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  1. 1.   Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes
  2. Gagliardi, Alessia; Porter, Vanessa L; Zong, Zusheng; Bowlby, Reanne; Titmuss, Emma; Namirembe, Constance; Griner, Nicholas B; Petrello, Hilary; Bowen, Jay; Chan, Simon K; Culibrk, Luka; Darragh, Teresa M; Stoler, Mark H; Wright, Thomas C; Gesuwan, Patee; Dyer,Maureen; Ma, Yussanne; Mungall, Karen L; Jones, Steven J M; Nakisige, Carolyn; Novik, Karen; Orem, Jackson; Origa, Martin; Gastier-Foster, Julie M; Yarchoan, Robert; Casper, Corey; Mills, Gordon B; Rader, Janet S; Ojesina, Akinyemi I; Gerhard, Daniela S; Mungall, Andrew J; Marra, Marco A
  3. Nature genetics. 2020, Aug; 52(8): 800-810.
  1. 2.   Modeling ligand docking to RNA in the design of RNA-based nanostructures
  2. Kasprzak,Wojciech; Ahmed, Nour Ali; Shapiro,Bruce
  3. Current opinion in biotechnology. 2020, JUN; 63: 16-25.
  1. 3.   Integrated genomic and molecular characterization of cervical cancer
  2. Burk, Robert D.; Chen, Zigui; Saller, Charles; Tarvin, Katherine; Carvalho, Andre L.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.; Fregnani, Jose H.; Creighton, Chad J.; Anderson, Matthew L.; Castro, Patricia; Wang, Sophia S.; Yau, Christina; Benz, Christopher; Robertson, A. Gordon; Mungall, Karen; Lim, Lynette; Bowlby, Reanne; Sadeghi, Sara; Brooks, Denise; Sipahimalani, Payal; Mar, Richard; Ally, Adrian; Clarke, Amanda; Mungall, Andrew J.; Tam, Angela; Lee, Darlene; Chuah, Eric; Schein, Jacqueline E.; Tse, Kane; Kasaian, Katayoon; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Balasundaram, Miruna; Thiessen, Nina; Dhalla, Noreen; Carlsen, Rebecca; Moore, Richard A.; Holt, Robert A.; Jones, Steven J. M.; Wong, Tina; Pantazi, Angeliki; Parfenov, Michael; Kucherlapati, Raju; Hadjipanayis, Angela; Seidman, Jonathan; Kucherlapati, Melanie; Ren, Xiaojia; Xu, Andrew W.; Yang, Lixing; Park, Peter J.; Lee, Semin; Rabeno, Brenda; Huelsenbeck-Dill, Lori; Borowsky, Mark; Cadungog, Mark; Iacocca, Mary; Petrelli, Nicholas; Swanson, Patricia; Ojesina, Akinyemi I.; Le, Xuan; Sandusky, George; Adebamowo, Sally N.; Akeredolu, Teniola; Adebamowo, Clement; Reynolds, Sheila M.; Shmulevich, Ilya; Shelton, Candace; Crain, Daniel; Mallery, David; Curley, Erin; Gardner, Johanna; Penny, Robert; Morris, Scott; Shelton, Troy; Liu, Jia; Lolla, Laxmi; Chudamani, Sudha; Wu, Ye; Birrer, Michael; McLellan, Michael D.; Bailey, Matthew H.; Miller, Christopher A.; Wyczalkowski, Matthew A.; Fulton, Robert S.; Fronick, Catrina C.; Lu, Charles; Mardis, Elaine R.; Appelbaum, Elizabeth L.; Schmidt, Heather K.; Fulton, Lucinda A.; Cordes, Matthew G.; Li, Tiandao; Ding, Li; Wilson, Richard K.; Rader, Janet S.; Behmaram, Behnaz; Uyar, Denise; Bradley, William; Wrangle, John; Pastore, Alessandro; Levine, Douglas A.; Dao, Fanny; Gao, Jianjiong; Schultz, Nikolaus; Sander, Chris; Ladanyi, Marc; Einstein, Mark; Teeter, Randall; Benz, Stephen; Wentzensen, Nicolas; Felau, Ina; Zenklusen, Jean C.; Bodelon, Clara; Demchok, John A.; Yang, Liming; Sheth, Margi; Ferguson, Martin L.; Tarnuzzer, Roy; Yang, Hannah; Schiffman, Mark; Zhang, Jiashan; Wang, Zhining; Davidsen, Tanja; Olaniyan, Olayinka; Hutter, Carolyn M.; Sofia, Heidi J.; Gordenin, Dmitry A.; Chan, Kin; Roberts, Steven A.; Klimczak, Leszek J.; Van Waes, Carter; Chen, Zhong; Saleh, Anthony D.; Cheng, Hui; Parfitt, Jeremy; Bartlett, John; Albert, Monique; Arnaout, Angel; Sekhon, Harman; Gilbert, Sebastien; Peto, Myron; Myers, Jerome; Harr, Jodi; Eckman, John; Bergsten, Julie; Tucker, Kelinda; Zach, Leigh Anne; Karlan, Beth Y.; Lester, Jenny; Orsulic, Sandra; Sun, Qiang; Naresh, Rashi; Pihl, Todd; Wan, Yunhu; Zaren, Howard; Sapp, Jennifer; Miller, Judy; Drwiega, Paul; Ojesina, Akinyemi I.; Murray, Bradley A.; Zhang, Hailei; Cherniack, Andrew D.; Sougnez, Carrie; Pedamallu, Chandra Sekhar; Lichtenstein, Lee; Meyerson, Matthew; Noble, Michael S.; Heiman, David I.; Voet, Doug; Getz, Gad; Saksena, Gordon; Kim, Jaegil; Shih, Juliann; Cho, Juok; Lawrence, Michael S.; Gehlenborg, Nils; Lin, Pei; Beroukhim, Rameen; Frazer, Scott; Gabriel, Stacey B.; Schumacher, Steven E.; Leraas, Kristen M.; Lichtenberg, Tara M.; Zmuda, Erik; Bowen, Jay; Frick, Jessica; Gastier-Foster, Julie M.; Wise, Lisa; Gerken, Mark; Ramirez, Nilsa C.; Danilova, Ludmila; Cope, Leslie; Baylin, Stephen B.; Salvesen, Helga B.; Vellano, Christopher P.; Ju, Zhenlin; Diao, Lixia; Zhao, Hao; Chong, Zechen; Ryan, Michael C.; Martinez-Ledesma, Emmanuel; Verhaak, Roeland G.; Byers, Lauren Averett; Yuan, Yuan; Chen, Ken; Ling, Shiyun; Mills, Gordon B.; Lu, Yiling; Akbani, Rehan; Seth, Sahil; Liang, Han; Wang, Jing; Han, Leng; Weinstein, John N.; Bristow, Christopher A.; Zhang, Wei; Mahadeshwar, Harshad S.; Sun, Huandong; Tang, Jiabin; Zhang, Jianhua; Song, Xingzhi; Protopopov, Alexei; Shaw, Kenna R. Mills; Chin, Lynda; Olabode, Oluwole; Ojesina, Akinyemi I.; DiSaia, Philip; Radenbaugh, Amie; Haussler, David; Zhu, Jingchun; Stuart, Josh; Chalise, Prabhakar; Koestler, Devin; Fridley, Brooke L.; Godwin, Andrew K.; Madan, Rashna; Ciriello, Giovanni; Martinez, Cathleen; Higgins, Kelly; Bocklage, Therese; Auman, J. Todd; Perou, Charles M.; Tan, Donghui; Parker, Joel S.; Hoadley, Katherine A.; Wilkerson, Matthew D.; Mieczkowski, Piotr A.; Skelly, Tara; Veluvolu, Umadevi; Hayes, D. Neil; Rathmell, W. Kimryn; Hoyle, Alan P.; Simons, Janae V.; Wu, Junyuan; Mose, Lisle E.; Soloway, Matthew G.; Balu, Saianand; Meng, Shaowu; Jefferys, Stuart R.; Bodenheimer, Tom; Shi, Yan; Roach, Jeffrey; Thorne, Leigh B.; Boice, Lori; Huang, Mei; Jones, Corbin D.; Zuna, Rosemary; Walker, Joan; Gunderson, Camille; Snowbarger, Carie; Brown, David; Moxley, Katherine; Moore, Kathleen; Andrade, Kelsi; Landrum, Lisa; Mannel, Robert; McMeekin, Scott; Johnson, Starla; Nelson, Tina; Elishaev, Esther; Dhir, Rajiv; Edwards, Robert; Bhargava, Rohit; Tiezzi, Daniel G.; Andrade, Jurandyr M.; Noushmehr, Houtan; Carlotti, Carlos Gilberto; Tirapelli, Daniela Pretti da Cunha; Weisenberger, Daniel J.; Van Den Berg, David J.; Maglinte, Dennis T.; Bootwalla, Moiz S.; Lai, Phillip H.; Triche, Timothy; Swisher, Elizabeth M.; Agnew, Kathy J.; Shelley, Carl Simon; Laird, Peter W.; Schwarz, Julie; Grigsby, Perry; Mutch, David
  3. NATURE. 2017, Mar 16; 543(7645): 378-384.
  1. 4.   Integrated genomic and molecular characterization of cervical cancer
  2. Burk, Robert D.; Chen, Zigui; Saller, Charles; Tarvin, Katherine; Carvalho, Andre L.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.; Fregnani, Jose H.; Creighton, Chad J.; Anderson, Matthew L.; Castro, Patricia; Wang, Sophia S.; Yau, Christina; Benz, Christopher; Robertson, A. Gordon; Mungall, Karen; Lim, Lynette; Bowlby, Reanne; Sadeghi, Sara; Brooks, Denise; Sipahimalani, Payal; Mar, Richard; Ally, Adrian; Clarke, Amanda; Mungall, Andrew J.; Tam, Angela; Lee, Darlene; Chuah, Eric; Schein, Jacqueline E.; Tse, Kane; Kasaian, Katayoon; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Balasundaram, Miruna; Thiessen, Nina; Dhalla, Noreen; Carlsen, Rebecca; Moore, Richard A.; Holt, Robert A.; Jones, Steven J. M.; Wong, Tina; Pantazi, Angeliki; Parfenov, Michael; Kucherlapati, Raju; Hadjipanayis, Angela; Seidman, Jonathan; Kucherlapati, Melanie; Ren, Xiaojia; Xu, Andrew W.; Yang, Lixing; Park, Peter J.; Lee, Semin; Rabeno, Brenda; Huelsenbeck-Dill, Lori; Borowsky, Mark; Cadungog, Mark; Iacocca, Mary; Petrelli, Nicholas; Swanson, Patricia; Ojesina, Akinyemi I.; Le, Xuan; Sandusky, George; Adebamowo, Sally N.; Akeredolu, Teniola; Adebamowo, Clement; Reynolds, Sheila M.; Shmulevich, Ilya; Shelton, Candace; Crain, Daniel; Mallery, David; Curley, Erin; Gardner, Johanna; Penny, Robert; Morris, Scott; Shelton, Troy; Liu, Jia; Lolla, Laxmi; Chudamani, Sudha; Wu, Ye; Birrer, Michael; McLellan, Michael D.; Bailey, Matthew H.; Miller, Christopher A.; Wyczalkowski, Matthew A.; Fulton, Robert S.; Fronick, Catrina C.; Lu, Charles; Mardis, Elaine R.; Appelbaum, Elizabeth L.; Schmidt, Heather K.; Fulton, Lucinda A.; Cordes, Matthew G.; Li, Tiandao; Ding, Li; Wilson, Richard K.; Rader, Janet S.; Behmaram, Behnaz; Uyar, Denise; Bradley, William; Wrangle, John; Pastore, Alessandro; Levine, Douglas A.; Dao, Fanny; Gao, Jianjiong; Schultz, Nikolaus; Sander, Chris; Ladanyi, Marc; Einstein, Mark; Teeter, Randall; Benz, Stephen; Wentzensen, Nicolas; Felau, Ina; Zenklusen, Jean C.; Bodelon, Clara; Demchok, John A.; Yang, Liming; Sheth, Margi; Ferguson, Martin L.; Tarnuzzer, Roy; Yang, Hannah; Schiffman, Mark; Zhang, Jiashan; Wang, Zhining; Davidsen, Tanja; Olaniyan, Olayinka; Hutter, Carolyn M.; Sofia, Heidi J.; Gordenin, Dmitry A.; Chan, Kin; Roberts, Steven A.; Klimczak, Leszek J.; Van Waes, Carter; Chen, Zhong; Saleh, Anthony D.; Cheng, Hui; Parfitt, Jeremy; Bartlett, John; Albert, Monique; Arnaout, Angel; Sekhon, Harman; Gilbert, Sebastien; Peto, Myron; Myers, Jerome; Harr, Jodi; Eckman, John; Bergsten, Julie; Tucker, Kelinda; Zach, Leigh Anne; Karlan, Beth Y.; Lester, Jenny; Orsulic, Sandra; Sun, Qiang; Naresh, Rashi; Pihl, Todd; Wan, Yunhu; Zaren, Howard; Sapp, Jennifer; Miller, Judy; Drwiega, Paul; Ojesina, Akinyemi I.; Murray, Bradley A.; Zhang, Hailei; Cherniack, Andrew D.; Sougnez, Carrie; Pedamallu, Chandra Sekhar; Lichtenstein, Lee; Meyerson, Matthew; Noble, Michael S.; Heiman, David I.; Voet, Doug; Getz, Gad; Saksena, Gordon; Kim, Jaegil; Shih, Juliann; Cho, Juok; Lawrence, Michael S.; Gehlenborg, Nils; Lin, Pei; Beroukhim, Rameen; Frazer, Scott; Gabriel, Stacey B.; Schumacher, Steven E.; Leraas, Kristen M.; Lichtenberg, Tara M.; Zmuda, Erik; Bowen, Jay; Frick, Jessica; Gastier-Foster, Julie M.; Wise, Lisa; Gerken, Mark; Ramirez, Nilsa C.; Danilova, Ludmila; Cope, Leslie; Baylin, Stephen B.; Salvesen, Helga B.; Vellano, Christopher P.; Ju, Zhenlin; Diao, Lixia; Zhao, Hao; Chong, Zechen; Ryan, Michael C.; Martinez-Ledesma, Emmanuel; Verhaak, Roeland G.; Byers, Lauren Averett; Yuan, Yuan; Chen, Ken; Ling, Shiyun; Mills, Gordon B.; Lu, Yiling; Akbani, Rehan; Seth, Sahil; Liang, Han; Wang, Jing; Han, Leng; Weinstein, John N.; Bristow, Christopher A.; Zhang, Wei; Mahadeshwar, Harshad S.; Sun, Huandong; Tang, Jiabin; Zhang, Jianhua; Song, Xingzhi; Protopopov, Alexei; Shaw, Kenna R. Mills; Chin, Lynda; Olabode, Oluwole; Ojesina, Akinyemi I.; DiSaia, Philip; Radenbaugh, Amie; Haussler, David; Zhu, Jingchun; Stuart, Josh; Chalise, Prabhakar; Koestler, Devin; Fridley, Brooke L.; Godwin, Andrew K.; Madan, Rashna; Ciriello, Giovanni; Martinez, Cathleen; Higgins, Kelly; Bocklage, Therese; Auman, J. Todd; Perou, Charles M.; Tan, Donghui; Parker, Joel S.; Hoadley, Katherine A.; Wilkerson, Matthew D.; Mieczkowski, Piotr A.; Skelly, Tara; Veluvolu, Umadevi; Hayes, D. Neil; Rathmell, W. Kimryn; Hoyle, Alan P.; Simons, Janae V.; Wu, Junyuan; Mose, Lisle E.; Soloway, Matthew G.; Balu, Saianand; Meng, Shaowu; Jefferys, Stuart R.; Bodenheimer, Tom; Shi, Yan; Roach, Jeffrey; Thorne, Leigh B.; Boice, Lori; Huang, Mei; Jones, Corbin D.; Zuna, Rosemary; Walker, Joan; Gunderson, Camille; Snowbarger, Carie; Brown, David; Moxley, Katherine; Moore, Kathleen; Andrade, Kelsi; Landrum, Lisa; Mannel, Robert; McMeekin, Scott; Johnson, Starla; Nelson, Tina; Elishaev, Esther; Dhir, Rajiv; Edwards, Robert; Bhargava, Rohit; Tiezzi, Daniel G.; Andrade, Jurandyr M.; Noushmehr, Houtan; Carlotti, Carlos Gilberto; Tirapelli, Daniela Pretti da Cunha; Weisenberger, Daniel J.; Van Den Berg, David J.; Maglinte, Dennis T.; Bootwalla, Moiz S.; Lai, Phillip H.; Triche, Timothy; Swisher, Elizabeth M.; Agnew, Kathy J.; Shelley, Carl Simon; Laird, Peter W.; Schwarz, Julie; Grigsby, Perry; Mutch, David
  3. Nature. 2017, Mar 16; 543(7645): 378-384.
  1. 5.   Comparison of Nine Programs Predicting pK(a) Values of Pharmaceutical Substances
  2. Liao, C. Z.; Nicklaus, M. C.
  3. Journal of Chemical Information and Modeling. 2009, Dec; 49(12): 2801-2812.
  1. 6.   CCL3L1 and HIV/AIDS susceptibility
  2. Urban, T. J.; Weintrob, A. C.; Fellay, J.; Colombo, S.; Shianna, K. V.; Gumbs, C.; Rotger, M.; Pelak, K.; Dang, K. K.; Detels, R.; Martinson, J. J.; O'Brien, S. J.; Letvin, N. L.; McMichael, A. J.; Haynes, B. F.; Carrington, M.; Telenti, A.
  3. Nature Medicine. 2009 15(10): 1110-1112.
  1. 7.   Substitution of Aminomethyl at the Meta-Position Enhances the Inactivation of O-6-Alkylguanine-DNA Alkyltransferase by O-6-Benzylguanine
  2. Pauly, G. T.; Loktionova, N. A.; Fang, Q. M.; Vankayala, S. L.; Guida, W. C.; Pegg, A. E.
  3. Journal of Medicinal Chemistry. 2008 51(22): 7144-7153.
  1. 8.   Numerology versus reality: a voice in a recent dispute
  2. Jaskolski, M.; Gilski, M.; Dauter, Z.; Wlodawer, A.
  3. Acta Crystallographica Section D-Biological Crystallography. 2007, Dec; 63: 1282-1283.
  1. 9.   Sculpting the bicyclo 3.1.0 hexane template of carbocyclic nucleosides to improve recognition by herpes thymidine kinase
  2. Comin, M. J.; Agbaria, R.; Ben-Kasus, T.; Huleihel, M.; Liao, C. Z.; Sun, G. Y.; Nicklaus, M. C.; Deschamps, J. R.; Parrish, D. A.; Marquez, V. E.
  3. Journal of the American Chemical Society. 2007, May; 129(19): 6216-6222.
  1. 10.   Mass spectrometry reveals specific and global molecular transformations during viral infection
  2. Go, E. P.; Wikoff, W. R.; Shen, Z. X.; O'Maille, G.; Morita, H.; Conrads, T. P.; Nordstrom, A.; Trauger, S. A.; Uritboonthai, W.; Lucas, D. A.; Chan, K. C.; Veenstra, T. D.; Lewicki, H.; Oldstone, M. B.; Schneemann, A.; Siuzdak, G.
  3. Journal of Proteome Research. 2006, Sep; 5(9): 2405-2416.
  1. 11.   Development of a quantitative cell-based ELISA, for a humanized anti-IL-2/IL-15 receptor beta antibody (HuMik beta(1)), and correlation with functional activity using an antigen-transfected murine cell line
  2. Yang, X. Y.; Chen, E.; Jiang, H. G.; Hartmann, W. K.; Mitra, G.; Hecht, T.; Soman, G.
  3. Journal of Immunological Methods. 2006, APR 20; 311(1-2): 71-80.
  1. 12.   Optimization of multiple-sequence alignment based on multiple-structure alignment
  2. Shatsky, M.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2006, JAN 1; 62(1): 209-217.
  1. 13.   Carbohydrate array analysis of anti-Tn antibodies and lectins reveals unexpected specificities: Implications for diagnostic and vaccine development
  2. Manimala, J. C.; Li, Z. T.; Jain, A.; VedBrat, S.; Gildersleeve, J. C.
  3. Chembiochem. 2005, DEC; 6(12): 2229-2241.
  1. 14.   Measuring fifteen endogenous estrogens simultaneously in human urine by high-performance liquid chromatography-mass spectrometry
  2. Xu, X.; Veenstra, T. D.; Fox, S. D.; Roman, J. M.; Issaq, H. J.; Falk, R.; Saavedra, J. E.; Keefer, L. K.; Ziegler, R. G.
  3. Analytical Chemistry. 2005, OCT 15; 77(20): 6646-6654.
  1. 15.   Whole cell segmentation in solid tissue sections
  2. Baggett, D.; Nakaya, M. A.; McAuliffe, M.; Yamaguchi, T. P.; Lockett, S.
  3. Cytometry Part A. 2005, OCT; 67A(2): 137-143.
  1. 16.   Simian immunodeficiency virus integration preference is similar to that of human immunodeficiency virus type 1
  2. Crise, B.; Li, Y.; Yuan, C. C.; Morcock, D. R.; Whitby, D.; Munroe, D. J.; Arthur, L. O.; Wu, X. L.
  3. Journal of Virology. 2005, OCT; 79(19): 12199-12204.
  1. 17.   STRA13 expression and subcellular localisation in normal and tumour tissues: implications for use as a diagnostic and differentiation marker
  2. Ivanova, A.; Liao, S. Y.; Lerman, M. I.; Ivanov, S.; Stanbridge, E. J.
  3. Journal of Medical Genetics. 2005, JUL; 42(7): 565-576.
  1. 18.   Plasmid partition system of the P1par family from the pWR100 virulence plasmid of Shigella flexneri
  2. Sergueev, K.; Dabrazhynetskaya, A.; Austin, S.
  3. Journal of Bacteriology. 2005, MAY; 187(10): 3369-3373.
  1. 19.   Surprising dependence on postsegregational killing of host cells for maintenance of the large virulence plasmid of Shigella flexneri
  2. Sayeed, S.; Brendler, T.; Davis, M.; Reaves, L.; Austin, S.
  3. Journal of Bacteriology. 2005, APR; 187(8): 2768-2773.
  1. 20.   Risk calculations for cystic fibrosis in neonatal screening by immunoreactive trypsinogen and CFTR mutation tests
  2. Ogino, S.; Flodman, P.; Wilson, R. B.; Gold, B.; Grody, W. W.
  3. Genetics in Medicine. 2005, MAY-JUN; 7(5): 317-327.
  1. 21.   Investigation of the mouse serum proteome
  2. Hood, B. L.; Zhou, M.; Chan, K. C.; Lucas, D. A.; Kim, G. J.; Issaq, H. J.; Veenstra, T. D.; Conrads, T. P.
  3. Journal of Proteome Research. 2005, SEP-OCT; 4(5): 1561-1568.
  1. 22.   New insights on the evolution of the SMN1 and SMN2 region: simulation and meta-analysis for allele and haplotype frequency calculations
  2. Ogino, S.; Wilson, R. B.; Gold, B.
  3. European Journal of Human Genetics. 2004, DEC; 12(12): 1015-1023.
  1. 23.   Measuring seven endogenous ketolic estrogens simultaneously in human urine by high-performance liquid chromatography-mass spectrometry
  2. Xu, X.; Keefer, L. K.; Waterhouse, D. J.; Saavedra, J. E.; Veenstra, T. D.; Ziegler, R. G.
  3. Analytical Chemistry. 2004, OCT 1; 76(19): 5829-5836.
  1. 24.   Moderate hypermutability of a transgenic lacZ reporter gene in Myc-dependent inflammation-induced plasma cell tumors in mice
  2. Felix, K.; Polack, A.; Pretsch, W.; Jackson, S. H.; Feigenbaum, L.; Bornkamm, G. W.; Janz, S.
  3. Cancer Research. 2004 64(2): 530-537.
  1. 25.   Theoretical study of the low lying electronic states of oxoX(salen) (X = Mn, Mn-, Fe, and Cr-) complexes
  2. Ivanic, J.; Collins, J. R.; Burt, S. K.
  3. Journal of Physical Chemistry A. 2004 108(12): 2314-2323.
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