-
1
-
-
78449312755
-
-
Accelrys Software Inc, formerly Genetics Computer Group Inc (GCG). 10188 Telesis Court, Suite 100. San Diego, CA 92121 USA
-
Accelrys Software Inc, formerly Genetics Computer Group Inc (GCG). 10188 Telesis Court, Suite 100. San Diego, CA 92121, USA.
-
(2000)
-
-
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
-
3
-
-
0030801002
-
G apped BLASTand PSI-BLAST: a new generation of protein database search programs
-
Altschul, S.F. et al. (1997)G apped BLASTand PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
4
-
-
33751099863
-
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures
-
Andersen, P.H. et al. (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci., 15, 2558-2567.
-
(2006)
Protein Sci
, vol.15
, pp. 2558-2567
-
-
Andersen, P.H.1
-
5
-
-
75549090745
-
AntigenDB: an immunoinformatics database of pathogen antigens
-
Ansari,H.R. et al. (2010) AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res., 38(Suppl. 1), D847-D853.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.SUPPL. 1
-
-
Ansari, H.R.1
-
6
-
-
0034948896
-
A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes
-
Baldi,P. and Long,A.D. (2001) A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics, 17, 509-519.
-
(2001)
Bioinformatics
, vol.17
, pp. 509-519
-
-
Baldi, P.1
Long, A.D.2
-
7
-
-
48849115545
-
A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi
-
Barbour,A.G. et al. (2008) A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi. Infect. Immun., 76, 3374-3389.
-
(2008)
Infect. Immun.
, vol.76
, pp. 3374-3389
-
-
Barbour, A.G.1
-
8
-
-
0141514712
-
External validation is necessary in prediction research: a clinical example
-
Bleeker,S.E. et al. (2003) External validation is necessary in prediction research: a clinical example. J. Clin. Epidemiol., 56, 826-832.
-
(2003)
J. Clin. Epidemiol.
, vol.56
, pp. 826-832
-
-
Bleeker, S.E.1
-
9
-
-
11144246404
-
Benchmarking B cell epitope prediction: underperformance of existing methods
-
Blythe, M.J. and Flower, D.R. (2005) Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci., 14, 246-248.
-
(2005)
Protein Sci
, vol.14
, pp. 246-248
-
-
Blythe, M.J.1
Flower, D.R.2
-
11
-
-
23144465987
-
SCRATCH: a protein structure and structural feature prediction server
-
Cheng, J. et al. (2005) SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res., 33(Suppl. 2), W72-W76.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.SUPPL. 2
-
-
Cheng, J.1
-
12
-
-
33745101459
-
DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks
-
Cheng, J. et al. (2006) DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks. Data Min. Knowl. Discov., 13, 1-10.
-
(2006)
Data Min. Knowl. Discov.
, vol.13
, pp. 1-10
-
-
Cheng, J.1
-
13
-
-
54249152284
-
Sick lecelltraitis associated with a delayed on set of Malaria: implications for time-to-event analysis in clinical studies of Malaria
-
Crompton,P.D.etal.(2008)SicklecelltraitisassociatedwithadelayedonsetofMalaria: implications for time-to-event analysis in clinical studies of Malaria. J. Infect. Dis., 198, 1265-1275.
-
(2008)
J. Infect. Dis.
, vol.198
, pp. 1265-1275
-
-
Crompton, P.D.1
-
14
-
-
77951078453
-
A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray
-
Crompton,P.D. et al. (2010) A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proc. Natl Acad. Sci., 107, 6958-6963.
-
(2010)
Proc. Natl Acad. Sci.
, vol.107
, pp. 6958-6963
-
-
Crompton, P.D.1
-
15
-
-
20044369888
-
Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery
-
Davies,D.H. et al. (2005) Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc. Natl Acad. Sci., 102, 547-552.
-
(2005)
Proc. Natl Acad. Sci.
, vol.102
, pp. 547-552
-
-
Davies, D.H.1
-
16
-
-
0000259511
-
Approximate statistical tests for comparing supervised classification learning algorithms
-
Dietterich,T.G. (1998) Approximate statistical tests for comparing supervised classification learning algorithms. Neural Comput., 10, 1895-1923.
-
(1998)
Neural Comput
, vol.10
, pp. 1895-1923
-
-
Dietterich, T.G.1
-
17
-
-
80053403826
-
Ensemble methods in machine learning
-
Dietterich,T.G. (2000) Ensemble methods in machine learning. Lect. Notes Comput. Sci., 1857, 1-15.
-
(2000)
Lect. Notes Comput. Sci.
, vol.1857
, pp. 1-15
-
-
Dietterich, T.G.1
-
18
-
-
33845195440
-
Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties
-
Doytchinova,I.A. and Flower,D.R. (2007a) Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties. Vaccine, 25, 856-866.
-
(2007)
Vaccine
, vol.25
, pp. 856-866
-
-
Doytchinova, I.A.1
Flower, D.R.2
-
19
-
-
33847031827
-
VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines
-
Doytchinova,I.A. and Flower,D.R. (2007b)VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8,4.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 4
-
-
Doytchinova, I.A.1
Flower, D.R.2
-
20
-
-
74449088827
-
Bioinformatic approach for identifying parasite and fungal candidate subunit vaccines
-
Doytchinova,I.A. and Flower,D.R. (2008) Bioinformatic approach for identifying parasite and fungal candidate subunit vaccines. Open Vaccine J., 1, 22-26.
-
(2008)
Open Vaccine J
, vol.1
, pp. 22-26
-
-
Doytchinova, I.A.1
Flower, D.R.2
-
22
-
-
34447577676
-
Immunodominant Francisella tularensis antigens identified using proteome microarray
-
Eyles,J.E. et al. (2007) Immunodominant Francisella tularensis antigens identified using proteome microarray. Proteomics, 7, 2172-2183.
-
(2007)
Proteomics
, vol.7
, pp. 2172-2183
-
-
Eyles, J.E.1
-
23
-
-
29144499905
-
Working set selection using second order information for training support vector machines
-
Fan,R.E. et al. (2005) Working set selection using second order information for training support vector machines. J. Mach. Learn. Res., 6, 1889-1918.
-
(2005)
J. Mach. Learn. Res.
, vol.6
, pp. 1889-1918
-
-
Fan, R.E.1
-
24
-
-
69449101951
-
A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens
-
Felgner,P.L. et al. (2009) A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Proc. Natl Acad. Sci., 106, 13499- 13504.
-
(2009)
Proc. Natl Acad. Sci.
, vol.106
, pp. 13499-13504
-
-
Felgner, P.L.1
-
25
-
-
34248581488
-
Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools
-
Greenbaum,J.A. et al. (2007) Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J. Mol. Recogn., 20, 75-82.
-
(2007)
J. Mol. Recogn.
, vol.20
, pp. 75-82
-
-
Greenbaum, J.A.1
-
26
-
-
0000448982
-
Prediction of protein antigenic determinants from amino acid sequences
-
Hopp,T.P. and Woods,K.R. (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl Acad. Sci. USA, 78, 3824-3828.
-
(1981)
Proc. Natl Acad. Sci. USA
, vol.78
, pp. 3824-3828
-
-
Hopp, T.P.1
Woods, K.R.2
-
27
-
-
11244346557
-
Variance stabilization applied to microarray data calibration and to the quantification of differential expression
-
Huber,W. et al. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18(Suppl. 1), S96-S104.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Huber, W.1
-
28
-
-
32144443802
-
A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli
-
Idicula-Thomas,S. et al. (2006) A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli. Bioinformatics, 22, 278-284.
-
(2006)
Bioinformatics
, vol.22
, pp. 278-284
-
-
Idicula-Thomas, S.1
-
29
-
-
0019287872
-
Thermostability and aliphatic index of globular proteins
-
Ikai,A. (1980) Thermostability and aliphatic index of globular proteins. J. Biochem., 88, 1895-1898.
-
(1980)
J. Biochem.
, vol.88
, pp. 1895-1898
-
-
Ikai, A.1
-
30
-
-
85164392958
-
A study of cross-validation and bootstrap for accuracy estimation and model selection
-
Morgan Kaufmann, San Francisco, CA, USA
-
Kohavi,R. (1995) A study of cross-validation and bootstrap for accuracy estimation and model selection. In Proceedings of the 14th International Joint Conference on Artificial Intelligence. Morgan Kaufmann, San Francisco, CA, USA, pp. 1137-1143.
-
(1995)
Proceedings of the 14th International Joint Conference on Artificial Intelligence
, pp. 1137-1143
-
-
Kohavi, R.1
-
31
-
-
0031381525
-
Wrappers for feature subset selection
-
Kohavi,R. and John,G.H. (1997) Wrappers for feature subset selection. Artif. Intell., 97, 273-324.
-
(1997)
Artif. Intell.
, vol.97
, pp. 273-324
-
-
Kohavi, R.1
John, G.H.2
-
32
-
-
0025605617
-
A semi-empirical method for prediction of antigenic determinants on protein antigens
-
Kolaskar,A.S. and Tongaonkar,P.C. (1990) A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett., 276, 172-174.
-
(1990)
FEBS Lett
, vol.276
, pp. 172-174
-
-
Kolaskar, A.S.1
Tongaonkar, P.C.2
-
33
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
-
Krogh,A. et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 567-580
-
-
Krogh, A.1
-
34
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte,J. and Doolittle,R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157, 105-132.
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
35
-
-
33751104704
-
Improved method for predicting linear B-cell epitopes
-
Larsen,J. et al. (2006) Improved method for predicting linear B-cell epitopes. Immun. Res., 2,2.
-
(2006)
Immun. Res.
, vol.2
, pp. 2
-
-
Larsen, J.1
-
36
-
-
77955286458
-
Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens
-
Liang,L. et al. (2010)L arge scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens. PLoS Negl. Trop. Dis., 4, e673.
-
(2010)
PLoS Negl. Trop. Dis.
, vol.4
-
-
Liang, L.1
-
37
-
-
69949162927
-
SOLpro: accurate sequence-based prediction of protein solubility
-
Magnan,C.N. et al. (2009) SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics, 25, 2200-2207.
-
(2009)
Bioinformatics
, vol.25
, pp. 2200-2207
-
-
Magnan, C.N.1
-
38
-
-
77950420271
-
Serological profiling of a Candida albicans protein microarray reveals permanent host-pathogen interplay and stage-specific responses during Candidemia
-
Mochon,A.B. et al. (2010) Serological profiling of a Candida albicans protein microarray reveals permanent host-pathogen interplay and stage-specific responses during Candidemia. PLoS Pathog., 6, e1000827.
-
(2010)
PLoS Pathog
, vol.6
-
-
Mochon, A.B.1
-
39
-
-
0032972509
-
PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization
-
Nakai,K. and Horton,P. (1999) PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization. Trends Biochem. Sci., 24, 34.
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 34
-
-
Nakai, K.1
Horton, P.2
-
40
-
-
0037263777
-
BEPITOPE: predicting the location of continuous epitopes and patterns in proteins
-
Odorico,M. and Pellequer,J.L. (2003) BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. J. Mol. Recogn., 16, 20-22.
-
(2003)
J. Mol. Recogn.
, vol.16
, pp. 20-22
-
-
Odorico, M.1
Pellequer, J.L.2
-
41
-
-
0025272240
-
Rapid and sensitive sequence comparison with FASTP and FASTA
-
Pearson,W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 183, 63-98.
-
(1990)
Methods Enzymol
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
42
-
-
20944447214
-
The immune epitope database and analysis resource: from vision to blueprint
-
Peters,B. et al. (2005) The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol., 3, 379-381.
-
(2005)
PLoS Biol
, vol.3
, pp. 379-381
-
-
Peters, B.1
-
43
-
-
0034629284
-
Identification of vaccine candidates against serogroup B Meningococcus by whole-genome sequencing
-
Pizza,M. et al. (2000) Identification of vaccine candidates against serogroup B Meningococcus by whole-genome sequencing. Science, 287, 1816-1820.
-
(2000)
Science
, vol.287
, pp. 1816-1820
-
-
Pizza, M.1
-
44
-
-
37749042370
-
Antibody-protein interactions: benchmark datasets and prediction tools evaluation
-
Ponomarenko,J. and Bourne,P. (2007) Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct. Biol., 7, 64.
-
(2007)
BMC Struct. Biol.
, vol.7
, pp. 64
-
-
Ponomarenko, J.1
Bourne, P.2
-
45
-
-
0035925596
-
Reverse vaccinology, a genome-based approach to vaccine development
-
Rappuoli,R. (2001) Reverse vaccinology, a genome-based approach to vaccine development. Vaccine, 19, 2688-2691.
-
(2001)
Vaccine
, vol.19
, pp. 2688-2691
-
-
Rappuoli, R.1
-
46
-
-
0142147304
-
Reverse vaccinology and genomics
-
Rappuoli,R. and Covacci,A. (2003) Reverse vaccinology and genomics. Science, 302, 602.
-
(2003)
Science
, vol.302
, pp. 602
-
-
Rappuoli, R.1
Covacci, A.2
-
47
-
-
32344453260
-
Characterization and identification of vaccine candidate proteins through analysis of the groupAStreptococcus surface proteome
-
Rodriguez-Ortega,M.J. et al. (2006) Characterization and identification of vaccine candidate proteins through analysis of the groupAStreptococcus surface proteome. Nat. Biotech., 24, 191-197.
-
(2006)
Nat. Biotech.
, vol.24
, pp. 191-197
-
-
Rodriguez-Ortega, M.J.1
-
48
-
-
59249095901
-
A machine-learning approach for predicting B-cell epitopes
-
Rubinstein,N.D. et al. (2009) A machine-learning approach for predicting B-cell epitopes. Mol. Immunol., 46, 840-847.
-
(2009)
Mol. Immunol.
, vol.46
, pp. 840-847
-
-
Rubinstein, N.D.1
-
49
-
-
25444509811
-
Bcipep: a database of B-cell epitopes
-
Saha,S. et al. (2005) Bcipep: a database of B-cell epitopes. BMC Genomics, 6, 79.
-
(2005)
BMC Genomics
, vol.6
, pp. 79
-
-
Saha, S.1
-
50
-
-
33748254730
-
Prediction of continuous B-cell epitopes in an antigen using recurrent neural network
-
Saha,S. and Raghava,G.P.S. (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins Struct. Funct. Bioinformatics, 65, 40-48.
-
(2006)
Proteins Struct. Funct. Bioinformatics
, vol.65
, pp. 40-48
-
-
Saha, S.1
Raghava, G.P.S.2
-
51
-
-
0024910640
-
Development and application of synthetic peptides as vaccines
-
Schmidt,M.A. (1989) Development and application of synthetic peptides as vaccines. Biotechnol. Adv., 7, 187-213.
-
(1989)
Biotechnol. Adv.
, vol.7
, pp. 187-213
-
-
Schmidt, M.A.1
-
52
-
-
35748966976
-
Protein solubility: sequence based prediction and experimental verification
-
Smialowski,P. et al. (2007) Protein solubility: sequence based prediction and experimental verification. Bioinformatics, 23, 2536-2542.
-
(2007)
Bioinformatics
, vol.23
, pp. 2536-2542
-
-
Smialowski, P.1
-
53
-
-
33745030152
-
Machine learning approaches for prediction of linear B-cell epitopes on proteins
-
Söllner,J. and Mayer,B. (2006) Machine learning approaches for prediction of linear B-cell epitopes on proteins. J. Mol. Recogn., 19, 200-208.
-
(2006)
J. Mol. Recogn.
, vol.19
, pp. 200-208
-
-
Söllner, J.1
Mayer, B.2
-
54
-
-
33747886203
-
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
-
Sundaresh,S. et al. (2006) Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics, 22, 1760-1766.
-
(2006)
Bioinformatics
, vol.22
, pp. 1760-1766
-
-
Sundaresh, S.1
-
55
-
-
34547852232
-
From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis
-
Sundaresh,S. et al. (2007) From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. Bioinformatics, 23, i508-i518.
-
(2007)
Bioinformatics
, vol.23
-
-
Sundaresh, S.1
-
56
-
-
45449086674
-
PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure
-
Sweredoski,M.J. and Baldi,P. (2008) PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics, 24, 1459-1460.
-
(2008)
Bioinformatics
, vol.24
, pp. 1459-1460
-
-
Sweredoski, M.J.1
Baldi, P.2
-
57
-
-
60749128663
-
COBEpro: a novel system for predicting continuous B-cell epitopes
-
Sweredoski,M.J. and Baldi,P. (2009) COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng. Des. Sel., 22, 113-120.
-
(2009)
Protein Eng. Des. Sel.
, vol.22
, pp. 113-120
-
-
Sweredoski, M.J.1
Baldi, P.2
-
58
-
-
33846041078
-
The Universal Protein Resource
-
The UniProt Consortium
-
The UniProt Consortium (2007) The Universal Protein Resource. Nucleic Acids Res., 35, D193.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
-
59
-
-
0022668738
-
Location of 'continuous' antigenic determinants in the protruding regions of proteins
-
Thornton,J.M. et al. (1986) Location of 'continuous' antigenic determinants in the protruding regions of proteins. EMBO J., 5, 409-413.
-
(1986)
EMBO J
, vol.5
, pp. 409-413
-
-
Thornton, J.M.1
-
60
-
-
28544438391
-
AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data
-
Toseland,C. et al. (2005) AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immun. Res., 1,4.
-
(2005)
Immun. Res.
, vol.1
, pp. 4
-
-
Toseland, C.1
-
61
-
-
77955393671
-
Identification of the feline humoral immune response to Bartonella henselae infection by protein microarray
-
Vigil,A. et al. (2010) Identification of the feline humoral immune response to Bartonella henselae infection by protein microarray. PLoS ONE, 5, e11447.
-
(2010)
PLoS ONE
, vol.5
-
-
Vigil, A.1
-
62
-
-
0022236552
-
Prediction of sequential antigenic regions in proteins
-
Welling,G.W. et al. (1985) Prediction of sequential antigenic regions in proteins. FEBS Lett., 188, 215-218.
-
(1985)
FEBS Lett
, vol.188
, pp. 215-218
-
-
Welling, G.W.1
-
63
-
-
0003957032
-
-
2nd edn, M. Kaufmann Series in Data Management Systems San Francisco, CA, USA
-
Witten,I.H. and Frank,E. (2005) Data Mining: Practical Machine Learning Tools and Techniques, 2nd edn, M. Kaufmann Series in Data Management Systems.San Francisco, CA, USA.
-
(2005)
Data Mining: Practical Machine Learning Tools and Techniques
-
-
Witten, I.H.1
Frank, E.2
-
64
-
-
0027215340
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DNA and peptide sequences and chemical processes multivariately modelled by principal component analysis and partial least-squares projections to latent structures
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Wold,S. et al. (1993) DNA and peptide sequences and chemical processes multivariately modelled by principal component analysis and partial least-squares projections to latent structures. Anal. Chim. Acta, 277, 239-253.
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(1993)
Anal. Chim. Acta
, vol.277
, pp. 239-253
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Wold, S.1
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