-
1
-
-
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
-
2
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
W.F. Doolittle Phylogenetic classification and the universal tree Science 284 1999 2124 2129
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
3
-
-
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
-
5
-
-
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
-
7
-
-
0035546223
-
Detection of lateral gene transfer among microbial genomes
-
M.A. Ragan Detection of lateral gene transfer among microbial genomes Curr. Opin. Genet. Dev. 11 2001 620 626
-
(2001)
Curr. Opin. Genet. Dev.
, vol.11
, pp. 620-626
-
-
Ragan, M.A.1
-
8
-
-
0028069540
-
Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen
-
G. Blum, M. Ott, A. Lischewski, A. Ritter, H. Imrich, and H. Tschape Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen Infect. Immun. 62 1994 606 614
-
(1994)
Infect. Immun.
, vol.62
, pp. 606-614
-
-
Blum, G.1
Ott, M.2
Lischewski, A.3
Ritter, A.4
Imrich, H.5
Tschape, H.6
-
9
-
-
2442449227
-
Genomic islands in pathogenic and environmental microorganisms
-
U. Dobrindt, B. Hochhut, U. Hentschel, and J. Hacker Genomic islands in pathogenic and environmental microorganisms Nat. Rev., Microbiol. 2 2004 414 424
-
(2004)
Nat. Rev., Microbiol.
, vol.2
, pp. 414-424
-
-
Dobrindt, U.1
Hochhut, B.2
Hentschel, U.3
Hacker, J.4
-
10
-
-
0033758756
-
Pathogenicity islands and the evolution of microbes
-
J. Hacker, and J.B. Kaper Pathogenicity islands and the evolution of microbes Annu. Rev. Microbiol. 54 2000 641 679
-
(2000)
Annu. Rev. Microbiol.
, vol.54
, pp. 641-679
-
-
Hacker, J.1
Kaper, J.B.2
-
11
-
-
3042849253
-
Biased biological functions of horizontally transferred genes in prokaryotic genomes
-
Y. Nakamura, T. Itoh, H. Matsuda, and T. Gojobori Biased biological functions of horizontally transferred genes in prokaryotic genomes Nat. Genet. 36 2004 760 766
-
(2004)
Nat. Genet.
, vol.36
, pp. 760-766
-
-
Nakamura, Y.1
Itoh, T.2
Matsuda, H.3
Gojobori, T.4
-
12
-
-
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. U. S. A. 96 1999 3801 3806
-
(1999)
Proc. Natl. Acad. Sci. U. S. A.
, vol.96
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.C.2
Lake, J.A.3
-
13
-
-
0033609333
-
Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima
-
K.E. Nelson, R.A. Clayton, S.R. Gill, M.L. Gwinn, R.J. Dodson, and D.H. Haft Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima Nature 399 1999 323 329
-
(1999)
Nature
, vol.399
, pp. 323-329
-
-
Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
Gwinn, M.L.4
Dodson, R.J.5
Haft, D.H.6
-
14
-
-
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
-
15
-
-
0042902833
-
The COG database: An updated version includes Eukaryotes
-
R.L. Tatusov, N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, and E.V. Koonin 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
-
16
-
-
2942519433
-
SIGI: Score-based identification of genomic islands
-
R. Merkl SIGI: Score-based identification of genomic islands BMC Bioinformatics 5 2004 22
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 22
-
-
Merkl, R.1
-
17
-
-
0037250152
-
STRING: A database of predicted functional associations between proteins
-
C. von Mering, M. Huynen, D. Jaeggi, S. Schmidt, P. Bork, and B. Snel STRING: a database of predicted functional associations between proteins Nucleic Acids Res. 31 2003 258 261
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 258-261
-
-
Von Mering, C.1
Huynen, M.2
Jaeggi, D.3
Schmidt, S.4
Bork, P.5
Snel, B.6
-
19
-
-
0035988323
-
The genome of Methanosarcina mazei: Evidence for lateral gene transfer between Bacteria and Archaea
-
U. Deppenmeier, A. Johann, T. Hartsch, R. Merkl, R.A. Schmitz, and R. Martinez-Arias The genome of Methanosarcina mazei: evidence for lateral gene transfer between Bacteria and Archaea J. Mol. Microbiol. Biotechnol. 4 2002 453 461
-
(2002)
J. Mol. Microbiol. Biotechnol.
, vol.4
, pp. 453-461
-
-
Deppenmeier, U.1
Johann, A.2
Hartsch, T.3
Merkl, R.4
Schmitz, R.A.5
Martinez-Arias, R.6
-
20
-
-
2342586677
-
The genome sequence of the extreme thermophile Thermus thermophilus
-
A. Henne, H. Brüggemann, C. Raasch, A. Wiezer, T. Hartsch, and H. Liesegang The genome sequence of the extreme thermophile Thermus thermophilus Nat. Biotechnol. 22 2004 547 553
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 547-553
-
-
Henne, A.1
Brüggemann, H.2
Raasch, C.3
Wiezer, A.4
Hartsch, T.5
Liesegang, H.6
-
21
-
-
0035955375
-
Comparative genomics of Listeria species
-
P. Glaser, L. Frangeul, C. Buchrieser, C. Rusniok, A. Amend, and F. Baquero Comparative genomics of Listeria species Science 294 2001 849 852
-
(2001)
Science
, vol.294
, pp. 849-852
-
-
Glaser, P.1
Frangeul, L.2
Buchrieser, C.3
Rusniok, C.4
Amend, A.5
Baquero, F.6
-
22
-
-
0018879196
-
Codon catalog usage and the genome hypothesis
-
R. Grantham, C. Gautier, M. Gouy, R. Mercier, and A. Pave Codon catalog usage and the genome hypothesis Nucleic Acids Res. 8 1980 r49 r62
-
(1980)
Nucleic Acids Res.
, vol.8
-
-
Grantham, R.1
Gautier, C.2
Gouy, M.3
Mercier, R.4
Pave, A.5
-
23
-
-
0038648028
-
Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content
-
R. Sandberg, C.I. Bränden, I. Ernberg, and J. Cöster Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content Gene 311 2003 35 42
-
(2003)
Gene
, vol.311
, pp. 35-42
-
-
Sandberg, R.1
Bränden, C.I.2
Ernberg, I.3
Cöster, J.4
-
24
-
-
0035961748
-
Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
-
T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii, and K. Yokoyama Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12 DNA Res. 8 2001 11 22
-
(2001)
DNA Res.
, vol.8
, pp. 11-22
-
-
Hayashi, T.1
Makino, K.2
Ohnishi, M.3
Kurokawa, K.4
Ishii, K.5
Yokoyama, K.6
-
25
-
-
0035945586
-
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
-
N.T. Perna, G. Plunkett III, V. Burland, B. Mau, J.D. Glasner, and D.J. Rose Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 Nature 409 2001 529 533
-
(2001)
Nature
, vol.409
, pp. 529-533
-
-
Perna, N.T.1
Plunkett III, G.2
Burland, V.3
Mau, B.4
Glasner, J.D.5
Rose, D.J.6
-
26
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
F.R. Blattner, G. Plunkett III, C.A. Bloch, N.T. Perna, V. Burland, and M. Riley The complete genome sequence of Escherichia coli K-12 Science 277 1997 1453 1474
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett III, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
Riley, M.6
-
27
-
-
0036225678
-
The genome of M. acetivorans reveals extensive metabolic and physiological diversity
-
J.E. Galagan, C. Nusbaum, A. Roy, M.G. Endrizzi, P. Macdonald, and W. FitzHugh The genome of M. acetivorans reveals extensive metabolic and physiological diversity Genome Res. 12 2002 532 542
-
(2002)
Genome Res.
, vol.12
, pp. 532-542
-
-
Galagan, J.E.1
Nusbaum, C.2
Roy, A.3
Endrizzi, M.G.4
MacDonald, P.5
Fitzhugh, W.6
-
29
-
-
0034739881
-
Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti
-
T. Kaneko, Y. Nakamura, S. Sato, E. Asamizu, T. Kato, and S. Sasamoto Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti DNA Res. 7 2000 331 338
-
(2000)
DNA Res.
, vol.7
, pp. 331-338
-
-
Kaneko, T.1
Nakamura, Y.2
Sato, S.3
Asamizu, E.4
Kato, T.5
Sasamoto, S.6
-
30
-
-
0035958746
-
The composite genome of the legume symbiont Sinorhizobium meliloti
-
F. Galibert, T.M. Finan, S.R. Long, A. Pühler, P. Abola, and F. Ampe The composite genome of the legume symbiont Sinorhizobium meliloti Science 293 2001 668 672
-
(2001)
Science
, vol.293
, pp. 668-672
-
-
Galibert, F.1
Finan, T.M.2
Long, S.R.3
Pühler, A.4
Abola, P.5
Ampe, F.6
-
31
-
-
0032574728
-
Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene
-
J.T. Sullivan, and C.W. Ronson Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene Proc. Natl. Acad. Sci. U. S. A. 95 1998 5145 5149
-
(1998)
Proc. Natl. Acad. Sci. U. S. A.
, vol.95
, pp. 5145-5149
-
-
Sullivan, J.T.1
Ronson, C.W.2
-
32
-
-
13044313472
-
Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1
-
O. White, J.A. Eisen, J.F. Heidelberg, E.K. Hickey, J.D. Peterson, and R.J. Dodson Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1 Science 286 1999 1571 1577
-
(1999)
Science
, vol.286
, pp. 1571-1577
-
-
White, O.1
Eisen, J.A.2
Heidelberg, J.F.3
Hickey, E.K.4
Peterson, J.D.5
Dodson, R.J.6
-
33
-
-
0022448655
-
Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp
-
Y. Koyama, T. Hoshino, N. Tomizuka, and K. Furukawa Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp J. Bacteriol. 166 1986 338 340
-
(1986)
J. Bacteriol.
, vol.166
, pp. 338-340
-
-
Koyama, Y.1
Hoshino, T.2
Tomizuka, N.3
Furukawa, K.4
-
34
-
-
0036151806
-
Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27
-
A. Friedrich, C. Prust, T. Hartsch, A. Henne, and B. Averhoff Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27 Appl. Environ. Microbiol. 68 2002 745 755
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 745-755
-
-
Friedrich, A.1
Prust, C.2
Hartsch, T.3
Henne, A.4
Averhoff, B.5
-
35
-
-
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. U. S. A. 95 1998 9413 9417
-
(1998)
Proc. Natl. Acad. Sci. U. S. A.
, vol.95
, pp. 9413-9417
-
-
Lawrence, J.G.1
Ochman, H.2
-
36
-
-
0035399931
-
Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
-
S. Karlin Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes Trends Microbiol. 9 2001 335 343
-
(2001)
Trends Microbiol.
, vol.9
, pp. 335-343
-
-
Karlin, S.1
-
37
-
-
0035040364
-
Analysis of codon usage patterns of bacterial genomes using the self-organizing map
-
H.C. Wang, J. Badger, P. Kearney, and M. Li Analysis of codon usage patterns of bacterial genomes using the self-organizing map Mol. Biol. Evol. 18 2001 792 800
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 792-800
-
-
Wang, H.C.1
Badger, J.2
Kearney, P.3
Li, M.4
-
38
-
-
0142093984
-
Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis
-
Q. Tu, and D. Ding Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis FEMS Microbiol. Lett. 221 2003 269 275
-
(2003)
FEMS Microbiol. Lett.
, vol.221
, pp. 269-275
-
-
Tu, Q.1
Ding, D.2
-
39
-
-
0242500968
-
Informatics for unveiling hidden genome signatures
-
T. Abe, S. Kanaya, M. Kinouchi, Y. Ichiba, T. Kozuki, and T. Ikemura Informatics for unveiling hidden genome signatures Genome Res. 13 2003 693 702
-
(2003)
Genome Res.
, vol.13
, pp. 693-702
-
-
Abe, T.1
Kanaya, S.2
Kinouchi, M.3
Ichiba, Y.4
Kozuki, T.5
Ikemura, T.6
-
40
-
-
0034727087
-
The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum
-
A. Ruepp, W. Graml, M.L. Santos-Martinez, K.K. Koretke, C. Volker, and H.W. Mewes The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum Nature 407 2000 508 513
-
(2000)
Nature
, vol.407
, pp. 508-513
-
-
Ruepp, A.1
Graml, W.2
Santos-Martinez, M.L.3
Koretke, K.K.4
Volker, C.5
Mewes, H.W.6
-
41
-
-
0035106010
-
Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria
-
C.L. Nesbø, S. L'Haridon, K.O. Stetter, and W.F. Doolittle Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria Mol. Biol. Evol. 18 2001 362 375
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 362-375
-
-
Nesbø, C.L.1
L'Haridon, S.2
Stetter, K.O.3
Doolittle, W.F.4
-
42
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
S. Garcia-Vallvé, 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-Vallvé, S.1
Romeu, A.2
Palau, J.3
-
43
-
-
0242424342
-
Targeting clusters of transferred genes in Thermotoga maritima
-
C.L. Nesbø, and W.F. Doolittle Targeting clusters of transferred genes in Thermotoga maritima Environ. Microbiol. 5 2003 1144 1154
-
(2003)
Environ. Microbiol.
, vol.5
, pp. 1144-1154
-
-
Nesbø, C.L.1
Doolittle, W.F.2
-
44
-
-
0642312312
-
The source of laterally transferred genes in bacterial genomes
-
V. Daubin, E. Lerat, and G. Perrière The source of laterally transferred genes in bacterial genomes Genome Biol. 4 2003 R57
-
(2003)
Genome Biol.
, vol.4
, pp. 57
-
-
Daubin, V.1
Lerat, E.2
Perrière, G.3
-
45
-
-
0034163439
-
Horizontal gene transfer and the origin of species: Lessons from bacteria
-
F. de la Cruz, and J. Davies Horizontal gene transfer and the origin of species: lessons from bacteria Trends Microbiol. 8 2000 128 133
-
(2000)
Trends Microbiol.
, vol.8
, pp. 128-133
-
-
De La Cruz, F.1
Davies, J.2
-
47
-
-
2042421069
-
Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease
-
D.M. Faguy Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease BMC Infect. Dis. 3 2003 13
-
(2003)
BMC Infect. Dis.
, vol.3
, pp. 13
-
-
Faguy, D.M.1
-
48
-
-
1542327668
-
Trends between gene content and genome size in prokaryotic species with larger genomes
-
K.T. Konstantinidis, and J.M. Tiedje Trends between gene content and genome size in prokaryotic species with larger genomes Proc. Natl. Acad. Sci. U. S. A. 101 2004 3160 3165
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, pp. 3160-3165
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
49
-
-
0031945225
-
Cell wall polymers in Archaea (Archaebacteria)
-
O. Kandler, and H. König Cell wall polymers in Archaea (Archaebacteria) Cell. Mol. Life Sci. 54 1998 305 308
-
(1998)
Cell. Mol. Life Sci.
, vol.54
, pp. 305-308
-
-
Kandler, O.1
König, H.2
-
50
-
-
0032766490
-
Comparative genomics of the Archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell
-
K.S. Makarova, L. Aravind, M.Y. Galperin, N.V. Grishin, R.L. Tatusov, and Y.I. Wolf Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell Genome Res. 9 1999 608 628
-
(1999)
Genome Res.
, vol.9
, pp. 608-628
-
-
Makarova, K.S.1
Aravind, L.2
Galperin, M.Y.3
Grishin, N.V.4
Tatusov, R.L.5
Wolf, Y.I.6
-
51
-
-
0015598484
-
Aerobic bacteria occurring in the hind-gut of the cockroach, Blatta orientalis
-
N.R. Burgess, S.N. McDermott, and J. Whiting Aerobic bacteria occurring in the hind-gut of the cockroach, Blatta orientalis J. Hyg. (Lond.) 71 1973 1 7
-
(1973)
J. Hyg. (Lond.)
, vol.71
, pp. 1-7
-
-
Burgess, N.R.1
McDermott, S.N.2
Whiting, J.3
-
52
-
-
0032777154
-
Insights into the evolutionary process of genome degradation
-
J.O. Andersson, and S.G. Andersson Insights into the evolutionary process of genome degradation Curr. Opin. Genet. Dev. 9 1999 664 671
-
(1999)
Curr. Opin. Genet. Dev.
, vol.9
, pp. 664-671
-
-
Andersson, J.O.1
Andersson, S.G.2
-
53
-
-
0035931926
-
Massive gene decay in the leprosy bacillus
-
S.T. Cole, K. Eiglmeier, J. Parkhill, K.D. James, N.R. Thomson, and P.R. Wheeler Massive gene decay in the leprosy bacillus Nature 409 2001 1007 1011
-
(2001)
Nature
, vol.409
, pp. 1007-1011
-
-
Cole, S.T.1
Eiglmeier, K.2
Parkhill, J.3
James, K.D.4
Thomson, N.R.5
Wheeler, P.R.6
-
54
-
-
0035479142
-
Deletional bias and the evolution of bacterial genomes
-
A. Mira, H. Ochman, and N.A. Moran Deletional bias and the evolution of bacterial genomes Trends Genet. 17 2001 589 596
-
(2001)
Trends Genet.
, vol.17
, pp. 589-596
-
-
Mira, A.1
Ochman, H.2
Moran, N.A.3
-
55
-
-
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
-
56
-
-
0028027521
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Hyperrecombination in the terminus region of the Escherichia coli chromosome: Possible relation to nucleoid organization
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J. Louarn, F. Cornet, V. Francois, J. Patte, and J.M. Louarn Hyperrecombination in the terminus region of the Escherichia coli chromosome: possible relation to nucleoid organization J. Bacteriol. 176 1994 7524 7531
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(1994)
J. Bacteriol.
, vol.176
, pp. 7524-7531
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Louarn, J.1
Cornet, F.2
Francois, V.3
Patte, J.4
Louarn, J.M.5
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