent the role that inclusive fitness has played in the theory of social evolution by which understanding social behaviour in a variety of disciplines has developed and flourished. By discarding inclusive fitness on the basis of its limitations, they create a conceptual tension which, we argue, is unnecessary, and potentially dangerous for evolutionary biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferriere, Regis -- Michod, Richard E -- England -- Nature. 2011 Mar 24;471(7339):E6-8; author reply E9-10. doi: 10.1038/nature09834.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430724" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Altruism ; Animals ; *Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; *Genetic Fitness/genetics ; Genetics, Population ; Heredity/genetics ; Male ; *Models, Biological ; Phenotype ; Reproducibility of Results ; Selection, Genetic/genetics ; Sex Ratio
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  • 48
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    Publication Date: 2011-01-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Samuel Reich, Eugenie -- England -- Nature. 2011 Jan 13;469(7329):139-40. doi: 10.1038/469139a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21228842" target="_blank"〉PubMed〈/a〉
    Keywords: Clinical Trials as Topic/ethics/*standards ; Gene Expression Profiling ; Humans ; *Neoplasms ; North Carolina ; Pharmacogenetics/standards ; Precision Medicine/standards ; Reproducibility of Results ; *Research Design/standards ; Research Personnel/ethics/standards ; Scientific Misconduct
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  • 49
    Publication Date: 2011-02-25
    Description: Rare copy number variants (CNVs) have a prominent role in the aetiology of schizophrenia and other neuropsychiatric disorders. Substantial risk for schizophrenia is conferred by large (〉500-kilobase) CNVs at several loci, including microdeletions at 1q21.1 (ref. 2), 3q29 (ref. 3), 15q13.3 (ref. 2) and 22q11.2 (ref. 4) and microduplication at 16p11.2 (ref. 5). However, these CNVs collectively account for a small fraction (2-4%) of cases, and the relevant genes and neurobiological mechanisms are not well understood. Here we performed a large two-stage genome-wide scan of rare CNVs and report the significant association of copy number gains at chromosome 7q36.3 with schizophrenia. Microduplications with variable breakpoints occurred within a 362-kilobase region and were detected in 29 of 8,290 (0.35%) patients versus 2 of 7,431 (0.03%) controls in the combined sample. All duplications overlapped or were located within 89 kilobases upstream of the vasoactive intestinal peptide receptor gene VIPR2. VIPR2 transcription and cyclic-AMP signalling were significantly increased in cultured lymphocytes from patients with microduplications of 7q36.3. These findings implicate altered vasoactive intestinal peptide signalling in the pathogenesis of schizophrenia and indicate the VPAC2 receptor as a potential target for the development of new antipsychotic drugs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351382/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351382/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vacic, Vladimir -- McCarthy, Shane -- Malhotra, Dheeraj -- Murray, Fiona -- Chou, Hsun-Hua -- Peoples, Aine -- Makarov, Vladimir -- Yoon, Seungtai -- Bhandari, Abhishek -- Corominas, Roser -- Iakoucheva, Lilia M -- Krastoshevsky, Olga -- Krause, Verena -- Larach-Walters, Veronica -- Welsh, David K -- Craig, David -- Kelsoe, John R -- Gershon, Elliot S -- Leal, Suzanne M -- Dell Aquila, Marie -- Morris, Derek W -- Gill, Michael -- Corvin, Aiden -- Insel, Paul A -- McClellan, Jon -- King, Mary-Claire -- Karayiorgou, Maria -- Levy, Deborah L -- DeLisi, Lynn E -- Sebat, Jonathan -- 072894/Z/03/Z/Wellcome Trust/United Kingdom -- GM66232/GM/NIGMS NIH HHS/ -- HG04222/HG/NHGRI NIH HHS/ -- MH044245/MH/NIMH NIH HHS/ -- MH061399/MH/NIMH NIH HHS/ -- MH071523/MH/NIMH NIH HHS/ -- MH076431/MH/NIMH NIH HHS/ -- MH082945/MH/NIMH NIH HHS/ -- MH083989/MH/NIMH NIH HHS/ -- P41 HG004222/HG/NHGRI NIH HHS/ -- P41 HG004222-04S1/HG/NHGRI NIH HHS/ -- P41 HG004222-04S2/HG/NHGRI NIH HHS/ -- R00 HL091061/HL/NHLBI NIH HHS/ -- R01 MH061399/MH/NIMH NIH HHS/ -- R01 MH076431/MH/NIMH NIH HHS/ -- R01 MH076431-06/MH/NIMH NIH HHS/ -- R01 MH082945/MH/NIMH NIH HHS/ -- R01 MH091350/MH/NIMH NIH HHS/ -- England -- Nature. 2011 Mar 24;471(7339):499-503. doi: 10.1038/nature09884. Epub 2011 Feb 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 12824, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21346763" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Chromosomes, Human, Pair 7/genetics ; Cohort Studies ; Cyclic AMP/metabolism ; DNA Copy Number Variations/*genetics ; Female ; Gene Dosage/genetics ; Genes, Duplicate/*genetics ; Genetic Predisposition to Disease/*genetics ; Genome-Wide Association Study ; Humans ; Inheritance Patterns/genetics ; Male ; Pedigree ; Receptors, Vasoactive Intestinal Peptide, Type II/*genetics/metabolism ; Reproducibility of Results ; Schizophrenia/*genetics/metabolism ; Signal Transduction ; Transcription, Genetic/genetics
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  • 50
    Publication Date: 2011-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rykaczewski, Ryan R -- Dunne, John P -- England -- Nature. 2011 Apr 14;472(7342):E5-6; discussion E8-9. doi: 10.1038/nature09952.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University Corporation for Atmospheric Research, Boulder, Colorado 80307-3000 USA. rrykacze@ucar.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21490624" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/growth & development/isolation & purification/metabolism ; Bias (Epidemiology) ; Biomass ; Chlorophyll/*analysis ; Data Collection/methods ; Ecosystem ; Oceans and Seas ; Phytoplankton/growth & development/isolation & purification/metabolism ; Reproducibility of Results ; Seawater/analysis/*chemistry ; Time Factors
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  • 51
    Publication Date: 2011-07-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2011 Jul 6;475(7354):123-8. doi: 10.1038/475123a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21734709" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autistic Disorder/genetics/physiopathology ; Automation ; *Behavior, Animal/physiology ; Cues ; *Disease Models, Animal ; Environment ; Fragile X Syndrome/genetics/physiopathology ; Gene Knockout Techniques ; Grooming/physiology ; Housing, Animal ; Humans ; Informatics/methods ; Mental Disorders/diagnosis/*genetics/*physiopathology ; Mice ; Motor Activity/physiology ; Muscular Atrophy, Spinal/genetics/physiopathology ; Obesity/genetics/physiopathology ; Obsessive-Compulsive Disorder/genetics/physiopathology ; Rats ; Reproducibility of Results ; Rett Syndrome/genetics/physiopathology ; Schizophrenia/genetics/physiopathology ; Video Recording/instrumentation/methods
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  • 52
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    Publication Date: 2011-04-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2011 Mar 31;471(7340):661-5. doi: 10.1038/471661a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21455183" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Testing Alternatives/instrumentation/*methods ; Animals ; Bioengineering/instrumentation/*methods ; Biomimetics/instrumentation/*methods ; Cell Culture Techniques/instrumentation/methods ; Drug Evaluation, Preclinical/instrumentation/methods ; Humans ; *Lab-On-A-Chip Devices ; Liver/drug effects/pathology/physiology/physiopathology ; Lung/blood supply/cytology/drug effects/immunology/physiology ; Mice ; Models, Animal ; *Models, Biological ; Nanotechnology/instrumentation/methods ; *Organ Specificity ; Reproducibility of Results ; Silicon/chemistry
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  • 53
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    Nature Publishing Group (NPG)
    Publication Date: 2011-01-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mandavilli, Apoorva -- England -- Nature. 2011 Jan 20;469(7330):286-7. doi: 10.1038/469286a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21248816" target="_blank"〉PubMed〈/a〉
    Keywords: Aged, 80 and over ; Bias (Epidemiology) ; Bibliometrics ; Blogging/trends/*utilization ; Genome-Wide Association Study ; Humans ; Longevity/genetics ; Oligonucleotide Array Sequence Analysis ; Peer Review, Research/*methods/standards/trends ; Reproducibility of Results ; *Research Personnel/standards ; Time Factors
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  • 54
    Publication Date: 2011-02-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2011 Feb 24;470(7335):446-7. doi: 10.1038/470446a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350457" target="_blank"〉PubMed〈/a〉
    Keywords: Conflict of Interest ; *Faculty ; Glass/chemistry ; Japan ; Metals/chemistry ; Reproducibility of Results ; *Research Personnel ; Scientific Misconduct/*legislation & jurisprudence ; *Universities/organization & administration
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  • 55
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    Nature Publishing Group (NPG)
    Publication Date: 2011-01-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cyranoski, David -- England -- Nature. 2011 Jan 13;469(7329):148-9. doi: 10.1038/469148a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21228849" target="_blank"〉PubMed〈/a〉
    Keywords: Clinical Medicine/*instrumentation/*methods ; Complementary Therapies ; Diagnostic Errors/prevention & control/statistics & numerical data ; Evidence-Based Medicine ; Humans ; Japan ; Male ; Mental Disorders/*diagnosis ; Reproducibility of Results ; Spectroscopy, Near-Infrared/*utilization
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  • 56
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    Nature Publishing Group (NPG)
    Publication Date: 2011-04-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marchant, Jo -- England -- Nature. 2011 Apr 28;472(7344):404-6. doi: 10.1038/472404a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21525906" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cold Climate ; DNA/*analysis/*genetics/isolation & purification ; DNA, Mitochondrial/genetics ; Egypt ; Female ; Hot Temperature ; Humans ; Male ; *Mummies ; Reproducibility of Results ; *Sequence Analysis, DNA/methods/standards/trends ; Y Chromosome/genetics
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  • 57
    Publication Date: 2011-06-07
    Description: Chronic lymphocytic leukaemia (CLL), the most frequent leukaemia in adults in Western countries, is a heterogeneous disease with variable clinical presentation and evolution. Two major molecular subtypes can be distinguished, characterized respectively by a high or low number of somatic hypermutations in the variable region of immunoglobulin genes. The molecular changes leading to the pathogenesis of the disease are still poorly understood. Here we performed whole-genome sequencing of four cases of CLL and identified 46 somatic mutations that potentially affect gene function. Further analysis of these mutations in 363 patients with CLL identified four genes that are recurrently mutated: notch 1 (NOTCH1), exportin 1 (XPO1), myeloid differentiation primary response gene 88 (MYD88) and kelch-like 6 (KLHL6). Mutations in MYD88 and KLHL6 are predominant in cases of CLL with mutated immunoglobulin genes, whereas NOTCH1 and XPO1 mutations are mainly detected in patients with unmutated immunoglobulins. The patterns of somatic mutation, supported by functional and clinical analyses, strongly indicate that the recurrent NOTCH1, MYD88 and XPO1 mutations are oncogenic changes that contribute to the clinical evolution of the disease. To our knowledge, this is the first comprehensive analysis of CLL combining whole-genome sequencing with clinical characteristics and clinical outcomes. It highlights the usefulness of this approach for the identification of clinically relevant mutations in cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322590/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322590/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Puente, Xose S -- Pinyol, Magda -- Quesada, Victor -- Conde, Laura -- Ordonez, Gonzalo R -- Villamor, Neus -- Escaramis, Georgia -- Jares, Pedro -- Bea, Silvia -- Gonzalez-Diaz, Marcos -- Bassaganyas, Laia -- Baumann, Tycho -- Juan, Manel -- Lopez-Guerra, Monica -- Colomer, Dolors -- Tubio, Jose M C -- Lopez, Cristina -- Navarro, Alba -- Tornador, Cristian -- Aymerich, Marta -- Rozman, Maria -- Hernandez, Jesus M -- Puente, Diana A -- Freije, Jose M P -- Velasco, Gloria -- Gutierrez-Fernandez, Ana -- Costa, Dolors -- Carrio, Anna -- Guijarro, Sara -- Enjuanes, Anna -- Hernandez, Lluis -- Yague, Jordi -- Nicolas, Pilar -- Romeo-Casabona, Carlos M -- Himmelbauer, Heinz -- Castillo, Ester -- Dohm, Juliane C -- de Sanjose, Silvia -- Piris, Miguel A -- de Alava, Enrique -- San Miguel, Jesus -- Royo, Romina -- Gelpi, Josep L -- Torrents, David -- Orozco, Modesto -- Pisano, David G -- Valencia, Alfonso -- Guigo, Roderic -- Bayes, Monica -- Heath, Simon -- Gut, Marta -- Klatt, Peter -- Marshall, John -- Raine, Keiran -- Stebbings, Lucy A -- Futreal, P Andrew -- Stratton, Michael R -- Campbell, Peter J -- Gut, Ivo -- Lopez-Guillermo, Armando -- Estivill, Xavier -- Montserrat, Emili -- Lopez-Otin, Carlos -- Campo, Elias -- 088340/Wellcome Trust/United Kingdom -- 093867/Wellcome Trust/United Kingdom -- England -- Nature. 2011 Jun 5;475(7354):101-5. doi: 10.1038/nature10113.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departamento de Bioquimica y Biologia Molecular, Instituto Universitario de Oncologia, Universidad de Oviedo, 33006 Oviedo, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21642962" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/genetics ; DNA Mutational Analysis ; Genome, Human/*genetics ; Humans ; Karyopherins/genetics ; Leukemia, Lymphocytic, Chronic, B-Cell/*genetics ; Molecular Sequence Data ; Mutation/*genetics ; Myeloid Differentiation Factor 88/chemistry/genetics ; Receptor, Notch1/genetics ; Receptors, Cytoplasmic and Nuclear/genetics ; Reproducibility of Results
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  • 58
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    Nature Publishing Group (NPG)
    Publication Date: 2011-07-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Ruth -- England -- Nature. 2011 Jul 13;475(7355):S5-7. doi: 10.1038/475S5a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21760581" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/*diagnosis/immunology/*metabolism/therapy ; Amyloid beta-Peptides/analysis/antagonists & inhibitors/metabolism ; Antibodies/analysis/immunology ; Biomarkers/analysis/metabolism ; Case-Control Studies ; Cognition Disorders/diagnosis/metabolism ; Disease Progression ; Humans ; Magnetic Resonance Imaging ; Multicenter Studies as Topic ; Positron-Emission Tomography ; Prognosis ; Public-Private Sector Partnerships ; Reproducibility of Results ; tau Proteins/analysis/metabolism
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  • 59
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    Nature Publishing Group (NPG)
    Publication Date: 2011-03-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buchen, Lizzie -- England -- Nature. 2011 Mar 24;471(7339):428-32. doi: 10.1038/471428a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430749" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Biomarkers, Tumor/*blood ; CA-125 Antigen/blood ; Clinical Trials as Topic ; Early Detection of Cancer/*methods/standards ; Female ; Gene Expression Profiling ; Humans ; Male ; Models, Statistical ; Ovarian Neoplasms/blood/diagnosis ; Predictive Value of Tests ; Reproducibility of Results ; United States ; United States Food and Drug Administration/legislation & jurisprudence
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  • 60
    Publication Date: 2011-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McQuatters-Gollop, Abigail -- Reid, Philip C -- Edwards, Martin -- Burkill, Peter H -- Castellani, Claudia -- Batten, Sonia -- Gieskes, Winfried -- Beare, Doug -- Bidigare, Robert R -- Head, Erica -- Johnson, Rod -- Kahru, Mati -- Koslow, J Anthony -- Pena, Angelica -- England -- Nature. 2011 Apr 14;472(7342):E6-7; discussion E8-9. doi: 10.1038/nature09950.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sir Alister Hardy Foundation for Ocean Science, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK. abiqua@sahfos.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21490625" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/growth & development/*isolation & purification/metabolism ; Atlantic Ocean ; Bias (Epidemiology) ; Biomass ; Chlorophyll/analysis ; Data Collection/methods ; *Ecosystem ; Fisheries ; Phytoplankton/growth & development/*isolation & purification/metabolism ; Reproducibility of Results ; Seawater/chemistry/microbiology ; Time Factors
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  • 61
    Publication Date: 2011-07-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edwards, David P -- Fisher, Brendan -- Wilcove, David S -- England -- Nature. 2011 Jul 13;475(7355):174. doi: 10.1038/475174d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21753837" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*methods ; Animals ; Biodiversity ; Cacao ; *Conservation of Natural Resources/methods ; Forestry/*methods ; Plant Oils ; Reproducibility of Results ; Saccharum ; Soybeans
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    Publication Date: 2011-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borrell, Brendan -- England -- Nature. 2011 Feb 17;470(7334):320-2. doi: 10.1038/470320a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21331018" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollutants/analysis ; Case-Control Studies ; Child ; Diet/statistics & numerical data ; Environmental Exposure/*analysis ; Environmental Monitoring/instrumentation/methods ; Health Surveys/*instrumentation/*methods ; Humans ; Memory/physiology ; Monitoring, Physiologic/instrumentation/methods ; Motor Activity/physiology ; Photography/instrumentation/methods ; Reproducibility of Results ; Research Design ; Self Report/standards/utilization ; Surveys and Questionnaires/standards/utilization
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    Publication Date: 2011-01-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2011 Jan 13;469(7329):132. doi: 10.1038/469132a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21228830" target="_blank"〉PubMed〈/a〉
    Keywords: Bipolar Disorder/diagnosis ; Diagnosis, Differential ; Diagnostic Errors/prevention & control/statistics & numerical data ; Evidence-Based Medicine/*standards/trends ; Humans ; Japan ; Mental Disorders/*diagnosis ; Reproducibility of Results ; Spectroscopy, Near-Infrared/*utilization
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    Publication Date: 2011-05-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hayden, Erika Check -- England -- Nature. 2011 May 26;473(7348):432. doi: 10.1038/473432a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21614050" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA/analysis/genetics ; Exons/genetics ; Genetic Predisposition to Disease/genetics ; Genomics/trends ; Humans ; *Models, Genetic ; RNA Editing/genetics/*physiology ; RNA, Messenger/analysis/*genetics/*metabolism ; Reproducibility of Results ; Research Design ; Ribosomes/metabolism ; Sequence Analysis, RNA/standards
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    Publication Date: 2011-04-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ledford, Heidi -- England -- Nature. 2011 Apr 21;472(7343):273. doi: 10.1038/472273a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512545" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Movement ; Cells, Cultured ; *Epithelial-Mesenchymal Transition ; Humans ; Mice ; *Models, Biological ; Neoplasm Metastasis/*pathology ; Neoplasms/*pathology ; Reproducibility of Results
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  • 66
    Publication Date: 2011-03-25
    Description: Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Arguably the defining characteristic of the scientific process is its capacity for self-criticism and correction. Nowak et al. challenge proposed connections between relatedness and the evolution of eusociality, suggest instead that defensible nests and "spring-loaded" traits are key, and present alternative modelling approaches. They then dismiss the utility of Hamilton's insight that relatedness has a profound evolutionary effect, formalized in his widely accepted inclusive fitness theory as Hamilton's rule ("Rise and fall of inclusive fitness theory"). However, we believe that Nowak et al. fail to make their case for logical, theoretical and empirical reasons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herre, Edward Allen -- Wcislo, William T -- England -- Nature. 2011 Mar 24;471(7339):E8-9; author reply E9-10. doi: 10.1038/nature09835.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430725" target="_blank"〉PubMed〈/a〉
    Keywords: Altruism ; Animals ; Biological Evolution ; Cooperative Behavior ; Female ; Game Theory ; *Genetic Fitness ; Genetics, Population ; Heredity ; Male ; *Models, Biological ; Models, Genetic ; Reproducibility of Results ; Selection, Genetic ; Sex Ratio
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  • 67
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    Nature Publishing Group (NPG)
    Publication Date: 2011-02-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abramson, Steven B -- England -- Nature. 2011 Feb 24;470(7335):465. doi: 10.1038/470465a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350471" target="_blank"〉PubMed〈/a〉
    Keywords: *Cancer Vaccines/administration & dosage/immunology ; Dendritic Cells/immunology ; Faculty ; New York City ; Reproducibility of Results ; Research Personnel/*standards ; Schools, Medical ; Scientific Misconduct
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 68
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    Nature Publishing Group (NPG)
    Publication Date: 2011-03-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Callaway, Ewen -- England -- Nature. 2011 Mar 17;471(7338):282-5. doi: 10.1038/471282a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21412308" target="_blank"〉PubMed〈/a〉
    Keywords: Fatigue Syndrome, Chronic/*etiology/*virology ; Humans ; Patients/psychology ; Reproducibility of Results ; *Research Personnel/psychology/standards ; *Xenotropic murine leukemia virus-related virus
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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