-
1
-
-
18744382506
-
PROTTEST: Selection of best-fit models of protein evolution
-
doi:10.1093/bioinformatics/bti263
-
Abascal, F., Zardoya, R. & Posada, D. 2005 PROTTEST: selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105. (doi:10.1093/bioinformatics/bti263)
-
(2005)
Bioinformatics
, vol.21
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
0141993683
-
A functional link between RubisCO-like protein of Bacillus and photosynthetic RubisCO
-
doi:10.1126/science.1086997
-
Ashida, H., Saito, Y., Kojima, C., Kobayashi, K., Ogasawara, N. & Yokota, A. 2003 A functional link between RubisCO-like protein of Bacillus and photosynthetic RubisCO. Science 302, 286-290. (doi:10.1126/science.1086997)
-
(2003)
Science
, vol.302
, pp. 286-290
-
-
Ashida, H.1
Saito, Y.2
Kojima, C.3
Kobayashi, K.4
Ogasawara, N.5
Yokota, A.6
-
3
-
-
20444419762
-
Was photosynthetic RubisCO recruited by acquisitive evolution from RubisCO-like proteins involved in sulfur metabolism?
-
doi:10.1016/j.resmic. 2005.01.014
-
Ashida, H., Danchin, A. & Yokota, A. 2005 Was photosynthetic RubisCO recruited by acquisitive evolution from RubisCO-like proteins involved in sulfur metabolism? Res. Microbiol. 156, 611-618. (doi:10.1016/j.resmic. 2005.01.014)
-
(2005)
Res. Microbiol
, vol.156
, pp. 611-618
-
-
Ashida, H.1
Danchin, A.2
Yokota, A.3
-
4
-
-
33747687786
-
A new RubisCO-like protein coexists with a photosynthetic RubisCO in the planktonic cyanobacteria Microcystis
-
doi:10.1074/jbc.M602973200
-
Carre-Mlouka, A. et al. 2006 A new RubisCO-like protein coexists with a photosynthetic RubisCO in the planktonic cyanobacteria Microcystis. J. Biol. Chem. 281, 24 462-24 471. (doi:10.1074/jbc.M602973200)
-
(2006)
J. Biol. Chem
, vol.281
-
-
Carre-Mlouka, A.1
-
5
-
-
0026559592
-
The consistency of several phylogeny-inference methods under varying evolutionary rates
-
DeBry, R. W. 1992 The consistency of several phylogeny-inference methods under varying evolutionary rates. Mol. Biol. Evol. 9, 537-551.
-
(1992)
Mol. Biol. Evol
, vol.9
, pp. 537-551
-
-
DeBry, R.W.1
-
6
-
-
2642524290
-
2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation
-
doi:10.1016/j.femsre.2004.01. 002
-
2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation. FEMS Microbiol. Rev. 28, 353-376. (doi:10.1016/j.femsre.2004.01. 002)
-
(2004)
FEMS Microbiol. Rev
, vol.28
, pp. 353-376
-
-
Dubbs, J.M.1
Tabita, F.R.2
-
7
-
-
0033582465
-
Presence of a structurally novel type ribulose-bisphosphate carboxylase/ oxygenase in the hyperthermophilic archaeo, Pyrococcus kodakaraensis KOD1
-
doi:10.1074/jbc.274.8.5078
-
Ezaki, S., Maeda, N., Kishimoto, T., Atomi, H. & Imanaka, T. 1999 Presence of a structurally novel type ribulose-bisphosphate carboxylase/ oxygenase in the hyperthermophilic archaeo, Pyrococcus kodakaraensis KOD1. J. Biol. Chem. 274, 5078-5082. (doi:10.1074/jbc.274.8.5078)
-
(1999)
J. Biol. Chem
, vol.274
, pp. 5078-5082
-
-
Ezaki, S.1
Maeda, N.2
Kishimoto, T.3
Atomi, H.4
Imanaka, T.5
-
8
-
-
0038643328
-
Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea
-
doi:10.1128/JB.185.10.3049-3059.2003
-
Finn, M. W. & Tabita, F. R. 2003 Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea. J. Bacteriol. 185, 3049-3059. (doi:10.1128/JB.185.10.3049-3059.2003)
-
(2003)
J. Bacteriol
, vol.185
, pp. 3049-3059
-
-
Finn, M.W.1
Tabita, F.R.2
-
9
-
-
4544272017
-
Modified pathway to synthesize ribulose 1,5-bisphosphate in methanogenic archaea
-
doi:10.1128/JB.186.19.6360-6366.2004
-
Finn, M. W. & Tabita, F. R. 2004 Modified pathway to synthesize ribulose 1,5-bisphosphate in methanogenic archaea. J. Bacteriol. 186, 6360-6366. (doi:10.1128/JB.186.19.6360-6366.2004)
-
(2004)
J. Bacteriol
, vol.186
, pp. 6360-6366
-
-
Finn, M.W.1
Tabita, F.R.2
-
10
-
-
0027096383
-
A methanogenic archaeon from Ace Lake, Antarctica - Methanococcoides-Burtonii Sp-Nov
-
Franzmann, P. D., Springer, N., Ludwig, W., Demacario, E. C. & Rohde, M. 1992 A methanogenic archaeon from Ace Lake, Antarctica - Methanococcoides-Burtonii Sp-Nov. Syst. Appl. Microbiol. 15, 573-581.
-
(1992)
Syst. Appl. Microbiol
, vol.15
, pp. 573-581
-
-
Franzmann, P.D.1
Springer, N.2
Ludwig, W.3
Demacario, E.C.4
Rohde, M.5
-
11
-
-
10044245551
-
Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry
-
doi:10.1021/pr0498988
-
Goodchild, A., Raftery, M., Saunders, N. F. W., Guilhaus, M. & Cavicchioli, R. 2004a Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. J. Proteome Res. 3, 1164-1176. (doi:10.1021/pr0498988)
-
(2004)
J. Proteome Res
, vol.3
, pp. 1164-1176
-
-
Goodchild, A.1
Raftery, M.2
Saunders, N.F.W.3
Guilhaus, M.4
Cavicchioli, R.5
-
12
-
-
3142596395
-
A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii
-
doi:10.1111/j.1365-2958.2004.04130.x
-
Goodchild, A., Saunders, N. F. W., Ertan, H., Raftery, M., Guilhaus, M., Curmi, P. M. G. & Cavicchioli, R. 2004b A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii. Mol. Microbiol. 53, 309-321. (doi:10.1111/j.1365-2958.2004.04130.x)
-
(2004)
Mol. Microbiol
, vol.53
, pp. 309-321
-
-
Goodchild, A.1
Saunders, N.F.W.2
Ertan, H.3
Raftery, M.4
Guilhaus, M.5
Curmi, P.M.G.6
Cavicchioli, R.7
-
13
-
-
17444384908
-
Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT
-
doi:10.1021/pr049760p
-
Goodchild, A., Raftery, M., Saunders, N. F. W., Guilhaus, M. & Cavicchioli, R. 2005 Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT. J. Proteome Res. 4, 473-480. (doi:10.1021/pr049760p)
-
(2005)
J. Proteome Res
, vol.4
, pp. 473-480
-
-
Goodchild, A.1
Raftery, M.2
Saunders, N.F.W.3
Guilhaus, M.4
Cavicchioli, R.5
-
14
-
-
0035836695
-
A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress
-
doi:10.1073/pnas. 081610398
-
Hanson, T. E. & Tabita, F. R. 2001 A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc. Natl Acad. Sci. USA 98, 4397-4402. (doi:10.1073/pnas. 081610398)
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 4397-4402
-
-
Hanson, T.E.1
Tabita, F.R.2
-
15
-
-
0347506350
-
Insights into the stress response and sulfur metabolism revealed by proteome analysis of a Chlorobium tepidum mutant lacking the RubisCO-like protein
-
doi:10.1023/B:PRES.0000006829.41444.3d
-
Hanson, T. E. & Tabita, F. R. 2003 Insights into the stress response and sulfur metabolism revealed by proteome analysis of a Chlorobium tepidum mutant lacking the RubisCO-like protein. Photosynth. Res. 78, 231-248. (doi:10.1023/B:PRES.0000006829.41444.3d)
-
(2003)
Photosynth. Res
, vol.78
, pp. 231-248
-
-
Hanson, T.E.1
Tabita, F.R.2
-
16
-
-
34047237283
-
Mechanistic diversity in the RubisCO superfamily: The 'enolase' in the methionine salvage pathway in Geobacillus kaustophilus
-
doi:10.1021/bi7000483
-
Imker, H. J., Fedorov, A. A., Fedorov, E. V., Almo, S. C. & Gerlt, J. A. 2007 Mechanistic diversity in the RubisCO superfamily: the 'enolase' in the methionine salvage pathway in Geobacillus kaustophilus. Biochemistry 46, 4077-4089. (doi:10.1021/bi7000483)
-
(2007)
Biochemistry
, vol.46
, pp. 4077-4089
-
-
Imker, H.J.1
Fedorov, A.A.2
Fedorov, E.V.3
Almo, S.C.4
Gerlt, J.A.5
-
17
-
-
0034984584
-
Crystal structure of a novel-type archaeal RubisCO with pentagonal symmetry
-
doi:10.1016/S0969-2126(01)00608- 6
-
Kitano, K., Maeda, N., Fukui, T., Atomi, H., Imanaka, T. & Miki, K. 2001 Crystal structure of a novel-type archaeal RubisCO with pentagonal symmetry. Structure 9, 473-481. (doi:10.1016/S0969-2126(01)00608- 6)
-
(2001)
Structure
, vol.9
, pp. 473-481
-
-
Kitano, K.1
Maeda, N.2
Fukui, T.3
Atomi, H.4
Imanaka, T.5
Miki, K.6
-
18
-
-
33847716348
-
2 specificity
-
doi:10.1074/jbc.M609399200
-
2 specificity. J. Biol. Chem. 282, 1341-1351. (doi:10.1074/jbc.M609399200)
-
(2007)
J. Biol. Chem
, vol.282
, pp. 1341-1351
-
-
Kreel, N.E.1
Tabita, F.R.2
-
19
-
-
33745634395
-
CD-HIT: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
doi:10.1093/bioinformatics/btl158
-
Li, W. & Godzik, A. 2006 CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659. (doi:10.1093/bioinformatics/btl158)
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
20
-
-
18944389308
-
Crystal structure of a RubisCO-like protein from the green sulfur bacterium Chlorobium tepidum
-
doi:10.1016/j.str. 2005.02.017
-
Li, H., Sawaya, M. R., Tabita, F. R. & Eisenberg, D. 2005 Crystal structure of a RubisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure 13, 779-789. (doi:10.1016/j.str. 2005.02.017)
-
(2005)
Structure
, vol.13
, pp. 779-789
-
-
Li, H.1
Sawaya, M.R.2
Tabita, F.R.3
Eisenberg, D.4
-
22
-
-
33645023824
-
Can improvement in photosynthesis increase crop yields?
-
doi:10.1111/j.1365-3040.2005.01493.x
-
Long, S. P., Zhu, X.-G., Naidu, S. L. & Ort, D. R. 2006b Can improvement in photosynthesis increase crop yields? Plant Cell Environ. 29, 315-330. (doi:10.1111/j.1365-3040.2005.01493.x)
-
(2006)
Plant Cell Environ
, vol.29
, pp. 315-330
-
-
Long, S.P.1
Zhu, X.-G.2
Naidu, S.L.3
Ort, D.R.4
-
23
-
-
0025741291
-
Crystal structure of activated ribulose-1,5-bisphosphate carboxylase complexed with its substrate, ribulose-1,5-bisphosphate
-
Lundqvist, T. & Schneider, G. 1991 Crystal structure of activated ribulose-1,5-bisphosphate carboxylase complexed with its substrate, ribulose-1,5-bisphosphate. J. Biol. Chem. 266, 12 604-12 611.
-
(1991)
J. Biol. Chem
, vol.266
-
-
Lundqvist, T.1
Schneider, G.2
-
24
-
-
33847643705
-
Hon-yaku: A biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
-
doi:10.1186/1471-2105-8- 47
-
Makita, Y., de Hoon, M. J. & Danchin, A. 2007 Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. BMC Bioinform. 8, 47. (doi:10.1186/1471-2105-8- 47)
-
(2007)
BMC Bioinform
, vol.8
, pp. 47
-
-
Makita, Y.1
de Hoon, M.J.2
Danchin, A.3
-
25
-
-
0000528384
-
Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301
-
doi:10.1107/S090744499300530X
-
Newman, J., Branden, C. I. & Jones, T. A. 1993 Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301. Acta Crystallogr. Sect. D 49, 548-560. (doi:10.1107/S090744499300530X)
-
(1993)
Acta Crystallogr. Sect. D
, vol.49
, pp. 548-560
-
-
Newman, J.1
Branden, C.I.2
Jones, T.A.3
-
26
-
-
34047227131
-
The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: Organelle genomes of the smallest eukaryote are examples of compaction
-
doi:10.1093/molbev/msm012
-
Robbens, S., Derelle, E., Ferraz, C., Wuyts, J., Moreau, H. & Van de Peer, Y. 2007 The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction. Mol. Biol. Evol. 24, 956-968. (doi:10.1093/molbev/msm012)
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 956-968
-
-
Robbens, S.1
Derelle, E.2
Ferraz, C.3
Wuyts, J.4
Moreau, H.5
Van de Peer, Y.6
-
27
-
-
33847157932
-
Archaeal type III RubisCOs function in a pathway for AMP metabolism
-
doi:10.1126/science.1135999
-
Sato, T., Atomi, H. & Imanaka, T. 2007 Archaeal type III RubisCOs function in a pathway for AMP metabolism. Science 315, 1003-1006. (doi:10.1126/science.1135999)
-
(2007)
Science
, vol.315
, pp. 1003-1006
-
-
Sato, T.1
Atomi, H.2
Imanaka, T.3
-
28
-
-
17444376059
-
Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii
-
doi:10.1021/pr049797
-
Saunders, N. F. W., Goodchild, A., Raftery, M., Guilhaus, M., Curmi, P. M. G. & Cavicchioli, R. 2005 Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii. J. Proteome Res. 4, 464-472. (doi:10.1021/pr049797+)
-
(2005)
J. Proteome Res
, vol.4
, pp. 464-472
-
-
Saunders, N.F.W.1
Goodchild, A.2
Raftery, M.3
Guilhaus, M.4
Curmi, P.M.G.5
Cavicchioli, R.6
-
29
-
-
0041663412
-
Positive and negative bioselection of mutant forms of prokaryotic (cyanobacterial) ribulose-1, 5-bisphosphate carboxylase/oxygenase
-
doi:10.1016/S0022-2836(03)00786-1
-
Smith, S. A. & Tabita, F. R. 2003 Positive and negative bioselection of mutant forms of prokaryotic (cyanobacterial) ribulose-1, 5-bisphosphate carboxylase/oxygenase. J. Mol. Biol. 331, 557-569. (doi:10.1016/S0022-2836(03)00786-1)
-
(2003)
J. Mol. Biol
, vol.331
, pp. 557-569
-
-
Smith, S.A.1
Tabita, F.R.2
-
30
-
-
2942590258
-
Glycine 176 affects catalytic properties and stability of the Synechococcus sp. strain PCC 6301 ribulose 1,5-bisphosphate carboxylase/oxygenase
-
doi:10.1074/jbc.M401360200
-
Smith, S. A. & Tabita, F. R. 2004 Glycine 176 affects catalytic properties and stability of the Synechococcus sp. strain PCC 6301 ribulose 1,5-bisphosphate carboxylase/oxygenase. J. Biol. Chem. 279, 25 632-25 637. (doi:10.1074/jbc.M401360200)
-
(2004)
J. Biol. Chem
, vol.279
-
-
Smith, S.A.1
Tabita, F.R.2
-
31
-
-
0037001967
-
RubisCO: Structure, regulatory interactions, and possibilities for a better enzyme
-
doi:10.1146/annurev.arplant.53.100301. 135233
-
Spreitzer, R. J. & Salvucci, M. E. 2002 RubisCO: structure, regulatory interactions, and possibilities for a better enzyme. Annu. Rev. Plant Biol. 53, 449-475. (doi:10.1146/annurev.arplant.53.100301. 135233)
-
(2002)
Annu. Rev. Plant Biol
, vol.53
, pp. 449-475
-
-
Spreitzer, R.J.1
Salvucci, M.E.2
-
32
-
-
0032840522
-
Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective
-
doi:10.1023/A:1006211417981
-
Tabita, F. R. 1999 Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a different perspective. Photosynth. Res. 60, 1-28. (doi:10.1023/A:1006211417981)
-
(1999)
Photosynth. Res
, vol.60
, pp. 1-28
-
-
Tabita, F.R.1
-
33
-
-
37349069540
-
Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs
-
doi:10.1128/MMBR.00015-07
-
Tabita, F. R., Hanson, T. E., Li, H., Satagopan, S., Singh, J. & Chan, S. 2007 Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol. Mol. Biol. Rev. 71, 576-599. (doi:10.1128/MMBR.00015-07)
-
(2007)
Microbiol. Mol. Biol. Rev
, vol.71
, pp. 576-599
-
-
Tabita, F.R.1
Hanson, T.E.2
Li, H.3
Satagopan, S.4
Singh, J.5
Chan, S.6
-
34
-
-
34547781750
-
-
Tamura, K, Dudley, J, Nei, M. & Kumar, S. 2007 MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599, doi:10.1093/molbev/msm092
-
Tamura, K., Dudley, J., Nei, M. & Kumar, S. 2007 MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599. (doi:10.1093/molbev/msm092)
-
-
-
-
35
-
-
33646583168
-
Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases my be perfectly optimized
-
doi:10.1073/pnas.0600605103
-
Tcherkez, G. G. B., Farquhar, G. & Andrews, T. J. 2006 Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases my be perfectly optimized. Proc. Natl Acad. Sci. USA 103, 7246-7251. (doi:10.1073/pnas.0600605103)
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 7246-7251
-
-
Tcherkez, G.G.B.1
Farquhar, G.2
Andrews, T.J.3
-
36
-
-
33645635990
-
An unsupervised classification scheme for improving predictions of prokaryotic TIS
-
doi:10.1186/1471-2105-7-121
-
Tech, M. & Meinicke, P. 2006 An unsupervised classification scheme for improving predictions of prokaryotic TIS. BMC Bioinform. 7, 121. (doi:10.1186/1471-2105-7-121)
-
(2006)
BMC Bioinform
, vol.7
, pp. 121
-
-
Tech, M.1
Meinicke, P.2
-
37
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
doi:10.1093/nar/22.22.4673
-
Thompson, J. D., Higgins, D. G. & Gibson, T. J. 1994 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, 4673-4680. (doi:10.1093/nar/22.22.4673)
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
38
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
doi:10.1038/nature02340
-
Tyson, G. W. et al. 2004 Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43. (doi:10.1038/nature02340)
-
(2004)
Nature
, vol.428
, pp. 37-43
-
-
Tyson, G.W.1
-
39
-
-
0033027258
-
Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic archaea
-
Watson, G. M., Yu, J. P. & Tabita, F. R. 1999 Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic archaea. J. Bacteriol. 181, 1569-1575.
-
(1999)
J. Bacteriol
, vol.181
, pp. 1569-1575
-
-
Watson, G.M.1
Yu, J.P.2
Tabita, F.R.3
-
40
-
-
33947235074
-
The Sorcerer II global ocean sampling expedition: Expanding the universe of protein families
-
doi:10.1371/journal.pbio.0050016
-
Yooseph, S. et al. 2007 The Sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biol. 5, e16. (doi:10.1371/journal.pbio.0050016)
-
(2007)
PLoS Biol
, vol.5
-
-
Yooseph, S.1
-
41
-
-
0028053255
-
Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate
-
Zhang, K. Y., Cascio, D. & Eisenberg, D. 1994 Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate. Protein Sci. 3, 64-69.
-
(1994)
Protein Sci
, vol.3
, pp. 64-69
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Zhang, K.Y.1
Cascio, D.2
Eisenberg, D.3
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