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ENCODE Project Consortium; Birney, E; Stamatoyannopoulos, JA; Dutta, A; Guigó, R; Gingeras, TR; Margulies, EH; Weng, Z; Snyder, M «Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.». Nature, 447, 7146, 2007, pàg. 799–816. DOI: 10.1038/nature05874. PMC: 2212820. PMID: 17571346.
Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF «Structured RNAs in the ENCODE selected regions of the human genome.». Genome Res, 17, 6, 2007, pàg. 852–64. DOI: 10.1101/gr.5650707. PMC: 1891344. PMID: 17568003.
Madison JT, Everett GA, Kung H «Nucleotide sequence of a yeast tyrosine transfer RNA.». Science, 153, 735, 1966, pàg. 531–4. DOI: 10.1126/science.153.3735.531. PMID: 5938777.
Dudock BS, Katz G, Taylor EK, Holley RW «Primary structure of wheat germ phenylalanine transfer RNA». Proc. Natl. Acad. Sci. U.S.A., 62, 3, març 1969, pàg. 941-5. DOI: 10.1073/pnas.62.3.941. PMC: 223689. PMID: 5257014 [Consulta: 3 setembre 2010].
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Kim SH, Quigley GJ, Suddath FL, et al. «Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain». Science, 179, 70, 1973, pàg. 285–8. DOI: 10.1126/science.179.4070.285. PMID: 4566654.
Eddy SR «Non-coding RNA genes and the modern RNA world». Nat. Rev. Genet., 2, 12, desembre 2001, pàg. 919–29. DOI: 10.1038/35103511. PMID: 11733745 [Consulta: 3 setembre 2010].
Jeffares DC, Poole AM, Penny D «Relics from the RNA world.». J Mol Evol, 46, 1, 1998, pàg. 18–36. DOI: 10.1007/PL00006280. PMID: 9419222.
Poole AM, Jeffares DC, Penny D «The path from the RNA world.». J Mol Evol, 46, 1, 1998, pàg. 1–17. DOI: 10.1007/PL00006275. PMID: 9419221.
Ban N, Nissen P, Hansen J, Moore P, Steitz T «The complete atomic structure of the large ribosomal subunit at 2.4 ångström resolution». Science, 289, 5481, 2000, pàg. 905–20. DOI: 10.1126/science.289.5481.905. PMID: 10937989.
Zhu Y, Stribinskis V, Ramos KS, Li Y «Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA». RNA, 12, 5, 2006, pàg. 699–706. DOI: 10.1261/ARN.2284906. PMC: 1440897. PMID: 16540690.
Kishore S, Stamm S «The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C». Science, 311, 5758, 2006, pàg. 230–231. DOI: 10.1126/science.1118265. PMID: 16357227.
Reiner R, Ben-Asouli Y, Krilovetzky I, Jarrous N «A role for the catalytic ribonucleoprotein RNAse P in RNA polymerase III transcription.». Genes Dev, 20, 12, 2006, pàg. 1621–35. DOI: 10.1101/gad.386706. PMC: 1482482. PMID: 16778078.
Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA «B2 RNA binds directly to RNA polymerase II to repress transcript synthesis.». Nat Struct Mol Biol, 11, 9, 2004, pàg. 822–9. DOI: 10.1038/nsmb812. PMID: 15300239.
Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T, Ohta K «Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs.». Nature, 456, 7218, 2008, pàg. 130–4. DOI: 10.1038/nature07348. PMID: 18820678.
Park Y, Kelley RL, Oh H, Kuroda MI, Meller VH «Extent of chromatin spreading determined by roX RNA recruitment of MSL proteins.». Science, 298, 5598, 2002, pàg. 1620–3. DOI: 10.1126/science.1076686. PMID: 12446910.
Wadler CS, Vanderpool CK «A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide.». Proc Natl Acad Sci USA, 104, 51, 2007, pàg. 20454–9. DOI: 10.1073/pnas.0708102104. PMC: 2154452. PMID: 18042713.
Dinger ME, Pang KC, Mercer TR, Mattick JS «Differentiating protein-coding and noncoding RNA: challenges and ambiguities.». PLoS Comput Biol, 4, 11, 2008, pàg. e1000176. DOI: 10.1371/journal.pcbi.1000176. PMC: 2518207. PMID: 19043537.
Ender C, Krek A, Friedländer MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G «A human snoRNA with microRNA-like functions.». Mol Cell, 32, 4, 2008, pàg. 519–28. DOI: 10.1016/j.molcel.2008.10.017. PMID: 19026782.
Leygue E «Steroid receptor RNA activator (SRA1): unusual bifaceted gene products with suspected relevance to breast cancer.». Nucl Recept Signal, 5, 2007, pàg. e006. DOI: 10.1621/nrs.05006. PMC: 1948073. PMID: 17710122.
Kloc M, Wilk K, Vargas D, Shirato Y, Bilinski S, Etkin LD «Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes.». Development, 132, 15, 2005, pàg. 3445–57. DOI: 10.1242/dev.01919. PMID: 16000384.
Jenny A, Hachet O, Závorszky P, Cyrklaff A, Weston MD, Johnston DS, Erdélyi M, Ephrussi A «A translation-independent role of oskar RNA in early Drosophila oogenesis.». Development, 133, 15, 2006, pàg. 2827–33. DOI: 10.1242/dev.02456. PMID: 16835436.
Gultyaev AP, Roussis A «Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants.». Nucleic Acids Res, 35, 9, 2007, pàg. 3144-52. DOI: 10.1093/nar/gkm173. PMC: 1888808. PMID: 17452360.
Pibouin L, Villaudy J, Ferbus D, Muleris M, Prospéri MT, Remvikos Y, Goubin G «Cloning of the mRNA of overexpression in colon carcinoma-1: a sequence overexpressed in a subset of colon carcinomas». Cancer Genet Cytogenet, 133, 1, 2002, pàg. 55–60. DOI: 10.1016/S0165-4608(01)00634-3. PMID: 11890990.
Fu X, Ravindranath L, Tran N, Petrovics G, Srivastava S «Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1». DNA Cell Biol, 25, 3, 2006, pàg. 135–41. DOI: 10.1089/dna.2006.25.135. PMID: 16569192.
Mourtada-Maarabouni M, Pickard MR, Hedge VL, Farzaneh F, Williams GT «GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer.». Oncogene, 28, 2, 2009, pàg. 195–208. DOI: 10.1038/onc.2008.373. PMID: 18836484.
Christov CP, Trivier E, Krude T «Noncoding human Y RNAs are overexpressed in tumours and required for cell proliferation». Br J Cancer, 98, 5, 2008, pàg. 981–8. DOI: 10.1038/sj.bjc.6604254. PMC: 2266855. PMID: 18283318.
Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP «The widespread impact of mammalian MicroRNAs on mRNA repression and evolution». Science, 310, 5755, 2005, pàg. 1817–21. DOI: 10.1126/science.1121158. PMID: 16308420.
Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM «Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs». Nature, 433, 7027, 2005, pàg. 769–73. DOI: 10.1038/nature03315. PMID: 15685193.
Christov CP, Gardiner TJ, Szüts D, Krude T «Functional requirement of noncoding Y RNAs for human chromosomal DNA replication». Mol Cell Biol, 26, 18, 2006, pàg. 6993-7004. DOI: 10.1128/MCB.01060-06. PMC: 1592862. PMID: 16943439.
Calin, GA; Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM «Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia». Proc Natl Acad Sci USA, 99, 24, 2002, pàg. 15524–15529. DOI: 10.1073/pnas.242606799. PMC: 137750. PMID: 12434020.
Hu Z, Chen J, Tian T, Zhou X, Gu H, Xu L, Zeng Y, Miao R, Jin G, Ma H, Chen Y, Shen H «Genetic variants of miRNA sequences and non-small cell lung cancer survival». J Clin Invest, 118, 7, 2008, pàg. 2600–8. DOI: 10.1172/JCI34934. PMC: 2402113. PMID: 18521189.
Shen J, Ambrosone CB, Zhao H «Novel genetic variants in microRNA genes and familial breast cancer». Int J Cancer, 124, 5, 2009, pàg. 1178–82. DOI: 10.1002/ijc.24008. PMID: 19048628.
Sahoo T, del Gaudio D, German JR, Shinawi M, Peters SU, Person RE, Garnica A, Cheung SW, Beaudet AL «Prader–Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster.». Nat Genet, 40, 6, 2008, pàg. 719–21. DOI: 10.1038/ng.158. PMC: 2705197. PMID: 18500341.
Ding F, Li HH, Zhang S, Solomon NM, Camper SA, Cohen P, Francke U «SnoRNA Snord116 (Pwcr1/MBII-85) deletion causes growth deficiency and hyperphagia in mice.». PLoS ONE, 3, 3, 2008, pàg. e1709. DOI: 10.1371/journal.pone.0001709. PMC: 2248623. PMID: 18320030.
Ding F, Prints Y, Dhar MS, Johnson DK, Garnacho-Montero C, Nicholls RD, Francke U «Lack of Pwcr1/MBII-85 snoRNA is critical for neonatal lethality in Prader–Willi syndrome mouse models.». Mamm Genome, 16, 6, 2005, pàg. 424–31. DOI: 10.1007/s00335-005-2460-2. PMID: 16075369.
Bazeley PS, Shepelev V, Talebizadeh Z, Butler MG, Fedorova L, Filatov V, Fedorov A «snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions.». Gene, 408, 1-2, 2008, pàg. 172–9. DOI: 10.1016/j.gene.2007.10.037. PMID: 18160232.
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Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR «Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.». Science, 308, 5725, 2005, pàg. 1149–54. DOI: 10.1126/science.1108625. PMID: 15790807.
ENCODE Project Consortium; Birney, E; Stamatoyannopoulos, JA; Dutta, A; Guigó, R; Gingeras, TR; Margulies, EH; Weng, Z; Snyder, M «Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.». Nature, 447, 7146, 2007, pàg. 799–816. DOI: 10.1038/nature05874. PMC: 2212820. PMID: 17571346.
Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF «Structured RNAs in the ENCODE selected regions of the human genome.». Genome Res, 17, 6, 2007, pàg. 852–64. DOI: 10.1101/gr.5650707. PMC: 1891344. PMID: 17568003.
Madison JT, Everett GA, Kung H «Nucleotide sequence of a yeast tyrosine transfer RNA.». Science, 153, 735, 1966, pàg. 531–4. DOI: 10.1126/science.153.3735.531. PMID: 5938777.
Zachau HG, Dütting D, Feldmann H, Melchers F, Karau W «Serine specific transfer ribonucleic acids. XIV. Comparison of nucleotide sequences and secondary structure models». Cold Spring Harb. Symp. Quant. Biol., 31, 1966, pàg. 417–24. PMID: 5237198 [Consulta: 3 setembre 2010].
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Cramer F, Doepner H, Haar F VD, Schlimme E, Seidel H «On the conformation of transfer RNA». Proc. Natl. Acad. Sci. U.S.A., 61, 4, desembre 1968, pàg. 1384–91. DOI: 10.1073/pnas.61.4.1384. PMC: 225267. PMID: 4884685 [Consulta: 3 setembre 2010].
Ladner JE, Jack A, Robertus JD, et al. «Structure of yeast phenylalanine transfer RNA at 2.5 A resolution». Proc. Natl. Acad. Sci. U.S.A., 72, 11, novembre 1975, pàg. 4414–8. DOI: 10.1073/pnas.72.11.4414. PMC: 388732. PMID: 1105583 [Consulta: 3 setembre 2010].
Kim SH, Quigley GJ, Suddath FL, et al. «Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain». Science, 179, 70, 1973, pàg. 285–8. DOI: 10.1126/science.179.4070.285. PMID: 4566654.
Eddy SR «Non-coding RNA genes and the modern RNA world». Nat. Rev. Genet., 2, 12, desembre 2001, pàg. 919–29. DOI: 10.1038/35103511. PMID: 11733745 [Consulta: 3 setembre 2010].
Jeffares DC, Poole AM, Penny D «Relics from the RNA world.». J Mol Evol, 46, 1, 1998, pàg. 18–36. DOI: 10.1007/PL00006280. PMID: 9419222.
Poole AM, Jeffares DC, Penny D «The path from the RNA world.». J Mol Evol, 46, 1, 1998, pàg. 1–17. DOI: 10.1007/PL00006275. PMID: 9419221.
Ban N, Nissen P, Hansen J, Moore P, Steitz T «The complete atomic structure of the large ribosomal subunit at 2.4 ångström resolution». Science, 289, 5481, 2000, pàg. 905–20. DOI: 10.1126/science.289.5481.905. PMID: 10937989.
Zhu Y, Stribinskis V, Ramos KS, Li Y «Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA». RNA, 12, 5, 2006, pàg. 699–706. DOI: 10.1261/ARN.2284906. PMC: 1440897. PMID: 16540690.
Kishore S, Stamm S «The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C». Science, 311, 5758, 2006, pàg. 230–231. DOI: 10.1126/science.1118265. PMID: 16357227.
Reiner R, Ben-Asouli Y, Krilovetzky I, Jarrous N «A role for the catalytic ribonucleoprotein RNAse P in RNA polymerase III transcription.». Genes Dev, 20, 12, 2006, pàg. 1621–35. DOI: 10.1101/gad.386706. PMC: 1482482. PMID: 16778078.
Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA «B2 RNA binds directly to RNA polymerase II to repress transcript synthesis.». Nat Struct Mol Biol, 11, 9, 2004, pàg. 822–9. DOI: 10.1038/nsmb812. PMID: 15300239.
Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T, Ohta K «Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs.». Nature, 456, 7218, 2008, pàg. 130–4. DOI: 10.1038/nature07348. PMID: 18820678.
Park Y, Kelley RL, Oh H, Kuroda MI, Meller VH «Extent of chromatin spreading determined by roX RNA recruitment of MSL proteins.». Science, 298, 5598, 2002, pàg. 1620–3. DOI: 10.1126/science.1076686. PMID: 12446910.
Wadler CS, Vanderpool CK «A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide.». Proc Natl Acad Sci USA, 104, 51, 2007, pàg. 20454–9. DOI: 10.1073/pnas.0708102104. PMC: 2154452. PMID: 18042713.
Dinger ME, Pang KC, Mercer TR, Mattick JS «Differentiating protein-coding and noncoding RNA: challenges and ambiguities.». PLoS Comput Biol, 4, 11, 2008, pàg. e1000176. DOI: 10.1371/journal.pcbi.1000176. PMC: 2518207. PMID: 19043537.
Ender C, Krek A, Friedländer MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G «A human snoRNA with microRNA-like functions.». Mol Cell, 32, 4, 2008, pàg. 519–28. DOI: 10.1016/j.molcel.2008.10.017. PMID: 19026782.
Leygue E «Steroid receptor RNA activator (SRA1): unusual bifaceted gene products with suspected relevance to breast cancer.». Nucl Recept Signal, 5, 2007, pàg. e006. DOI: 10.1621/nrs.05006. PMC: 1948073. PMID: 17710122.
Zhang J, King ML «Xenopus VegT RNA is localized to the vegetal cortex during oogenesis and encodes a novel T-box transcription factor involved in mesodermal patterning.». Development, 122, 12, 1996, pàg. 4119–29. PMID: 9012531.
Kloc M, Wilk K, Vargas D, Shirato Y, Bilinski S, Etkin LD «Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes.». Development, 132, 15, 2005, pàg. 3445–57. DOI: 10.1242/dev.01919. PMID: 16000384.
Jenny A, Hachet O, Závorszky P, Cyrklaff A, Weston MD, Johnston DS, Erdélyi M, Ephrussi A «A translation-independent role of oskar RNA in early Drosophila oogenesis.». Development, 133, 15, 2006, pàg. 2827–33. DOI: 10.1242/dev.02456. PMID: 16835436.
Gultyaev AP, Roussis A «Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants.». Nucleic Acids Res, 35, 9, 2007, pàg. 3144-52. DOI: 10.1093/nar/gkm173. PMC: 1888808. PMID: 17452360.
Pibouin L, Villaudy J, Ferbus D, Muleris M, Prospéri MT, Remvikos Y, Goubin G «Cloning of the mRNA of overexpression in colon carcinoma-1: a sequence overexpressed in a subset of colon carcinomas». Cancer Genet Cytogenet, 133, 1, 2002, pàg. 55–60. DOI: 10.1016/S0165-4608(01)00634-3. PMID: 11890990.
Fu X, Ravindranath L, Tran N, Petrovics G, Srivastava S «Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1». DNA Cell Biol, 25, 3, 2006, pàg. 135–41. DOI: 10.1089/dna.2006.25.135. PMID: 16569192.
Mourtada-Maarabouni M, Pickard MR, Hedge VL, Farzaneh F, Williams GT «GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer.». Oncogene, 28, 2, 2009, pàg. 195–208. DOI: 10.1038/onc.2008.373. PMID: 18836484.
Christov CP, Trivier E, Krude T «Noncoding human Y RNAs are overexpressed in tumours and required for cell proliferation». Br J Cancer, 98, 5, 2008, pàg. 981–8. DOI: 10.1038/sj.bjc.6604254. PMC: 2266855. PMID: 18283318.
Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP «The widespread impact of mammalian MicroRNAs on mRNA repression and evolution». Science, 310, 5755, 2005, pàg. 1817–21. DOI: 10.1126/science.1121158. PMID: 16308420.
Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM «Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs». Nature, 433, 7027, 2005, pàg. 769–73. DOI: 10.1038/nature03315. PMID: 15685193.
Christov CP, Gardiner TJ, Szüts D, Krude T «Functional requirement of noncoding Y RNAs for human chromosomal DNA replication». Mol Cell Biol, 26, 18, 2006, pàg. 6993-7004. DOI: 10.1128/MCB.01060-06. PMC: 1592862. PMID: 16943439.
Calin, GA; Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM «Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia». Proc Natl Acad Sci USA, 99, 24, 2002, pàg. 15524–15529. DOI: 10.1073/pnas.242606799. PMC: 137750. PMID: 12434020.
Hu Z, Chen J, Tian T, Zhou X, Gu H, Xu L, Zeng Y, Miao R, Jin G, Ma H, Chen Y, Shen H «Genetic variants of miRNA sequences and non-small cell lung cancer survival». J Clin Invest, 118, 7, 2008, pàg. 2600–8. DOI: 10.1172/JCI34934. PMC: 2402113. PMID: 18521189.
Shen J, Ambrosone CB, Zhao H «Novel genetic variants in microRNA genes and familial breast cancer». Int J Cancer, 124, 5, 2009, pàg. 1178–82. DOI: 10.1002/ijc.24008. PMID: 19048628.
Sahoo T, del Gaudio D, German JR, Shinawi M, Peters SU, Person RE, Garnica A, Cheung SW, Beaudet AL «Prader–Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster.». Nat Genet, 40, 6, 2008, pàg. 719–21. DOI: 10.1038/ng.158. PMC: 2705197. PMID: 18500341.
Ding F, Li HH, Zhang S, Solomon NM, Camper SA, Cohen P, Francke U «SnoRNA Snord116 (Pwcr1/MBII-85) deletion causes growth deficiency and hyperphagia in mice.». PLoS ONE, 3, 3, 2008, pàg. e1709. DOI: 10.1371/journal.pone.0001709. PMC: 2248623. PMID: 18320030.
Ding F, Prints Y, Dhar MS, Johnson DK, Garnacho-Montero C, Nicholls RD, Francke U «Lack of Pwcr1/MBII-85 snoRNA is critical for neonatal lethality in Prader–Willi syndrome mouse models.». Mamm Genome, 16, 6, 2005, pàg. 424–31. DOI: 10.1007/s00335-005-2460-2. PMID: 16075369.
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