-
1
-
-
0035870985
-
Campylobacter jejuni infections: Update on emerging issues and trends
-
B.M. Allos Campylobacter jejuni infections: Update on emerging issues and trends Clin. Infect. Dis. 32 2001 1201 1206
-
(2001)
Clin. Infect. Dis.
, vol.32
, pp. 1201-1206
-
-
Allos, B.M.1
-
2
-
-
0033552961
-
Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori
-
R.A. Alm, L.S. Ling, D.T. Moir, B.L. King, E.D. Brown, P.C. Doig, and D.R. Smith Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori Nature 397 1999 176 180
-
(1999)
Nature
, vol.397
, pp. 176-180
-
-
Alm, R.A.1
Ling, L.S.2
Moir, D.T.3
King, B.L.4
Brown, E.D.5
Doig, P.C.6
Smith, D.R.7
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
4
-
-
0031736121
-
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles
-
L. Aravind, R.L. Tatusov, Y.I. Wolf, D.R. Walker, and E.V. Koonin Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles Trends Genet. 14 1998 442 444
-
(1998)
Trends Genet.
, vol.14
, pp. 442-444
-
-
Aravind, L.1
Tatusov, R.L.2
Wolf, Y.I.3
Walker, D.R.4
Koonin, E.V.5
-
5
-
-
0141705354
-
Complete genome sequence and analysis of Wolinella succinogenes
-
C. Baar, M. Eppinger, G. Raddatz, J. Simon, C. Lanz, O. Klimmek, and R. Nandakumar Complete genome sequence and analysis of Wolinella succinogenes Proc. Natl. Acad. Sci. USA 100 2003 11690 11695
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 11690-11695
-
-
Baar, C.1
Eppinger, M.2
Raddatz, G.3
Simon, J.4
Lanz, C.5
Klimmek, O.6
Nandakumar, R.7
-
6
-
-
2542448032
-
Phylogeny of γ-Proteobacteria: Resolution of one branch of the universal tree?
-
J.R. Brown, and C. Volker Phylogeny of γ-Proteobacteria: Resolution of one branch of the universal tree? Bioessays 26 2004 463 468
-
(2004)
Bioessays
, vol.26
, pp. 463-468
-
-
Brown, J.R.1
Volker, C.2
-
7
-
-
4844221596
-
Bacterial α2-macroglobulins: Colonisation factors acquired by horizontal gene transfer from the metazoan genome?
-
A. Budd, S. Blandin, E.A. Levashina, and T.J. Gibson Bacterial α2-macroglobulins: Colonisation factors acquired by horizontal gene transfer from the metazoan genome? Genome Biol. 5 2004 R38
-
(2004)
Genome Biol.
, vol.5
, pp. 38
-
-
Budd, A.1
Blandin, S.2
Levashina, E.A.3
Gibson, T.J.4
-
8
-
-
0020003603
-
Genetic and biochemical analyses of pantothenate biosynthesis in Escherichia coli and Salmonella typhimurium
-
J.E. Cronan, K.J. Little, and S. Jackowski Genetic and biochemical analyses of pantothenate biosynthesis in Escherichia coli and Salmonella typhimurium J. Bacteriol. 149 1982 916 922
-
(1982)
J. Bacteriol.
, vol.149
, pp. 916-922
-
-
Cronan, J.E.1
Little, K.J.2
Jackowski, S.3
-
9
-
-
0032404453
-
You are what you eat: A gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes
-
W.F. Doolittle You are what you eat: A gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes Trends Genet. 14 1998 307 311
-
(1998)
Trends Genet.
, vol.14
, pp. 307-311
-
-
Doolittle, W.F.1
-
10
-
-
0032870331
-
Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis
-
S. Garcia-Vallve, J. Palau, and A. Ramau Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis Mol. Biol. Evol. 16 1999 1125 1134
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1125-1134
-
-
Garcia-Vallve, S.1
Palau, J.2
Ramau, A.3
-
11
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
S. Garcia-Vallve, A. Romeu, and J. Palau Horizontal gene transfer in bacterial and archaeal complete genomes Genome Res. 10 2000 1719 1725
-
(2000)
Genome Res.
, vol.10
, pp. 1719-1725
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
-
12
-
-
0033995545
-
Horizontal gene transfer of glycosyl hydrolases of the rumen fungi
-
S. Garcia-Vallve, A. Romeu, and J. Palau Horizontal gene transfer of glycosyl hydrolases of the rumen fungi Mol. Biol. Evol. 17 2000 352 361
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 352-361
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
-
13
-
-
0037250391
-
HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes
-
S. Garcia-Vallve, E. Guzman, M.A. Montero, and A. Romeu HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes Nucleic Acids Res. 31 2003 187 189
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 187-189
-
-
Garcia-Vallve, S.1
Guzman, E.2
Montero, M.A.3
Romeu, A.4
-
14
-
-
0033752775
-
About the last common ancestor, the universal life-tree and lateral gene transfer: A reappraisal
-
N. Glansdorff About the last common ancestor, the universal life-tree and lateral gene transfer: A reappraisal Mol. Microbiol. 38 2000 177 185
-
(2000)
Mol. Microbiol.
, vol.38
, pp. 177-185
-
-
Glansdorff, N.1
-
17
-
-
0032415865
-
How to interpret an anonymous bacterial genome: Machine learning approach to gene identification
-
W.S. Hayes, and M. Borodovsky How to interpret an anonymous bacterial genome: Machine learning approach to gene identification Genome Res. 8 1998 1154 1171
-
(1998)
Genome Res.
, vol.8
, pp. 1154-1171
-
-
Hayes, W.S.1
Borodovsky, M.2
-
18
-
-
0033616714
-
Horizontal gene transfer among genomes: The complexity hypothesis
-
R. Jain, M.C. Rivera, and J.A. Lake Horizontal gene transfer among genomes: The complexity hypothesis Proc. Natl. Acad. Sci. USA 96 1999 3801 3806
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.C.2
Lake, J.A.3
-
19
-
-
0242371471
-
Horizontal gene transfer accelerates genome innovation and evolution
-
R. Jain, M.C. Rivera, J.E. Moore, and J.A. Lake Horizontal gene transfer accelerates genome innovation and evolution Mol. Biol. Evol. 20 2003 1598 1602
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 1598-1602
-
-
Jain, R.1
Rivera, M.C.2
Moore, J.E.3
Lake, J.A.4
-
20
-
-
0031757669
-
Multiple sequence alignment with ClustalX
-
F. Jeanmougin, J.D. Thompson, M. Gouy, D.G. Higgins, and T.J. Gibson Multiple sequence alignment with ClustalX Trends Biochem. Sci. 23 1998 403 405
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 403-405
-
-
Jeanmougin, F.1
Thompson, J.D.2
Gouy, M.3
Higgins, D.G.4
Gibson, T.J.5
-
21
-
-
0027139172
-
Lateral transfer in natural populations of eukaryotes
-
M.G. Kidwell Lateral transfer in natural populations of eukaryotes Annu. Rev. Genet. 27 1993 235 256
-
(1993)
Annu. Rev. Genet.
, vol.27
, pp. 235-256
-
-
Kidwell, M.G.1
-
22
-
-
0034780910
-
Horizontal gene transfer in prokaryotes: Quantification and classification
-
E.V. Koonin, K.S. Makarova, and L. Aravind Horizontal gene transfer in prokaryotes: Quantification and classification Annu. Rev. Microbiol. 55 2001 709 742
-
(2001)
Annu. Rev. Microbiol.
, vol.55
, pp. 709-742
-
-
Koonin, E.V.1
Makarova, K.S.2
Aravind, L.3
-
23
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbour
-
L. Koski, and G.B. Golding The closest BLAST hit is often not the nearest neighbour J. Mol. Evol. 52 2001 540 542
-
(2001)
J. Mol. Evol.
, vol.52
, pp. 540-542
-
-
Koski, L.1
Golding, G.B.2
-
24
-
-
0035099964
-
Codon bias and base composition are poor indicators of horizontally transferred genes
-
L.B. Koski, R.A. Morton, and B.G. Golding Codon bias and base composition are poor indicators of horizontally transferred genes Mol. Biol. Evol. 18 2001 404 412
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 404-412
-
-
Koski, L.B.1
Morton, R.A.2
Golding, B.G.3
-
25
-
-
0038486918
-
The balance of driving forces during genome evolution in prokaryotes
-
V. Kunin, and C.A. Ouzounis The balance of driving forces during genome evolution in prokaryotes Genome Res. 13 2003 1589 1594
-
(2003)
Genome Res.
, vol.13
, pp. 1589-1594
-
-
Kunin, V.1
Ouzounis, C.A.2
-
27
-
-
0030994798
-
Amelioration of bacterial genomes: Rates of change and exchange
-
J.G. Lawrence, and H. Ochman Amelioration of bacterial genomes: Rates of change and exchange J. Mol. Evol. 44 1997 383 397
-
(1997)
J. Mol. Evol.
, vol.44
, pp. 383-397
-
-
Lawrence, J.G.1
Ochman, H.2
-
28
-
-
0032482924
-
Molecular archaeology of the Escherichia coli genome
-
J.G. Lawrence, and H. Ochman Molecular archaeology of the Escherichia coli genome Proc. Natl. Acad. Sci. USA 95 1998 9413 9417
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 9413-9417
-
-
Lawrence, J.G.1
Ochman, H.2
-
29
-
-
0036145420
-
Reconciling the many faces of lateral gene transfer
-
J.G. Lawrence, and H. Ochman Reconciling the many faces of lateral gene transfer Trends Microbiol. 10 2002 1 4
-
(2002)
Trends Microbiol.
, vol.10
, pp. 1-4
-
-
Lawrence, J.G.1
Ochman, H.2
-
31
-
-
3042849253
-
Biased biological function of horizontally transferred genes in prokaryotic genomes
-
Y. Nakamura, T. Itoh, H. Matsuda, and T. Gojobori Biased biological function of horizontally transferred genes in prokaryotic genomes Nature Genet. 36 2004 760 766
-
(2004)
Nature Genet.
, vol.36
, pp. 760-766
-
-
Nakamura, Y.1
Itoh, T.2
Matsuda, H.3
Gojobori, T.4
-
32
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
H. Ochman, J.G. Lawrence, and E.A. Groisman Lateral gene transfer and the nature of bacterial innovation Nature 405 2000 299 304
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
33
-
-
0034542621
-
Horizontal transfer of archaeal genes into the Deinococcaceae: Detection by molecular and computer-based approaches
-
L. Olendzenski, L. Liu, O. Zhaxybayeva, R. Murphey, D.G. Shin, and P.J. Gogarten Horizontal transfer of archaeal genes into the Deinococcaceae: Detection by molecular and computer-based approaches J. Mol. Evol. 51 2000 587 599
-
(2000)
J. Mol. Evol.
, vol.51
, pp. 587-599
-
-
Olendzenski, L.1
Liu, L.2
Zhaxybayeva, O.3
Murphey, R.4
Shin, D.G.5
Gogarten, P.J.6
-
34
-
-
0036032121
-
Extragastric Helicobacter species
-
S.L. On, S. Hynes, and T. Wadstrom Extragastric Helicobacter species Helicobacter 7 Suppl. 1 2002 63 67
-
(2002)
Helicobacter
, vol.7
, Issue.1 SUPPL.
, pp. 63-67
-
-
On, S.L.1
Hynes, S.2
Wadstrom, T.3
-
35
-
-
0346104824
-
Speciation in Chlamydia: Genomewide phylogenetic analysis identified a reliable set of acquired genes
-
C. Ortutay, Z. Gaspari, G. Toth, E. Jager, G. Vida, L. Orosz, and T. Vellai Speciation in Chlamydia: Genomewide phylogenetic analysis identified a reliable set of acquired genes J. Mol. Evol. 57 2003 672 680
-
(2003)
J. Mol. Evol.
, vol.57
, pp. 672-680
-
-
Ortutay, C.1
Gaspari, Z.2
Toth, G.3
Jager, E.4
Vida, G.5
Orosz, L.6
Vellai, T.7
-
36
-
-
0030203863
-
TREEVIEW: An application to display phylogenetic trees on personal computers
-
R.D.M. Page TREEVIEW: An application to display phylogenetic trees on personal computers Comp. App. Biosci. 12 1996 357 358
-
(1996)
Comp. App. Biosci.
, vol.12
, pp. 357-358
-
-
Page, R.D.M.1
-
37
-
-
0034628526
-
The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences
-
J. Parkhill, B.W. Wren, K. Mungall, J.M. Ketley, C. Churcher, D. Basham, and T. Chillingworth The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences Nature 403 2000 665 668
-
(2000)
Nature
, vol.403
, pp. 665-668
-
-
Parkhill, J.1
Wren, B.W.2
Mungall, K.3
Ketley, J.M.4
Churcher, C.5
Basham, D.6
Chillingworth, T.7
-
38
-
-
0009183442
-
-
Ph.D. thesis, University of Nottingham, UK
-
J.F. Peden, Analysis of codon usage, Ph.D. thesis, University of Nottingham, UK, 1999
-
(1999)
Analysis of Codon Usage
-
-
Peden, J.F.1
-
40
-
-
0035943134
-
On surrogate methods for detecting lateral gene transfer
-
M.A. Ragan On surrogate methods for detecting lateral gene transfer FEMS Microbiol. Lett. 201 2001 187 191
-
(2001)
FEMS Microbiol. Lett.
, vol.201
, pp. 187-191
-
-
Ragan, M.A.1
-
41
-
-
0035546223
-
Detection of lateral gene transfer among microbial genomes
-
M.A. Ragan Detection of lateral gene transfer among microbial genomes Curr. Opin. Gen. Dev. 11 2001 620 626
-
(2001)
Curr. Opin. Gen. Dev.
, vol.11
, pp. 620-626
-
-
Ragan, M.A.1
-
42
-
-
0035989433
-
Distributional profiles of homologous open reading frames among bacterial phyla: Implications for vertical and lateral transmission
-
M.A. Ragan, and R.L. Charlebois Distributional profiles of homologous open reading frames among bacterial phyla: Implications for vertical and lateral transmission Int. J. Syst. Evol. Microbiol. 52 2002 777 787
-
(2002)
Int. J. Syst. Evol. Microbiol.
, vol.52
, pp. 777-787
-
-
Ragan, M.A.1
Charlebois, R.L.2
-
43
-
-
2242447089
-
Whole-genome analysis of photosynthetic prokaryotes
-
J. Raymond, O. Zhaxybayeva, P.J. Gogarten, S.Y. Gerdes, and R.E. Blankenschip Whole-genome analysis of photosynthetic prokaryotes Science 298 2002 1616 1620
-
(2002)
Science
, vol.298
, pp. 1616-1620
-
-
Raymond, J.1
Zhaxybayeva, O.2
Gogarten, P.J.3
Gerdes, S.Y.4
Blankenschip, R.E.5
-
45
-
-
0023375195
-
The neighbour-joining method: A new method for reconstructing phylogenetic trees
-
N. Saitou, and M. Nei The neighbour-joining method: A new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
46
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
H.A. Schmidt, K. Strimmer, M. Vingron, and A. von Haeseler TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing Bioinformatics 18 2002 502 504
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
47
-
-
0036143446
-
Genomes in flux: The evolution of archaeal and proteobacterial gene content
-
B. Snel, P. Bork, and M.A. Huynen Genomes in flux: The evolution of archaeal and proteobacterial gene content Genome Res. 12 2002 17 25
-
(2002)
Genome Res.
, vol.12
, pp. 17-25
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
48
-
-
0029836454
-
Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
-
K. Strimmer, and A. von Haeseler Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies Mol. Biol. Evol. 13 1996 964 969
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 964-969
-
-
Strimmer, K.1
Von Haeseler, A.2
-
49
-
-
0038610618
-
The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus
-
S. Suerbaum, C. Josenhans, T. Sterzenbach, B. Drescher, B. Brandt, M. Bell, and M. Dröge The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus Proc. Natl. Acad. Sci. USA 100 2003 7901 7906
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 7901-7906
-
-
Suerbaum, S.1
Josenhans, C.2
Sterzenbach, T.3
Drescher, B.4
Brandt, B.5
Bell, M.6
Dröge, M.7
-
50
-
-
0028606283
-
Horizontal gene transfer: Evidence and possible consequences
-
M. Syvanen Horizontal gene transfer: Evidence and possible consequences Annu. Rev. Genet. 28 1994 237 261
-
(1994)
Annu. Rev. Genet.
, vol.28
, pp. 237-261
-
-
Syvanen, M.1
-
51
-
-
0030660581
-
A genomic perspective on protein families
-
R.L. Tatusov, E.V. Koonin, and D.J. Lipman A genomic perspective on protein families Science 278 1997 631 637
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
52
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
R.L. Tatusov, N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, E.V. Koonin, and D.M. Krylov The COG database: An updated version includes eukaryotes BMC Bioinformatics 4 2003 41
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
Krylov, D.M.7
-
53
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
54
-
-
0030835739
-
The complete genome sequence of the gastric pathogen Helicobacter pylori
-
J.F. Tomb, O. White, A.R. Kerlavage, R.A. Clayton, G.G. Sutton, R.D. Fleischmann, and K.A. Ketchum The complete genome sequence of the gastric pathogen Helicobacter pylori Nature 388 1997 539 547
-
(1997)
Nature
, vol.388
, pp. 539-547
-
-
Tomb, J.F.1
White, O.2
Kerlavage, A.R.3
Clayton, R.A.4
Sutton, G.G.5
Fleischmann, R.D.6
Ketchum, K.A.7
-
55
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
J.C. Venter, K. Remington, J.F. Heidelberg, A.L. Halpern, D. Rusch, J.A. Eisen, and D. Wu Environmental genome shotgun sequencing of the Sargasso Sea Science 304 2004 66 74
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
Wu, D.7
-
56
-
-
0032962345
-
Rickettsiae and Chlamydiae - Evidence of horizontal gene transfer and gene exchange
-
Y.I. Wolf, L. Aravind, and E.V. Koonin Rickettsiae and Chlamydiae - evidence of horizontal gene transfer and gene exchange Trends Genet. 15 1999 173 175
-
(1999)
Trends Genet.
, vol.15
, pp. 173-175
-
-
Wolf, Y.I.1
Aravind, L.2
Koonin, E.V.3
-
57
-
-
0001240972
-
Cytochrome-producing anaerobic vibrio, Vibrio succinogenes, sp. n.
-
M.J. Wolin, E.A. Wolin, and N.J. Jacobs Cytochrome-producing anaerobic vibrio, Vibrio succinogenes, sp. n. J. Bacteriol. 81 1961 911 917
-
(1961)
J. Bacteriol.
, vol.81
, pp. 911-917
-
-
Wolin, M.J.1
Wolin, E.A.2
Jacobs, N.J.3
-
58
-
-
0034141421
-
Structural analysis of DNA sequence: Evidence for lateral gene transfer in Thermotoga maritima
-
P. Worning, L.J. Jensen, K.E. Nelson, S. Brunak, and D.W. Ussery Structural analysis of DNA sequence: Evidence for lateral gene transfer in Thermotoga maritima Nucleic Acids Res. 28 2000 706 709
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 706-709
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Worning, P.1
Jensen, L.J.2
Nelson, K.E.3
Brunak, S.4
Ussery, D.W.5
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