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  • 1
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    PDB-wide collection of binding data: current status of the PDBbind database (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-29
    Description: Motivation: Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank (PDB). It thus provides the linkage between structural information and energetic properties of biomolecular complexes, which is especially desirable for computational studies or statistical analyses. Results: Since its first public release in 2004, the PDBbind database has been updated on an annual basis. The latest release (version 2013) provides experimental binding affinity data for 10 776 biomolecular complexes in PDB, including 8302 protein–ligand complexes and 2474 other types of complexes. In this article, we will describe the current methods used for compiling PDBbind and the updated status of this database. We will also review some typical applications of PDBbind published in the scientific literature. Availability and implementation: All contents of this database are freely accessible at the PDBbind-CN Web server at http://www.pdbbind-cn.org/ . Contact: wangrx@mail.sioc.ac.cn . Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation [Cell Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-02-23
    Description: Histone methylation has an important role in transcriptional regulation. However, unlike H3K4 and H3K9 methylation, the role of H4K20 monomethylation (H4K20me-1) in transcriptional regulation remains unclear. Here, we show that Wnt3a specifically stimulates H4K20 monomethylation at the T cell factor (TCF)-binding element through the histone methylase SET8. Additionally, SET8 is crucial for activation of the Wnt reporter gene and target genes in both mammalian cells and zebrafish. Furthermore, SET8 interacts with lymphoid enhancing factor-1 (LEF1)/TCF4 directly, and this interaction is regulated by Wnt3a. Therefore, we conclude that SET8 is a Wnt signaling mediator and is recruited by LEF1/TCF4 to regulate the transcription of Wnt-activated genes, possibly through H4K20 monomethylation at the target gene promoters. Our findings also indicate that H4K20me-1 is a marker for gene transcription activation, at least in canonical Wnt signaling.
    Keywords: Feature Articles
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    Spin fluctuation induced Weyl semimetal state in the paramagnetic phase of EuCd2As2 (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Weyl fermions as emergent quasiparticles can arise in Weyl semimetals (WSMs) in which the energy bands are nondegenerate, resulting from inversion or time-reversal symmetry breaking. Nevertheless, experimental evidence for magnetically induced WSMs is scarce. Here, using photoemission spectroscopy, we observe that the degeneracy of Bloch bands is already lifted in the paramagnetic phase of EuCd〈sub〉2〈/sub〉As〈sub〉2〈/sub〉. We attribute this effect to the itinerant electrons experiencing quasi-static and quasi–long-range ferromagnetic fluctuations. Moreover, the spin-nondegenerate band structure harbors a pair of ideal Weyl nodes near the Fermi level. Hence, we show that long-range magnetic order and the spontaneous breaking of time-reversal symmetry are not essential requirements for WSM states in centrosymmetric systems and that WSM states can emerge in a wider range of condensed matter systems than previously thought.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Autistic phenotype from MEF2C knockout cells (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-01-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lipton, Stuart A -- Li, Hao -- Zaremba, Jeffrey D -- McKercher, Scott R -- Cui, Jiankun -- Kang, Yeon-Joo -- Nie, Zhiguo -- Soussou, Walid -- Talantova, Maria -- Okamoto, Shu-Ichi -- Nakanishi, Nobuki -- New York, N.Y. -- Science. 2009 Jan 9;323(5911):208. doi: 10.1126/science.323.5911.208b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19131610" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autistic Disorder/*genetics/*physiopathology ; Embryonic Stem Cells/physiology ; Gene Knockout Techniques ; MEF2 Transcription Factors ; Mice ; Mice, Knockout ; Myogenic Regulatory Factors/*genetics/*physiology ; *Neurogenesis ; Neurons/cytology/*physiology ; Phenotype ; Rett Syndrome/genetics/physiopathology ; Synapses/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Step-growth polymerization of inorganic nanoparticles (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-07-10
    Description: Self-organization of nanoparticles is an efficient strategy for producing nanostructures with complex, hierarchical architectures. The past decade has witnessed great progress in nanoparticle self-assembly, yet the quantitative prediction of the architecture of nanoparticle ensembles and of the kinetics of their formation remains a challenge. We report on the marked similarity between the self-assembly of metal nanoparticles and reaction-controlled step-growth polymerization. The nanoparticles act as multifunctional monomer units, which form reversible, noncovalent bonds at specific bond angles and organize themselves into a colloidal polymer. We show that the kinetics and statistics of step-growth polymerization enable a quantitative prediction of the architecture of linear, branched, and cyclic self-assembled nanostructures; their aggregation numbers and size distribution; and the formation of structural isomers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Kun -- Nie, Zhihong -- Zhao, Nana -- Li, Wei -- Rubinstein, Michael -- Kumacheva, Eugenia -- 1-R01-HL077546-03A2/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2010 Jul 9;329(5988):197-200. doi: 10.1126/science.1189457.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616274" target="_blank"〉PubMed〈/a〉
    Keywords: Cetrimonium Compounds/chemistry ; Colloids ; Cyclization ; Gold ; Isomerism ; Kinetics ; Metal Nanoparticles/*chemistry ; Microscopy, Electron, Transmission ; Nanotechnology/methods ; Physicochemical Processes ; Polymers ; Polystyrenes/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Ethanol augments GABAergic transmission in the central amygdala via CRF1 receptors (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-06
    Description: The central amygdala (CeA) plays a role in the relationship among stress, corticotropin-releasing factor (CRF), and alcohol abuse. In whole-cell recordings, both CRF and ethanol enhanced gamma-aminobutyric acid-mediated (GABAergic) neurotransmission in CeA neurons from wild-type and CRF2 receptor knockout mice, but not CRF1 receptor knockout mice. CRF1 (but not CRF2) receptor antagonists blocked both CRF and ethanol effects in wild-type mice. These data indicate that CRF1 receptors mediate ethanol enhancement of GABAergic synaptic transmission in the CeA, and they suggest a cellular mechanism underlying involvement of CRF in ethanol's behavioral and motivational effects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nie, Zhiguo -- Schweitzer, Paul -- Roberts, Amanda J -- Madamba, Samuel G -- Moore, Scott D -- Siggins, George Robert -- AA06420/AA/NIAAA NIH HHS/ -- AA10994/AA/NIAAA NIH HHS/ -- DA03665/DA/NIDA NIH HHS/ -- DA13658/DA/NIDA NIH HHS/ -- New York, N.Y. -- Science. 2004 Mar 5;303(5663):1512-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuropharmacology and Alcohol Research Center, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15001778" target="_blank"〉PubMed〈/a〉
    Keywords: Alcohol Drinking ; Amygdala/drug effects/*physiology ; Animals ; Corticotropin-Releasing Hormone/pharmacology ; Dose-Response Relationship, Drug ; Ethanol/*pharmacology ; Evoked Potentials/drug effects ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Neurons/drug effects/*physiology ; Patch-Clamp Techniques ; Receptors, Corticotropin-Releasing Hormone/antagonists & ; inhibitors/genetics/*metabolism ; Receptors, GABA-A/metabolism ; Stress, Psychological/physiopathology ; Synaptic Transmission/*drug effects ; gamma-Aminobutyric Acid/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Temporal diagnostics of femtosecond electron bunches with complex structures using sparsity-based algorithm (2018)
    American Physical Society (APS)
    Details
    Publication Date: 2018-11-03
    Description: Author(s): Q. Q. Su, J. F. Hua, Z. Nie, Y. Ma, S. Liu, Y. F. Zheng, C.-H. Pai, and W. Lu Femtosecond electron bunches with complex temporal structures play a crucial role in terahertz generation, free-electron lasers, and plasma wakefield accelerators. However, diagnostics of electron beam current profiles with femtosecond resolution are still challenging. Coherent transition radiation ... [Phys. Rev. Accel. Beams 21, 112801] Published Fri Nov 02, 2018
    Keywords: Beam Control, Diagnostics, and Feedback
    Electronic ISSN: 1098-4402
    Topics: Physics
    Published by American Physical Society (APS)
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  • 8
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    Pollution threatens migratory shorebirds (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-01-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Zhenwu -- Huang, Qifei -- Nie, Zhiqiang -- Yang, Yufei -- New York, N.Y. -- Science. 2015 Dec 4;350(6265):1176-7. doi: 10.1126/science.350.6265.1176-c.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Research Academy, North China Electric Power University, Beijing, 102206, China. ; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China. huangqf@craes.org.cn. ; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26785469" target="_blank"〉PubMed〈/a〉
    Keywords: *Animal Migration ; Animals ; *Birds
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Chiral Majorana fermion modes in a quantum anomalous Hall insulator-superconductor structure (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-07-21
    Description: Majorana fermion is a hypothetical particle that is its own antiparticle. We report transport measurements that suggest the existence of one-dimensional chiral Majorana fermion modes in the hybrid system of a quantum anomalous Hall insulator thin film coupled with a superconductor. As the external magnetic field is swept, half-integer quantized conductance plateaus are observed at the locations of magnetization reversals, giving a distinct signature of the Majorana fermion modes. This transport signature is reproducible over many magnetic field sweeps and appears at different temperatures. This finding may open up an avenue to control Majorana fermions for implementing robust topological quantum computing.
    Keywords: Physics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Experimental evidence of hourglass fermion in the candidate nonsymmorphic topological insulator KHgSb (2017)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2017-05-06
    Description: Topological insulators (TIs) host novel states of quantum matter characterized by nontrivial conducting boundary states connecting valence and conduction bulk bands. All TIs discovered experimentally so far rely on either time-reversal or mirror crystal symmorphic symmetry to protect massless Dirac-like boundary states. Several materials were recently proposed to be TIs with nonsymmorphic symmetry, where a glide mirror protects exotic surface fermions with hourglass-shaped dispersion. However, an experimental confirmation of this new fermion is missing. Using angle-resolved photoemission spectroscopy, we provide experimental evidence of hourglass fermions on the (010) surface of crystalline KHgSb, whereas the (001) surface has no boundary state, in agreement with first-principles calculations. Our study will stimulate further research activities of topological properties of nonsymmorphic materials.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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