-
1
-
-
34548825690
-
Towards a theory of biological robustness
-
Kitano H, (2007) Towards a theory of biological robustness. Mol Syst Biol 3: 137.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 137
-
-
Kitano, H.1
-
2
-
-
1542619848
-
Cancer as a robust system: implications for anticancer therapy
-
Kitano H, (2004) Cancer as a robust system: implications for anticancer therapy. Nat Rev Cancer 4: 227-235.
-
(2004)
Nat Rev Cancer
, vol.4
, pp. 227-235
-
-
Kitano, H.1
-
3
-
-
0033552946
-
Robustness in bacterial chemotaxis
-
Alon U, Surette MG, Barkai N, Leibler S, (1999) Robustness in bacterial chemotaxis. Nature 397: 168-171.
-
(1999)
Nature
, vol.397
, pp. 168-171
-
-
Alon, U.1
Surette, M.G.2
Barkai, N.3
Leibler, S.4
-
4
-
-
33745470929
-
Robustness trade-offs and host-microbial symbiosis in the immune system
-
2006.0022
-
Kitano H, Oda K, (2006) Robustness trade-offs and host-microbial symbiosis in the immune system. Mol Syst Biol 2: 2006.0022.
-
(2006)
Mol Syst Biol
, vol.2
-
-
Kitano, H.1
Oda, K.2
-
5
-
-
60749109846
-
Cell cycle, CDKs and cancer: a changing paradigm
-
Malumbres M, Barbacid M, (2009) Cell cycle, CDKs and cancer: a changing paradigm. Nature Reviews in Cancer 9: 153-166.
-
(2009)
Nature Reviews in Cancer
, vol.9
, pp. 153-166
-
-
Malumbres, M.1
Barbacid, M.2
-
6
-
-
78049380554
-
The patterns and dynamics of genomic instability in metastatic pancreatic cancer
-
Campbell PJ, Yachida S, Mudie LJ, Stephens PJ, Pleasance ED, et al. (2010) The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467: 1109-1113.
-
(2010)
Nature
, vol.467
, pp. 1109-1113
-
-
Campbell, P.J.1
Yachida, S.2
Mudie, L.J.3
Stephens, P.J.4
Pleasance, E.D.5
-
7
-
-
0029849620
-
Cancer cell cycles
-
Sherr CJ, (1996) Cancer cell cycles. Science 274: 1672-1677.
-
(1996)
Science
, vol.274
, pp. 1672-1677
-
-
Sherr, C.J.1
-
8
-
-
1842687878
-
The yeast cell-cycle network is robustly designed
-
Li FT, Long T, Lu Y, Ouyang Q, Tang C, (2004) The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci U S A 101: 4781-4786.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 4781-4786
-
-
Li, F.T.1
Long, T.2
Lu, Y.3
Ouyang, Q.4
Tang, C.5
-
9
-
-
45849093636
-
Boolean network model predicts cell cycle sequence of fission yeast
-
Davidich M, Bornholdt S, (2008) Boolean network model predicts cell cycle sequence of fission yeast. PLoS ONE 3: e1672.
-
(2008)
PLoS ONE
, vol.3
-
-
Davidich, M.1
Bornholdt, S.2
-
10
-
-
33747874092
-
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
-
Faure A, Naldi A, Chaouiya C, Thieffry D, (2006) Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22(14): e124-e131.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Faure, A.1
Naldi, A.2
Chaouiya, C.3
Thieffry, D.4
-
11
-
-
77953783859
-
Process-based network decomposition reveals backbone motif structure
-
Wang G, Du C, Simha R, Rong Y, Xiao Y, et al. (2010) Process-based network decomposition reveals backbone motif structure. Proc Natl Acad Sci U S A 107: 10478-10483.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 10478-10483
-
-
Wang, G.1
Du, C.2
Simha, R.3
Rong, Y.4
Xiao, Y.5
-
13
-
-
3042767202
-
MicroRNAs: small RNAs with a big role in gene regulation
-
He L, Hannon GJ, (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5: 522-531.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 522-531
-
-
He, L.1
Hannon, G.J.2
-
14
-
-
33144490646
-
A microRNA expression signature of human solid tumors defines cancer gene targets
-
Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, et al. (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103: 2257-2261.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 2257-2261
-
-
Volinia, S.1
Calin, G.A.2
Liu, C.G.3
Ambs, S.4
Cimmino, A.5
-
15
-
-
51549115859
-
The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition
-
Cloonan N, Brown MK, Steptoe AL, Wani S, Chan WL, et al. (2008) The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition. Genome Biology 9: R127.
-
(2008)
Genome Biology
, vol.9
-
-
Cloonan, N.1
Brown, M.K.2
Steptoe, A.L.3
Wani, S.4
Chan, W.L.5
-
16
-
-
33750376591
-
Mir-17-5p Regulates Breast Cancer Cell Proliferation by Inhibiting Translation of AIB1 mRNA
-
Hossain A, Kuo MT, Saunders GF, (2006) Mir-17-5p Regulates Breast Cancer Cell Proliferation by Inhibiting Translation of AIB1 mRNA. Molecular and Cellular Biology 26: 8191-8201.
-
(2006)
Molecular and Cellular Biology
, vol.26
, pp. 8191-8201
-
-
Hossain, A.1
Kuo, M.T.2
Saunders, G.F.3
-
17
-
-
0036467506
-
Regulation of G1 cell-cycle progression by oncogenes and tumor suppressor genes
-
Ho A, Dowdy SF, (2002) Regulation of G1 cell-cycle progression by oncogenes and tumor suppressor genes. Curr Opin Genet Dev 12: 47C52.
-
(2002)
Curr Opin Genet Dev
, vol.12
-
-
Ho, A.1
Dowdy, S.F.2
-
18
-
-
81555202890
-
Cell Cycle Control by Oncogenes and Tumor Suppressors: Driving the Transformation of Normal Cells into Cancerous Cells
-
Chow AY, (2010) Cell Cycle Control by Oncogenes and Tumor Suppressors: Driving the Transformation of Normal Cells into Cancerous Cells. Nature Education 3: 7.
-
(2010)
Nature Education
, vol.3
, pp. 7
-
-
Chow, A.Y.1
-
19
-
-
58149382580
-
MicroRNA regulation of a cancer network: consequences of the feedback loops involving miR-17-92, E2F, and Myc
-
Aguda BD, Kim Y, Piper-Hunter MG, Friedman A, Marsh CB, (2008) MicroRNA regulation of a cancer network: consequences of the feedback loops involving miR-17-92, E2F, and Myc. Proc Natl Acad Sci U S A 105: 19678-19683.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 19678-19683
-
-
Aguda, B.D.1
Kim, Y.2
Piper-Hunter, M.G.3
Friedman, A.4
Marsh, C.B.5
-
20
-
-
0033453231
-
The kinetic origins of the restriction point in the mammalian cell cycle
-
Aguda BD, Tang Y, (1999) The kinetic origins of the restriction point in the mammalian cell cycle. Cell Prolif 32: 321-335.
-
(1999)
Cell Prolif
, vol.32
, pp. 321-335
-
-
Aguda, B.D.1
Tang, Y.2
-
21
-
-
3042778898
-
A structural analysis of the qualitative networks regulating the cell cycle and apoptosis
-
Aguda BD, Algar CK, (2003) A structural analysis of the qualitative networks regulating the cell cycle and apoptosis. Cell Cycle 2: 538-544.
-
(2003)
Cell Cycle
, vol.2
, pp. 538-544
-
-
Aguda, B.D.1
Algar, C.K.2
-
22
-
-
34548381748
-
"Myc'ed messages': myc induces transcription of E2F1 while inhibiting its translation via a microRNA polycistron
-
Coller HA, Forman JJ, Legesse-Miller A, (2007) "Myc'ed messages': myc induces transcription of E2F1 while inhibiting its translation via a microRNA polycistron. PLoS Genet 3: e146.
-
(2007)
PLoS Genet
, vol.3
-
-
Coller, H.A.1
Forman, J.J.2
Legesse-Miller, A.3
-
23
-
-
34249892465
-
Do scale-free regulatory networks allow more expression than random ones?
-
Fortuna MA, Melián CJ, (2007) Do scale-free regulatory networks allow more expression than random ones? J Theor Biol 247: 331-336.
-
(2007)
J Theor Biol
, vol.247
, pp. 331-336
-
-
Fortuna, M.A.1
Melián, C.J.2
-
25
-
-
74549172058
-
ON/OFF and Beyond - A Boolean Model of Apoptosis
-
Schlatter R, Schmich K, Avalos Vizcarra I, Scheurich P, Sauter T, et al. (2009) ON/OFF and Beyond- A Boolean Model of Apoptosis. PLoS Comput Biol 5: e1000595.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Schlatter, R.1
Schmich, K.2
Avalos Vizcarra, I.3
Scheurich, P.4
Sauter, T.5
-
26
-
-
58149328931
-
miR-17 and miR-20a temper an E2F1-induced G1 checkpoint to regulate cell cycle progression
-
Pickering MT, Stadler BM, Kowalik TF, (2009) miR-17 and miR-20a temper an E2F1-induced G1 checkpoint to regulate cell cycle progression. Oncogene 28: 140-145.
-
(2009)
Oncogene
, vol.28
, pp. 140-145
-
-
Pickering, M.T.1
Stadler, B.M.2
Kowalik, T.F.3
-
27
-
-
0034014307
-
Involvement of Myc activity in a G1/S-promoting mechanism parallel to the pRb/E2F pathway
-
Santoni-Rugiu E, Falck J, Mailand N, Bartek J, Lukas J, (2000) Involvement of Myc activity in a G1/S-promoting mechanism parallel to the pRb/E2F pathway. Mol Cell Biol 20: 3497-3509.
-
(2000)
Mol Cell Biol
, vol.20
, pp. 3497-3509
-
-
Santoni-Rugiu, E.1
Falck, J.2
Mailand, N.3
Bartek, J.4
Lukas, J.5
-
28
-
-
0026099022
-
The MYC protein activates transcription of the α-prothymosin gene
-
Eilers M, Schirm S, Bishop JM, (1991) The MYC protein activates transcription of the α-prothymosin gene. EMBO J 10: 133-141.
-
(1991)
EMBO J
, vol.10
, pp. 133-141
-
-
Eilers, M.1
Schirm, S.2
Bishop, J.M.3
-
29
-
-
0028930840
-
An E-Box-Mediated Increase in cad Transcription at the G1/S-Phase Boundary Is Suppressed by Inhibitory c-Myc Mutants
-
Miltenberger RJ, Sukow KA, Farnham PJ, (1995) An E-Box-Mediated Increase in cad Transcription at the G1/S-Phase Boundary Is Suppressed by Inhibitory c-Myc Mutants. Mol Cell Biol 15: 2527-2535.
-
(1995)
Mol Cell Biol
, vol.15
, pp. 2527-2535
-
-
Miltenberger, R.J.1
Sukow, K.A.2
Farnham, P.J.3
-
30
-
-
0033214080
-
Direct induction of cyclin D2 by Myc contributes to cell cycle induction and sequestration of p27
-
Bouchard C, Thieke K, Maier A, Saffrich R, Hanley-Hyde J, et al. (1999) Direct induction of cyclin D2 by Myc contributes to cell cycle induction and sequestration of p27. EMBO J 18: 5321-5333.
-
(1999)
EMBO J
, vol.18
, pp. 5321-5333
-
-
Bouchard, C.1
Thieke, K.2
Maier, A.3
Saffrich, R.4
Hanley-Hyde, J.5
-
31
-
-
0026701339
-
Cyclin E/Cdk2 and cyclin A/CDK2 kinases associate with p107 and E2F in a temporally distinct manner
-
Lees E, Faha B, Dulic V, Reed SI, Harlow E, (1992) Cyclin E/Cdk2 and cyclin A/CDK2 kinases associate with p107 and E2F in a temporally distinct manner. Genes Dev 6: 1874-1885.
-
(1992)
Genes Dev
, vol.6
, pp. 1874-1885
-
-
Lees, E.1
Faha, B.2
Dulic, V.3
Reed, S.I.4
Harlow, E.5
-
32
-
-
0029009876
-
Different Roles for Cyclins D1 and E in Regulation of the G1-to-S Transition
-
Resnitzky D, Reed SI, (1995) Different Roles for Cyclins D1 and E in Regulation of the G1-to-S Transition. Mol Cell Biol 15: 3463-3469.
-
(1995)
Mol Cell Biol
, vol.15
, pp. 3463-3469
-
-
Resnitzky, D.1
Reed, S.I.2
-
33
-
-
0032568043
-
Functional capabilities of molecular network components controlling the mammalian G1/S cell cycle phase transition
-
Kohn KW, (1998) Functional capabilities of molecular network components controlling the mammalian G1/S cell cycle phase transition. Oncogene 16: 1065-1075.
-
(1998)
Oncogene
, vol.16
, pp. 1065-1075
-
-
Kohn, K.W.1
-
34
-
-
0344931628
-
CDC25A phosphatase is a target of E2F and is required for efficient E2F-induced S phase
-
Vigo E, Muller H, Prosperini E, Hateboer G, Cartwright P, et al. (1999) CDC25A phosphatase is a target of E2F and is required for efficient E2F-induced S phase. Mol Cell Biol 19: 6379-6395.
-
(1999)
Mol Cell Biol
, vol.19
, pp. 6379-6395
-
-
Vigo, E.1
Muller, H.2
Prosperini, E.3
Hateboer, G.4
Cartwright, P.5
-
35
-
-
0036613246
-
Suppression of the p53- or pRBmediated G1 checkpoint is required for E2F-induced S-phase entry
-
Lomazzi M, Moroni MC, Jensen MR, Frittoli E, Helin K, (2002) Suppression of the p53- or pRBmediated G1 checkpoint is required for E2F-induced S-phase entry. Nature Genetics 31: 190-194.
-
(2002)
Nature Genetics
, vol.31
, pp. 190-194
-
-
Lomazzi, M.1
Moroni, M.C.2
Jensen, M.R.3
Frittoli, E.4
Helin, K.5
-
36
-
-
0037325853
-
Deregulated degradation of the cdk inhibitor p27 and malignant transformation
-
Bloom J, Pagano M, (2003) Deregulated degradation of the cdk inhibitor p27 and malignant transformation. Semin Cancer Biol 13: 41-47.
-
(2003)
Semin Cancer Biol
, vol.13
, pp. 41-47
-
-
Bloom, J.1
Pagano, M.2
-
37
-
-
0029024015
-
Role of the ubiquitin-proteasome pathway in regulating abundance of the cyclin dependent kinase inhibitor p27
-
Pagano M, Tam SW, Theodoras AM, Beer-Romero P, Del Sal G, et al. (1995) Role of the ubiquitin-proteasome pathway in regulating abundance of the cyclin dependent kinase inhibitor p27. Science 269: 682-685.
-
(1995)
Science
, vol.269
, pp. 682-685
-
-
Pagano, M.1
Tam, S.W.2
Theodoras, A.M.3
Beer-Romero, P.4
Del Sal, G.5
-
38
-
-
0031008465
-
Cyclin E-induced S phase without activation of the pRb/E2F pathway
-
Lukas J, Herzinger T, Hansen K, Moroni MC, Resnitzky D, et al. (1997) Cyclin E-induced S phase without activation of the pRb/E2F pathway. Genes Dev 11: 1479-1492.
-
(1997)
Genes Dev
, vol.11
, pp. 1479-1492
-
-
Lukas, J.1
Herzinger, T.2
Hansen, K.3
Moroni, M.C.4
Resnitzky, D.5
-
39
-
-
0032766844
-
Ectopic Expression of Cdc25A Accelerates the G1/S Transition and Leads to Premature Activation of Cyclin E- and Cyclin A-Dependent Kinases
-
Blomberg I, Hoffmann I, (1999) Ectopic Expression of Cdc25A Accelerates the G1/S Transition and Leads to Premature Activation of Cyclin E- and Cyclin A-Dependent Kinases. Mol Cell Biol. 19: 6183-6194.
-
(1999)
Mol Cell Biol
, vol.19
, pp. 6183-6194
-
-
Blomberg, I.1
Hoffmann, I.2
-
41
-
-
84864957848
-
Finding a periodic attractor of a Boolean network
-
Akutsu T, Kosub S, Melkman AA, Tamura T, (2012) Finding a periodic attractor of a Boolean network. IEEE/ACM Trans Comput Biol Bioinform 9: 1410-1421.
-
(2012)
IEEE/ACM Trans Comput Biol Bioinform
, vol.9
, pp. 1410-1421
-
-
Akutsu, T.1
Kosub, S.2
Melkman, A.A.3
Tamura, T.4
-
42
-
-
80053121012
-
Determining a singleton attractor of a boolean network with nested canalyzing functions
-
Akutsu T, Melkman AA, Tamura T, Yamamoto M, (2011) Determining a singleton attractor of a boolean network with nested canalyzing functions. J Comput Biol 18: 1275-1290.
-
(2011)
J Comput Biol
, vol.18
, pp. 1275-1290
-
-
Akutsu, T.1
Melkman, A.A.2
Tamura, T.3
Yamamoto, M.4
-
43
-
-
34250800265
-
Algorithms for finding small attractors in Boolean networks
-
Zhang SQ, Hayashida M, Akutsu T, Ching WK, Ng MK, (2007) Algorithms for finding small attractors in Boolean networks. EURASIP J Bioinform Syst Biol 2: 20180.
-
(2007)
EURASIP J Bioinform Syst Biol
, vol.2
, pp. 20180
-
-
Zhang, S.Q.1
Hayashida, M.2
Akutsu, T.3
Ching, W.K.4
Ng, M.K.5
-
44
-
-
34147102223
-
Basin entropy in Boolean network ensembles
-
Krawitz P, Shmulevich I, (2007) Basin entropy in Boolean network ensembles. Phys Rev Lett 98: 158701.
-
(2007)
Phys Rev Lett
, vol.98
, pp. 158701
-
-
Krawitz, P.1
Shmulevich, I.2
-
45
-
-
84869799148
-
Attractor Landscape Analysis Reveals Feedback Loops in the p53 Network That Control the Cellular Response to DNA Damage
-
Choi M, Shi J, Jung SH, Chen X, Cho K-H, (2012) Attractor Landscape Analysis Reveals Feedback Loops in the p53 Network That Control the Cellular Response to DNA Damage. Sci Signal 5: ra83.
-
(2012)
Sci Signal
, vol.5
-
-
Choi, M.1
Shi, J.2
Jung, S.H.3
Chen, X.4
Cho, K.-H.5
-
46
-
-
84860450630
-
Identifying targets for intervention by analyzing basins of attraction
-
Verdicchio MP, Kim S (2011) Identifying targets for intervention by analyzing basins of attraction. Pac Symp Biocomput 350-361.
-
(2011)
Pac Symp Biocomput
, pp. 350-361
-
-
Verdicchio, M.P.1
Kim, S.2
-
47
-
-
84867010562
-
Escherichia coli noncoding RNAs can affect gene expression and physiology of Caenorhabditis elegans
-
Liu H, Wang X, Wang HD, Wu J, Ren J, et al. (2012) Escherichia coli noncoding RNAs can affect gene expression and physiology of Caenorhabditis elegans. Nature Communications 25: 1073.
-
(2012)
Nature Communications
, vol.25
, pp. 1073
-
-
Liu, H.1
Wang, X.2
Wang, H.D.3
Wu, J.4
Ren, J.5
-
48
-
-
84864475934
-
Signals from noncoding RNAs: Unconventional roles for conventional pol III transcripts
-
Hu S, Wu J, Chen L, Shan G, (2012) Signals from noncoding RNAs: Unconventional roles for conventional pol III transcripts. Int J Biochem Cell Biol 44: 1847-1851.
-
(2012)
Int J Biochem Cell Biol
, vol.44
, pp. 1847-1851
-
-
Hu, S.1
Wu, J.2
Chen, L.3
Shan, G.4
-
49
-
-
84863236972
-
Noncoding RNAs: different roles in tumorigenesis
-
LIN M, WU J, SHAN G, (2012) Noncoding RNAs: different roles in tumorigenesis. Chinese Science Bulletin 57: 959-965.
-
(2012)
Chinese Science Bulletin
, vol.57
, pp. 959-965
-
-
Lin, M.1
Wu, J.2
Shan, G.3
-
50
-
-
84857691987
-
Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis
-
Gong J, Tong Y, Zhang HM, Wang K, Hu T, et al. (2012) Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis. Hum Mutat 33: 254C263.
-
(2012)
Hum Mutat
, vol.33
-
-
Gong, J.1
Tong, Y.2
Zhang, H.M.3
Wang, K.4
Hu, T.5
-
51
-
-
77954386712
-
RNA interference as a gene knockdown technique
-
Shan G, (2010) RNA interference as a gene knockdown technique. Int J Biochem Cell Biol 42: 1243C1251.
-
(2010)
Int J Biochem Cell Biol
, vol.42
-
-
Shan, G.1
-
52
-
-
84861889741
-
Evaluation of attractors and basins of asynchronous random Boolean networks
-
Yang M, Chu T, (2012) Evaluation of attractors and basins of asynchronous random Boolean networks. Phys Rev E 85: 056105.
-
(2012)
Phys Rev E
, vol.85
, pp. 056105
-
-
Yang, M.1
Chu, T.2
-
53
-
-
77955496931
-
Attractor analysis of asynchronous Boolean models of signal transduction networks
-
Saadatpour A, Albert I, Albert R, (2010) Attractor analysis of asynchronous Boolean models of signal transduction networks. J Theor Biol 266: 641-656.
-
(2010)
J Theor Biol
, vol.266
, pp. 641-656
-
-
Saadatpour, A.1
Albert, I.2
Albert, R.3
-
54
-
-
33947361606
-
Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity
-
Braunewell S, Bornholdt S, (2007) Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity. J Theor Biol 245(4): 638C643.
-
(2007)
J Theor Biol
, vol.245
, Issue.4
-
-
Braunewell, S.1
Bornholdt, S.2
-
55
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382.
-
(2007)
Nat Protoc
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
Kuchinsky, A.4
Landys, N.5
-
56
-
-
79551587720
-
Cytoscape 2.8: new features for data integration and network visualization
-
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T, (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
-
(2011)
Bioinformatics
, vol.27
, pp. 431-432
-
-
Smoot, M.E.1
Ono, K.2
Ruscheinski, J.3
Wang, P.L.4
Ideker, T.5
-
57
-
-
0002226683
-
Pajek C A program for large network analysis
-
Batagelj V, Mrvar A, (1998) Pajek C A program for large network analysis. Connections 21: 47-57.
-
(1998)
Connections
, vol.21
, pp. 47-57
-
-
Batagelj, V.1
Mrvar, A.2
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