Niu Huang, Ph.D. - Publications

Affiliations: 
2007- NIBS, Beijing 
Area:
Computer-aided Drug Design, Computational Chemistry
Website:
http://www.huanglab.org.cn/

74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Gao L, Su C, Du X, Wang R, Chen S, Zhou Y, Liu C, Liu X, Tian R, Zhang L, Xie K, Chen S, Guo Q, Guo L, Hano Y, ... ... Huang N, et al. FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis. Nature Chemistry. PMID 32451436 DOI: 10.1038/s41557-020-0467-7  0.4
2020 Li G, Zhang W, Xie Y, Li Y, Cao R, Zheng G, Huang N, Zhou Y. Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors. Journal of Chemical Information and Modeling. PMID 32407627 DOI: 10.1021/acs.jcim.0c00245  0.4
2020 Ju D, Zhang W, Yan J, Zhao H, Li W, Wang J, Liao M, Xu Z, Wang Z, Zhou G, Mei L, Hou N, Ying S, Cai T, Chen S, ... ... Huang N, et al. Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals. Science Translational Medicine. 12. PMID 32376767 DOI: 10.1126/scitranslmed.aba0769  0.44
2020 Peng S, Li W, Hou N, Huang N. A Review of 1-Regulated Metabolic Diseases and Related Drug Discoveries. Cells. 9. PMID 31936903 DOI: 10.3390/cells9010184  0.32
2019 Li G, Li W, Xie Y, Wan X, Zheng G, Huang N, Zhou Y. Discovery of Novel Pim-1 Kinase Inhibitors with a Flexible-Receptor Docking Protocol. Journal of Chemical Information and Modeling. PMID 31609618 DOI: 10.1021/acs.jcim.9b00494  0.44
2019 Jones AX, Cao Y, Tang YL, Wang JH, Ding YH, Tan H, Chen ZL, Fang RQ, Yin J, Chen RC, Zhu X, She Y, Huang N, Shao F, Ye K, et al. Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers. Nature Communications. 10: 3911. PMID 31477730 DOI: 10.1038/s41467-019-11917-z  0.56
2019 Wang Y, Fu Q, Zhou Y, Du Y, Huang N. The Replacement of Protein Binding-site Waters Contributes to Favorable Halogen Bond Interactions. Journal of Chemical Information and Modeling. PMID 31187992 DOI: 10.1021/acs.jcim.9b00128  0.4
2019 Peng S, Xiao W, Ju D, Sun B, Hou N, Liu Q, Wang Y, Zhao H, Gao C, Zhang S, Cao R, Li P, Huang H, Ma Y, Wang Y, ... ... Huang N, et al. Identification of entacapone as a chemical inhibitor of FTO mediating metabolic regulation through FOXO1. Science Translational Medicine. 11. PMID 30996080 DOI: 10.1126/scitranslmed.aau7116  0.4
2019 Zhang C, Qin S, Hu B, Lv J, Yang Z, Yan W, Wang J, Huang N, Huang Z. Disruption of nucleobase stacking to restore reactivity. Nucleosides, Nucleotides & Nucleic Acids. 1-11. PMID 30922168 DOI: 10.1080/15257770.2019.1576882  0.44
2019 Sun L, Ma L, Zhang H, Cao Y, Wang C, Hou N, Huang N, von Deneen KM, Zhao C, Shi Y, Pan Y, Wang M, Ji G, Nie Y. Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice via Alterations in Gut Microbiota. Theranostics. 9: 721-733. PMID 30809304 DOI: 10.7150/thno.31562  0.56
2018 Zhou Y, Wang Y, Li P, Huang XP, Qi X, Du Y, Huang N. Exploring Halogen Bonds in 5-Hydroxytryptamine 2B Receptor-Ligand Interactions. Acs Medicinal Chemistry Letters. 9: 1019-1024. PMID 30344910 DOI: 10.1021/acsmedchemlett.8b00300  0.4
2018 Lei Z, Chai N, Tian M, Zhang Y, Wang G, Liu J, Tian Z, Yi X, Chen D, Li X, Yu P, Hu H, Xu B, Jian C, Bian Z, ... ... Huang N, et al. Novel peptide GX1 inhibits angiogenesis by specifically binding to transglutaminase-2 in the tumorous endothelial cells of gastric cancer. Cell Death & Disease. 9: 579. PMID 29785022 DOI: 10.1038/s41419-018-0594-x  0.44
2017 He L, Li H, Huang N, Zhou X, Tian J, Li T, Wu J, Tian Y, Yin Y, Yao K. Alpha-ketoglutarate suppresses the NF-κB-mediated inflammatory pathway and enhances the PXR-regulated detoxification pathway. Oncotarget. 8: 102974-102988. PMID 29262538 DOI: 10.18632/oncotarget.16875  0.44
2017 He L, Zhou X, Huang N, Li H, Cui Z, Tian J, Jiang Q, Liu S, Wu J, Li T, Yao K, Yin Y. Administration of alpha-ketoglutarate improves epithelial restitution under stress injury in early-weaning piglets. Oncotarget. 8: 91965-91978. PMID 29190890 DOI: 10.18632/oncotarget.20555  0.44
2017 Ren S, Caforio A, Yang Q, Sun B, Yu F, Zhu X, Wang J, Dou C, Fu Q, Huang N, Sun Q, Nie C, Qi S, Gong X, He J, et al. Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes. Cell Research. PMID 28961231 DOI: 10.1038/cr.2017.122  0.44
2017 Wang Y, Sun Y, Cao R, Liu D, Xie Y, Li L, Qi X, Huang N. In Silico Identification of a Novel Hinge-Binding Scaffold for Kinase Inhibitor Discovery. Journal of Medicinal Chemistry. PMID 28945083 DOI: 10.1021/acs.jmedchem.7b01075  0.4
2017 Zhang L, Sun H, Chen Z, Liu Z, Huang N, Qian F. Intermolecular interactions between co-encapsulated drugs inhibit drug crystallization and enhance colloidal stability of polymeric micelles. Molecular Pharmaceutics. PMID 28829143 DOI: 10.1021/acs.molpharmaceut.7b00591  0.32
2017 He L, Zhou X, Huang N, Li H, Li T, Yao K, Tian Y, Hu CA, Yin Y. Functions of pregnane X receptor in self-detoxification. Amino Acids. PMID 28534176 DOI: 10.1007/s00726-017-2435-0  0.44
2017 He L, Li H, Huang N, Zhou X, Tian J, Li T, Wu J, Tian Y, Yin Y, Yao K. Alpha-ketoglutarate suppresses the NF-κB-mediated inflammatory pathway and enhances the PXR-regulated detoxification pathway. Oncotarget. PMID 28430654 DOI: 10.18632/oncotarget.16875  0.44
2017 He L, Huang N, Li H, Tian J, Zhou X, Li T, Yao K, Wu G, Yin Y. The AMPK/α-ketoglutarate axis regulates intestinal water and ions homeostasis in young pigs. Journal of Agricultural and Food Chemistry. PMID 28241728 DOI: 10.1021/acs.jafc.7b00324  0.44
2016 Bao C, Li F, Wang J, Sun P, Huang N, Sun Y, Fang L, Wang L, Sun X. One-Pot Solvothermal in Situ Growth of 1D Single-Crystalline NiSe on Ni Foil as Efficient and Stable Transparent Conductive Oxide Free Counter Electrodes for Dye-Sensitized Solar Cells. Acs Applied Materials & Interfaces. 8: 32788-32796. PMID 27934175 DOI: 10.1021/acsami.6b10198  0.44
2016 Liu X, Dong T, Zhou Y, Huang N, Lei X. Exploring the Binding Proteins of Glycolipids with Bifunctional Chemical Probes. Angewandte Chemie (International Ed. in English). PMID 27762087 DOI: 10.1002/anie.201608827  0.4
2016 He L, Zhou X, Huang N, Li H, Tian J, Li T, Yao K, Wu G, Nyachoti CM, Kim SW, Yin Y. The Mechanism of AMPK Regulation on Glucose, Lipid and Protein Metabolic Homeostasis and Its Related Physiologically Nutritional Significance. Current Protein & Peptide Science. PMID 27356941  0.44
2016 Liu JJ, Niu CY, Wu Y, Tan D, Wang Y, Ye MD, Liu Y, Zhao W, Zhou K, Liu QS, Dai J, Yang X, Dong MQ, Huang N, Wang HW. CryoEM structure of yeast cytoplasmic exosome complex. Cell Research. PMID 27174052 DOI: 10.1038/cr.2016.56  0.32
2016 He L, Li H, Huang N, Tian J, Liu Z, Zhou X, Yao K, Li T, Yin Y. Effects of Alpha-Ketoglutarate on Glutamine Metabolism in Piglet Enterocytes in Vivo and in Vitro. Journal of Agricultural and Food Chemistry. PMID 27018713 DOI: 10.1021/acs.jafc.6b00433  0.44
2015 Zhou Y, Ma J, Lin X, Huang XP, Wu K, Huang N. Structure-Based Discovery of Novel and Selective 5-Hydroxytryptamine 2B Receptor Antagonists for the Treatment of Irritable Bowel Syndrome. Journal of Medicinal Chemistry. PMID 26700945 DOI: 10.1021/acs.jmedchem.5b01631  0.4
2015 Cao R, Wang Y, Huang N. Discovery of 2-Acylaminothiophene-3-Carboxamides as Multitarget Inhibitors for BCR-ABL Kinase and Microtubules. Journal of Chemical Information and Modeling. PMID 26501568 DOI: 10.1021/acs.jcim.5b00540  0.84
2015 Hu Z, Wan X, Hao R, Zhang H, Li L, Li L, Xie Q, Wang P, Gao Y, Chen S, Wei M, Luan Z, Zhang A, Huang N, Chen L. Phosphorylation of mutationally introduced tyrosine in the activation loop of HER2 confers gain-of-function activity. Plos One. 10: e0123623. PMID 25853726 DOI: 10.1371/journal.pone.0123623  0.44
2015 Dong T, Li C, Wang X, Dian L, Zhang X, Li L, Chen S, Cao R, Li L, Huang N, He S, Lei X. Ainsliadimer A selectively inhibits IKKα/β by covalently binding a conserved cysteine. Nature Communications. 6: 6522. PMID 25813672 DOI: 10.1038/ncomms7522  0.4
2015 Zhou Y, Huang N. Binding site druggability assessment in fragment-based drug design. Methods in Molecular Biology (Clifton, N.J.). 1289: 13-21. PMID 25709029 DOI: 10.1007/978-1-4939-2486-8_2  0.84
2014 Yao Q, Zhang L, Wan X, Chen J, Hu L, Ding X, Li L, Karar J, Peng H, Chen S, Huang N, Rauscher FJ, Shao F. Structure and specificity of the bacterial cysteine methyltransferase effector NleE suggests a novel substrate in human DNA repair pathway. Plos Pathogens. 10: e1004522. PMID 25412445 DOI: 10.1371/journal.ppat.1004522  0.84
2014 Yao Q, Lu Q, Wan X, Song F, Xu Y, Hu M, Zamyatina A, Liu X, Huang N, Zhu P, Shao F. A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family. Elife. 3. PMID 25310236 DOI: 10.7554/eLife.03714  0.44
2014 Cao R, Huang N, Wang Y. Evaluation and application of MD-PB/SA in structure-based hierarchical virtual screening. Journal of Chemical Information and Modeling. 54: 1987-96. PMID 24977649 DOI: 10.1021/ci5003203  0.4
2014 Deng M, Lu Z, Zheng J, Wan X, Chen X, Hirayasu K, Sun H, Lam Y, Chen L, Wang Q, Song C, Huang N, Gao GF, Jiang Y, Arase H, et al. A motif in LILRB2 critical for Angptl2 binding and activation. Blood. 124: 924-35. PMID 24899623 DOI: 10.1182/blood-2014-01-549162  0.44
2014 Zhou Y, Wu C, Zhao L, Huang N. Exploring the early stages of the pH-induced conformational change of influenza hemagglutinin. Proteins. 82: 2412-28. PMID 24854389 DOI: 10.1002/prot.24606  0.4
2014 Sun H, Zhao L, Peng S, Huang N. Incorporating replacement free energy of binding-site waters in molecular docking. Proteins. 82: 1765-76. PMID 24549784 DOI: 10.1002/prot.24530  0.32
2013 Cao R, Li W, Sun HZ, Zhou Y, Huang N. [Computational chemistry in structure-based drug design]. Yao Xue Xue Bao = Acta Pharmaceutica Sinica. 48: 1041-52. PMID 24133970  0.4
2013 Bu C, Liu Y, Yu Z, You S, Huang N, Liang L, Zhao XZ. Highly transparent carbon counter electrode prepared via an in situ carbonization method for bifacial dye-sensitized solar cells. Acs Applied Materials & Interfaces. 5: 7432-8. PMID 23806279 DOI: 10.1021/am4017472  0.32
2013 Wan X, Ma Y, McClendon CL, Huang LJ, Huang N. Ab initio modeling and experimental assessment of Janus Kinase 2 (JAK2) kinase-pseudokinase complex structure. Plos Computational Biology. 9: e1003022. PMID 23592968 DOI: 10.1371/journal.pcbi.1003022  0.84
2013 Wan X, Zhang W, Li L, Xie Y, Li W, Huang N. A new target for an old drug: identifying mitoxantrone as a nanomolar inhibitor of PIM1 kinase via kinome-wide selectivity modeling. Journal of Medicinal Chemistry. 56: 2619-29. PMID 23442188 DOI: 10.1021/jm400045y  0.44
2013 Liang L, Liu Y, Bu C, Guo K, Sun W, Huang N, Peng T, Sebo B, Pan M, Liu W, Guo S, Zhao XZ. Highly uniform, bifunctional core/double-shell-structured β-NaYF4:Er3+, Yb3+ @ SiO2@TiO2 hexagonal sub-microprisms for high-performance dye sensitized solar cells. Advanced Materials (Deerfield Beach, Fla.). 25: 2174-80. PMID 23420696 DOI: 10.1002/adma.201204847  0.32
2013 Wu Y, Dai X, Huang N, Zhao L. A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space. Journal of Computational Chemistry. 34: 1271-82. PMID 23420684 DOI: 10.1002/jcc.23249  0.32
2013 Wang Y, Liu M, Cao R, Zhang W, Yin M, Xiao X, Liu Q, Huang N. A soluble bis-chelated gold(I) diphosphine compound with strong anticancer activity and low toxicity. Journal of Medicinal Chemistry. 56: 1455-66. PMID 23362983 DOI: 10.1021/jm3009822  0.4
2013 Peng T, Sun W, Sun X, Huang N, Liu Y, Bu C, Guo S, Zhao XZ. Direct tri-constituent co-assembly of highly ordered mesoporous carbon counter electrode for dye-sensitized solar cells. Nanoscale. 5: 337-41. PMID 23165970 DOI: 10.1039/c2nr32536e  0.32
2012 Yao Q, Cui J, Wang J, Li T, Wan X, Luo T, Gong YN, Xu Y, Huang N, Shao F. Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis. Proceedings of the National Academy of Sciences of the United States of America. 109: 20395-400. PMID 23175788 DOI: 10.1073/pnas.1210831109  0.44
2012 Liu Y, Zhai H, Guo F, Huang N, Sun W, Bu C, Peng T, Yuan J, Zhao X. Synergistic effect of surface plasmon resonance and constructed hierarchical TiO2 spheres for dye-sensitized solar cells. Nanoscale. 4: 6863-9. PMID 23023266 DOI: 10.1039/c2nr31954c  0.32
2012 Cao R, Liu M, Yin M, Liu Q, Wang Y, Huang N. Discovery of novel tubulin inhibitors via structure-based hierarchical virtual screening. Journal of Chemical Information and Modeling. 52: 2730-40. PMID 22992059 DOI: 10.1021/ci300302c  0.4
2012 Lin X, Huang XP, Chen G, Whaley R, Peng S, Wang Y, Zhang G, Wang SX, Wang S, Roth BL, Huang N. Life beyond kinases: structure-based discovery of sorafenib as nanomolar antagonist of 5-HT receptors. Journal of Medicinal Chemistry. 55: 5749-59. PMID 22694093 DOI: 10.1021/jm300338m  0.84
2012 Peng S, Lin X, Guo Z, Huang N. Identifying multiple-target ligands via computational chemogenomics approaches. Current Topics in Medicinal Chemistry. 12: 1363-75. PMID 22690683  0.36
2012 Chen P, Song Z, Qi Y, Feng X, Xu N, Sun Y, Wu X, Yao X, Mao Q, Li X, Dong W, Wan X, Huang N, Shen X, Liang Z, et al. Molecular determinants of enterovirus 71 viral entry: cleft around GLN-172 on VP1 protein interacts with variable region on scavenge receptor B 2. The Journal of Biological Chemistry. 287: 6406-20. PMID 22219187 DOI: 10.1074/jbc.M111.301622  0.44
2011 Christofferson A, Zhao L, Sun H, Huang Z, Huang N. Theoretical studies of the base pair fidelity of selenium-modified DNA. The Journal of Physical Chemistry. B. 115: 10041-8. PMID 21770426 DOI: 10.1021/jp204204x  0.32
2010 Huang N, Jacobson MP. Binding-site assessment by virtual fragment screening. Plos One. 5: e10109. PMID 20404926 DOI: 10.1371/journal.pone.0010109  0.84
2009 Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y. Automated docking screens: a feasibility study. Journal of Medicinal Chemistry. 52: 5712-20. PMID 19719084 DOI: 10.1021/jm9006966  0.84
2009 Rapp CS, Schonbrun C, Jacobson MP, Kalyanaraman C, Huang N. Automated site preparation in physics-based rescoring of receptor ligand complexes. Proteins. 77: 52-61. PMID 19382204 DOI: 10.1002/prot.22415  0.84
2009 Yao Q, Cui J, Zhu Y, Wang G, Hu L, Long C, Cao R, Liu X, Huang N, Chen S, Liu L, Shao F. A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle. Proceedings of the National Academy of Sciences of the United States of America. 106: 3716-21. PMID 19225106 DOI: 10.1073/pnas.0900212106  0.44
2008 Huang Z, Feng Y, Chen D, Wu X, Huang S, Wang X, Xiao X, Li W, Huang N, Gu L, Zhong G, Chai J. Structural basis for activation and inhibition of the secreted chlamydia protease CPAF. Cell Host & Microbe. 4: 529-42. PMID 19064254 DOI: 10.1016/j.chom.2008.10.005  0.4
2008 Huang N, Shoichet BK. Exploiting ordered waters in molecular docking. Journal of Medicinal Chemistry. 51: 4862-5. PMID 18680357 DOI: 10.1021/jm8006239  0.84
2008 Chen L, Wang H, Zhang J, Gu L, Huang N, Zhou JM, Chai J. Structural basis for the catalytic mechanism of phosphothreonine lyase. Nature Structural & Molecular Biology. 15: 101-2. PMID 18084305 DOI: 10.1038/nsmb1329  0.36
2007 Ji Q, Zhou Y, Peng H, Huang N, Qi J, Xiong DS, Gao YD, Yang M, Yang CZ. [Design and activity determination of small molecular inhibitors of integrin alphavbeta3]. Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae. 29: 347-52. PMID 17633460  0.4
2007 Huang N, Jacobson MP. Physics-based methods for studying protein-ligand interactions. Current Opinion in Drug Discovery & Development. 10: 325-31. PMID 17554859  0.84
2006 Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. Molecular mechanics methods for predicting protein-ligand binding. Physical Chemistry Chemical Physics : Pccp. 8: 5166-77. PMID 17203140 DOI: 10.1039/b608269f  0.84
2006 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. Journal of Medicinal Chemistry. 49: 6789-801. PMID 17154509 DOI: 10.1021/jm0608356  0.84
2006 Banavali NK, Huang N, MacKerell AD. Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix. The Journal of Physical Chemistry. B. 110: 10997-1004. PMID 16771353 DOI: 10.1021/jp0561322  1
2006 Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. Journal of Chemical Information and Modeling. 46: 243-53. PMID 16426060 DOI: 10.1021/ci0502855  0.84
2005 Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 1: 153-68. PMID 26641126 DOI: 10.1021/ct049930p  1
2005 Huang N, MacKerell AD. Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. Journal of Molecular Biology. 345: 265-74. PMID 15571720 DOI: 10.1016/j.jmb.2004.10.042  1
2005 Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD. Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator Journal of Chemical Theory and Computation. 1: 153-168. DOI: 10.1021/ct049930p  0.84
2004 Huang N, MacKerell AD. Atomistic view of base flipping in DNA. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 362: 1439-60. PMID 15306460 DOI: 10.1098/rsta.2004.1383  1
2004 Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X. Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Research. 32: 3877-86. PMID 15273274 DOI: 10.1093/nar/gkh701  0.84
2004 Huang N, Nagarsekar A, Xia G, Hayashi J, MacKerell AD. Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site. Journal of Medicinal Chemistry. 47: 3502-11. PMID 15214778 DOI: 10.1021/jm030470e  1
2004 Peng H, Qi J, Huang N, Xie P, Wang JX, Yang CZ. [Molecular design and biological activity of BCR-ABL tyrosine kinase inhibitors]. Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae. 26: 145-9. PMID 15171550  0.32
2003 Peng H, Huang N, Qi J, Xie P, Xu C, Wang J, Yang C. Identification of novel inhibitors of BCR-ABL tyrosine kinase via virtual screening. Bioorganic & Medicinal Chemistry Letters. 13: 3693-9. PMID 14552760 DOI: 10.1016/j.bmcl.2003.08.014  0.44
2003 Pan Y, Huang N, Cho S, MacKerell AD. Consideration of molecular weight during compound selection in virtual target-based database screening Journal of Chemical Information and Computer Sciences. 43: 267-272. PMID 12546562 DOI: 10.1021/ci020055f  0.84
2003 Huang N, Banavali NK, MacKerell AD. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proceedings of the National Academy of Sciences of the United States of America. 100: 68-73. PMID 12506195 DOI: 10.1073/pnas.0135427100  1
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