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Mary Frances Lopez, PhD

Mary Frances Lopez PhD
Medicine Research
Endocrinology Research
Hospital Title:
Medical Staff
Academic Title:
Assistant Professor of Pediatrics, Harvard Medical School
Contact Via Email
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  1. Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong G, Zhong N, Zhao L, Aebersold R, Arrowsmith CH, Emili A, Frappier L, Gingras AC, Gstaiger M, Paulovich AG, Koide S, Kossiakoff AA, Sidhu SS, Wodak SJ, Gräslund S, Greenblatt JF, Edwards AM. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat Methods. 2015 Aug; 12(8):725-31.
  2. Gauthier MS, Pérusse JR, Awan Z, Bouchard A, Tessier S, Champagne J, Krastins B, Byram G, Chabot K, Garneau P, Rabasa-Lhoret R, Faubert D, Lopez MF, Seidah NG, Coulombe B. A semi-automated mass spectrometric immunoassay coupled to selected reaction monitoring (MSIA-SRM) reveals novel relationships between circulating PCSK9 and metabolic phenotypes in patient cohorts. Methods. 2015 Jun 15; 81:66-73.
  3. Singh RJ, Hines JM, Lopez MF, Krastins B, Hoofnagle AN. Mass spectrometric immunoassay raises doubt for the existence of parathyroid hormone fragment 7-84. Clin Chem. 2015 Mar; 61(3):558-60.
  4. Lopez MF, Krastins B, Sarracino DA, Byram G, Vogelsang MS, Prakash A, Peterman S, Ahmad S, Vadali G, Deng W, Inglessis I, Wickham T, Feeney K, Dec GW, Palacios I, Buonanno FS, Lo EH, Ning M. Proteomic signatures of serum albumin-bound proteins from stroke patients with and without endovascular closure of PFO are significantly different and suggest a novel mechanism for cholesterol efflux. Clin Proteomics. 2015; 12(1):2.
  5. Korbakis D, Prassas I, Brinc D, Batruch I, Krastins B, Lopez MF, Diamandis EP. Delineating monoclonal antibody specificity by mass spectrometry. J Proteomics. 2015 Jan 30; 114:115-24.
  6. Prakash A, Peterman S, Ahmad S, Sarracino D, Frewen B, Vogelsang M, Byram G, Krastins B, Vadali G, Lopez M. Hybrid data acquisition and processing strategies with increased throughput and selectivity: pSMART analysis for global qualitative and quantitative analysis. J Proteome Res. 2014 Dec 5; 13(12):5415-30.
  7. Ritter SY, Collins J, Krastins B, Sarracino D, Lopez M, Losina E, Aliprantis AO. Mass spectrometry assays of plasma biomarkers to predict radiographic progression of knee osteoarthritis. Arthritis Res Ther. 2014; 16(5):456.
  8. Couchman L, Taylor DR, Krastins B, Lopez MF, Moniz CF. LC-MS candidate reference methods for the harmonisation of parathyroid hormone (PTH) measurement: a review of recent developments and future considerations. Clin Chem Lab Med. 2014 Sep; 52(9):1251-63.
  9. Hoggart CJ, Venturini G, Mangino M, Gomez F, Ascari G, Zhao JH, Teumer A, Winkler TW, Tšernikova N, Luan J, Mihailov E, Ehret GB, Zhang W, Lamparter D, Esko T, Macé A, Rüeger S, Bochud PY, Barcella M, Dauvilliers Y, Benyamin B, Evans DM, Hayward C, Lopez MF, Franke L, Russo A, Heid IM, Salvi E, Vendantam S, Arking DE, Boerwinkle E, Chambers JC, Fiorito G, Grallert H, Guarrera S, Homuth G, Huffman JE, Porteous D, Moradpour D, Iranzo A, Hebebrand J, Kemp JP, Lammers GJ, Aubert V, Heim MH, Martin NG, Montgomery GW, Peraita-Adrados R, Santamaria J, Negro F, Schmidt CO, Scott RA, Spector TD, Strauch K, Völzke H, Wareham NJ, Yuan W, Bell JT, Chakravarti A, Kooner JS, Peters A, Matullo G, Wallaschofski H, Whitfield JB, Paccaud F, Vollenweider P, Bergmann S, Beckmann JS, Tafti M, Hastie ND, Cusi D, Bochud M, Frayling TM, Metspalu A, Jarvelin MR, Scherag A, Smith GD, Borecki IB, Rousson V, Hirschhorn JN, Rivolta C, Loos RJ, Kutalik Z. Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index. PLoS Genet. 2014 Jul; 10(7):e1004508.
  10. Peterman S, Niederkofler EE, Phillips DA, Krastins B, Kiernan UA, Tubbs KA, Nedelkov D, Prakash A, Vogelsang MS, Schoeder T, Couchman L, Taylor DR, Moniz CF, Vadali G, Byram G, Lopez MF. An automated, high-throughput method for targeted quantification of intact insulin and its therapeutic analogs in human serum or plasma coupling mass spectrometric immunoassay with high resolution and accurate mass detection (MSIA-HR/AM). Proteomics. 2014 Jun; 14(12):1445-56.
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  12. Lopez MF, Krastins B, Ning M. The role of apolipoprotein E in neurodegeneration and cardiovascular disease. Expert Rev Proteomics. 2014 Jun; 11(3):371-81.
  13. Oran PE, Trenchevska O, Nedelkov D, Borges CR, Schaab MR, Rehder DS, Jarvis JW, Sherma ND, Shen L, Krastins B, Schwenke DC, Reaven PD, Nelson RW. Parallel workflow for high-throughput (&gt1,000 samples/day) quantitative analysis of human insulin-like growth factor 1 using mass spectrometric immunoassay. PLoS One. 2014; 9(3):e92801.
  14. Niederkofler EE, Phillips DA, Krastins B, Kulasingam V, Kiernan UA, Tubbs KA, Peterman SM, Prakash A, Diamandis EP, Lopez MF, Nedelkov D. Targeted selected reaction monitoring mass spectrometric immunoassay for insulin-like growth factor 1. PLoS One. 2013; 8(11):e81125.
  15. Ritter SY, Subbaiah R, Bebek G, Crish J, Scanzello CR, Krastins B, Sarracino D, Lopez MF, Crow MK, Aigner T, Goldring MB, Goldring SR, Lee DM, Gobezie R, Aliprantis AO. Proteomic analysis of synovial fluid from the osteoarthritic knee: comparison with transcriptome analyses of joint tissues. Arthritis Rheum. 2013 Apr; 65(4):981-92.
  16. Krastins B, Prakash A, Sarracino DA, Nedelkov D, Niederkofler EE, Kiernan UA, Nelson R, Vogelsang MS, Vadali G, Garces A, Sutton JN, Peterman S, Byram G, Darbouret B, Pérusse JR, Seidah NG, Coulombe B, Gobom J, Portelius E, Pannee J, Blennow K, Kulasingam V, Couchman L, Moniz C, Lopez MF. Rapid development of sensitive, high-throughput, quantitative and highly selective mass spectrometric targeted immunoassays for clinically important proteins in human plasma and serum. Clin Biochem. 2013 Apr; 46(6):399-410.
  17. Lopez MF, Sarracino DA, Vogelsang M, Sutton JN, Athanas M, Krastins B, Garces A, Prakash A, Peterman S, Demirjian Z, Inglessis-Azuaje I, Feeney K, Elia M, McMullin D, Dec GW, Palacios I, Lo EH, Buonanno F, Ning M. Heart-brain signaling in patent foramen ovale-related stroke: differential plasma proteomic expression patterns revealed with a 2-pass liquid chromatography-tandem mass spectrometry discovery workflow. J Investig Med. 2012 Dec; 60(8):1122-30.
  18. Lopez MF, Tollervey J, Krastins B, Garces A, Sarracino D, Prakash A, Vogelsang M, Geesman G, Valderrama A, Jordan IK, Lunyak VV. Depletion of nuclear histone H2A variants is associated with chronic DNA damage signaling upon drug-evoked senescence of human somatic cells. Aging (Albany NY). 2012 Nov; 4(11):823-42.
  19. Prakash A, Rezai T, Krastins B, Sarracino D, Athanas M, Russo P, Zhang H, Tian Y, Li Y, Kulasingam V, Drabovich A, Smith CR, Batruch I, Oran PE, Fredolini C, Luchini A, Liotta L, Petricoin E, Diamandis EP, Chan DW, Nelson R, Lopez MF. Interlaboratory reproducibility of selective reaction monitoring assays using multiple upfront analyte enrichment strategies. J Proteome Res. 2012 Aug 3; 11(8):3986-95.
  20. Lopez MF, Sarracino DA, Prakash A, Athanas M, Krastins B, Rezai T, Sutton JN, Peterman S, Gvozdyak O, Chou S, Lo E, Buonanno F, Ning M. Discrimination of ischemic and hemorrhagic strokes using a multiplexed, mass spectrometry-based assay for serum apolipoproteins coupled to multi-marker ROC algorithm. Proteomics Clin Appl. 2012 Apr; 6(3-4):190-200.
  21. Lopez MF, Sarracino D, Athanas M, Krastins B, Prakash A, Garces A. Global profiling and relative quantifiction of histones, histone PTMs and histone-modifying enzymes in mesenchymal stem cells using LC-MS/MS and a novel PerfectPair mass difference algorithm. Cell Cycle. 2011 Dec 15; 10(24):4181-3.
  22. Campbell J, Rezai T, Prakash A, Krastins B, Dayon L, Ward M, Robinson S, Lopez M. Evaluation of absolute peptide quantitation strategies using selected reaction monitoring. Proteomics. 2011 Mar; 11(6):1148-52.
  23. Li Y, Tian Y, Rezai T, Prakash A, Lopez MF, Chan DW, Zhang H. Simultaneous analysis of glycosylated and sialylated prostate-specific antigen revealing differential distribution of glycosylated prostate-specific antigen isoforms in prostate cancer tissues. Anal Chem. 2011 Jan 1; 83(1):240-5.
  24. Ning M, Sarracino DA, Buonanno FS, Krastins B, Chou S, McMullin D, Wang X, Lopez M, Lo EH. Proteomic Protease Substrate Profiling of tPA Treatment in Acute Ischemic Stroke Patients: A Step Toward Individualizing Thrombolytic Therapy at the Bedside. Transl Stroke Res. 2010 Dec 1; 1(4):268-75.
  25. Garces A, Atmakuri K, Chase MR, Woodworth JS, Krastins B, Rothchild AC, Ramsdell TL, Lopez MF, Behar SM, Sarracino DA, Fortune SM. EspA acts as a critical mediator of ESX1-dependent virulence in Mycobacterium tuberculosis by affecting bacterial cell wall integrity. PLoS Pathog. 2010; 6(6):e1000957.
  26. Lopez MF, Kuppusamy R, Sarracino DA, Prakash A, Athanas M, Krastins B, Rezai T, Sutton JN, Peterman S, Nicolaides K. Mass spectrometric discovery and selective reaction monitoring (SRM) of putative protein biomarker candidates in first trimester Trisomy 21 maternal serum. J Proteome Res. 2011 Jan 7; 10(1):133-42.
  27. Zhu H, Shah S, Shyh-Chang N, Shinoda G, Einhorn WS, Viswanathan SR, Takeuchi A, Grasemann C, Rinn JL, Lopez MF, Hirschhorn JN, Palmert MR, Daley GQ. Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies. Nat Genet. 2010 Jul; 42(7):626-30.
  28. Nilsson CL, Dillon R, Devakumar A, Shi SD, Greig M, Rogers JC, Krastins B, Rosenblatt M, Kilmer G, Major M, Kaboord BJ, Sarracino D, Rezai T, Prakash A, Lopez M, Ji Y, Priebe W, Lang FF, Colman H, Conrad CA. Quantitative phosphoproteomic analysis of the STAT3/IL-6/HIF1alpha signaling network: an initial study in GSC11 glioblastoma stem cells. J Proteome Res. 2010 Jan; 9(1):430-43.
  29. Liang L, Guo WH, Esquiliano DR, Asai M, Rodriguez S, Giraud J, Kushner JA, White MF, Lopez MF. Insulin-like growth factor 2 and the insulin receptor, but not insulin, regulate fetal hepatic glycogen synthesis. Endocrinology. 2010 Feb; 151(2):741-7.
  30. Lopez MF, Rezai T, Sarracino DA, Prakash A, Krastins B, Athanas M, Singh RJ, Barnidge DR, Oran P, Borges C, Nelson RW. Selected reaction monitoring-mass spectrometric immunoassay responsive to parathyroid hormone and related variants. Clin Chem. 2010 Feb; 56(2):281-90.
  31. Silva D, Dikkes P, Barnes M, Lopez MF. Decreased motoneuron survival in Igf2 null mice after sciatic nerve transection. Neuroreport. 2009 Oct 28; 20(16):1414-8.
  32. Esquiliano DR, Guo W, Liang L, Dikkes P, Lopez MF. Placental glycogen stores are increased in mice with H19 null mutations but not in those with insulin or IGF type 1 receptor mutations. Placenta. 2009 Aug; 30(8):693-9.
  33. Diamandis EP, Hanash S, Lopez M, Carr S, Petricoin EF. Protein quantification by mass spectrometry: is it ready for prime time? Clin Chem. 2009 Jul; 55(7):1427-30.
  34. Liu C, Shea N, Rucker S, Harvey L, Russo P, Saul R, Lopez MF, Mikulskis A, Kuzdzal S, Golenko E, Fishman D, Vonderheid E, Booher S, Cowen EW, Hwang ST, Whiteley GR. Proteomic patterns for classification of ovarian cancer and CTCL serum samples utilizing peak pairs indicative of post-translational modifications. Proteomics. 2007 Nov; 7(22):4045-52.
  35. Fisher WG, Rosenblatt KP, Fishman DA, Whiteley GR, Mikulskis A, Kuzdzal SA, Lopez MF, Tan NC, German DC, Garner HR. A robust biomarker discovery pipeline for high-performance mass spectrometry data. J Bioinform Comput Biol. 2007 Oct; 5(5):1023-45.
  36. Dikkes P, B Jaffe D, Guo WH, Chao C, Hemond P, Yoon K, Zurakowski D, Lopez MF. IGF2 knockout mice are resistant to kainic acid-induced seizures and neurodegeneration. Brain Res. 2007 Oct 17; 1175:85-95.
  37. Lopez MF, Mikulskis A, Kuzdzal S, Golenko E, Petricoin EF, Liotta LA, Patton WF, Whiteley GR, Rosenblatt K, Gurnani P, Nandi A, Neill S, Cullen S, O'Gorman M, Sarracino D, Lynch C, Johnson A, Mckenzie W, Fishman D. A novel, high-throughput workflow for discovery and identification of serum carrier protein-bound peptide biomarker candidates in ovarian cancer samples. Clin Chem. 2007 Jun; 53(6):1067-74.
  38. Dikkes P, Hawkes C, Kar S, Lopez MF. Effect of kainic acid treatment on insulin-like growth factor-2 receptors in the IGF2-deficient adult mouse brain. Brain Res. 2007 Feb 2; 1131(1):77-87.
  39. Silva D, Venihaki M, Guo WH, Lopez MF. Igf2 deficiency results in delayed lung development at the end of gestation. Endocrinology. 2006 Dec; 147(12):5584-91.
  40. Scrivener E, Boghigian BA, Golenko E, Bogdanova A, Jackson P, Mikulskis A, Denoyer E, Courtney P, Lopez MF, Patton WF. Performance validation of an improved Xenon-arc lamp-based CCD camera system for multispectral imaging in proteomics. Proteomics. 2005 Nov; 5(17):4354-66.
  41. Kuzdzal S, Lopez M, Mikulskis A, Golenko E, DiCesare J, Denoyer E, Patton W, Ediger R, Sapp L, Ziegert T, Ackloo S, Wall MR, Mannion DP, della Cioppa G, Wolfe G, Bennett D, Melov S. Biomarker discovery and analysis platform: application to Alzheimer's disease. Biotechniques. 2005 Oct; 39(4):606-7.
  42. Lopez MF, Mikulskis A, Kuzdzal S, Bennett DA, Kelly J, Golenko E, DiCesare J, Denoyer E, Patton WF, Ediger R, Sapp L, Ziegert T, Lynch C, Kramer S, Whiteley GR, Wall MR, Mannion DP, Della Cioppa G, Rakitan JS, Wolfe GM. High-resolution serum proteomic profiling of Alzheimer disease samples reveals disease-specific, carrier-protein-bound mass signatures. Clin Chem. 2005 Oct; 51(10):1946-54.
  43. Lopez MF, Mikulskis A, Golenko E, Melov S, Bennett D, Cherkasskiy A, Kuzdzal S, Kramer S, Sissors D. Microscale fractionation facilitates detection of differentially expressed proteins in Alzheimer's disease brain samples. Electrophoresis. 2004 Aug; 25(15):2557-63.
  44. Friedman JS, Lopez MF, Fleming MD, Rivera A, Martin FM, Welsh ML, Boyd A, Doctrow SR, Burakoff SJ. SOD2-deficiency anemia: protein oxidation and altered protein expression reveal targets of damage, stress response, and antioxidant responsiveness. Blood. 2004 Oct 15; 104(8):2565-73.
  45. Lopez MF, Melov S, Johnson F, Nagulko N, Golenko E, Kuzdzal S, Ackloo S, Mikulskis A. Proteomic analysis of mitochondrial proteins. Int Rev Neurobiol. 2004; 61:31-48.
  46. Lopez MF, Mikulskis A, Golenko E, Herick K, Spibey CA, Taylor I, Bobrow M, Jackson P. High-content proteomics: fluorescence multiplexing using an integrated, high-sensitivity, multiwavelength charge-coupled device imaging system. Proteomics. 2003 Jul; 3(7):1109-16.
  47. Lopez MF, Pluskal MG. Protein micro- and macroarrays: digitizing the proteome. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5; 787(1):19-27.
  48. Berggren KN, Schulenberg B, Lopez MF, Steinberg TH, Bogdanova A, Smejkal G, Wang A, Patton WF. An improved formulation of SYPRO Ruby protein gel stain: comparison with the original formulation and with a ruthenium II tris (bathophenanthroline disulfonate) formulation. Proteomics. 2002 May; 2(5):486-98.
  49. Lopez MF, Melov S. Applied proteomics: mitochondrial proteins and effect on function. Circ Res. 2002 Mar 8; 90(4):380-9.
  50. Pluskal MG, Bogdanova A, Lopez M, Gutierrez S, Pitt AM. Multiwell in-gel protein digestion and microscale sample preparation for protein identification by mass spectrometry. Proteomics. 2002 Feb; 2(2):145-50.
  51. Berggren KN, Chernokalskaya E, Lopez MF, Beechem JM, Patton WF. Comparison of three different fluorescent visualization strategies for detecting Escherichia coli ATP synthase subunits after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Proteomics. 2001 Jan; 1(1):54-65.
  52. Lopez MF, Berggren K, Chernokalskaya E, Lazarev A, Robinson M, Patton WF. A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling. Electrophoresis. 2000 Nov; 21(17):3673-83.
  53. Lopez MF, Kristal BS, Chernokalskaya E, Lazarev A, Shestopalov AI, Bogdanova A, Robinson M. High-throughput profiling of the mitochondrial proteome using affinity fractionation and automation. Electrophoresis. 2000 Oct; 21(16):3427-40.
  54. Berggren K, Chernokalskaya E, Steinberg TH, Kemper C, Lopez MF, Diwu Z, Haugland RP, Patton WF. Background-free, high sensitivity staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex. Electrophoresis. 2000 Jul; 21(12):2509-21.
  55. Lopez MF. Better approaches to finding the needle in a haystack: optimizing proteome analysis through automation. Electrophoresis. 2000 Apr; 21(6):1082-93.
  56. Steinberg TH, Chernokalskaya E, Berggren K, Lopez MF, Diwu Z, Haugland RP, Patton WF. Ultrasensitive fluorescence protein detection in isoelectric focusing gels using a ruthenium metal chelate stain. Electrophoresis. 2000 Feb; 21(3):486-96.
  57. Berggren K, Steinberg TH, Lauber WM, Carroll JA, Lopez MF, Chernokalskaya E, Zieske L, Diwu Z, Haugland RP, Patton WF. A luminescent ruthenium complex for ultrasensitive detection of proteins immobilized on membrane supports. Anal Biochem. 1999 Dec 15; 276(2):129-43.
  58. Lopez MF, Dikkes P, Zurakowski D, Villa-Komaroff L, Majzoub JA. Regulation of hepatic glycogen in the insulin-like growth factor II-deficient mouse. Endocrinology. 1999 Mar; 140(3):1442-8.
  59. Lopez MF. 2-D electrophoresis using carrier ampholytes in the first dimension (IEF). Methods Mol Biol. 1999; 112:111-27.
  60. Lopez MF, Patton WF. Reproducibility of polypeptide spot positions in two-dimensional gels run using carrier ampholytes in the isoelectric focusing dimension. Electrophoresis. 1997 Mar-Apr; 18(3-4):338-43.
  61. Lim MJ, Patton WF, Lopez MF, Spofford KH, Shojaee N, Shepro D. A luminescent europium complex for the sensitive detection of proteins and nucleic acids immobilized on membrane supports. Anal Biochem. 1997 Feb 15; 245(2):184-95.
  62. Lopez MF, Dikkes P, Zurakowski D, Villa-Komaroff L. Insulin-like growth factor II affects the appearance and glycogen content of glycogen cells in the murine placenta. Endocrinology. 1996 May; 137(5):2100-8.
  63. Lopez MF, Patton WF, Sawlivich WB, Erdjument-Bromage H, Barry P, Gmyrek K, Hines T, Tempst P, Skea WM. A glutathione S-transferase (GST) isozyme from broccoli with significant sequence homology to the mammalian theta-class of GSTs. Biochim Biophys Acta. 1994 Mar 16; 1205(1):29-38.
  64. Barnard R, Thordarson G, Lopez MF, Yamaguchi M, Edens A, Cramer SD, Ogren L, Talamantes F. Expression of growth hormone-binding protein with a hydrophilic carboxyl terminus by the mouse placenta: studies in vivo and in vitro. J Endocrinol. 1994 Jan; 140(1):125-35.
  65. Patton WF, Lopez MF, Barry P, Skea WM. A mechanically strong matrix for protein electrophoresis with enhanced silver staining properties. Biotechniques. 1992 Apr; 12(4):580-5.
  66. Lopez MF, Patton WF, Utterback BL, Chung-Welch N, Barry P, Skea WM, Cambria RP. Effect of various detergents on protein migration in the second dimension of two-dimensional gels. Anal Biochem. 1991 Nov 15; 199(1):35-44.
  67. Lopez MF, Carrion FA, Talamantes F. Pituitary-placental interaction: hypophysectomy modulates the secretion of mouse placental lactogen-I. Endocrinology. 1991 Nov; 129(5):2325-8.
  68. Patton WF, Chung-Welch N, Lopez MF, Cambria RP, Utterback BL, Skea WM. Tris-tricine and Tris-borate buffer systems provide better estimates of human mesothelial cell intermediate filament protein molecular weights than the standard Tris-glycine system. Anal Biochem. 1991 Aug 15; 197(1):25-33.
  69. Patton WF, Pluskal MG, Skea WM, Buecker JL, Lopez MF, Zimmermann R, Belanger LM, Hatch PD. Development of a dedicated two-dimensional gel electrophoresis system that provides optimal pattern reproducibility and polypeptide resolution. Biotechniques. 1990 May; 8(5):518-27.
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