-
1
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR 2010. A method and server for predicting damaging missense mutations. Nat Methods. 7:248-249.
-
(2010)
Nat Methods.
, vol.7
, pp. 248-249
-
-
Adzhubei, I.A.1
Schmidt, S.2
Peshkin, L.3
Ramensky, V.E.4
Gerasimova, A.5
Bork, P.6
Kondrashov, A.S.7
Sunyaev, S.R.8
-
2
-
-
38149063370
-
Selection on domestication traits and quantitative trait loci in crop-wild sunflower hybrids
-
Baack EJ, Sapir Y, Chapman MA Burke JM, Rieseberg LH. 2008. Selection on domestication traits and quantitative trait loci in crop-wild sunflower hybrids. Mol Ecol. 17:666-677.
-
(2008)
Mol Ecol.
, vol.17
, pp. 666-677
-
-
Baack, E.J.1
Sapir, Y.2
Ma, C.3
Burke, J.M.4
Rieseberg, L.H.5
-
3
-
-
54149092976
-
Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years
-
Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW, Knapp SJ, Rieseberg LH. 2008. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol Biol Evol. 25:2445-2455.
-
(2008)
Mol Biol Evol.
, vol.25
, pp. 2445-2455
-
-
Barker, M.S.1
Kane, N.C.2
Matvienko, M.3
Kozik, A.4
Michelmore, R.W.5
Knapp, S.J.6
Rieseberg, L.H.7
-
4
-
-
84925278690
-
Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives
-
Baute GJ, Kane NC, Grassa CJ, Lai Z, Rieseberg LH. 2015. Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives. New Phytol. 206:830-838.
-
(2015)
New Phytol.
, vol.206
, pp. 830-838
-
-
Baute, G.J.1
Kane, N.C.2
Grassa, C.J.3
Lai, Z.4
Rieseberg, L.H.5
-
5
-
-
80052184682
-
Sunflower domestication alleles support single domestication center in eastern North America
-
Blackman BK, Scascitelli M, Kane NC, Luton HH, Rasmussen DA Bye RA Lentz DL, Rieseberg LH. 2011. Sunflower domestication alleles support single domestication center in eastern North America. Proc Natl Acad Sci USA. 108:14360-14365.
-
(2011)
Proc Natl Acad Sci USA.
, vol.108
, pp. 14360-14365
-
-
Blackman, B.K.1
Scascitelli, M.2
Kane, N.C.3
Luton, H.H.4
Rasmussen, D.A.5
Bye, R.A.6
Lentz, D.L.7
Rieseberg, L.H.8
-
8
-
-
84867301515
-
Predicting the functional effect of amino acid substitutions and indels
-
Choi Y, Sims GE, Murphy S, Miller JR Chan AP. 2012. Predicting the functional effect of amino acid substitutions and indels. PLoS One 7:e46688.
-
(2012)
PLoS One
, vol.7
, pp. e46688
-
-
Choi, Y.1
Sims, G.E.2
Murphy, S.3
Miller, J.R.4
Chan, A.P.5
-
9
-
-
54149110152
-
The legacy of domestication: Accumulation of deleterious mutations in the dog genome
-
Cruz F, Vila C, Webster MT. 2008. The legacy of domestication: accumulation of deleterious mutations in the dog genome. Mol Biol Evol. 25:2331-2336.
-
(2008)
Mol Biol Evol.
, vol.25
, pp. 2331-2336
-
-
Cruz, F.1
Vila, C.2
Webster, M.T.3
-
10
-
-
57749119798
-
Crop domestication in the Compositae: A family-wide trait assessment
-
Dempewolf H, Rieseberg LH, Cronk QC 2008. Crop domestication in the Compositae: a family-wide trait assessment. Genet Resour Crop Evol. 55:1141-1157.
-
(2008)
Genet Resour Crop Evol.
, vol.55
, pp. 1141-1157
-
-
Dempewolf, H.1
Rieseberg, L.H.2
Cronk, Q.C.3
-
11
-
-
84926169268
-
No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans
-
Do R Balick D, Li H, Adzhubei I, Sunyaev S, Reich D. 2015. No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans. Nat Genet. 47:126-131.
-
(2015)
Nat Genet.
, vol.47
, pp. 126-131
-
-
Do, R.1
Balick, D.2
Li, H.3
Adzhubei, I.4
Sunyaev, S.5
Reich, D.6
-
14
-
-
34447546660
-
The distribution of fitness effects of new mutations
-
Eyre-Walker A, Keightley PD. 2007. The distribution of fitness effects of new mutations. Nat Rev Genet 8:610-618.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 610-618
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
15
-
-
0016110957
-
The evolutionary advantage of recombination
-
Felsenstein J. 1974. The evolutionary advantage of recombination. Genetics 78:737-756.
-
(1974)
Genetics
, vol.78
, pp. 737-756
-
-
Felsenstein, J.1
-
16
-
-
84855597512
-
Sunflower
-
Vollmann J, Rajcan I, editors New York Springer.
-
Fernandez-Martinez JM, Perez-Vich B, Velasco L 2009. Sunflower. In: Vollmann J, Rajcan I, editors. Oil crops. New York Springer. p. 155-232.
-
(2009)
Oil Crops
, pp. 155-232
-
-
Fernandez-Martinez, J.M.1
Perez-Vich, B.2
Velasco, L.3
-
17
-
-
84872143942
-
Analysis of 6, 515 exomes reveals the recent origin of most human protein-coding variants
-
Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Altshuler D, Shendure J, Nickerson DA, et al. 2012. Analysis of 6, 515 exomes reveals the recent origin of most human protein-coding variants. Nature 493:216-220.
-
(2012)
Nature
, vol.493
, pp. 216-220
-
-
Fu, W.1
O'Connor, T.D.2
Jun, G.3
Kang, H.M.4
Abecasis, G.5
Leal, S.M.6
Gabriel, S.7
Altshuler, D.8
Shendure, J.9
Nickerson, D.A.10
-
18
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 29:644-652.
-
(2011)
Nat Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
-
19
-
-
77955504857
-
Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice
-
Günther T, Schmid KJ. 2010. Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice. Theor Appl Genet. 121:157-168.
-
(2010)
Theor Appl Genet.
, vol.121
, pp. 157-168
-
-
Günther, T.1
Schmid, K.J.2
-
20
-
-
34447522201
-
Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over
-
Haddrill PR, Halligan DL, Tomaras D, Charlesworth B. 2007. Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over. Genome Biol. 8:R18.
-
(2007)
Genome Biol.
, vol.8
, pp. R18
-
-
Haddrill, P.R.1
Halligan, D.L.2
Tomaras, D.3
Charlesworth, B.4
-
21
-
-
3142653666
-
Origin of extant domesticated sunflowers in eastern North America
-
Harter AV, Gardner KA, Falush D, Lentz DL, Bye RA, Rieseberg LH. 2004. Origin of extant domesticated sunflowers in eastern North America. Nature 430:201-205.
-
(2004)
Nature
, vol.430
, pp. 201-205
-
-
Harter, A.V.1
Gardner, K.A.2
Falush, D.3
Lentz, D.L.4
Bye, R.A.5
Rieseberg, L.H.6
-
23
-
-
84890147590
-
Genomics of Compositae crops: Reference transcriptome assemblies and evidence of hybridization with wild relatives
-
Hodgins KA, Lai Z, Oliveira LO, Still DW, Scascitelli M, Barker M, Kane NC, Dempewolf H, Kozik A, Kesseli RV, et al. 2014. Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives. Mol Ecol Res. 14:166-177.
-
(2014)
Mol Ecol Res.
, vol.14
, pp. 166-177
-
-
Hodgins, K.A.1
Lai, Z.2
Oliveira, L.O.3
Still, D.W.4
Scascitelli, M.5
Barker, M.6
Kane, N.C.7
Dempewolf, H.8
Kozik, A.9
Kesseli, R.V.10
-
24
-
-
77649219524
-
Population genomics of parallel adaptation in threespine stickleback using sequenced RAD Tags
-
Hohenlohe P, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA. 2009. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD Tags. PLoS Genet. 6:e1000862.
-
(2009)
PLoS Genet.
, vol.6
, pp. e1000862
-
-
Hohenlohe, P.1
Bassham, S.2
Etter, P.D.3
Stiffler, N.4
Johnson, E.A.5
Cresko, W.A.6
-
25
-
-
0033367922
-
Wild relatives and crop cultivars: Detecting natural introgression and farmer selection of new genetic combinations in agroecosystems
-
Jarvis DI, Hodgkin T. 1999. Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems. Mol Ecol. 8:S159-S173.
-
(1999)
Mol Ecol.
, vol.8
, pp. S159-S173
-
-
Jarvis, D.I.1
Hodgkin, T.2
-
26
-
-
79961230602
-
Progress towards a reference genome for sunflower
-
Kane NC, Gill N, King MG, Bowers JE, Berges H. 2011. Progress towards a reference genome for sunflower. Botany 89:429-437.
-
(2011)
Botany
, vol.89
, pp. 429-437
-
-
Kane, N.C.1
Gill, N.2
King, M.G.3
Bowers, J.E.4
Berges, H.5
-
27
-
-
68149126536
-
Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent Helianthus species
-
Kane NC, King MG, Barker MS, Raduski A, Karrenberg S, Yatabe Y, Knapp SJ, Rieseberg LH. 2009. Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent Helianthus species. Evolution 63:2061-2075.
-
(2009)
Evolution
, vol.63
, pp. 2061-2075
-
-
Kane, N.C.1
King, M.G.2
Barker, M.S.3
Raduski, A.4
Karrenberg, S.5
Yatabe, Y.6
Knapp, S.J.7
Rieseberg, L.H.8
-
28
-
-
37349012643
-
Genetics and evolution of weedy Helianthus annuus populations: Adaptation of an agricultural weed
-
Kane NC, Rieseberg LH. 2008. Genetics and evolution of weedy Helianthus annuus populations: adaptation of an agricultural weed. Mol Ecol. 17:384-394.
-
(2008)
Mol Ecol.
, vol.17
, pp. 384-394
-
-
Kane, N.C.1
Rieseberg, L.H.2
-
29
-
-
33244467305
-
The fate of mutations surfing on the wave of a range expansion
-
Klopfstein S, Currat M, Excoffier L. 2006. The fate of mutations surfing on the wave of a range expansion. Mol Biol Evol. 23:482-490.
-
(2006)
Mol Biol Evol.
, vol.23
, pp. 482-490
-
-
Klopfstein, S.1
Currat, M.2
Excoffier, L.3
-
30
-
-
0023737547
-
Deleterious mutations and the evolution of sexual reproduction
-
Kondrashov AS. 1988. Deleterious mutations and the evolution of sexual reproduction. Nature 336:435-440.
-
(1988)
Nature
, vol.336
, pp. 435-440
-
-
Kondrashov, A.S.1
-
31
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
32
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
34
-
-
39749139577
-
Proportionally more deleterious genetic variation in European than in African populations
-
Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, et al. 2008. Proportionally more deleterious genetic variation in European than in African populations. Nature 451:994-997.
-
(2008)
Nature
, vol.451
, pp. 994-997
-
-
Lohmueller, K.E.1
Indap, A.R.2
Schmidt, S.3
Boyko, A.R.4
Hernandez, R.D.5
Hubisz, M.J.6
Sninsky, J.J.7
White, T.J.8
Sunyaev, S.R.9
Nielsen, R.10
-
35
-
-
84899624756
-
Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests
-
Lotterhos KE, Whitlock MC. 2014. Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests. Mol Ecol. 23:2178-2192.
-
(2014)
Mol Ecol.
, vol.23
, pp. 2178-2192
-
-
Lotterhos, K.E.1
Whitlock, M.C.2
-
36
-
-
33344458581
-
The accumulation of deleterious mutations in rice genomes: A hypothesis on the cost of domestication
-
Lu J, Tang T, Tang H, Huang J, Shi S, Wu CI. 2006. The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet. 22:126-131.
-
(2006)
Trends Genet.
, vol.22
, pp. 126-131
-
-
Lu, J.1
Tang, T.2
Tang, H.3
Huang, J.4
Shi, S.5
Wu, C.I.6
-
37
-
-
84879858533
-
Agriculture: Feeding the future
-
McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, et al. 2013. Agriculture: feeding the future. Nature 499:23-24.
-
(2013)
Nature
, vol.499
, pp. 23-24
-
-
McCouch, S.1
Baute, G.J.2
Bradeen, J.3
Bramel, P.4
Bretting, P.K.5
Buckler, E.6
Burke, J.M.7
Charest, D.8
Cloutier, S.9
Cole, G.10
-
38
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. 2010. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-1303.
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
Kernytsky, A.6
Garimella, K.7
Altshuler, D.8
Gabriel, S.9
Daly, M.10
-
39
-
-
68449094455
-
Genetic properties of the maize nested association mapping population
-
McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, et al. 2009. Genetic properties of the maize nested association mapping population. Science 325:737-740.
-
(2009)
Science
, vol.325
, pp. 737-740
-
-
McMullen, M.D.1
Kresovich, S.2
Villeda, H.S.3
Bradbury, P.4
Li, H.5
Sun, Q.6
Flint-Garcia, S.7
Thornsberry, J.8
Acharya, C.9
Bottoms, C.10
-
42
-
-
0043122919
-
SIFT: Predicting amino acid changes that affect protein function
-
Ng PC, Henikoff S. 2003. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31:3812-3814.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3812-3814
-
-
Ng, P.C.1
Henikoff, S.2
-
43
-
-
0027020232
-
The nearly neutral theory of molecular evolution
-
Ohta T. 1992. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst. 23:263-286.
-
(1992)
Annu Rev Ecol Syst.
, vol.23
, pp. 263-286
-
-
Ohta, T.1
-
44
-
-
84890120078
-
On the accumulation of deleterious mutations during range expansions
-
Peischl S, Dupanloup I, Kirkpatrick M, Excoffier L. 2013. On the accumulation of deleterious mutations during range expansions. Mol Ecol. 22:5972-5982.
-
(2013)
Mol Ecol.
, vol.22
, pp. 5972-5982
-
-
Peischl, S.1
Dupanloup, I.2
Kirkpatrick, M.3
Excoffier, L.4
-
46
-
-
85103046475
-
Early history of sunflower
-
Schneiter AA, editor Madison (WI): American Society of Agronomy/Crop Science Society of America/Soil Science Society of America.
-
Putt ED. 1997. Early history of sunflower. In: Schneiter AA, editor. Sunflower technology and production. Madison (WI): American Society of Agronomy/Crop Science Society of America/Soil Science Society of America. p. 1-19.
-
(1997)
Sunflower Technology and Production
, pp. 1-19
-
-
Putt, E.D.1
-
47
-
-
84863304598
-
-
R Core Team. Vienna (Austria): R Foundation for Statistical Computing
-
R Core Team. 2013. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing. Available from: http://www.R-project.org/.
-
(2013)
R: A Language and Environment for Statistical Computing
-
-
-
48
-
-
84878596895
-
The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq
-
Renaut S, Grassa C, Moyers B, Kane N, Rieseberg L. 2012. The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq. Biology 1:575-596.
-
(2012)
Biology
, vol.1
, pp. 575-596
-
-
Renaut, S.1
Grassa, C.2
Moyers, B.3
Kane, N.4
Rieseberg, L.5
-
49
-
-
84878589154
-
Data from: Genomic islands of divergence are not affected by geography of speciation in sunflowers
-
Renaut S, Grassa CJ, Yeaman S, Lai Z, Kane NK, Moyers BT, Bowers JE, Burke JM, Rieseberg LH. 2013. Data from: genomic islands of divergence are not affected by geography of speciation in sunflowers. Nat Commun. Available from: http://dx.doi.org/10.5061/dryad.9q1n4.
-
(2013)
Nat Commun
-
-
Renaut, S.1
Grassa, C.J.2
Yeaman, S.3
Lai, Z.4
Kane, N.K.5
Moyers, B.T.6
Bowers, J.E.7
Burke, J.M.8
Rieseberg, L.H.9
-
50
-
-
84878589154
-
Genomic islands of divergence are not affected by geography of speciation in sunflowers
-
Renaut S, Grassa CJ, Yeaman S, Moyers BT, Lai Z, Kane NC, Bowers JE, Burke JM, Rieseberg LH. 2013. Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nat Commun. 4:1827.
-
(2013)
Nat Commun.
, vol.4
, pp. 1827
-
-
Renaut, S.1
Grassa, C.J.2
Yeaman, S.3
Moyers, B.T.4
Lai, Z.5
Kane, N.C.6
Bowers, J.E.7
Burke, J.M.8
Rieseberg, L.H.9
-
51
-
-
0034201441
-
EMBOSS: The European molecular biology open software suite
-
Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European molecular biology open software suite. Trends Genet. 16:276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
52
-
-
84865798797
-
Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa
-
Scaglione D, Lanteri S, Acquadro A, Lai Z, Knapp SJ, Rieseberg L, Portis E. 2012. Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa. Plant Biotechnol J. 10:956-969.
-
(2012)
Plant Biotechnol J.
, vol.10
, pp. 956-969
-
-
Scaglione, D.1
Lanteri, S.2
Acquadro, A.3
Lai, Z.4
Knapp, S.J.5
Rieseberg, L.6
Portis, E.7
-
53
-
-
84895867277
-
The deleterious mutation load is insensitive to recent population history
-
Simons YB, Turchin MC, Pritchard JK, Sella G. 2014. The deleterious mutation load is insensitive to recent population history. Nat Genet. 46:220-224.
-
(2014)
Nat Genet.
, vol.46
, pp. 220-224
-
-
Simons, Y.B.1
Turchin, M.C.2
Pritchard, J.K.3
Sella, G.4
-
54
-
-
84864430562
-
SIFT web server: Predicting effects of amino acid substitutions on proteins
-
Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC. 2012. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res. 40:W452-W457.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W452-W457
-
-
Sim, N.L.1
Kumar, P.2
Hu, J.3
Henikoff, S.4
Schneider, G.5
Ng, P.C.6
-
55
-
-
33747595222
-
Eastern North America as an independent center of plant domestication
-
Smith BD. 2006. Eastern North America as an independent center of plant domestication. Proc Natl Acad Sci USA. 103:12223-12228.
-
(2006)
Proc Natl Acad Sci USA.
, vol.103
, pp. 12223-12228
-
-
Smith, B.D.1
-
56
-
-
0032229295
-
Fecundity, phenology, and seed dormancy of F1 wild-crop hybrids in Sunflower (Helianthus annuus, Asteraceae)
-
Snow A, Moran-Palma P, Rieseberg L, Wszelaki A, Seiler G. 1998. Fecundity, phenology, and seed dormancy of F1 wild-crop hybrids in Sunflower (Helianthus annuus, Asteraceae). Am J Bot. 85:794.
-
(1998)
Am J Bot.
, vol.85
, pp. 794
-
-
Snow, A.1
Moran-Palma, P.2
Rieseberg, L.3
Wszelaki, A.4
Seiler, G.5
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