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Items: 1 to 50 of 56

1.

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.

Ellrott K, Buchanan A, Creason A, Mason M, Schaffter T, Hoff B, Eddy J, Chilton JM, Yu T, Stuart JM, Saez-Rodriguez J, Stolovitzky G, Boutros PC, Guinney J.

Genome Biol. 2019 Sep 10;20(1):195. doi: 10.1186/s13059-019-1794-0.

2.

Relative contribution of clinicopathological variables, genomic markers, transcriptomic subtyping and microenvironment features for outcome prediction in stage II/III colorectal cancer.

Dienstmann R, Villacampa G, Sveen A, Mason MJ, Niedzwiecki D, Nesbakken A, Moreno V, Warren RS, Lothe RA, Guinney J.

Ann Oncol. 2019 Aug 27. pii: mdz287. doi: 10.1093/annonc/mdz287. [Epub ahead of print]

PMID:
31504112
3.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I.

Immunity. 2019 Aug 20;51(2):411-412. doi: 10.1016/j.immuni.2019.08.004. No abstract available.

4.

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M; AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J.

Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2.

5.

The evolution and multi-molecular properties of NF1 cutaneous neurofibromas originating from C-fiber sensory endings and terminal Schwann cells at normal sites of sensory terminations in the skin.

Rice FL, Houk G, Wymer JP, Gosline SJC, Guinney J, Wu J, Ratner N, Jankowski MP, La Rosa S, Dockum M, Storey JR, Carroll SL, Albrecht PJ, Riccardi VM.

PLoS One. 2019 May 20;14(5):e0216527. doi: 10.1371/journal.pone.0216527. eCollection 2019.

6.

American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange: From Inception to First Data Release and Beyond-Lessons Learned and Member Institutions' Perspectives.

Micheel CM, Sweeney SM, LeNoue-Newton ML, André F, Bedard PL, Guinney J, Meijer GA, Rollins BJ, Sawyers CL, Schultz N, Shaw KRM, Velculescu VE, Levy MA; AACR Project GENIE Consortium.

JCO Clin Cancer Inform. 2018 Dec;2:1-14. doi: 10.1200/CCI.17.00083. Review.

7.

Colorectal premalignancy is associated with consensus molecular subtypes 1 and 2.

Chang K, Willis JA, Reumers J, Taggart MW, San Lucas FA, Thirumurthi S, Kanth P, Delker DA, Hagedorn CH, Lynch PM, Ellis LM, Hawk ET, Scheet PA, Kopetz S, Arts J, Guinney J, Dienstmann R, Vilar E.

Ann Oncol. 2018 Oct 1;29(10):2061-2067. doi: 10.1093/annonc/mdy337.

8.

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.

Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC.

Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5.

9.

Spatiotemporal Loss of NF1 in Schwann Cell Lineage Leads to Different Types of Cutaneous Neurofibroma Susceptible to Modification by the Hippo Pathway.

Chen Z, Mo J, Brosseau JP, Shipman T, Wang Y, Liao CP, Cooper JM, Allaway RJ, Gosline SJC, Guinney J, Carroll TJ, Le LQ.

Cancer Discov. 2019 Jan;9(1):114-129. doi: 10.1158/2159-8290.CD-18-0151. Epub 2018 Oct 22.

PMID:
30348677
10.

Probing the chemical-biological relationship space with the Drug Target Explorer.

Allaway RJ, La Rosa S, Guinney J, Gosline SJC.

J Cheminform. 2018 Aug 20;10(1):41. doi: 10.1186/s13321-018-0297-4.

11.

Traditional and systems biology based drug discovery for the rare tumor syndrome neurofibromatosis type 2.

Synodos for NF2 Consortium, Allaway R, Angus SP, Beauchamp RL, Blakeley JO, Bott M, Burns SS, Carlstedt A, Chang LS, Chen X, Clapp DW, Desouza PA, Erdin S, Fernandez-Valle C, Guinney J, Gusella JF, Haggarty SJ, Johnson GL, La Rosa S, Morrison H, Petrilli AM, Plotkin SR, Pratap A, Ramesh V, Sciaky N, Stemmer-Rachamimov A, Stuhlmiller TJ, Talkowski ME, Welling DB, Yates CW, Zawistowski JS, Zhao WN.

PLoS One. 2018 Jun 13;13(6):e0197350. doi: 10.1371/journal.pone.0197350. eCollection 2018.

12.

Pharmacological and genomic profiling of neurofibromatosis type 1 plexiform neurofibroma-derived schwann cells.

Ferrer M, Gosline SJC, Stathis M, Zhang X, Guo X, Guha R, Ryman DA, Wallace MR, Kasch-Semenza L, Hao H, Ingersoll R, Mohr D, Thomas C, Verma S, Guinney J, Blakeley JO.

Sci Data. 2018 Jun 12;5:180106. doi: 10.1038/sdata.2018.106.

13.

Alternative models for sharing confidential biomedical data.

Guinney J, Saez-Rodriguez J.

Nat Biotechnol. 2018 May 9;36(5):391-392. doi: 10.1038/nbt.4128. No abstract available.

PMID:
29734317
14.

Cutaneous neurofibromas in the genomics era: current understanding and open questions.

Allaway RJ, Gosline SJC, La Rosa S, Knight P, Bakker A, Guinney J, Le LQ.

Br J Cancer. 2018 Jun;118(12):1539-1548. doi: 10.1038/s41416-018-0073-2. Epub 2018 Apr 26. Review.

15.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5. Erratum in: Immunity. 2019 Aug 20;51(2):411-412.

16.

Functional Precision Medicine Identifies Novel Druggable Targets and Therapeutic Options in Head and Neck Cancer.

Xu C, Nikolova O, Basom RS, Mitchell RM, Shaw R, Moser RD, Park H, Gurley KE, Kao MC, Green CL, Schaub FX, Diaz RL, Swan HA, Jang IS, Guinney J, Gadi VK, Margolin AA, Grandori C, Kemp CJ, Méndez E.

Clin Cancer Res. 2018 Jun 15;24(12):2828-2843. doi: 10.1158/1078-0432.CCR-17-1339. Epub 2018 Mar 29.

17.

Multi-targeting Drug Community Challenge.

Schlessinger A, Abagyan R, Carlson HA, Dang KK, Guinney J, Cagan RL.

Cell Chem Biol. 2017 Dec 21;24(12):1434-1435. doi: 10.1016/j.chembiol.2017.12.006. No abstract available.

18.

Colorectal Cancer Consensus Molecular Subtypes Translated to Preclinical Models Uncover Potentially Targetable Cancer Cell Dependencies.

Sveen A, Bruun J, Eide PW, Eilertsen IA, Ramirez L, Murumägi A, Arjama M, Danielsen SA, Kryeziu K, Elez E, Tabernero J, Guinney J, Palmer HG, Nesbakken A, Kallioniemi O, Dienstmann R, Lothe RA.

Clin Cancer Res. 2018 Feb 15;24(4):794-806. doi: 10.1158/1078-0432.CCR-17-1234. Epub 2017 Dec 14.

19.

Community mining of open clinical trial data.

Laajala TD, Guinney J, Costello JC.

Oncotarget. 2017 Sep 13;8(47):81721-81722. doi: 10.18632/oncotarget.20853. eCollection 2017 Oct 10. No abstract available.

20.

A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer.

Seyednasrollah F, Koestler DC, Wang T, Piccolo SR, Vega R, Greiner R, Fuchs C, Gofer E, Kumar L, Wolfinger RD, Kanigel Winner K, Bare C, Neto EC, Yu T, Shen L, Abdallah K, Norman T, Stolovitzky G, Soule HR, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Elo LL, Zhou FL, Guinney J, Costello JC; Prostate Cancer DREAM Challenge Community.

JCO Clin Cancer Inform. 2017 Nov;1:1-15. doi: 10.1200/CCI.17.00018.

21.

KRAS Mutation and Consensus Molecular Subtypes 2 and 3 Are Independently Associated with Reduced Immune Infiltration and Reactivity in Colorectal Cancer.

Lal N, White BS, Goussous G, Pickles O, Mason MJ, Beggs AD, Taniere P, Willcox BE, Guinney J, Middleton GW.

Clin Cancer Res. 2018 Jan 1;24(1):224-233. doi: 10.1158/1078-0432.CCR-17-1090. Epub 2017 Oct 23.

22.

Reply to the letter to the editor 'Including lynch syndrome in personalized prognostication and follow-up of stage II and III colon cancer' by Sciallero et al.

Dienstmann R, Guinney J.

Ann Oncol. 2017 Nov 1;28(11):2889-2890. doi: 10.1093/annonc/mdx415. No abstract available.

PMID:
29045507
23.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.

Cell Rep. 2017 Aug 29;20(9):2201-2214. doi: 10.1016/j.celrep.2017.08.010.

24.

Prediction of overall survival in stage II and III colon cancer beyond TNM system: a retrospective, pooled biomarker study.

Dienstmann R, Mason MJ, Sinicrope FA, Phipps AI, Tejpar S, Nesbakken A, Danielsen SA, Sveen A, Buchanan DD, Clendenning M, Rosty C, Bot B, Alberts SR, Milburn Jessup J, Lothe RA, Delorenzi M, Newcomb PA, Sargent D, Guinney J.

Ann Oncol. 2017 May 1;28(5):1023-1031. doi: 10.1093/annonc/mdx052.

25.

A high-throughput molecular data resource for cutaneous neurofibromas.

Gosline SJ, Weinberg H, Knight P, Yu T, Guo X, Prasad N, Jones A, Shrestha S, Boone B, Levy SE, La Rosa S, Guinney J, Bakker A.

Sci Data. 2017 Apr 11;4:170045. doi: 10.1038/sdata.2017.45.

26.

Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer.

Dienstmann R, Vermeulen L, Guinney J, Kopetz S, Tejpar S, Tabernero J.

Nat Rev Cancer. 2017 Mar 23;17(4):268. doi: 10.1038/nrc.2017.24. No abstract available.

PMID:
28332502
27.

Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer.

Dienstmann R, Vermeulen L, Guinney J, Kopetz S, Tejpar S, Tabernero J.

Nat Rev Cancer. 2017 Feb;17(2):79-92. doi: 10.1038/nrc.2016.126. Epub 2017 Jan 4. Review. Erratum in: Nat Rev Cancer. 2017 Mar 23;17 (4):268.

PMID:
28050011
28.

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.

Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC; Prostate Cancer Challenge DREAM Community.

Lancet Oncol. 2017 Jan;18(1):132-142. doi: 10.1016/S1470-2045(16)30560-5. Epub 2016 Nov 16.

29.

BRAF V600E Mutant Colorectal Cancer Subtypes Based on Gene Expression.

Barras D, Missiaglia E, Wirapati P, Sieber OM, Jorissen RN, Love C, Molloy PL, Jones IT, McLaughlin S, Gibbs P, Guinney J, Simon IM, Roth AD, Bosman FT, Tejpar S, Delorenzi M.

Clin Cancer Res. 2017 Jan 1;23(1):104-115. doi: 10.1158/1078-0432.CCR-16-0140. Epub 2016 Jun 27.

30.

American Joint Committee on Cancer acceptance criteria for inclusion of risk models for individualized prognosis in the practice of precision medicine.

Kattan MW, Hess KR, Amin MB, Lu Y, Moons KG, Gershenwald JE, Gimotty PA, Guinney JH, Halabi S, Lazar AJ, Mahar AL, Patel T, Sargent DJ, Weiser MR, Compton C; members of the AJCC Precision Medicine Core.

CA Cancer J Clin. 2016 Sep;66(5):370-4. doi: 10.3322/caac.21339. Epub 2016 Jan 19.

31.

PERSONALIZED HYPOTHESIS TESTS FOR DETECTING MEDICATION RESPONSE IN PARKINSON DISEASE PATIENTS USING iPHONE SENSOR DATA.

Chaibub Neto E, Bot BM, Perumal T, Omberg L, Guinney J, Kellen M, Klein A, Friend SH, Trister AD.

Pac Symp Biocomput. 2016;21:273-84.

32.

rCGH: a comprehensive array-based genomic profile platform for precision medicine.

Commo F, Guinney J, Ferté C, Bot B, Lefebvre C, Soria JC, André F.

Bioinformatics. 2016 May 1;32(9):1402-4. doi: 10.1093/bioinformatics/btv718. Epub 2015 Dec 26.

33.

The consensus molecular subtypes of colorectal cancer.

Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S.

Nat Med. 2015 Nov;21(11):1350-6. doi: 10.1038/nm.3967. Epub 2015 Oct 12.

34.

The NIH BD2K center for big data in translational genomics.

Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van't Veer L, Wold B, Haussler D.

J Am Med Inform Assoc. 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047. Epub 2015 Jul 13.

35.

Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors.

Dienstmann R, Jang IS, Bot B, Friend S, Guinney J.

Cancer Discov. 2015 Feb;5(2):118-23. doi: 10.1158/2159-8290.CD-14-1118.

36.
37.

Impact of centralization on aCGH-based genomic profiles for precision medicine in oncology.

Commo F, Ferté C, Soria JC, Friend SH, André F, Guinney J.

Ann Oncol. 2015 Mar;26(3):582-8. doi: 10.1093/annonc/mdu582. Epub 2014 Dec 23.

38.

Social interactomes for enabling research communities.

Guinney J, Dienstmann R, Ferté C, Friend S, McCormick F.

Cancer Discov. 2014 Nov;4(11):1265-8. doi: 10.1158/2159-8290.CD-14-0774.

39.

Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes.

Sinicrope FA, Shi Q, Smyrk TC, Thibodeau SN, Dienstmann R, Guinney J, Bot BM, Tejpar S, Delorenzi M, Goldberg RM, Mahoney M, Sargent DJ, Alberts SR.

Gastroenterology. 2015 Jan;148(1):88-99. doi: 10.1053/j.gastro.2014.09.041. Epub 2014 Oct 8.

40.

CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer.

Kemp CJ, Moore JM, Moser R, Bernard B, Teater M, Smith LE, Rabaia NA, Gurley KE, Guinney J, Busch SE, Shaknovich R, Lobanenkov VV, Liggitt D, Shmulevich I, Melnick A, Filippova GN.

Cell Rep. 2014 May 22;7(4):1020-9. doi: 10.1016/j.celrep.2014.04.004. Epub 2014 May 1.

41.

Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data.

Jang IS, Neto EC, Guinney J, Friend SH, Margolin AA.

Pac Symp Biocomput. 2014:63-74.

42.

Modeling RAS phenotype in colorectal cancer uncovers novel molecular traits of RAS dependency and improves prediction of response to targeted agents in patients.

Guinney J, Ferté C, Dry J, McEwen R, Manceau G, Kao KJ, Chang KM, Bendtsen C, Hudson K, Huang E, Dougherty B, Ducreux M, Soria JC, Friend S, Derry J, Laurent-Puig P.

Clin Cancer Res. 2014 Jan 1;20(1):265-272. doi: 10.1158/1078-0432.CCR-13-1943. Epub 2013 Oct 29.

43.

Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology.

Ferté C, Trister AD, Huang E, Bot BM, Guinney J, Commo F, Sieberts S, André F, Besse B, Soria JC, Friend SH.

Clin Cancer Res. 2013 Aug 15;19(16):4315-25. doi: 10.1158/1078-0432.CCR-12-3937. Epub 2013 Jun 18. Review.

44.

Improving breast cancer survival analysis through competition-based multidimensional modeling.

Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA.

PLoS Comput Biol. 2013;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047. Epub 2013 May 9.

45.

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer.

Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HK, Rueda OM, Guinney J, Deflaux NA, Hoff B, Schildwachter X, Russnes HG, Park D, Vang VO, Pirtle T, Youseff L, Citro C, Curtis C, Kristensen VN, Hellerstein J, Friend SH, Stolovitzky G, Aparicio S, Caldas C, Børresen-Dale AL.

Sci Transl Med. 2013 Apr 17;5(181):181re1. doi: 10.1126/scitranslmed.3006112.

46.

GSVA: gene set variation analysis for microarray and RNA-seq data.

Hänzelmann S, Castelo R, Guinney J.

BMC Bioinformatics. 2013 Jan 16;14:7. doi: 10.1186/1471-2105-14-7.

47.

Genome-wide methylation profiles reveal quantitative views of human aging rates.

Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, Zhang K.

Mol Cell. 2013 Jan 24;49(2):359-367. doi: 10.1016/j.molcel.2012.10.016. Epub 2012 Nov 21.

48.

Integrating genetic association, genetics of gene expression, and single nucleotide polymorphism set analysis to identify susceptibility Loci for type 2 diabetes mellitus.

Greenawalt DM, Sieberts SK, Cornelis MC, Girman CJ, Zhong H, Yang X, Guinney J, Qi L, Hu FB.

Am J Epidemiol. 2012 Sep 1;176(5):423-30. doi: 10.1093/aje/kws123. Epub 2012 Aug 2.

49.

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge.

Huang CL, Lamb J, Chindelevitch L, Kostrowicki J, Guinney J, Delisi C, Ziemek D.

BMC Bioinformatics. 2012 Mar 23;13:46. doi: 10.1186/1471-2105-13-46.

50.

Evidence for type II cells as cells of origin of K-Ras-induced distal lung adenocarcinoma.

Xu X, Rock JR, Lu Y, Futtner C, Schwab B, Guinney J, Hogan BL, Onaitis MW.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4910-5. doi: 10.1073/pnas.1112499109. Epub 2012 Mar 12.

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