| Year |
Citation |
Score |
| 2018 |
Azad RN, Zafiropoulos D, Ober D, Jiang Y, Chiu TP, Sagendorf JM, Rohs R, Tullius TD. Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations. Nucleic Acids Research. PMID 29390080 DOI: 10.1093/Nar/Gky033 |
0.763 |
|
| 2015 |
Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R. 28 GBshape: a genome browser database for DNA shape annotations. Journal of Biomolecular Structure & Dynamics. 33: 16. PMID 26103240 DOI: 10.1080/07391102.2015.1032568 |
0.418 |
|
| 2015 |
Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R. GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Research. 43: D103-9. PMID 25326329 DOI: 10.1093/Nar/Gku977 |
0.497 |
|
| 2014 |
Ingle S, Azad RN, Jain SS, Tullius TD. Chemical probing of RNA with the hydroxyl radical at single-atom resolution. Nucleic Acids Research. 42: 12758-67. PMID 25313156 DOI: 10.1093/Nar/Gku934 |
0.674 |
|
| 2014 |
Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, ... ... Tullius TD, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415 |
0.325 |
|
| 2013 |
Subramanian HK, Bernard SE, Chiang C, J. Parker SC, Tullius TD. 120 Genome-wide mapping of DNA strand breaks inSaccharomyces cerevisiae Journal of Biomolecular Structure and Dynamics. 31: 76-76. DOI: 10.1080/07391102.2013.786362 |
0.471 |
|
| 2011 |
Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. Acs Chemical Biology. 6: 1314-20. PMID 21967305 DOI: 10.1021/Cb200155T |
0.538 |
|
| 2011 |
Parker SC, Harlap A, Tullius TD. A computational method to search for DNA structural motifs in functional genomic elements. Methods in Molecular Biology (Clifton, N.J.). 759: 367-79. PMID 21863498 DOI: 10.1007/978-1-61779-173-4_21 |
0.532 |
|
| 2011 |
Parker SC, Tullius TD. DNA shape, genetic codes, and evolution. Current Opinion in Structural Biology. 21: 342-7. PMID 21439813 DOI: 10.1016/J.Sbi.2011.03.002 |
0.435 |
|
| 2009 |
Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH. Local DNA topography correlates with functional noncoding regions of the human genome. Science (New York, N.Y.). 324: 389-92. PMID 19286520 DOI: 10.1126/Science.1169050 |
0.505 |
|
| 2008 |
Parker SC, Margulies EH, Tullius TD. The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome. Genome Informatics. International Conference On Genome Informatics. 20: 199-211. PMID 19425134 DOI: 10.11234/Gi1990.20.199 |
0.468 |
|
| 2008 |
Jain SS, Tullius TD. Footprinting protein-DNA complexes using the hydroxyl radical. Nature Protocols. 3: 1092-1100. PMID 18546600 DOI: 10.1038/Nprot.2008.72 |
0.524 |
|
| 2007 |
Wang Q, Tullius TD, Levin JR. Effects of discontinuities in the DNA template on abortive initiation and promoter escape by Escherichia coli RNA polymerase. The Journal of Biological Chemistry. 282: 26917-27. PMID 17650506 DOI: 10.1074/Jbc.M702473200 |
0.436 |
|
| 2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Tullius TD, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.622 |
|
| 2007 |
Greenbaum JA, Pang B, Tullius TD. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Research. 17: 947-53. PMID 17568010 DOI: 10.1101/Gr.6073107 |
0.742 |
|
| 2007 |
Greenbaum JA, Parker SC, Tullius TD. Detection of DNA structural motifs in functional genomic elements. Genome Research. 17: 940-6. PMID 17568009 DOI: 10.1101/Gr.5602807 |
0.717 |
|
| 2005 |
Danford AJ, Wang D, Wang Q, Tullius TD, Lippard SJ. Platinum anticancer drug damage enforces a particular rotational setting of DNA in nucleosomes. Proceedings of the National Academy of Sciences of the United States of America. 102: 12311-6. PMID 16116097 DOI: 10.1073/Pnas.0506025102 |
0.581 |
|
| 2005 |
Tullius TD, Greenbaum JA. Mapping nucleic acid structure by hydroxyl radical cleavage. Current Opinion in Chemical Biology. 9: 127-34. PMID 15811796 DOI: 10.1016/J.Cbpa.2005.02.009 |
0.654 |
|
| 2003 |
Guo H, Tullius TD. Gapped DNA is anisotropically bent. Proceedings of the National Academy of Sciences of the United States of America. 100: 3743-7. PMID 12644712 DOI: 10.1073/Pnas.0737062100 |
0.527 |
|
| 2002 |
Tullius TD. Probing DNA structure with hydroxyl radicals. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 6.7. PMID 18428898 DOI: 10.1002/0471142700.Nc0607S07 |
0.493 |
|
| 2002 |
Frazee RW, Taylor JA, Tullius TD. Interchange of DNA-binding modes in the deformed and ultrabithorax homeodomains: a structural role for the N-terminal arm. Journal of Molecular Biology. 323: 665-83. PMID 12419257 DOI: 10.1016/S0022-2836(02)00996-8 |
0.485 |
|
| 2002 |
Chen B, Jamieson ER, Tullius TD. A general synthesis of specifically deuterated nucleotides for studies of DNA and RNA. Bioorganic & Medicinal Chemistry Letters. 12: 3093-6. PMID 12372509 DOI: 10.1016/S0960-894X(02)00650-9 |
0.317 |
|
| 2000 |
Levin JR, Blake JJ, Ganunis RA, Tullius TD. The roles of specific template nucleosides in the formation of stable transcription complexes by Escherichia coli RNA polymerase Journal of Biological Chemistry. 275: 6885-6893. PMID 10702248 DOI: 10.1074/Jbc.275.10.6885 |
0.426 |
|
| 2000 |
Wu M, Stoermer D, Tullius TD, Townsend CA. Calicheamicin - Homeodomain conjugate as an efficient, sequence-specific DNA cleavage and mapping tool [11] Journal of the American Chemical Society. 122: 12884-12885. DOI: 10.1021/Ja002280O |
0.336 |
|
| 2000 |
Ottinger LM, Tullius TD. High-resolution in vivo footprinting of a protein - DNA complex using γ-radiation [13] Journal of the American Chemical Society. 122: 5901-5902. DOI: 10.1021/Ja000285F |
0.405 |
|
| 1999 |
Widlund HR, Kuduvalli PN, Bengtsson M, Cao H, Tullius TD, Kubista M. Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence Journal of Biological Chemistry. 274: 31847-31852. PMID 10542209 DOI: 10.1074/jbc.274.45.31847 |
0.315 |
|
| 1999 |
Jamison McDaniels CP, Jensen LT, Srinivasan C, Winge DR, Tullius TD. The yeast transcription factor Mac1 binds to DNA in a modular fashion. The Journal of Biological Chemistry. 274: 26962-7. PMID 10480908 DOI: 10.1074/Jbc.274.38.26962 |
0.461 |
|
| 1998 |
Balasubramanian B, Pogozelski WK, Tullius TD. DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone Proceedings of the National Academy of Sciences of the United States of America. 95: 9738-9743. PMID 9707545 DOI: 10.1073/Pnas.95.17.9738 |
0.527 |
|
| 1998 |
Draganescu A, Tullius TD. The DNA binding specificity of engrailed homeodomain. Journal of Molecular Biology. 276: 529-36. PMID 9551094 DOI: 10.1006/Jmbi.1997.1567 |
0.535 |
|
| 1998 |
Tullius TD. Chemical snapshots of DNA Faseb Journal. 12. |
0.454 |
|
| 1997 |
Eijkelenboom AP, van den Ent FM, Vos A, Doreleijers JF, Hård K, Tullius TD, Plasterk RH, Kaptein R, Boelens R. The solution structure of the amino-terminal HHCC domain of HIV-2 integrase: a three-helix bundle stabilized by zinc. Current Biology : Cb. 7: 739-46. PMID 9368756 DOI: 10.1016/S0960-9822(06)00332-0 |
0.382 |
|
| 1997 |
Shadle SE, Allen DF, Guo H, Pogozelski WK, Bashkin JS, Tullius TD. Quantitative analysis of electrophoresis data: Novel curve fitting methodology and its application to the determination of a protein-DNA binding constant Nucleic Acids Research. 25: 850-860. PMID 9016637 DOI: 10.1093/Nar/25.4.850 |
0.344 |
|
| 1996 |
Ganunis RM, Guo H, Tullius TD. Effect of the crystallizing agent 2-methyl-2,4-pentanediol on the structure of adenine tract DNA in solution Biochemistry. 35: 13729-13732. PMID 8901514 DOI: 10.1021/Bi961880Q |
0.505 |
|
| 1996 |
Dixon WJ, Inouye C, Karin M, Tullius TD. CUP2 binds in a bipartite manner to upstream activation sequence c in the promoter of the yeast copper metallothionein gene Journal of Biological Inorganic Chemistry. 1: 451-459. DOI: 10.1007/S007750050078 |
0.403 |
|
| 1995 |
Kuduvalli PN, Townsend CA, Tullius TD. Cleavage by calicheamicin gamma 1I of DNA in a nucleosome formed on the 5S RNA gene of Xenopus borealis. Biochemistry. 34: 3899-906. PMID 7696253 DOI: 10.1021/Bi00012A005 |
0.51 |
|
| 1995 |
Kimball AS, Kimball ML, Jayaram M, Tullius TD. Chemical probe and missing nucleoside analysis of flp recombinase bound to the recombination target sequence Nucleic Acids Research. 23: 3009-3017. PMID 7659525 DOI: 10.1093/Nar/23.15.3009 |
0.476 |
|
| 1995 |
Draganescu A, Levin JR, Tullius TD. Homeodomain proteins: what governs their ability to recognize specific DNA sequences? Journal of Molecular Biology. 250: 595-608. PMID 7623378 DOI: 10.1006/Jmbi.1995.0401 |
0.494 |
|
| 1995 |
Chatterjee M, Mah SC, Tullius TD, Townsend CA. Role of the aryl iodide in the sequence-selective cleavage of DNA by calicheamicin. Importance of thermodynamic binding vs kinetic activation in the cleavage process Journal of the American Chemical Society. 117: 8074-8082. DOI: 10.1021/Ja00136A004 |
0.431 |
|
| 1995 |
Pogozelski WK, McNeese TJ, Tullius TD. What species is responsible for strand scission in the reaction of [FeIIEDTA]2- and H2O2 with DNA? Journal of the American Chemical Society. 117: 6428-6433. DOI: 10.1021/Ja00129A002 |
0.411 |
|
| 1994 |
Mah SC, Townsend CA, Tullius TD. Hydroxyl radical footprinting of calicheamicin. Relationship of DNA binding to cleavage. Biochemistry. 33: 614-21. PMID 8286393 DOI: 10.1021/Bi00168A029 |
0.498 |
|
| 1994 |
Mah SC, Price MA, Townsend CA, Tullius TD. Features of DNA recognition for oriented binding and cleavage by calicheamicin Tetrahedron. 50: 1361-1378. DOI: 10.1016/S0040-4020(01)80624-4 |
0.525 |
|
| 1993 |
Kimball AS, Lee J, Jayaram M, Tullius TD. Sequence-specific cleavage of DNA via nucleophilic attack of hydrogen peroxide, assisted by Flp recombinase Biochemistry. 32: 4698-4701. PMID 8490015 DOI: 10.1021/Bi00069A002 |
0.519 |
|
| 1993 |
Bashkin J, Hayes JJ, Tullius TD, Wolffe AP. Structure of DNA in a nucleosome core at high salt concentration and at high temperature Biochemistry. 32: 1895-1898. PMID 8383529 DOI: 10.1021/Bi00059A002 |
0.439 |
|
| 1993 |
Price MA, Tullius TD. How the structure of an adenine tract depends on sequence context: a new model for the structure of TnAn DNA sequences. Biochemistry. 32: 127-36. PMID 8380329 DOI: 10.1021/Bi00052A018 |
0.489 |
|
| 1993 |
Tullius TD. Structural details of complexes of metalloregulatory proteins with DNA Journal of Inorganic Biochemistry. 51: 580. DOI: 10.1016/0162-0134(93)85602-5 |
0.401 |
|
| 1992 |
Hayes JJ, Tullius TD. Structure of the TFIIIA-5 S DNA complex Journal of Molecular Biology. 227: 407-417. PMID 1404361 DOI: 10.1016/0022-2836(92)90897-S |
0.52 |
|
| 1992 |
Price MA, Tullius TD. Using hydroxyl radical to probe DNA structure Methods in Enzymology. 212: 194-219. PMID 1325598 DOI: 10.1016/0076-6879(92)12013-G |
0.552 |
|
| 1991 |
Dixon WJ, Hayes JJ, Levin JR, Weidner MF, Dombroski BA, Tullius TD. Hydroxyl radical footprinting. Methods in Enzymology. 208: 380-413. PMID 1664026 DOI: 10.1016/0076-6879(91)08021-9 |
0.524 |
|
| 1991 |
Hayes JJ, Bashkin J, Tullius TD, Wolffe AP. The histone core exerts a dominant constraint on the structure of DNA in a nucleosome. Biochemistry. 30: 8434-40. PMID 1653013 DOI: 10.1021/Bi00098A022 |
0.517 |
|
| 1991 |
Tullius TD. DNA footprinting with the hydroxyl radical Free Radical Research. 13: 521-529. DOI: 10.3109/10715769109145826 |
0.43 |
|
| 1991 |
Nakagawa KH, Inouye C, Hedman B, Karin M, Tullius TD, Hodgson KO. Evidence from EXAFS for a copper cluster in the metalloregulatory protein CUP2 from yeast Journal of the American Chemical Society. 113: 3621-3623. DOI: 10.1021/Ja00009A075 |
0.414 |
|
| 1991 |
Tullius TD. The use of chemical probes to analyse DNA and RNA structures Current Opinion in Structural Biology. 1: 428-434. DOI: 10.1016/0959-440X(91)90043-S |
0.495 |
|
| 1990 |
Guo Q, Lu M, Churchill ME, Tullius TD, Kallenbach NR. Asymmetric structure of a three-arm DNA junction. Biochemistry. 29: 10927-34. PMID 2176888 DOI: 10.1021/Bi00501A010 |
0.692 |
|
| 1990 |
Hayes JJ, Kam L, Tullius TD. Footprinting protein-DNA complexes with γ-rays Methods in Enzymology. 186: 545-549. PMID 2172714 DOI: 10.1016/0076-6879(90)86148-O |
0.489 |
|
| 1990 |
Hayes JJ, Tullius TD, Wolffe AP. The structure of DNA in a nucleosome Proceedings of the National Academy of Sciences of the United States of America. 87: 7405-7409. PMID 2170977 DOI: 10.1073/Pnas.87.19.7405 |
0.524 |
|
| 1990 |
Buchman C, Skroch P, Dixon W, Tullius TD, Karin M. A single amino acid change in CUP2 alters its mode of DNA binding Molecular and Cellular Biology. 10: 4778-4787. PMID 2167439 DOI: 10.1128/Mcb.10.9.4778 |
0.341 |
|
| 1990 |
Churchill ME, Tullius TD, Klug A. Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus. Proceedings of the National Academy of Sciences of the United States of America. 87: 5528-32. PMID 2164687 DOI: 10.1073/Pnas.87.14.5528 |
0.757 |
|
| 1990 |
Kimball A, Guo Q, Lu M, Cunningham RP, Kallenbach NR, Seeman NC, Tullius TD. Construction and analysis of parallel and antiparallel Holliday junctions. The Journal of Biological Chemistry. 265: 6544-7. PMID 2157702 |
0.311 |
|
| 1990 |
Churchill MEA, Hayes JJ, Tullius TD. Detection of drug binding to DNA by hydroxyl radical footprinting. Relationship of distamycin binding sites to DNA structure and positioned nucleosomes on 5S RNA genes of Xenopus Biochemistry. 29: 6043-6050. PMID 1696501 DOI: 10.1021/Bi00477A023 |
0.505 |
|
| 1989 |
Tullius TD. Physical studies of protein-DNA complexes by footprinting Annual Review of Biophysics and Biophysical Chemistry. 18: 213-237. PMID 2660824 |
0.326 |
|
| 1989 |
Hayes JJ, Tullius TD. The missing nucleoside experiment: A new technique to study recognition of DNA by protein Biochemistry. 28: 9521-9527. PMID 2611245 DOI: 10.1021/Bi00450A041 |
0.499 |
|
| 1989 |
Shafer GE, Price MA, Tullius TD. Use of the hydroxyl radical and gel electrophoresis to study DNA structure Electrophoresis. 10: 397-404. PMID 2504579 DOI: 10.1002/Elps.1150100518 |
0.522 |
|
| 1988 |
Churchill ME, Tullius TD, Kallenbach NR, Seeman NC. A Holliday recombination intermediate is twofold symmetric. Proceedings of the National Academy of Sciences of the United States of America. 85: 4653-6. PMID 3387432 DOI: 10.1073/Pnas.85.13.4653 |
0.72 |
|
| 1988 |
Burkhoff AM, Tullius TD. Structural details of an adenine tract that does not cause DNA to bend Nature. 331: 455-457. PMID 3340190 DOI: 10.1038/331455A0 |
0.515 |
|
| 1988 |
Chen JH, Churchill ME, Tullius TD, Kallenbach NR, Seeman NC. Construction and analysis of monomobile DNA junctions. Biochemistry. 27: 6032-8. PMID 3191106 DOI: 10.1021/Bi00416A031 |
0.66 |
|
| 1988 |
Vrana KE, Churchill ME, Tullius TD, Brown DD. Mapping functional regions of transcription factor TFIIIA. Molecular and Cellular Biology. 8: 1684-96. PMID 2837652 DOI: 10.1128/Mcb.8.4.1684 |
0.669 |
|
| 1988 |
Tullius TD. DNA footprinting with hydroxyl radical Nature. 332: 663-664. PMID 2833707 DOI: 10.1038/332663A0 |
0.473 |
|
| 1987 |
Burkhoff AM, Tullius TD. The unusual conformation adopted by the adenine tracts in kinetoplast DNA Cell. 48: 935-943. PMID 3030560 DOI: 10.1016/0092-8674(87)90702-1 |
0.524 |
|
| 1987 |
Tullius TD, Dombroski BA, Churchill MEA, Kam L. Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts Methods in Enzymology. 155: 537-558. PMID 2828876 DOI: 10.1016/0076-6879(87)55035-2 |
0.542 |
|
| 1987 |
Tullius TD. Chemical 'snapshots' of DNA: using the hydroxyl radical to study the structure of DNA and DNA-protein complexes Trends in Biochemical Sciences. 12: 297-300. DOI: 10.1016/0968-0004(87)90145-9 |
0.541 |
|
| 1986 |
Tullius TD, Dombroski BA. Hydroxyl radical 'footprinting': High-resolution information about DNA-protein contacts and application to λ repressor and Cro protein Proceedings of the National Academy of Sciences of the United States of America. 83: 5469-5473. PMID 3090544 DOI: 10.1073/Pnas.83.15.5469 |
0.521 |
|
| 1985 |
Tullius TD, Dombroski BA. Iron(II) EDTA used to measure the helical twist along any DNA molecule Science. 230: 679-681. PMID 2996145 DOI: 10.1126/Science.2996145 |
0.488 |
|
| 1985 |
Frank P, Licht A, Tullius TD, Hodgson KO, Pecht I. A selenomethionine-containing azurin from an auxotroph of Pseudomonas aeruginosa. The Journal of Biological Chemistry. 260: 5518-25. PMID 2985597 |
0.379 |
|
| 1982 |
Tullius TD, Lippard SJ. Ethidium bromide changes the nuclease-sensitive DNA binding sites of the antitumor drug cis-diamminedichloroplatinum(II). Proceedings of the National Academy of Sciences of the United States of America. 79: 3489-92. PMID 6954494 DOI: 10.1073/pnas.79.11.3489 |
0.448 |
|
| 1981 |
Ushay HM, Tullius TD, Lippard SJ. Inhibition of the BamHI cleavage and unwinding of pBR322 deoxyribonucleic acid by the antitumor drug cis-dichlorodiammineplatinum(II). Biochemistry. 20: 3744-8. PMID 6268142 DOI: 10.1021/Bi00516A012 |
0.374 |
|
| 1981 |
Tullius TD, Lippard SJ. cis-Diamminedichloroplatinum(II) binds in a unique manner to oligo(dG).oligo(dC) sequences in DNA - a new assay using exonuclease III Journal of the American Chemical Society. 103: 4620-4622. DOI: 10.1021/Ja00405A073 |
0.514 |
|
| 1980 |
Tullius TD, Gillum WO, Carlson RMK, Hodgson KO. Structural study of the vanadium complex in living ascidian blood cells by x-ray absorption spectroscopy Journal of the American Chemical Society. 102: 5670-5676. DOI: 10.1021/Ja00537A045 |
0.442 |
|
| 1979 |
Tullius TD, Kurtz DM, Conradson SD, Hodgson KO. The molybdenum site of xanthine oxidase. Structural evidence from x-ray absorption spectroscopy Journal of the American Chemical Society. 101: 2776-2779. DOI: 10.1021/Ja00504A069 |
0.396 |
|
| 1979 |
TULLIUS TD, KURTZ DMJ, CONRADSON SD, HODGSON KO. ChemInform Abstract: THE MOLYBDENUM SITE OF XANTHINE OXIDASE. STRUCTURAL EVIDENCE FROM X-RAY ABSORPTION SPECTROSCOPY Chemischer Informationsdienst. 10. DOI: 10.1002/chin.197934088 |
0.39 |
|
| 1978 |
Tullius TD, Frank P, Hodgson KO. Characterization of the blue copper site in oxidized azurin by extended x-ray absorption fine structure: Determination of a short Cu-S distance. Proceedings of the National Academy of Sciences of the United States of America. 75: 4069-73. PMID 16592557 DOI: 10.1073/Pnas.75.9.4069 |
0.378 |
|
| 1977 |
COLLMAN JP, ROTHROCK RK, SEN JP, TULLIUS TD, HODGSON KO. ChemInform Abstract: MOLECULAR STRUCTURE OF TRANS-BIS(BENZENESELENIDO)(DIFLUORO-3,3′-(TRIMETHYLENEDINITRILO)BIS(2-PENTANONE OXIMATO)BORATE)RHODIUM(III) Chemischer Informationsdienst. 8: no-no. DOI: 10.1002/Chin.197705062 |
0.454 |
|
| 1976 |
Collman JP, Rothrock RK, Sen JP, Tullius TD, Hodgson KO. Molecular structure of trans-bis(benzeneselenido)[difluoro-3,3'-(trimethylenedinitrilo)bis(2-pentanone oximato)borate]rhodium(III) Inorganic Chemistry. 15: 2947-2948. DOI: 10.1021/Ic50165A085 |
0.471 |
|
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