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  • 2005-2009  (1,342)
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  • 1
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    In:  Geophys. J. Int., Hannover, Elsevier, vol. 166, no. 2, pp. 767-781, pp. L15S14, (ISSN: 1340-4202)
    Publication Date: 2006
    Keywords: Plate tectonics ; hot ; spot ; USA ; Volcanology ; Receiver functions ; GJI ; convection, ; Hawaii,hotspots, ; mantle ; discontinuities, ; mantle ; plume, ; receiver ; functions ; Woelbern ; Wolbern
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  • 2
    Publication Date: 2006
    Keywords: TF VIII ; Task Force VIII ; Baby plumes in Central Europe
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  • 3
    Publication Date: 2008-04-11
    Description: Energy and glucose homeostasis are regulated by food intake and liver glucose production, respectively. The upper intestine has a critical role in nutrient digestion and absorption. However, studies indicate that upper intestinal lipids inhibit food intake as well in rodents and humans by the activation of an intestine-brain axis. In parallel, a brain-liver axis has recently been proposed to detect blood lipids to inhibit glucose production in rodents. Thus, we tested the hypothesis that upper intestinal lipids activate an intestine-brain-liver neural axis to regulate glucose homeostasis. Here we demonstrate that direct administration of lipids into the upper intestine increased upper intestinal long-chain fatty acyl-coenzyme A (LCFA-CoA) levels and suppressed glucose production. Co-infusion of the acyl-CoA synthase inhibitor triacsin C or the anaesthetic tetracaine with duodenal lipids abolished the inhibition of glucose production, indicating that upper intestinal LCFA-CoAs regulate glucose production in the preabsorptive state. Subdiaphragmatic vagotomy or gut vagal deafferentation interrupts the neural connection between the gut and the brain, and blocks the ability of upper intestinal lipids to inhibit glucose production. Direct administration of the N-methyl-d-aspartate ion channel blocker MK-801 into the fourth ventricle or the nucleus of the solitary tract where gut sensory fibres terminate abolished the upper-intestinal-lipid-induced inhibition of glucose production. Finally, hepatic vagotomy negated the inhibitory effects of upper intestinal lipids on glucose production. These findings indicate that upper intestinal lipids activate an intestine-brain-liver neural axis to inhibit glucose production, and thereby reveal a previously unappreciated pathway that regulates glucose homeostasis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Penny Y T -- Caspi, Liora -- Lam, Carol K L -- Chari, Madhu -- Li, Xiaosong -- Light, Peter E -- Gutierrez-Juarez, Roger -- Ang, Michelle -- Schwartz, Gary J -- Lam, Tony K T -- DK45024/DK/NIDDK NIH HHS/ -- DK47208/DK/NIDDK NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):1012-6. doi: 10.1038/nature06852. Epub 2008 Apr 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Toronto General Hospital Research Institute, University Health Network, Toronto M5G 1L7, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18401341" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Coenzyme A/biosynthesis/metabolism ; Animals ; Brain/drug effects/*metabolism ; Dietary Fats/administration & dosage/metabolism/*pharmacology ; Fatty Acids/chemistry/metabolism ; Glucose/*biosynthesis/metabolism ; Homeostasis/drug effects ; Insulin/metabolism ; Intestines/drug effects/innervation/*metabolism ; *Lipid Metabolism ; Liver/drug effects/innervation/*metabolism ; Rats ; Satiety Response/drug effects ; Tetracaine/pharmacology ; Triazenes/pharmacology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2008-04-15
    Description: Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly Drosophila melanogaster and compare it to that from the yeast Saccharomyces cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical -1, nucleosome-free region, +1 arrangement. However, Drosophila does not incorporate H2A.Z into the -1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735122/" 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/PMC2735122/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mavrich, Travis N -- Jiang, Cizhong -- Ioshikhes, Ilya P -- Li, Xiaoyong -- Venters, Bryan J -- Zanton, Sara J -- Tomsho, Lynn P -- Qi, Ji -- Glaser, Robert L -- Schuster, Stephan C -- Gilmour, David S -- Albert, Istvan -- Pugh, B Franklin -- GM47477/GM/NIGMS NIH HHS/ -- HG004160/HG/NHGRI NIH HHS/ -- R01 HG004160/HG/NHGRI NIH HHS/ -- R01 HG004160-01A1/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 May 15;453(7193):358-62. doi: 10.1038/nature06929. Epub 2008 Apr 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18408708" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conserved Sequence/genetics ; Drosophila melanogaster/embryology/enzymology/*genetics ; Gene Expression Regulation/genetics ; Genes, Insect/genetics ; Genome, Insect/*genetics ; Histones/metabolism ; Nucleosomes/*genetics/*metabolism ; Promoter Regions, Genetic/genetics ; RNA Polymerase II/metabolism ; Saccharomyces cerevisiae/genetics ; Transcription Initiation Site ; Transcription, Genetic/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2008-09-26
    Description: DNA methylation is an important epigenetic mark for transcriptional gene silencing (TGS) in diverse organisms. Recent studies suggest that the methylation status of a number of genes is dynamically regulated by methylation and demethylation. In Arabidopsis, active DNA demethylation is mediated by the ROS1 (repressor of silencing 1) subfamily of 5-methylcytosine DNA glycosylases through a base excision repair pathway. These demethylases have critical roles in erasing DNA methylation and preventing TGS of target genes. However, it is not known how the demethylases are targeted to specific sequences. Here we report the identification of ROS3, an essential regulator of DNA demethylation that contains an RNA recognition motif. Analysis of ros3 mutants and ros1 ros3 double mutants suggests that ROS3 acts in the same genetic pathway as ROS1 to prevent DNA hypermethylation and TGS. Gel mobility shift assays and analysis of ROS3 immunoprecipitate from plant extracts shows that ROS3 binds to small RNAs in vitro and in vivo. Immunostaining shows that ROS3 and ROS1 proteins co-localize in discrete foci dispersed throughout the nucleus. These results demonstrate a critical role for ROS3 in preventing DNA hypermethylation and suggest that DNA demethylation by ROS1 may be guided by RNAs bound to ROS3.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782394/" 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/PMC2782394/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zheng, Xianwu -- Pontes, Olga -- Zhu, Jianhua -- Miki, Daisuke -- Zhang, Fei -- Li, Wen-Xue -- Iida, Kei -- Kapoor, Avnish -- Pikaard, Craig S -- Zhu, Jian-Kang -- 1R01GM060380/GM/NIGMS NIH HHS/ -- R01 GM060380/GM/NIGMS NIH HHS/ -- R01 GM060380-08/GM/NIGMS NIH HHS/ -- R01 GM077590/GM/NIGMS NIH HHS/ -- R01 GM077590-03/GM/NIGMS NIH HHS/ -- R01GM059138/GM/NIGMS NIH HHS/ -- R01GM070795/GM/NIGMS NIH HHS/ -- R01GM077590/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Oct 30;455(7217):1259-62. doi: 10.1038/nature07305. Epub 2008 Sep 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18815596" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/cytology/*genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cell Nucleus/metabolism ; *DNA Methylation ; DNA-Directed RNA Polymerases/genetics/metabolism ; Gene Silencing ; Nuclear Proteins/genetics/metabolism ; RNA, Plant/genetics/metabolism ; RNA-Binding Proteins/genetics/*metabolism ; Transcription, Genetic
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2008-07-11
    Description: The recent emergence of highly pathogenic avian influenza A virus strains with subtype H5N1 pose a global threat to human health. Elucidation of the underlying mechanisms of viral replication is critical for development of anti-influenza virus drugs. The influenza RNA-dependent RNA polymerase (RdRp) heterotrimer has crucial roles in viral RNA replication and transcription. It contains three proteins: PA, PB1 and PB2. PB1 harbours polymerase and endonuclease activities and PB2 is responsible for cap binding; PA is implicated in RNA replication and proteolytic activity, although its function is less clearly defined. Here we report the 2.9 angstrom structure of avian H5N1 influenza A virus PA (PA(C), residues 257-716) in complex with the PA-binding region of PB1 (PB1(N), residues 1-25). PA(C) has a fold resembling a dragon's head with PB1(N) clamped into its open 'jaws'. PB1(N) is a known inhibitor that blocks assembly of the polymerase heterotrimer and abolishes viral replication. Our structure provides details for the binding of PB1(N) to PA(C) at the atomic level, demonstrating a potential target for novel anti-influenza therapeutics. We also discuss a potential nucleotide binding site and the roles of some known residues involved in polymerase activity. Furthermore, to explore the role of PA in viral replication and transcription, we propose a model for the influenza RdRp heterotrimer by comparing PA(C) with the lambda3 reovirus polymerase structure, and docking the PA(C) structure into an available low resolution electron microscopy map.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Xiaojing -- Zhou, Jie -- Bartlam, Mark -- Zhang, Rongguang -- Ma, Jianyuan -- Lou, Zhiyong -- Li, Xuemei -- Li, Jingjing -- Joachimiak, Andrzej -- Zeng, Zonghao -- Ge, Ruowen -- Rao, Zihe -- Liu, Yingfang -- England -- Nature. 2008 Aug 28;454(7208):1123-6. doi: 10.1038/nature07120. Epub 2008 Jul 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18615018" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Birds/*virology ; Crystallography, X-Ray ; Influenza A Virus, H5N1 Subtype/*enzymology ; Models, Molecular ; Multienzyme Complexes/chemistry/metabolism ; Nucleotides/metabolism ; Peptide Fragments/chemistry/metabolism ; Protein Binding ; Protein Structure, Quaternary ; RNA Replicase/*chemistry/metabolism ; Viral Proteins/*chemistry/*metabolism ; Virus Replication
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2009-02-06
    Description: The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenza H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuan, Puwei -- Bartlam, Mark -- Lou, Zhiyong -- Chen, Shoudeng -- Zhou, Jie -- He, Xiaojing -- Lv, Zongyang -- Ge, Ruowen -- Li, Xuemei -- Deng, Tao -- Fodor, Ervin -- Rao, Zihe -- Liu, Yingfang -- G0700848/Medical Research Council/United Kingdom -- England -- Nature. 2009 Apr 16;458(7240):909-13. doi: 10.1038/nature07720. Epub 2009 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194458" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Birds/virology ; Catalytic Domain ; Crystallography, X-Ray ; Endonucleases/*chemistry/genetics/*metabolism ; Influenza A Virus, H5N1 Subtype/*enzymology ; Influenza in Birds/*virology ; Models, Molecular ; Protein Subunits/chemistry/genetics/metabolism ; RNA Replicase/*chemistry/genetics/*metabolism ; Viral Proteins/*chemistry/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2009-10-10
    Description: The pluripotent state, which is first established in the primitive ectoderm cells of blastocysts, is lost progressively and irreversibly during subsequent development. For example, development of post-implantation epiblast cells from primitive ectoderm involves significant transcriptional and epigenetic changes, including DNA methylation and X chromosome inactivation, which create a robust epigenetic barrier and prevent their reversion to a primitive-ectoderm-like state. Epiblast cells are refractory to leukaemia inhibitory factor (LIF)-STAT3 signalling, but they respond to activin/basic fibroblast growth factor to form self-renewing epiblast stem cells (EpiSCs), which exhibit essential properties of epiblast cells and that differ from embryonic stem (ES) cells derived from primitive ectoderm. Here we show reprogramming of advanced epiblast cells from embryonic day 5.5-7.5 mouse embryos with uniform expression of N-cadherin and inactive X chromosome to ES-cell-like cells (rESCs) in response to LIF-STAT3 signalling. Cultured epiblast cells overcome the epigenetic barrier progressively as they proceed with the erasure of key properties of epiblast cells, resulting in DNA demethylation, X reactivation and expression of E-cadherin. The accompanying changes in the transcriptome result in a loss of phenotypic and epigenetic memory of epiblast cells. Using this approach, we report reversion of established EpiSCs to rESCs. Moreover, unlike epiblast and EpiSCs, rESCs contribute to somatic tissues and germ cells in chimaeras. Further studies may reveal how signalling-induced epigenetic reprogramming may promote reacquisition of pluripotency.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863718/" 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/PMC3863718/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bao, Siqin -- Tang, Fuchou -- Li, Xihe -- Hayashi, Katsuhiko -- Gillich, Astrid -- Lao, Kaiqin -- Surani, M Azim -- 083089/Wellcome Trust/United Kingdom -- G0800784/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2009 Oct 29;461(7268):1292-5. doi: 10.1038/nature08534.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19816418" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomarkers/metabolism ; Cadherins/metabolism ; Cells, Cultured ; Cellular Reprogramming ; DNA Methylation ; Ectoderm/cytology ; Embryo, Mammalian/cytology ; *Embryonic Development ; Embryonic Stem Cells/*cytology/*metabolism ; *Epigenesis, Genetic ; Gene Expression Profiling ; Germ Layers/*cytology/metabolism ; Leukemia Inhibitory Factor/metabolism ; Mice ; Pluripotent Stem Cells/*cytology/*metabolism ; STAT3 Transcription Factor/metabolism ; Y Chromosome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2006-07-22
    Description: The early morphogenetic mechanisms involved in heart formation are evolutionarily conserved. A screen for genes that control Drosophila heart development revealed a cardiac defect in which pericardial and cardial cells dissociate, which causes loss of cardiac function and embryonic lethality. This phenotype resulted from mutations in the genes encoding HMG-CoA reductase, downstream enzymes in the mevalonate pathway, and G protein Ggamma1, which is geranylgeranylated, thus representing an end point of isoprenoid biosynthesis. Our findings reveal a cardial cell-autonomous requirement of Ggamma1 geranylgeranylation for heart formation and suggest the involvement of the mevalonate pathway in congenital heart disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yi, Peng -- Han, Zhe -- Li, Xiumin -- Olson, Eric N -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1301-3. Epub 2006 Jul 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9148, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857902" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Animals, Genetically Modified ; Cell Adhesion ; Drosophila melanogaster/*embryology/genetics/metabolism ; Embryo, Nonmammalian/metabolism ; GTP-Binding Proteins/chemistry/genetics/*metabolism ; Heart/*embryology ; Heart Defects, Congenital/etiology ; Hydroxymethylglutaryl CoA Reductases/genetics/metabolism ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology ; Mevalonic Acid/*metabolism ; Models, Animal ; Mutation ; Myocardium/cytology/metabolism ; Pericardium/cytology ; Protein Prenylation ; Transgenes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2006-11-11
    Description: Metallic and semiconducting carbon nanotubes generally coexist in as-grown materials. We present a gas-phase plasma hydrocarbonation reaction to selectively etch and gasify metallic nanotubes, retaining the semiconducting nanotubes in near-pristine form. With this process, 100% of purely semiconducting nanotubes were obtained and connected in parallel for high-current transistors. The diameter- and metallicity-dependent "dry" chemical etching approach is scalable and compatible with existing semiconductor processing for future integrated circuits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Guangyu -- Qi, Pengfei -- Wang, Xinran -- Lu, Yuerui -- Li, Xiaolin -- Tu, Ryan -- Bangsaruntip, Sarunya -- Mann, David -- Zhang, Li -- Dai, Hongjie -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):974-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Laboratory for Advanced Materials, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095698" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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