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  • Amino Acid Motifs  (14)
  • American Association for the Advancement of Science (AAAS)  (14)
  • American Chemical Society
  • Cambridge University Press
  • International Union of Crystallography
  • National Academy of Sciences
  • 2000-2004  (14)
  • 1940-1944
  • 2000  (14)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (14)
  • American Chemical Society
  • Cambridge University Press
  • International Union of Crystallography
  • National Academy of Sciences
Years
  • 2000-2004  (14)
  • 1940-1944
Year
  • 1
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    Structure of the RNA polymerase domain of E. coli primase (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-03-31
    Description: All cellular organisms use specialized RNA polymerases called "primases" to synthesize RNA primers for the initiation of DNA replication. The high-resolution crystal structure of a primase, comprising the catalytic core of the Escherichia coli DnaG protein, was determined. The core structure contains an active-site architecture that is unrelated to other DNA or RNA polymerase palm folds, but is instead related to the "toprim" fold. On the basis of the structure, it is likely that DnaG binds nucleic acid in a groove clustered with invariant residues and that DnaG is positioned within the replisome to accept single-stranded DNA directly from the replicative helicase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keck, J L -- Roche, D D -- Lynch, A S -- Berger, J M -- New York, N.Y. -- Science. 2000 Mar 31;287(5462):2482-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, 229 Stanley Hall, no. 3206, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10741967" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; DNA Helicases/chemistry/metabolism ; DNA Primase/*chemistry/*metabolism ; DNA Replication ; DNA, Bacterial/metabolism ; DNA, Single-Stranded/*metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Escherichia coli/*enzymology/metabolism ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/biosynthesis ; Recombinant Proteins/chemistry/metabolism ; Templates, Genetic
    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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  • 2
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    Architecture of RNA polymerase II and implications for the transcription mechanism (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-04-28
    Description: A backbone model of a 10-subunit yeast RNA polymerase II has been derived from x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits exhibit a high degree of identity with the corresponding human proteins, and 9 of the 10 subunits are conserved among the three eukaryotic RNA polymerases I, II, and III. Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing complexes. A pore in the protein complex beneath the active center may allow entry of substrates for polymerization and exit of the transcript during proofreading and passage through pause sites in the DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cramer, P -- Bushnell, D A -- Fu, J -- Gnatt, A L -- Maier-Davis, B -- Thompson, N E -- Burgess, R R -- Edwards, A M -- David, P R -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 28;288(5466):640-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10784442" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Enzyme Stability ; Escherichia coli/enzymology ; Humans ; *Models, Molecular ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; RNA Polymerase II/*chemistry/genetics/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; Thermus/enzymology ; Transcription Factors/chemistry/metabolism ; *Transcription Factors, General ; *Transcription, Genetic ; *Transcriptional Elongation Factors
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  • 3
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    A potassium channel protein encoded by chlorella virus PBCV-1 (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-03-04
    Description: The large chlorella virus PBCV-1, which contains double-stranded DNA (dsDNA), encodes a 94-codon open reading frame (ORF) that contains a motif resembling the signature sequence of the pore domain of potassium channel proteins. Phylogenetic analyses of the encoded protein, Kcv, indicate a previously unidentified type of potassium channel. The messenger RNA encoded by the ORF leads to functional expression of a potassium-selective conductance in Xenopus laevis oocytes. The channel blockers amantadine and barium, but not cesium, inhibit this conductance, in addition to virus plaque formation. Thus, PBCV-1 encodes the first known viral protein that functions as a potassium-selective channel and is essential in the virus life cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Plugge, B -- Gazzarrini, S -- Nelson, M -- Cerana, R -- Van Etten, J L -- Derst, C -- DiFrancesco, D -- Moroni, A -- Thiel, G -- 971/Telethon/Italy -- GM32441/GM/NIGMS NIH HHS/ -- GM41333/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Mar 3;287(5458):1641-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Albrecht-von-Haller-Institut fur Pflanzenwissenschaften, Universitat Gottingen, 37073 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10698737" target="_blank"〉PubMed〈/a〉
    Keywords: Amantadine/pharmacology ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Barium/pharmacology ; Cesium/pharmacology ; Chlorella/virology ; Isoelectric Point ; Molecular Sequence Data ; Molecular Weight ; Oocytes ; Patch-Clamp Techniques ; Phycodnaviridae/chemistry/drug effects/*genetics/*physiology ; Potassium/metabolism ; Potassium Channels/*chemistry/genetics/*physiology ; RNA, Messenger/genetics/metabolism ; Recombinant Proteins/metabolism ; Sodium/metabolism ; Viral Plaque Assay ; *Viral Proteins ; Virus Replication/drug effects ; Xenopus laevis
    Print ISSN: 0036-8075
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  • 4
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    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-12-16
    Description: The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riechmann, J L -- Heard, J -- Martin, G -- Reuber, L -- Jiang, C -- Keddie, J -- Adam, L -- Pineda, O -- Ratcliffe, O J -- Samaha, R R -- Creelman, R -- Pilgrim, M -- Broun, P -- Zhang, J Z -- Ghandehari, D -- Sherman, B K -- Yu, G -- New York, N.Y. -- Science. 2000 Dec 15;290(5499):2105-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mendel Biotechnology, 21375 Cabot Boulevard, Hayward, CA 94545, USA. jriechmann@mendelbio.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11118137" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Arabidopsis/chemistry/*genetics ; Caenorhabditis elegans/chemistry/*genetics ; DNA/metabolism ; Drosophila melanogaster/chemistry/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; Gene Duplication ; *Genome ; Genome, Plant ; Protein Binding ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/chemistry/*genetics ; Transcription Factors/chemistry/*genetics/metabolism
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  • 5
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    Structure and function of a human TAFII250 double bromodomain module (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-05-29
    Description: TFIID is a large multiprotein complex that initiates assembly of the transcription machinery. It is unclear how TFIID recognizes promoters in vivo when templates are nucleosome-bound. Here, it is shown that TAFII250, the largest subunit of TFIID, contains two tandem bromodomain modules that bind selectively to multiply acetylated histone H4 peptides. The 2.1 angstrom crystal structure of the double bromodomain reveals two side-by-side, four-helix bundles with a highly polarized surface charge distribution. Each bundle contains an Nepsilon-acetyllysine binding pocket at its center, which results in a structure ideally suited for recognition of diacetylated histone H4 tails. Thus, TFIID may be targeted to specific chromatin-bound promoters and may play a role in chromatin recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobson, R H -- Ladurner, A G -- King, D S -- Tjian, R -- New York, N.Y. -- Science. 2000 May 26;288(5470):1422-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular and Cell Biology, 401 Barker Hall, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10827952" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Histone Acetyltransferases ; Histones/metabolism ; Humans ; Lysine/analogs & derivatives/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Nucleosomes/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; *TATA-Binding Protein Associated Factors ; *Transcription Factor TFIID ; *Transcription, Genetic
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  • 6
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    Crystal structure of rhodopsin: A G protein-coupled receptor (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-05
    Description: Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane alpha helices connected by six loops of varying lengths. We determined the structure of rhodopsin from diffraction data extending to 2.8 angstroms resolution. The highly organized structure in the extracellular region, including a conserved disulfide bridge, forms a basis for the arrangement of the seven-helix transmembrane motif. The ground-state chromophore, 11-cis-retinal, holds the transmembrane region of the protein in the inactive conformation. Interactions of the chromophore with a cluster of key residues determine the wavelength of the maximum absorption. Changes in these interactions among rhodopsins facilitate color discrimination. Identification of a set of residues that mediate interactions between the transmembrane helices and the cytoplasmic surface, where G-protein activation occurs, also suggests a possible structural change upon photoactivation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palczewski, K -- Kumasaka, T -- Hori, T -- Behnke, C A -- Motoshima, H -- Fox, B A -- Le Trong, I -- Teller, D C -- Okada, T -- Stenkamp, R E -- Yamamoto, M -- Miyano, M -- EY09339/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 4;289(5480):739-45.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ophthalmology, University of Washington, Seattle, WA 98195, USA. palczews@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10926528" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cattle ; Cell Membrane/chemistry ; Crystallography, X-Ray ; Heterotrimeric GTP-Binding Proteins/*metabolism ; Hydrogen Bonding ; Light ; Molecular Sequence Data ; Receptors, Cell Surface/*chemistry/metabolism ; Retinaldehyde/chemistry/metabolism ; Rhodopsin/*chemistry/metabolism ; Schiff Bases ; Stereoisomerism ; Vision, Ocular
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  • 7
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    Kinesin superfamily motor protein KIF17 and mLin-10 in NMDA receptor-containing vesicle transport (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-06-10
    Description: Experiments with vesicles containing N-methyl-D-aspartate (NMDA) receptor 2B (NR2B subunit) show that they are transported along microtubules by KIF17, a neuron-specific molecular motor in neuronal dendrites. Selective transport is accomplished by direct interaction of the KIF17 tail with a PDZ domain of mLin-10 (Mint1/X11), which is a constituent of a large protein complex including mLin-2 (CASK), mLin-7 (MALS/Velis), and the NR2B subunit. This interaction, specific for a neurotransmitter receptor critically important for plasticity in the postsynaptic terminal, may be a regulatory point for synaptic plasticity and neuronal morphogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Setou, M -- Nakagawa, T -- Seog, D H -- Hirokawa, N -- New York, N.Y. -- Science. 2000 Jun 9;288(5472):1796-802.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology and Anatomy, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10846156" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Biological Transport ; *Caenorhabditis elegans Proteins ; Cloning, Molecular ; Dendrites/*metabolism ; Dimerization ; Kinesin/chemistry/genetics/*metabolism ; Male ; *Membrane Proteins ; Mice ; Microtubules/metabolism ; Models, Biological ; Molecular Motor Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Molecular Weight ; Organelles/metabolism ; Precipitin Tests ; Protein Binding ; Proteins/chemistry/*metabolism ; Receptors, N-Methyl-D-Aspartate/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Two-Hybrid System Techniques
    Print ISSN: 0036-8075
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  • 8
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    Integration of multiple signals through cooperative regulation of the N-WASP-Arp2/3 complex (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-10-29
    Description: The protein N-WASP [a homolog to the Wiskott-Aldrich syndrome protein (WASP)] regulates actin polymerization by stimulating the actin-nucleating activity of the actin-related protein 2/3 (Arp2/3) complex. N-WASP is tightly regulated by multiple signals: Only costimulation by Cdc42 and phosphatidylinositol (4,5)-bisphosphate (PIP2) yields potent polymerization. We found that regulation requires N-WASP's constitutively active output domain (VCA) and two regulatory domains: a Cdc42-binding domain and a previously undescribed PIP(2)-binding domain. In the absence of stimuli, the regulatory modules together hold the VCA-Arp2/3 complex in an inactive "closed" conformation. In this state, both the Cdc42- and PIP2-binding sites are masked. Binding of either input destabilizes the closed state and enhances binding of the other input. This cooperative activation mechanism shows how combinations of simple binding domains can be used to integrate and amplify coincident signals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prehoda, K E -- Scott, J A -- Mullins, R D -- Lim, W A -- New York, N.Y. -- Science. 2000 Oct 27;290(5492):801-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-0450, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11052943" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Actin-Related Protein 2 ; Actin-Related Protein 3 ; Actins/*metabolism ; Amino Acid Motifs ; Binding Sites ; Biopolymers ; *Cytoskeletal Proteins ; GTP Phosphohydrolases/metabolism ; Humans ; Models, Biological ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Phosphatidylinositol 4,5-Diphosphate/metabolism ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; Thermodynamics ; Wiskott-Aldrich Syndrome Protein, Neuronal ; cdc42 GTP-Binding Protein/metabolism
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  • 9
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    Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-09-01
    Description: The atomic structures of two proteins in the histidine biosynthesis pathway consist of beta/alpha barrels with a twofold repeat pattern. It is likely that these proteins evolved by twofold gene duplication and gene fusion from a common half-barrel ancestor. These ancestral domains are not visible as independent domains in the extant proteins but can be inferred from a combination of sequence and structural analysis. The detection of subdomain structures may be useful in efforts to search genome sequences for functionally and structurally related proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lang, D -- Thoma, R -- Henn-Sax, M -- Sterner, R -- Wilmanns, M -- New York, N.Y. -- Science. 2000 Sep 1;289(5484):1546-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory (EMBL) Hamburg Outstation, EMBL c/o Deutsches Elektronen- Synchrotron (DESY), Notkestrasse 85, D-22603 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10968789" target="_blank"〉PubMed〈/a〉
    Keywords: Aldose-Ketose Isomerases/*chemistry/genetics/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Aminohydrolases/*chemistry/genetics/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; *Evolution, Molecular ; *Gene Duplication ; Histidine/biosynthesis ; Models, Molecular ; Molecular Sequence Data ; Protein Folding ; *Protein Structure, Tertiary ; *Recombination, Genetic ; Sequence Alignment ; Thermotoga maritima/enzymology
    Print ISSN: 0036-8075
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  • 10
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    Protein evolution. On the ancestry of barrels (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-09-19
    Description: Most proteins consist of several domains linked together in a single polypeptide chain, and many of these proteins have evolved by gene duplication and fusion. Miles and Davies discuss the study by Lang et al., who show that this type of protein evolution may also occur in b/a barrel proteins, a common single-domain protein fold. Other single domain proteins may have arisen from similar evolutionary mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miles, E W -- Davies, D R -- New York, N.Y. -- Science. 2000 Sep 1;289(5484):1490.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NIH, Bethesda, MD 20892-0830, USA. edithm@intra.niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10991737" target="_blank"〉PubMed〈/a〉
    Keywords: Aldose-Ketose Isomerases/*chemistry/genetics/metabolism ; Amino Acid Motifs ; Aminohydrolases/*chemistry/genetics/metabolism ; Catalysis ; Crystallography, X-Ray ; Dimerization ; *Evolution, Molecular ; Gene Duplication ; Models, Molecular ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Recombination, Genetic ; Thermotoga maritima/enzymology
    Print ISSN: 0036-8075
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