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Volumn 53, Issue 12, 2013, Pages 3244-3261

Binary classification of a large collection of environmental chemicals from estrogen receptor assays by quantitative structure-activity relationship and machine learning methods

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICALS; COMPUTATIONAL CHEMISTRY; DECISION TREES; DISCRIMINANT ANALYSIS; ENDOCRINE DISRUPTERS; INFORMATION MANAGEMENT; ORGANIC POLLUTANTS; RISK ASSESSMENT; STRUCTURES (BUILT OBJECTS); SUPPORT VECTOR MACHINES; SUPPORT VECTOR REGRESSION;

EID: 84896504827     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400527b     Document Type: Article
Times cited : (57)

References (68)
  • 3
    • 77954035810 scopus 로고    scopus 로고
    • Environmental causes of cancer: Endocrine disruptors as carcinogens
    • Soto, A. M.; Sonnenschein, C. Environmental causes of cancer: endocrine disruptors as carcinogens Nat. Rev. Endocrinol. 2010, 6 (7) 363-370
    • (2010) Nat. Rev. Endocrinol. , vol.6 , Issue.7 , pp. 363-370
    • Soto, A.M.1    Sonnenschein, C.2
  • 4
    • 77955277910 scopus 로고    scopus 로고
    • Developmental programming: Impact of fetal exposure to endocrine-disrupting chemicals on gonadotropin-releasing hormone and estrogen receptor RNA in sheep hypothalamus
    • Mahoney, M. M.; Padmanabhan, V. Developmental programming: impact of fetal exposure to endocrine-disrupting chemicals on gonadotropin-releasing hormone and estrogen receptor RNA in sheep hypothalamus Toxicol. Appl. Pharmacol. 2010, 247 (2) 98-104
    • (2010) Toxicol. Appl. Pharmacol. , vol.247 , Issue.2 , pp. 98-104
    • Mahoney, M.M.1    Padmanabhan, V.2
  • 5
    • 0038746906 scopus 로고    scopus 로고
    • Cancer and developmental exposure to endocrine disruptors
    • Birnbaum, L. S.; Fenton, S. E. Cancer and developmental exposure to endocrine disruptors Environ. Health Perspect. 2003, 111 (4) 389-394
    • (2003) Environ. Health Perspect. , vol.111 , Issue.4 , pp. 389-394
    • Birnbaum, L.S.1    Fenton, S.E.2
  • 14
    • 84896523544 scopus 로고    scopus 로고
    • U.S. EPA, Officeof Pollution Prevention and Toxics (OPPT)chemical reviews and tools case study. (accessed September 4)
    • U.S. EPA, Officeof Pollution Prevention and Toxics (OPPT)chemical reviews and tools case study. http://www.who.int/ifcs/documents/forums/forum5/ precaution/epa-en.pdf (accessed September 4, 2013).
    • (2013)
  • 15
    • 84896527287 scopus 로고    scopus 로고
    • Overview: Office of Pollution Prevention and Toxics laws and programs. (accessed September 4)
    • Overview: Office of Pollution Prevention and Toxics laws and programs. http://www.epa.gov/opptintr/pubs/oppt101-032008.pdf (accessed September 4, 2013).
    • (2013)
  • 16
    • 77953981125 scopus 로고    scopus 로고
    • Computational toxicology as implemented by the U.S. EPA: Providing high throughput decision support tools for screening and assessing chemical exposure, hazard and risk
    • Kavlock, R. J.; Dix, D. J. Computational toxicology as implemented by the U.S. EPA: providing high throughput decision support tools for screening and assessing chemical exposure, hazard and risk J. Toxicol. Environ. Health B. Crit. Rev. 2010, 13 (2-4) 197-217
    • (2010) J. Toxicol. Environ. Health B. Crit. Rev. , vol.13 , Issue.24 , pp. 197-217
    • Kavlock, R.J.1    Dix, D.J.2
  • 21
    • 33845620001 scopus 로고    scopus 로고
    • The ToxCast program for prioritizing toxicity testing of environmental chemicals
    • Dix, D. J.; Houck, K. A.; Martin, M. T.; Richard, A. M.; Setzer, R. W.; Kavlock, R. J. The ToxCast program for prioritizing toxicity testing of environmental chemicals Toxicol. Sci. 2007, 95 (1) 5-12
    • (2007) Toxicol. Sci. , vol.95 , Issue.1 , pp. 5-12
    • Dix, D.J.1    Houck, K.A.2    Martin, M.T.3    Richard, A.M.4    Setzer, R.W.5    Kavlock, R.J.6
  • 22
    • 44849090379 scopus 로고    scopus 로고
    • A Comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model
    • Judson, R. S.; Elloumi, F.; Setzer, R. W.; Li, Z.; Shah, I. A Comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model BMC Bioinf. 2008, 9, 241
    • (2008) BMC Bioinf. , vol.9 , pp. 241
    • Judson, R.S.1    Elloumi, F.2    Setzer, R.W.3    Li, Z.4    Shah, I.5
  • 23
    • 77958493840 scopus 로고    scopus 로고
    • A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression
    • DiMaggio, P. A.; Subramani, A.; Judson, R. S.; Floudas, C. A. A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression Toxicol. Sci. 2010, 118 (1) 251-265
    • (2010) Toxicol. Sci. , vol.118 , Issue.1 , pp. 251-265
    • Dimaggio, P.A.1    Subramani, A.2    Judson, R.S.3    Floudas, C.A.4
  • 24
    • 77956964002 scopus 로고    scopus 로고
    • Best practices for QSAR model development, validation, and exploitation
    • Tropsha, A. Best practices for QSAR model development, validation, and exploitation Mol. Inf. 2010, 29, 476-488
    • (2010) Mol. Inf. , vol.29 , pp. 476-488
    • Tropsha, A.1
  • 25
    • 84882809589 scopus 로고    scopus 로고
    • Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches
    • Zhang, L.; Sedykh, A.; Tripathi, A.; Zhu, H.; Afantitis, A.; Mouchlis, V. D.; Melagraki, G.; Rusyn, I.; Tropsha, A. Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches Toxicol. Appl. Pharmacol. 2013, 272 (1) 67-76
    • (2013) Toxicol. Appl. Pharmacol. , vol.272 , Issue.1 , pp. 67-76
    • Zhang, L.1    Sedykh, A.2    Tripathi, A.3    Zhu, H.4    Afantitis, A.5    Mouchlis, V.D.6    Melagraki, G.7    Rusyn, I.8    Tropsha, A.9
  • 26
    • 79952352704 scopus 로고    scopus 로고
    • Use of in vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in vivo toxicity
    • Sedykh, A.; Zhu, H.; Tang, H.; Zhang, L.; Richard, A. M.; Rusyn, I.; Tropsha, A. Use of in vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in vivo toxicity Environ. Health Perspect. 2011, 119 (3) 364-370
    • (2011) Environ. Health Perspect. , vol.119 , Issue.3 , pp. 364-370
    • Sedykh, A.1    Zhu, H.2    Tang, H.3    Zhang, L.4    Richard, A.M.5    Rusyn, I.6    Tropsha, A.7
  • 27
    • 69249097465 scopus 로고    scopus 로고
    • A novel two-step hierarchical quantitative structure-activity relationship modeling workflow for predicting acute toxicity of chemicals in rodents
    • Zhu, H.; Ye, L.; Richard, A. M.; Golbraikh, A.; Wright, F. A.; Rusyn, I.; Tropsha, A. A novel two-step hierarchical quantitative structure-activity relationship modeling workflow for predicting acute toxicity of chemicals in rodents Environ. Health Perspect. 2009, 117 (8) 1257-1264
    • (2009) Environ. Health Perspect. , vol.117 , Issue.8 , pp. 1257-1264
    • Zhu, H.1    Ye, L.2    Richard, A.M.3    Golbraikh, A.4    Wright, F.A.5    Rusyn, I.6    Tropsha, A.7
  • 28
    • 84857451787 scopus 로고    scopus 로고
    • The great descriptor melting pot: Mixing descriptors for the common good of QSAR models
    • Tseng, Y. J.; Hopfinger, A. J.; Esposito, E. X. The great descriptor melting pot: mixing descriptors for the common good of QSAR models J. Comput.-Aided Mol. Des. 2012, 26, 39-43
    • (2012) J. Comput.-Aided Mol. Des. , vol.26 , pp. 39-43
    • Tseng, Y.J.1    Hopfinger, A.J.2    Esposito, E.X.3
  • 29
    • 84862842130 scopus 로고    scopus 로고
    • In-silico predictive mutagenicity model generation using supervised learning approaches
    • Seal, A.; Passi, A.; Jaleel, U. C. A.; Wild, D. J. In-silico predictive mutagenicity model generation using supervised learning approaches J. Cheminf. 2012, 4 (1) 10
    • (2012) J. Cheminf. , vol.4 , Issue.1 , pp. 10
    • Seal, A.1    Passi, A.2    Jaleel, U.C.A.3    Wild, D.J.4
  • 30
    • 78049442434 scopus 로고    scopus 로고
    • In silico binary classification QSAR models based on 4D-fingerprints and MOE descriptors for prediction of hERG blockage
    • Su, B. H.; Shen, M. Y.; Esposito, E. X.; Hopfinger, A. J.; Tseng, Y. J. In silico binary classification QSAR models based on 4D-fingerprints and MOE descriptors for prediction of hERG blockage J. Chem. Inf. Model. 2010, 50 (7) 1304-1318
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.7 , pp. 1304-1318
    • Su, B.H.1    Shen, M.Y.2    Esposito, E.X.3    Hopfinger, A.J.4    Tseng, Y.J.5
  • 31
    • 79959469908 scopus 로고    scopus 로고
    • A comprehensive support vector machine binary hERG classification model based on extensive but biased end point hERG data sets
    • Shen, M. Y.; Su, B. H.; Esposito, E. X.; Hopfinger, A. J.; Tseng, Y. J. A comprehensive support vector machine binary hERG classification model based on extensive but biased end point hERG data sets Chem. Res. Toxicol. 2011, 24 (6) 934-949
    • (2011) Chem. Res. Toxicol. , vol.24 , Issue.6 , pp. 934-949
    • Shen, M.Y.1    Su, B.H.2    Esposito, E.X.3    Hopfinger, A.J.4    Tseng, Y.J.5
  • 32
    • 21144435586 scopus 로고    scopus 로고
    • Prediction of genotoxicity of chemical compounds by statistical learning methods
    • Li, H.; Ung, C. Y.; Yap, C. W.; Xue, Y.; Li, Z. R.; Cao, Z. W.; Chen, Y. Z. Prediction of genotoxicity of chemical compounds by statistical learning methods Chem. Res. Toxicol. 2005, 18 (6) 1071-1080
    • (2005) Chem. Res. Toxicol. , vol.18 , Issue.6 , pp. 1071-1080
    • Li, H.1    Ung, C.Y.2    Yap, C.W.3    Xue, Y.4    Li, Z.R.5    Cao, Z.W.6    Chen, Y.Z.7
  • 33
    • 33748702895 scopus 로고    scopus 로고
    • Classification of a diverse set of tetrahymena pyriformis toxicity chemical compounds from molecular descriptors by statistical learning methods
    • Xue, Y.; Li, H.; Ung, C. Y.; Yap, C. W.; Chen, Y. Z. Classification of a diverse set of tetrahymena pyriformis toxicity chemical compounds from molecular descriptors by statistical learning methods Chem. Res. Toxicol. 2006, 19 (8) 1030-1039
    • (2006) Chem. Res. Toxicol. , vol.19 , Issue.8 , pp. 1030-1039
    • Xue, Y.1    Li, H.2    Ung, C.Y.3    Yap, C.W.4    Chen, Y.Z.5
  • 34
    • 66449094983 scopus 로고    scopus 로고
    • Prediction of antibacterial compounds by machine learning approaches
    • Yang, X. G.; Chen, D.; Wang, M.; Xue, Y.; Chen, Y. Z. Prediction of antibacterial compounds by machine learning approaches J. Comput. Chem. 2009, 30 (8) 1202-1211
    • (2009) J. Comput. Chem. , vol.30 , Issue.8 , pp. 1202-1211
    • Yang, X.G.1    Chen, D.2    Wang, M.3    Xue, Y.4    Chen, Y.Z.5
  • 35
    • 33750982700 scopus 로고    scopus 로고
    • Prediction of estrogen receptor agonists and characterization of associated molecular descriptors by statistical learning methods
    • Li, H.; Ung, C. Y.; Yap, C. W.; Xue, Y.; Li, Z. R.; Chen, Y. Z. Prediction of estrogen receptor agonists and characterization of associated molecular descriptors by statistical learning methods J. Mol. Graph. Model. 2006, 25 (3) 313-323
    • (2006) J. Mol. Graph. Model. , vol.25 , Issue.3 , pp. 313-323
    • Li, H.1    Ung, C.Y.2    Yap, C.W.3    Xue, Y.4    Li, Z.R.5    Chen, Y.Z.6
  • 36
    • 80053385615 scopus 로고    scopus 로고
    • Classification models for neocryptolepine derivatives as inhibitors of the β-haematin formation
    • Dejaegher, B.; Dhooghe, L.; Goodarzi, M.; Apers, S.; Pieters, L.; Vander Heyden, Y. Classification models for neocryptolepine derivatives as inhibitors of the β-haematin formation Anal. Chim. Acta 2011, 705 (1-2) 98-110
    • (2011) Anal. Chim. Acta , vol.705 , Issue.12 , pp. 98-110
    • Dejaegher, B.1    Dhooghe, L.2    Goodarzi, M.3    Apers, S.4    Pieters, L.5    Vander Heyden, Y.6
  • 38
    • 79952229990 scopus 로고    scopus 로고
    • Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection
    • Cheng, T.; Li, Q.; Wang, Y.; Bryant, S. H. Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection J. Chem. Inf. Model. 2011, 51 (2) 229-236
    • (2011) J. Chem. Inf. Model. , vol.51 , Issue.2 , pp. 229-236
    • Cheng, T.1    Li, Q.2    Wang, Y.3    Bryant, S.H.4
  • 39
    • 5444272497 scopus 로고    scopus 로고
    • Effect of molecular descriptor feature selection in support vector machine classification of pharmacokinetic and toxicological properties of chemical agents
    • Xue, Y.; Li, Z. R.; Yap, C. W.; Sun, L. Z.; Chen, X.; Chen, Y. Z. Effect of molecular descriptor feature selection in support vector machine classification of pharmacokinetic and toxicological properties of chemical agents J. Chem. Inf. Comput. Sci. 2004, 44 (5) 1630-1638
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , Issue.5 , pp. 1630-1638
    • Xue, Y.1    Li, Z.R.2    Yap, C.W.3    Sun, L.Z.4    Chen, X.5    Chen, Y.Z.6
  • 40
    • 80054053316 scopus 로고    scopus 로고
    • Selecting relevant descriptors for classification by Bayesian estimates: A comparison with decision trees and support vector machines approaches for disparate data sets
    • Carbon-Mangels, M.; Hutter, M. C. Selecting relevant descriptors for classification by Bayesian estimates: a comparison with decision trees and support vector machines approaches for disparate data sets Mol. Inf. 2011, 30, 885-895
    • (2011) Mol. Inf. , vol.30 , pp. 885-895
    • Carbon-Mangels, M.1    Hutter, M.C.2
  • 41
    • 75849133755 scopus 로고    scopus 로고
    • A novel method for mining highly imbalanced high-throughput screening data in PubChem
    • Li, Q.; Wang, Y.; Bryant, S. H. A novel method for mining highly imbalanced high-throughput screening data in PubChem Bioinformatics 2009, 25 (24) 3310-3316
    • (2009) Bioinformatics , vol.25 , Issue.24 , pp. 3310-3316
    • Li, Q.1    Wang, Y.2    Bryant, S.H.3
  • 43
    • 84876551083 scopus 로고    scopus 로고
    • Oversampling to overcome overfitting: Exploring the relationship between data set composition, molecular descriptors, and predictive modeling methods
    • Chang, C. Y.; Hsu, M. T.; Esposito, E. X.; Tseng, Y. J. Oversampling to overcome overfitting: exploring the relationship between data set composition, molecular descriptors, and predictive modeling methods J. Chem. Inf. Model. 2013, 53 (4) 958-971
    • (2013) J. Chem. Inf. Model. , vol.53 , Issue.4 , pp. 958-971
    • Chang, C.Y.1    Hsu, M.T.2    Esposito, E.X.3    Tseng, Y.J.4
  • 44
    • 84859802343 scopus 로고    scopus 로고
    • In silico prediction of toxic action mechanisms of phenols for imbalanced data with random forest
    • Chen, J.; Tang, Y. Y.; Fang, B.; Guo, C. In silico prediction of toxic action mechanisms of phenols for imbalanced data with random forest J. Mol. Graph. Model. 2012, 35, 21-27
    • (2012) J. Mol. Graph. Model. , vol.35 , pp. 21-27
    • Chen, J.1    Tang, Y.Y.2    Fang, B.3    Guo, C.4
  • 45
    • 79960872876 scopus 로고    scopus 로고
    • Predicting disease risks from highly imbalanced data using random forest
    • Khalilia, M.; Chakraborty, S.; Popescu, M. Predicting disease risks from highly imbalanced data using random forest BMC Med. Inform. Decis. Mak. 2011, 11, 51
    • (2011) BMC Med. Inform. Decis. Mak. , vol.11 , pp. 51
    • Khalilia, M.1    Chakraborty, S.2    Popescu, M.3
  • 47
    • 0342645331 scopus 로고    scopus 로고
    • Chemical Computing Group: Montreal, Quebec, Canada
    • MOE (Molecular Operating Environment); Chemical Computing Group: Montreal, Quebec, Canada, 2012.
    • (2012) MOE (Molecular Operating Environment)
  • 48
    • 84896528721 scopus 로고    scopus 로고
    • version 3.2; Schrödinger: New York, USA
    • QikProp, version 3.2; Schrödinger: New York, USA, 2011.
    • (2011) QikProp
  • 50
    • 79953005609 scopus 로고    scopus 로고
    • PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints
    • Yap, C. W. PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints J. Comput. Chem. 2011, 32 (7) 1466-1474
    • (2011) J. Comput. Chem. , vol.32 , Issue.7 , pp. 1466-1474
    • Yap, C.W.1
  • 51
    • 84896507550 scopus 로고    scopus 로고
    • PubChem. (accessed August 8)
    • PubChem. http://pubchem.ncbi.nlm.nih.gov/ (accessed August 8, 2012).
    • (2012)
  • 54
    • 35348970485 scopus 로고    scopus 로고
    • GeneSrF and varSelRF: A web-based tool and R package for gene selection and classification using random forest
    • Diaz-Uriarte, R. GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest BMC Bioinf. 2007, 8, 328
    • (2007) BMC Bioinf. , vol.8 , pp. 328
    • Diaz-Uriarte, R.1
  • 55
    • 79952259201 scopus 로고    scopus 로고
    • A classification study of respiratory syncytial virus (RSV) inhibitors by variable selection with random forest
    • Hao, M.; Li, Y.; Wang, Y.; Zhang, S. A classification study of respiratory syncytial virus (RSV) inhibitors by variable selection with random forest Int. J. Mol. Sci. 2011, 12 (2) 1259-1280
    • (2011) Int. J. Mol. Sci. , vol.12 , Issue.2 , pp. 1259-1280
    • Hao, M.1    Li, Y.2    Wang, Y.3    Zhang, S.4
  • 56
    • 13844270855 scopus 로고    scopus 로고
    • Classification of the carcinogenicity of N-nitroso compounds based on support vector machines and linear discriminant analysis
    • Luan, F.; Zhang, R.; Zhao, C.; Yao, X.; Liu, M.; Hu, Z.; Fan, B. Classification of the carcinogenicity of N-nitroso compounds based on support vector machines and linear discriminant analysis Chem. Res. Toxicol. 2005, 18 (2) 198-203
    • (2005) Chem. Res. Toxicol. , vol.18 , Issue.2 , pp. 198-203
    • Luan, F.1    Zhang, R.2    Zhao, C.3    Yao, X.4    Liu, M.5    Hu, Z.6    Fan, B.7
  • 61
    • 33846864233 scopus 로고    scopus 로고
    • Classification of highly unbalanced CYP450 data of drugs using cost sensitive machine learning techniques
    • Eitrich, T.; Kless, A.; Druska, C.; Meyer, W.; Grotendorst, J. Classification of highly unbalanced CYP450 data of drugs using cost sensitive machine learning techniques J. Chem. Inf. Model. 2007, 47, 92-103
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 92-103
    • Eitrich, T.1    Kless, A.2    Druska, C.3    Meyer, W.4    Grotendorst, J.5
  • 64
    • 84855225473 scopus 로고    scopus 로고
    • 3-adrenergic receptor agonists using BCUT descriptors
    • 3-adrenergic receptor agonists using BCUT descriptors Mol. Divers. 2011, 15, 877-887
    • (2011) Mol. Divers. , vol.15 , pp. 877-887
    • Hao, M.1    Li, Y.2    Wang, Y.3    Zhang, S.4
  • 65
    • 27544491192 scopus 로고    scopus 로고
    • ROCR: Visualizing classifier performance in R
    • Sing, T.; Sander, O.; Beerenwinkel, N.; Lengauer, T. ROCR: visualizing classifier performance in R Bioinformatics 2005, 21 (20) 3940-3941
    • (2005) Bioinformatics , vol.21 , Issue.20 , pp. 3940-3941
    • Sing, T.1    Sander, O.2    Beerenwinkel, N.3    Lengauer, T.4
  • 66
    • 79961135005 scopus 로고    scopus 로고
    • R Development Core Team; R Foundation for Statistical Computing: Vienna, Austria, (accessed September 4, 2013)
    • R Development Core Team R: A language and environment for statistical computing; R Foundation for Statistical Computing: Vienna, Austria, 2011; http://www.R-project.org/ (accessed September 4, 2013).
    • (2011) R: A Language and Environment for Statistical Computing
  • 67
    • 0036156262 scopus 로고    scopus 로고
    • Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts
    • Hong, H.; Tong, W.; Fang, H.; Shi, L.; Xie, Q.; Wu, J.; Perkins, R.; Walker, J. D.; Branham, W.; Sheehan, D. M. Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts Environ. Health Perspect. 2002, 110 (1) 29-36
    • (2002) Environ. Health Perspect. , vol.110 , Issue.1 , pp. 29-36
    • Hong, H.1    Tong, W.2    Fang, H.3    Shi, L.4    Xie, Q.5    Wu, J.6    Perkins, R.7    Walker, J.D.8    Branham, W.9    Sheehan, D.M.10
  • 68
    • 78649790472 scopus 로고    scopus 로고
    • QSAR classification of estrogen receptor binders and pre-screening of potential pleiotropic EDCs
    • Li, J.; Gramatica, P. QSAR classification of estrogen receptor binders and pre-screening of potential pleiotropic EDCs SAR QSAR Environ. Res. 2010, 21 (7-8) 657-669
    • (2010) SAR QSAR Environ. Res. , vol.21 , Issue.78 , pp. 657-669
    • Li, J.1    Gramatica, P.2


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