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| Publications of the Quake Group |
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| 2009 |
| |
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105. |
Schwartz JJ, Stavrakis S, Quake SR "Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability" Nature Nanotech. doi:10.1038/nnano.2009.452  pdf |
104. |
Schwartz JJ, Quake SR "Single molecule measurement of the "speed limit" of DNA polymerase" Proc. Nat. Acad. Sci. 10.1073/pnas.0907404106 pdf
(Highlighted in Nature "Research Highlights")
|
103. |
Maerkl SJ, Quake SR "Experimental determination of the evolvability of a transcription factor" Proc. Nat. Acad. Sci. 106:44 18650-18655 pdf |
102. |
Bates SR, Quake SR "Highly parallel measurements of interaction kinetic constants with a microfabricated optomechanical device" Appl. Phys. Lett. 95, 073705 (21 August 2009) doi:10.1063/1.3211382 pdf |
101. |
Pushkarev D, Neff NF, Quake SR "Single-molecule Sequencing of an Individual Human Genome" Nature Biotech 27, 847-850 (10 August 2009) doi:10.1038 pdf
(Highlighted in a Nature Biotechnology Editorial and a Nature Reviews Genetics "Research Highlight")
|
100. |
Weinstein JA, Jiang N, White III RA, Fisher DS, Quake SR "High-Throughput Sequencing of the Zebrafish Antibody Repertoire" Science 8 May 2009: 807-810 pdf |
99. |
Fan HC, Blumenfeld YJ, El-Sayed YY, Chueh J, Quake SR "Micorfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy" Am J Obstet Gynecol 2009;200:543.e1-543.e7 pdf |
98. |
Wu AR, Hiatt JB, Lu R, Attema JL, Lobo NA, Weissman IL, Clarke MF, Quake SR "Automated microfluidic chromatin immunoprecipitation from 2,000 cells" Lab on a Chip 9, 1365-1370, 2009 pdf |
97. |
Melin J, Lee A, Foygel K, Leong DE, Quake SR, Yao MWM "In Vitro Embryo Culture in Defined, Sub-microliter Volumes" Dev. Dynamics. 238:950-955, 2009 pdf |
96. |
White III RA, Blainey PC, Fan CH, Quake SR. "Digital PCR provides sensitive and absolute calibration for high throughput sequencing" BMC Genomics 10:116 doi:10.1186/1471-2164-10-116 pdf |
95. |
Diehn M, Cho RW, Lobo NA, Kalisky T, Dorie MJ, Kulp AN, Qian D, Lam JS, Ailles LE, Wong M, Joshua B, Kaplan MJ, Wapnir I,
Dirbas F, Somlo G, Garberoglio C, Paz B, Shen J, Lau SK, Quake SR, Brown JM, Weissman IL, Clarke MF "Association of reactive oxygen species levels and radioresistance in cancer stem cells" Nature Feb 2009 doi:10.1038/nature07733 pdf |
94. |
Gerber D, Maerkl SJ, Quake SR. "An in vitro microfluidic approach to generating protein-interaction networks" Nature Methods 6:1 Jan 2009 10.1038/NMET.1289 pdf |
| 2008 |
93. |
Fan CH, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. "Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood " Proc. Nat. Acad. Sci. 10.1073/pnas.0808319105 pdf
(Highlighted in Nature News)
|
92. |
Einav S, Gerber D, Bryson PD, Sklan EH, Elazar M, Maerkl SJ, Glenn JS, Quake SR. "Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis" Nature Biotech. 26:9, 1019-1027 pdf |
91. |
Balagadde FK, Song H, Collins CH, Barnet M, Arnold FH, Quake SR, You L. "A synthetic Escherichia coli predator-prey ecosystem" Mol. Sys. Biol. 4:187, 1-8 pdf |
90. |
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, DiMeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. "Single-Molecule DNA Sequencing of a Viral Genome" Science. 4 April 2008 Vol. 320 pdf |
89. |
Zhong JF, Chen Y, Marcus JS, Scherer A, Quake SR, Taylor CR, Weiner LP. "A microfluidic processor for gene expression profiling of single human embryonic stem cells" Lab on a Chip. 8, 68-74 pdf |
| 2007 |
88. |
Warren LA, Rossi DJ, Schiebinger GR, Weissman IL, Kim SK, Quake SR. "Transcriptional instability is not a universal attribute of aging" Aging Cell. 6:6 775-782 pdf |
87. |
Gomez-Sjoberg R, Leyrat AA, Pirone DM, Chen CS, Quake SR. "Versatile, Fully Automated, Microfluidic Cell Culture System" Anal. Chem. 10.1021/ac071311w pdf |
86. |
Marcy Y, Oshoey T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SMD, Quake SR. "Nanoliter reactors improve multiple displacement amplification of genomes from single cells" PLoS Genet 3(9): e155. doi:10.1371/journal.pgen.0030155 pdf |
85. |
Fan HC , Quake SR. "Detection of aneuploidy with digital polymerase chain reaction" Anal. Chem. 10.1021/ac0709394 pdf |
84. |
Schwartz JJ, Quake SR. "High density single molecule surface patterning with colloidal epitaxy"
Appl. Phys. Lett. 91, 083902 2007 pdf |
83. |
Spletter ML, Liu J, Liu J, Su H, Giniger E, Komiyama T, Quake SR, Luo L. "Lola regulates Drosophila olfactory projection meuron identity and targeting specificity" Neural. Develop. 2:14 2007 pdf |
82. |
Marcy Y, Ouverney C, Blik EM, Losekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR. "Dissecting biological "dark matter" with single cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth" Proc. Nat. Acad. Sci. July 9, 2007, 10.1073/pnas.0704662104 pdf |
81. |
Kartalov EP, Scherer A, Quake SR, Taylor CR, Anderson WF. "Experimentally validated quantitative linear model for the device physics of elastomeric microfluidic valves" J. Appl. Phys. 101 (6) Mar 15 2007 pdf |
80. | Anderson MJ, DeLaBarre B, Raghunathan
A, Palsson BO, Brunger AT, Quake SR. "Crystal Structure
of a Hyperactive Escherichia coli Gylcerol Kinase Mutand
Gly230Asp Obtained Using
Microfluidic Crystallization Devices" Biochemistry 2007, 46,
5277-5731.
pdf |
79. |
Melin J, Quake SR. "Microfluidic Large-Scale Integration: The Evolution of Design Rules for Biological Automation" Annu. Rev. Biophys. Biomol. Struct. 36:213-31 pdf
|
78. |
Warren LA, Weinstein JA, Quake SR. "The Digital Array Response Curve" Preprint. pdf |
77. |
Huang Y, Castrataro P, Lee CC, Quake SR. "Solvent resistant microfluidic DNA synthesizer" Lab on a Chip. 2007, 7, 1 DOI: 10.1039/b613923j pdf |
76. |
Maerkl SJ, Quake SR. "A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors" Science. 12 January 2007, 315:233-237 pdf
(Highlighted in Nature Methods "Research Highlights")
|
| 2006 |
75. |
Ma Z, Gerton JM, Wade LA, Quake SR. "Fluorescence Near-Field Microscopy of DNA at Sub-10nm Resolution" Phys. Rev. Lett. 31 December 2006 97:26 (260801) pdf |
74. |
Ottesen EA, Hong JW, Quake SR, Leadbetter JR. "Microfluidic Digital PCR Enables Multigene Analysis of Individual Environmental Bacteria" Science. 1 December 2006, 314:1464-67 pdf |
73. |
Warren L, Bryder D, Weissman IL, Quake SR. "Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR" Proc. Nat. Acad. Sci. 2006 10.1073/pnas.0608512103 pdf |
72. |
Anderson MJ, Hansen CL, Quake SR. "Phase knowledge enables rational screens for protein crystallization " Proc. Nat. Acad. Sci. 2006 103: 16746-16751 pdf |
71. |
Psaltis D, Quake SR, Yang CH. "Developing optofluidic technology through the fusion of microfluidics and optics" Nature 442 (7101): 381-386 pdf |
70. |
Hong JW, Chen Y, Anderson WF, Quake SR. "Molecular Biology on a Microfluidic Chip" J. Cond. Matt. Phys . 2006 18 (18):S691-S701 May 10 2006 pdf |
69. |
Phillips R, Quake SR. "The Biological Frontier of Physics" Physics Today 2006 59 (5): 38-43 May 2006 pdf |
68. |
Liu J, Williams BA, Gwirtz RM, Wolf BJ, Quake SR. "Enhanced Signals and Fast Nucleic Acid Hybridization By Microfluidic Chaotic Mixing " Angew. Chem. 2006 45:3618-3623 pdf |
67. |
Gambin Y, Legrand O, Quake SR. "Microfabricated rubber microscope using soft solid immersion lenses" Appl. Phys. Lett. 88 (17) Art. No. 174102 pdf |
66. |
Marcus JS, Anderson WF, Quake SR. "Microfluidic Single-Cell mRNA Isolation and Analysis" Anal. Chem. 2006 Mar 31;10.1021/ac0518506. pdf |
65. |
Hansen CL, Classen S, Berger JM, Quake SR. "A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination" J. Am. Chem. Soc. 2006 Mar 15;128(10):3142-3. pdf |
64. |
Polin M, Grier DG, Quake SR. "Anomalous Vibrational Dispersion in Holographically Trapped Colloidal Arrays" Phys. Rev. Lett. 2006 Mar 3;96(8):088101 pdf |
63. |
Marcus JS, Anderson WF, Quake SR. "
Parallel Picoliter rt-PCR Assays Using Microfluidics." Anal. Chem. 2006 Feb 1;78(3):956-8. pdf |
62. |
Kartalov EP, Zhong JF, Scherer A, Quake SR, Taylor CR, Anderson WF. "
High-throughput multi-antigen microfluidic fluorescence immunoassays" Biotechniques. 2006 Jan;40(1):85-90. pdf |
61. |
Lacenere CJ, Garg NK, Stoltz BM, Quake SR. "Effects of a Modified Dye-Labeled Nucleotide Spacer Arm on Incorporation Thermophilic DNA Polymerases" Nucleosides, Nucleotides & Nucleic Acids. 25:9-15, 2006. pdf |
| 2005 |
60. |
Lee CC, Sui G, Elizarov A, Shu CJ, Shin YS, Dooley AN, Huang J, Daridon A, Wyatt P, Stout D, Kolb HC, Witte ON, Satyamurthy N, Heath JR, Phelps ME, Quake SR, Tseng HR.
"Multistep Synthesis of a Radiolabeled Imaging Probe Using Integrated Microfluidics"
Science. 16 December 2005: 1793-1796. pdf |
59. |
Squires TM, Quake SR. "Microfluidics: Fluid physics at the nanoliter scale" Rev. Mod. Phys. July 2005, 7:3 pp. 977-1026. pdf |
58. |
Adams ML, Johnston ML, Scherer A, Quake SR. "Polydimethylsiloxane based microfluidic diode" J. MicroMech. MicroEng. June 2005 15: 1517-1521 pdf |
57. |
Garg NK, Woodroofe CC, Lacenere CJ, Quake SR, Stoltz BM. "A ligand-free solid-supported system for Sonogashira couplings: applications in nucleoside chemistry" Chemical Communications. 2005, (36), 4551-4553. pdf |
56. |
Balagadde FK, You L, Hansen CL, Arnold FH, Quake SR. "Long-term monitoring of bacteria undergoing programmed population control in a microchemostat." Science. 2005 Jul 1;309(5731):137-40. pdf |
| 2004 |
55. |
Gerton JM, Wade LA, Lessard GA, Ma Z, Quake SR. "Tip-enhanced fluorescence microscopy at 10 nanometer resolution." Phys Rev Lett. 2004 Oct 29;93(18):180801. pdf |
54. |
Hansen CL, Sommer MO, Quake SR. "Systematic investigation of protein phase behavior with a microfluidic formulator." Proc. Natl. Acad. Sci . 2004 Oct 5;101(40):14431-6. pdf |
53. |
Kartalov EP, Quake SR. "Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis." Nucleic Acids Res. 2004 May 20;32(9):2873-9. pdf |
52. |
Hong JW, Studer V, Hang G, Anderson WF, Quake SR. "A nanoliter-scale nucleic acid processor with parallel architecture" Nat Biotechnol. 2004 Apr;22(4):435-9. pdf |
51. |
Vyawahare, S. Eyal, S. Mathews, K. D. Quake, S. R. " Nanometer-scale Fluorescence Resonance Optical Waveguides" Nano Lett.; (Comm.); 2004; 4 (6); 1035-1039. pdf |
50. |
Groisman A, Quake SR. "A microfluidic rectifier: anisotropic flow resistance at low Reynolds numbers." Phys Rev Lett. 2004 Mar 5;92(9):094501. pdf |
49. |
Rolland JP, Van Dam RM, Schorzman DA, Quake SR, DeSimone JM. "Solvent-resistant photocurable liquid fluoropolymers for microfluidic device fabrication" J. Am. Chem. Soc. 2004 Mar 3;126(8):2322-3. pdf |
48. |
Wade, LA, Shaprio IR, Ma Z, Quake SR, Collier PC. "Correlating AFM Probe Morphology to Image Resolution for Single-Wall Carbon Nanotube Tips" Nano Lett.; 2004; 4 (4); 725-731 pdf |
47. |
Studer V, Hang G, Pandolfi A, Ortiz M, Anderson WF, Quake SR. "Scaling properties of a low-actuation pressure microfluidic valve" J. Appl. Phys.; 95 (1) 393-398 pdf |
| 2003 |
46. |
Bao XR, Lee HJ, Quake SR. "Behavior of complex knots in single DNA molecules." Phys Rev Lett. 2003 Dec 31;91(26 Pt 1):265506. pdf |
45. |
Hong JW, Quake SR. "Integrated nanoliter systems." Nat Biotechnol. 2003 Oct;21(10):1179-83. Review. pdf |
44. |
Hansen C, Quake SR. "Microfluidics in structural biology: smaller, faster ... better." Curr Opin Struct Biol. 2003 Oct;13(5):538-44. Review. pdf |
43. |
Reese MO, van Dam RM, Scherer A, Quake SR. "Microfabricated fountain pens for high-density DNA arrays." Genome Res. 2003 Oct;13(10):2348-52. pdf |
42. |
Liu J, Hansen C, Quake SR. "Solving the "world-to-chip" interface problem with a microfluidic matrix." Anal Chem. 2003 Sep 15;75(18):4718-23. pdf |
41. |
Yi GR, Jeon SJ, Thorsen T, Manoharan VN, Quake SR, Pine DJ, Yang SM. "Generation of uniform photonic balls by template-assisted colloidal crystallization" Synth. Mat. 139 (3) 803-806 pdf |
40. |
Yi GR, Thorsen T, Manoharan VN, Hwang MJ, Jeon SJ, Pine DJ, Quake SR, Yang SM. "Generation of uniform colloidal assemblies in soft microfluidic devices" Adv. Mat. 2003 15 (15) 1300+ pdf |
39. |
Groisman A, Enzelberger M, Quake SR. "Microfluidic memory and control devices" Science. 2003 May 9;300(5621):955-8. pdf |
38. |
Wade LA, Shapiro I, Ma Z, Quake SR, Collier CP. "Single Molecule Fluorescence and Force Microscopy Employing Carbon Nanotubes" Nanotech 2003 Vol. 3 317-320 pdf |
37. |
Braslavsky I, Hebert B, Kartalov E, Quake SR, "Sequence Information can be obtained from Single DNA Molecules", Proc. Nat'l Acad. Sci. 100: 3960-3964 (2003). pdf |
36. |
Kartalov EP, Unger MA, Quake SR. "Polyelectrolyte surface interface for single-molecule fluorescence studies of DNA polymerase." Biotechniques. 2003 Mar;34(3):505-10. pdf |
35. |
Adams, ML, Enzelberger M, Quake SR, Scherer A. "Microfluidic integration on detector arrays for absorption and fluorescence micro-spectrometers" Sens. and Act. A. 104 (1):25-31 pdf |
34. |
Filippova EM, Monteleone DC, Trunk JG, Sutherland BM, Quake SR, Sutherland JC. "Quantifying double-strand breaks and clustered damages in DNA by single-molecule laser fluorescence sizing." Biophys. J. 2003 Feb;84(2 Pt 1):1281-90. pdf |
| 2002 |
33. |
Chiu CS, Jensen K, Sokolova I, Wang D, Li M, Deshpande P, Davidson N, Mody I, Quick MW, Quake SR, and Lester HA. "Number, density, and surface/cytoplasmic distribution of GABA transporters at presynaptic structures of knock-in mice carrying GABA transporter subtype 1-green fluorescent protein fusions." J Neurosci. 2002 Dec 1; 22 (23): 10251-66. pdf |
32. |
Hansen CL, Skordalakes E, Berger JM, Quake SR, "A Robust and Scalable Microfluidic Metering Method that Allows Protein Crystal Growth by Free Interface Diffusion", Proc. Nat'l Acad. Sci. 99: 16531-6 (2002). pdf |
31. |
Thorsen T, Maerkl SJ, Quake SR, "Microfluidic Large Scale Integration", Science 298: 580-584 (2002). pdf |
30. |
Brody JP, Williams BA, Wold BJ, Quake SR, "Significance and Statistical Errors in the Analysis of DNA Microarray Data", Proc. Nat'l Acad. Sci. 99: 12975-12978 (2002). pdf |
29. |
Thompson HGR, Harris JW, Wold BJ, Quake SR, Brody JP, "Identification and Confirmation of a Module of Coexpressed Genes", Genome Research 12: 1517-1522 (2002). pdf |
28. |
Adams M, DeRose G, Quake SR, Scherer A. "Fundamental approach for optoelectronic and microfluidic integration for miniaturizing spectroscopic devices", Proceedings of SPIE Vol. 4647 1-6 (2002). pdf |
27. |
Eyal S and Quake SR, "Velocity Independent Microfluidic Flow Cytometry", Electrophoresis 23: 2653-2657 (2002). pdf |
26. |
Liu J, Enzelberger M, Quake SR, "A Nanoliter Rotary Device for Polymerase Chain Reaction", Electrophoresis 23: 1531-1536 (2002). pdf |
25. |
Fu AY, Chou HP, Spence C, Arnold FH, Quake SR, "An Integrated Microfabricated Cell Sorter, Anal. Chem. (2002). pdf |
24. |
Van Dam RM, Quake SR, "Gene Expression Analysis with Universal n-mer Arrays", Genome Research 12: 145-152 (2002). pdf |
| 2001 |
23. |
Chou HP, Unger MA, Quake SR, "A Microfabricated Rotary Pump", Biomedical Microdevices 3: 323-330 (2001). pdf |
22. |
Thorsen T, Roberts RW, Arnold FH, Quake SR, "Dynamic Pattern Formation in a Vesicle-Generating Microfluidic Device", Phys. Rev. Lett. 86: 4163-6 (2001). pdf |
21. |
Chiu CS, Kartalov E, Unger MA, Quake SR, Lester H, "Single molecule measurements calibrate green fluorescent protein surface densities on transparent beads for use in "knock-in" animals and other expression systems", Journal of Neuroscience Methods 105: 55-63 (2001). pdf |
| 2000 |
20. |
Quake SR and Scherer A, "From Micro to Nano Fabrication with Soft Materials", Science 290: 1536-40 (2000). pdf |
19. |
Chou HP, Unger MA, Scherer A, Quake SR, "Integrated Elastomer Fluidic Lab on a Chip - Surface Patterning and DNA diagnostics", in Proceedings of the Solid State Actuator and Sensor Workshop , Hilton Head, S.C. (2000). pdf |
18. |
Meiners JC, Quake SR, "FemtoNewton Force Spectroscopy of Single Extended DNA Molecules", Phys. Rev. Lett. 84: 5014-7 (2000). pdf |
17. |
Quake SR, Yang TJ, Lessard GA, Unger A, Kartalov E, "Fluorescence apertureless near-field microscope: a step towards imaging information in DNA", Proceedings of SPIE Vol. 3922 199-204 (2000). pdf |
16. |
Unger MA, Chou HP, Thorsen T, Scherer A, Quake SR, "Monolithic Microfabricated Valves and Pumps by Multilayer Soft Lithography", Science 288: 113-116 (2000). pdf |
15. |
Yang TJ, Lessard GA, Quake SR, "An Apertureless Near-Field Microscope for Fluorescence Imaging", Applied Physics Letters 76: 378-380 (2000). pdf |
| 1999 |
14. |
Unger MA, Kartalov E, Chiu CS, Lester H, Quake SR, "Single Molecule Fluorescence Observed with Mercury Lamp Illumination", Biotechniques 27: 1008-1013 (1999). pdf |
13. |
Fu AY, Spence C, Scherer A, Arnold FH, Quake SR, "A Microfabricated Fluorescence-Activated Cell Sorter", Nature Biotechnology 17: 1109-1111 (1999). pdf |
12. |
Hatfield JW and Quake SR, "Dynamic Properties of an Extended Polymer in Solution", Phys Rev Lett 82: 3548-51 (1999). pdf |
11. |
Lessard G, Yang TJ, Barritault P, Quake SR, "A Scanning Apertureless Fluorescence Microscope", Proceedings of the SPIE, Vol. 3607 158-165 (1999) pdf |
10. |
Meiners JC and Quake SR, "A Direct Measurement of Hydrodynamic Cross Correlations Between Two Particles in an External Potential", Phys Rev Lett 82: 2211-2214 (1999). pdf |
9. |
Brody JP and Quake SR, "A Self-Assembled Microscopic Rotational Probe", Appl Phys Lett. volume 74, no. 1, 4 January 1999. pdf |
8. |
Chou HP, Spence C, Scherer A, Quake SR, "A Microfabricated Device for Sizing and Sorting DNA Molecules", Proc. Nat'l Acad. Sci. 96: 11-13 (1999). pdf |
| 1998 |
7. |
Quake SR, Chou HP, Spence C, Fu AY, Scherer A, "Disposable Microdevices for DNA Analysis and Cell Sorting", Proc. Solid-State Sensor and Actuator Workshop , Hilton Head, SC, June 8-11, 1998, pp.11-14. pdf |
6. |
Chou HP, Spence C, Scherer A, Quake SR, "Microfabricated devices for sizing DNA and sorting cells," in Micro- and Nanofabricated Structures and Devices for Biomedical Environmental Applications , Paul L. Gourley, Editor, Proceedings of SPIE Vol 3258, 181-7, (1998). pdf |
| 1997- |
5. |
Quake SR, Babcock H, Chu S, "The dynamics of partially extended single molecules of DNA", Nature 388 : 151-154 (1997). pdf |
4. |
Quake SR. "Fast Monte Carlo algorithms for knotted polymers" Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 1995 Jul; 52(1):1176-1180. pdf |
3. |
Quake SR. "Topological effects of knots in polymers" Phys. Rev. Lett. 1994 Dec 12; 73(24): 3317-3320. pdf |
2. |
Quake SR. "The Zimm model applied to extended single polymers" J. Chem Phys. 1994 Sept. 101 (5); 4307-4311 pdf |
1. |
Perkins TT, Quake SR, Smith DE, Chu S. "Relaxation of a single DNA molecule observed by optical microscopy" Science. 1994 May 6; 264(5160):822-6. pdf |
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