-
1
-
-
66249088017
-
The second wave of synthetic biology: From modules to systems
-
Purnick, P. E. M. and Weiss, R. (2009) The second wave of synthetic biology: From modules to systems Nat. Rev. Mol. Cell Biol. 10, 410 - 422
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 410-422
-
-
Purnick, P.E.M.1
Weiss, R.2
-
3
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli Nature 403, 339 - 342
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
4
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
Elowitz, M. B. and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators Nature 403, 335 - 338
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
5
-
-
57049159362
-
A fast, robust, and tunable synthetic gene oscillator
-
Stricker, J., Cookson, S., Bennett, M. R., Mather, W. H., Tsimring, L. S., and Hasty, J. (2008) A fast, robust, and tunable synthetic gene oscillator Nature 456, 516 - 519
-
(2008)
Nature
, vol.456
, pp. 516-519
-
-
Stricker, J.1
Cookson, S.2
Bennett, M.R.3
Mather, W.H.4
Tsimring, L.S.5
Hasty, J.6
-
6
-
-
58249117722
-
A tunable synthetic mammalian oscillator
-
Tigges, M., Marquez-Lago, T. T., Stelling, J., and Fussenegger, M. (2009) A tunable synthetic mammalian oscillator Nature 457, 309 - 312
-
(2009)
Nature
, vol.457
, pp. 309-312
-
-
Tigges, M.1
Marquez-Lago, T.T.2
Stelling, J.3
Fussenegger, M.4
-
7
-
-
84868619337
-
Genetic programs constructed from layered logic gates in single cells
-
Moon, T. S., Lou, C., Tamsir, A., Stanton, B. C., and Voigt, C. A. (2012) Genetic programs constructed from layered logic gates in single cells Nature 491, 249 - 253
-
(2012)
Nature
, vol.491
, pp. 249-253
-
-
Moon, T.S.1
Lou, C.2
Tamsir, A.3
Stanton, B.C.4
Voigt, C.A.5
-
8
-
-
84863454666
-
Programmable single-cell mammalian biocomputers
-
Ausländer, S., Ausländer, D., Müller, M., Wieland, M., and Fussenegger, M. (2012) Programmable single-cell mammalian biocomputers Nature 487, 123 - 127
-
(2012)
Nature
, vol.487
, pp. 123-127
-
-
Ausländer, S.1
Ausländer, D.2
Müller, M.3
Wieland, M.4
Fussenegger, M.5
-
9
-
-
67549145283
-
A synthetic genetic edge detection program
-
Tabor, J. J., Salis, H. M., Simpson, Z. B., Chevalier, A. A., Levskaya, A., Marcotte, E. M., Voigt, C. A., and Ellington, A. D. (2009) A synthetic genetic edge detection program Cell 137, 1272 - 1281
-
(2009)
Cell
, vol.137
, pp. 1272-1281
-
-
Tabor, J.J.1
Salis, H.M.2
Simpson, Z.B.3
Chevalier, A.A.4
Levskaya, A.5
Marcotte, E.M.6
Voigt, C.A.7
Ellington, A.D.8
-
10
-
-
84897954571
-
Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals
-
Olson, E. J., Hartsough, L. A., Landry, B. P., Shroff, R., and Tabor, J. J. (2014) Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals Nat. Methods 10.1038/NMETH.2884
-
(2014)
Nat. Methods
-
-
Olson, E.J.1
Hartsough, L.A.2
Landry, B.P.3
Shroff, R.4
Tabor, J.J.5
-
11
-
-
17844374314
-
A synthetic multicellular system for programmed pattern formation
-
Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H., and Weiss, R. (2005) A synthetic multicellular system for programmed pattern formation Nature 434, 1130 - 1134
-
(2005)
Nature
, vol.434
, pp. 1130-1134
-
-
Basu, S.1
Gerchman, Y.2
Collins, C.H.3
Arnold, F.H.4
Weiss, R.5
-
12
-
-
84889685663
-
The centrality of RNA for engineering gene expression
-
Chappell, J., Takahashi, M. K., Meyer, S., Loughrey, D., Watters, K. E., and Lucks, J. (2013) The centrality of RNA for engineering gene expression Biotechnol. J. 8, 1379 - 1395
-
(2013)
Biotechnol. J.
, vol.8
, pp. 1379-1395
-
-
Chappell, J.1
Takahashi, M.K.2
Meyer, S.3
Loughrey, D.4
Watters, K.E.5
Lucks, J.6
-
13
-
-
0037863216
-
In vivo evolution of an RNA-based transcriptional activator
-
Buskirk, A. R., Kehayova, P. D., Landrigan, A., and Liu, D. R. (2003) In vivo evolution of an RNA-based transcriptional activator Chem. Biol. 10, 533 - 540
-
(2003)
Chem. Biol.
, vol.10
, pp. 533-540
-
-
Buskirk, A.R.1
Kehayova, P.D.2
Landrigan, A.3
Liu, D.R.4
-
14
-
-
3042741121
-
Engineered riboregulators enable post-transcriptional control of gene expression
-
Isaacs, F. J., Dwyer, D. J., Ding, C., Pervouchine, D. D., Cantor, C. R., and Collins, J. J. (2004) Engineered riboregulators enable post-transcriptional control of gene expression Nat. Biotechnol. 22, 841 - 847
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 841-847
-
-
Isaacs, F.J.1
Dwyer, D.J.2
Ding, C.3
Pervouchine, D.D.4
Cantor, C.R.5
Collins, J.J.6
-
15
-
-
21444457242
-
Programmable ligand-controlled riboregulators of eukaryotic gene expression
-
Bayer, T. S. and Smolke, C. D. (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression Nat. Biotechnol. 23, 337 - 343
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 337-343
-
-
Bayer, T.S.1
Smolke, C.D.2
-
16
-
-
35448990907
-
A modular and extensible RNA-based gene-regulatory platform for engineering cellular function
-
Win, M. N. and Smolke, C. D. (2007) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function Proc. Natl. Acad. Sci. U.S.A. 104, 14283 - 14288
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 14283-14288
-
-
Win, M.N.1
Smolke, C.D.2
-
17
-
-
34447310821
-
A universal RNAi-based logic evaluator that operates in mammalian cells
-
Rinaudo, K., Bleris, L., Maddamsetti, R., Subramanian, S., Weiss, R., and Benenson, Y. (2007) A universal RNAi-based logic evaluator that operates in mammalian cells Nat. Biotechnol. 25, 795 - 801
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 795-801
-
-
Rinaudo, K.1
Bleris, L.2
Maddamsetti, R.3
Subramanian, S.4
Weiss, R.5
Benenson, Y.6
-
18
-
-
0032981770
-
Library of synthetic 5′ secondary structures to manipulate mRNA stability in Escherichia coli
-
Carrier, T. A. and Keasling, J. D. (1999) Library of synthetic 5′ secondary structures to manipulate mRNA stability in Escherichia coli Biotechnol. Prog. 15, 58 - 64
-
(1999)
Biotechnol. Prog.
, vol.15
, pp. 58-64
-
-
Carrier, T.A.1
Keasling, J.D.2
-
19
-
-
79957700542
-
Versatile RNA-sensing transcriptional regulators for engineering genetic networks
-
Lucks, J. B., Qi, L., Mutalik, V. K., Wang, D., and Arkin, A. P. (2011) Versatile RNA-sensing transcriptional regulators for engineering genetic networks Proc. Natl. Acad. Sci. U.S.A. 108, 8617 - 8622
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 8617-8622
-
-
Lucks, J.B.1
Qi, L.2
Mutalik, V.K.3
Wang, D.4
Arkin, A.P.5
-
20
-
-
84863226500
-
Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals
-
Qi, L., Lucks, J. B., Liu, C. C., Mutalik, V. K., and Arkin, A. P. (2012) Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals Nucleic Acids Res. 40, 5775 - 5786
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5775-5786
-
-
Qi, L.1
Lucks, J.B.2
Liu, C.C.3
Mutalik, V.K.4
Arkin, A.P.5
-
21
-
-
79960571755
-
Multiplexed RNA Structure Characterization with Selective 2′-Hydroxyl Acylation Analyzed by Primer Extension Sequencing (SHAPE-Seq)
-
Lucks, J. B., Mortimer, S. A., Trapnell, C., Luo, S., Aviran, S., Schroth, G. P., Pachter, L., Doudna, J. A., and Arkin, A. P. (2011) Multiplexed RNA Structure Characterization with Selective 2′-Hydroxyl Acylation Analyzed by Primer Extension Sequencing (SHAPE-Seq) Proc. Natl. Acad. Sci. U.S.A. 108, 11063 - 11068
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 11063-11068
-
-
Lucks, J.B.1
Mortimer, S.A.2
Trapnell, C.3
Luo, S.4
Aviran, S.5
Schroth, G.P.6
Pachter, L.7
Doudna, J.A.8
Arkin, A.P.9
-
22
-
-
84859842558
-
Rationally designed families of orthogonal RNA regulators of translation
-
Mutalik, V. K., Qi, L., Guimaraes, J. C., Lucks, J. B., and Arkin, A. P. (2012) Rationally designed families of orthogonal RNA regulators of translation Nat. Chem. Biol. 8, 447 - 454
-
(2012)
Nat. Chem. Biol.
, vol.8
, pp. 447-454
-
-
Mutalik, V.K.1
Qi, L.2
Guimaraes, J.C.3
Lucks, J.B.4
Arkin, A.P.5
-
23
-
-
84869097100
-
An adaptor from translational to transcriptional control enables predictable assembly of complex regulation
-
Liu, C. C., Qi, L., Lucks, J. B., Segall-Shapiro, T. H., Wang, D., Mutalik, V. K., and Arkin, A. P. (2012) An adaptor from translational to transcriptional control enables predictable assembly of complex regulation Nat. Methods 9, 1088 - 1094
-
(2012)
Nat. Methods
, vol.9
, pp. 1088-1094
-
-
Liu, C.C.1
Qi, L.2
Lucks, J.B.3
Segall-Shapiro, T.H.4
Wang, D.5
Mutalik, V.K.6
Arkin, A.P.7
-
24
-
-
84883467214
-
A modular strategy for engineering orthogonal chimeric RNA transcription regulators
-
Takahashi, M. K. and Lucks, J. B. (2013) A modular strategy for engineering orthogonal chimeric RNA transcription regulators Nucleic Acids Res. 41, 7577 - 7588
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 7577-7588
-
-
Takahashi, M.K.1
Lucks, J.B.2
-
25
-
-
80052456127
-
Multi-input RNAi-based logic circuit for identification of specific cancer cells
-
Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R., and Benenson, Y. (2011) Multi-input RNAi-based logic circuit for identification of specific cancer cells Science 333, 1307 - 1311
-
(2011)
Science
, vol.333
, pp. 1307-1311
-
-
Xie, Z.1
Wroblewska, L.2
Prochazka, L.3
Weiss, R.4
Benenson, Y.5
-
26
-
-
84874687019
-
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
-
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., and Lim, W. A. (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression Cell 152, 1173 - 1183
-
(2013)
Cell
, vol.152
, pp. 1173-1183
-
-
Qi, L.S.1
Larson, M.H.2
Gilbert, L.A.3
Doudna, J.A.4
Weissman, J.S.5
Arkin, A.P.6
Lim, W.A.7
-
27
-
-
0038392724
-
Response delays and the structure of transcription networks
-
Rosenfeld, N. and Alon, U. (2003) Response delays and the structure of transcription networks J. Mol. Biol. 329, 645 - 654
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 645-654
-
-
Rosenfeld, N.1
Alon, U.2
-
28
-
-
84886838580
-
Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology
-
Sun, Z. Z., Hayes, C. A., Shin, J., Caschera, F., Murray, R. M., and Noireaux, V. (2013) Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology J. Visualiz. Exp. 79, e50762
-
(2013)
J. Visualiz. Exp.
, vol.79
, pp. 50762
-
-
Sun, Z.Z.1
Hayes, C.A.2
Shin, J.3
Caschera, F.4
Murray, R.M.5
Noireaux, V.6
-
29
-
-
84863610029
-
An E. coli cell-free expression toolbox: Application to synthetic gene circuits and artificial cells
-
Shin, J. and Noireaux, V. (2012) An E. coli cell-free expression toolbox: Application to synthetic gene circuits and artificial cells ACS Synth. Biol. 1, 29 - 41
-
(2012)
ACS Synth. Biol.
, vol.1
, pp. 29-41
-
-
Shin, J.1
Noireaux, V.2
-
30
-
-
84860375823
-
Expression optimization and synthetic gene networks in cell-free systems
-
Karig, D. K., Iyer, S., Simpson, M. L., and Doktycz, M. J. (2012) Expression optimization and synthetic gene networks in cell-free systems Nucleic Acids Res. 40, 3763 - 3774
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 3763-3774
-
-
Karig, D.K.1
Iyer, S.2
Simpson, M.L.3
Doktycz, M.J.4
-
31
-
-
84885056795
-
Implementation of cell-free biological networks at steady state
-
Niederholtmeyer, H., Stepanova, V., and Maerkl, S. J. (2013) Implementation of cell-free biological networks at steady state Proc. Natl. Acad. Sci. U.S.A. 110, 15985 - 15990
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 15985-15990
-
-
Niederholtmeyer, H.1
Stepanova, V.2
Maerkl, S.J.3
-
32
-
-
83255164998
-
Cell-free synthetic biology: Thinking outside the cell
-
Hodgman, C. E. and Jewett, M. C. (2012) Cell-free synthetic biology: Thinking outside the cell Metab. Eng. 14, 261 - 269
-
(2012)
Metab. Eng.
, vol.14
, pp. 261-269
-
-
Hodgman, C.E.1
Jewett, M.C.2
-
33
-
-
84876382897
-
Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology
-
Chappell, J., Jensen, K., and Freemont, P. S. (2013) Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology Nucleic Acids Res. 41, 3471 - 3481
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 3471-3481
-
-
Chappell, J.1
Jensen, K.2
Freemont, P.S.3
-
34
-
-
0242268453
-
Principles of cell-free genetic circuit assembly
-
Noireaux, V., Bar-Ziv, R., and Libchaber, A. (2003) Principles of cell-free genetic circuit assembly Proc. Natl. Acad. Sci. U.S.A. 100, 12672 - 12677
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 12672-12677
-
-
Noireaux, V.1
Bar-Ziv, R.2
Libchaber, A.3
-
35
-
-
0034904102
-
Cell-free translation reconstituted with purified components
-
Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., and Ueda, T. (2001) Cell-free translation reconstituted with purified components Nat. Biotechnol. 19, 751 - 755
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 751-755
-
-
Shimizu, Y.1
Inoue, A.2
Tomari, Y.3
Suzuki, T.4
Yokogawa, T.5
Nishikawa, K.6
Ueda, T.7
-
36
-
-
84899918637
-
Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system
-
Sun, Z. Z., Yeung, E., Hayes, C. A., Noireaux, V., and Murray, R. M. (2013) Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system ACS Synth. Biol. 10.1021/sb400131a
-
(2013)
ACS Synth. Biol.
-
-
Sun, Z.Z.1
Yeung, E.2
Hayes, C.A.3
Noireaux, V.4
Murray, R.M.5
-
37
-
-
78649788244
-
Efficient cell-free expression with the endogenous E. coli RNA polymerase and sigma factor 70
-
Shin, J. and Noireaux, V. (2010) Efficient cell-free expression with the endogenous E. coli RNA polymerase and sigma factor 70 J. Biol. Eng. 4, 8
-
(2010)
J. Biol. Eng.
, vol.4
, pp. 8
-
-
Shin, J.1
Noireaux, V.2
-
38
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr, S. S., Milo, R., Mangan, S., and Alon, U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli Nat. Genet. 31, 64 - 68
-
(2002)
Nat. Genet.
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
39
-
-
0024473736
-
PT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator
-
Novick, R. P., Iordanescu, S., Projan, S. J., Kornblum, J., and Edelman, I. (1989) pT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator Cell 59, 395 - 404
-
(1989)
Cell
, vol.59
, pp. 395-404
-
-
Novick, R.P.1
Iordanescu, S.2
Projan, S.J.3
Kornblum, J.4
Edelman, I.5
-
40
-
-
0034021323
-
Antisense RNA-mediated transcriptional attenuation: An in vitro study of plasmid pT181
-
Brantl, S. and Wagner, E. G. (2000) Antisense RNA-mediated transcriptional attenuation: An in vitro study of plasmid pT181 Mol. Microbiol. 35, 1469 - 1482
-
(2000)
Mol. Microbiol.
, vol.35
, pp. 1469-1482
-
-
Brantl, S.1
Wagner, E.G.2
-
41
-
-
0033033283
-
Laser-mediated, site-specific inactivation of RNA transcripts
-
Grate, D. and Wilson, C. (1999) Laser-mediated, site-specific inactivation of RNA transcripts Proc. Natl. Acad. Sci. U.S.A. 96, 6131 - 6136
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 6131-6136
-
-
Grate, D.1
Wilson, C.2
-
42
-
-
84929602483
-
Resource usage and gene circuit performance characterization in a cell-free breadboard
-
Siegal-Gaskins, D., Tuza, Z. A., Kim, J., Noireaux, V., and Murray, R. M. (2013) Resource usage and gene circuit performance characterization in a cell-free breadboard bioRxiv 10.1101/000885
-
(2013)
BioRxiv
-
-
Siegal-Gaskins, D.1
Tuza, Z.A.2
Kim, J.3
Noireaux, V.4
Murray, R.M.5
-
43
-
-
0036233405
-
An antisense RNA-mediated transcriptional attenuation mechanism functions in Escherichia coli
-
Brantl, S. and Wagner, E. G. H. (2002) An antisense RNA-mediated transcriptional attenuation mechanism functions in Escherichia coli J. Bacteriol. 184, 2740 - 2747
-
(2002)
J. Bacteriol.
, vol.184
, pp. 2740-2747
-
-
Brantl, S.1
Wagner, E.G.H.2
-
44
-
-
30544433196
-
Engineering and characterization of a superfolder green fluorescent protein
-
Pédelacq, J.-D., Cabantous, S., Tran, T., Terwilliger, T. C., and Waldo, G. S. (2006) Engineering and characterization of a superfolder green fluorescent protein Nat. Biotechnol. 24, 79 - 88
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 79-88
-
-
Pédelacq, J.-D.1
Cabantous, S.2
Tran, T.3
Terwilliger, T.C.4
Waldo, G.S.5
-
45
-
-
35548995356
-
The RNA degradosome of Escherichia coli: An mRNA-degrading machine assembled on RNase e
-
Carpousis, A. J. (2007) The RNA degradosome of Escherichia coli: An mRNA-degrading machine assembled on RNase E Annu. Rev. Microbiol. 61, 71 - 87
-
(2007)
Annu. Rev. Microbiol.
, vol.61
, pp. 71-87
-
-
Carpousis, A.J.1
-
46
-
-
14844358192
-
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
-
Hooshangi, S., Thiberge, S., and Weiss, R. (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade Proc. Natl. Acad. Sci. U.S.A. 102, 3581 - 3586
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 3581-3586
-
-
Hooshangi, S.1
Thiberge, S.2
Weiss, R.3
-
47
-
-
0037062424
-
A monomeric red fluorescent protein
-
Campbell, R. E., Tour, O., Palmer, A. E., Steinbach, P. A., Baird, G. S., Zacharias, D. A., and Tsien, R. Y. (2002) A monomeric red fluorescent protein Proc. Natl. Acad. Sci. U.S.A. 99, 7877 - 7882
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 7877-7882
-
-
Campbell, R.E.1
Tour, O.2
Palmer, A.E.3
Steinbach, P.A.4
Baird, G.S.5
Zacharias, D.A.6
Tsien, R.Y.7
-
48
-
-
2442526837
-
Just-in-time transcription program in metabolic pathways
-
Zaslaver, A., Mayo, A. E., Rosenberg, R., Bashkin, P., Sberro, H., Tsalyuk, M., Surette, M. G., and Alon, U. (2004) Just-in-time transcription program in metabolic pathways Nat. Genet. 36, 486 - 491
-
(2004)
Nat. Genet.
, vol.36
, pp. 486-491
-
-
Zaslaver, A.1
Mayo, A.E.2
Rosenberg, R.3
Bashkin, P.4
Sberro, H.5
Tsalyuk, M.6
Surette, M.G.7
Alon, U.8
-
49
-
-
56649114274
-
A one pot, one step, precision cloning method with high throughput capability
-
Engler, C., Kandzia, R., and Marillonnet, S. (2008) A one pot, one step, precision cloning method with high throughput capability PLoS One 3, e3647
-
(2008)
PLoS One
, vol.3
, pp. 3647
-
-
Engler, C.1
Kandzia, R.2
Marillonnet, S.3
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