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Publications and Professional Activities

Methodological or major work: (*corresponding or senior author)
  1. Chi Song and George C. Tseng*. (2013) Hypothesis setting and order statistic for robust genomic meta-analysis. Annals of Applied Statistics. accepted. (software download)
  2. Luo JH, Ding Y, Chen R, Michalopoulos G, Nelson J, Tseng G*, Yu YP*.(2013) Genome-wide methylation analysis of prostate tissues reveals global methylation patterns of prostate cancer. American Journal of Pathology. (PMID: 23583283)
  3. Xingbin Wang§, Dongwan Kang§, Kui Shen§, Chi Song, Shuya Lu, Lunching Chang, Serena G. Liao, Zhiguang Huo, Naftali Kaminski, Etienne Sibille, Yan Lin, Jia Li* and George C. Tseng*. (2012) A Suite of R Packages for Quality Control, Differentially Expressed Gene and Enriched Pathway Detection in Microarray Meta-analysis. Bioinformatics. 28:2534-2536. (§ joint first author; * joint corresponding author) (pdf) (software download)(data and code used in the paper)
  4. George C. Tseng* (2012) Book Review for "Meta-analysis and Combining Information in Genetics and Genomics". Journal of the American Statistical Association. 107:497, 435-436.
  5. Xingbin Wang, Yan Lin, Chi Song, Etienne Sibille* and George C Tseng*. (2012) Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: with application to major depressive disorder. BMC Bioinformatics. 13:52. (pdf)
  6. George C. Tseng*, Debashis Ghosh and Eleanor Feingold. (2012) Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Research 40 (9): 3785-3799. (pdf)
  7. Ferdouse Begum, Debashis Ghosh, George C. Tseng*, Eleanor Feingold. (2012) Comprehensive literature review and statistical considerations for GWAS meta-analysis. Nucleic Acids Research 40 (9): 3777-3784. (pdf)
  8. Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng*. (2012) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. Nucleic Acids Research. 40(2):e15. (pdf) (software download)
  9. Nalesnik MA^, Tseng GC^, Ding Y, Xiang GS, Zheng ZL, Yu Y, March JW, Michalopoulos GK, Luo JH. (2012) Gene deletions and amplifications in human hepatocellular carcinomas: correlation with hepatocyte growth regulation. American Journal of Pathology. 180: 1495-1508. (^ joint first author)
  10. Yu YP^, Song C^, Tseng GC, Ren BG, Laframboise W, Michalopoulos G, Nelson J and Luo JH. (2012) Genome abnormalities precede prostate cancer and predict clinical relapse. American Journal of Pathology 180:2240-2248. (^ joint first author) (news release: AJP, post-gazette, UPMC)
  11. Rebecca D. Edmonds, Yoram Vodovotz, Claudio Lagoa, Joyeeta Dutta-Moscato, Yawching Yang, Mitchell P. Fink, Ryan M. Levy, Jose M. Prince, David J. Kaczorowski, George C. Tseng*, Timothy R. Billiar*. (2011) Transcriptomic response of murine liver to severe injury and hemorrhagic shock: a dual platform microarray analysis. Physiological Genomics. 43:1170-83. (* co-corresponding author)
  12. Jia Li and George C. Tseng*. (2011) An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies. Annals of Applied Statistics. 5:994-1019. (pdf) (software download)
  13. Sunghee Oh, Dongwan Kang, Guy N Brock and George C Tseng*. (2011) Biological impacts of missing value imputation on down-stream analyses in microarray data. Bioinformatics. 27:78-86. (PMID: 21045072; PMCID: PMC3008641)
  14. Zhibao Mi, Kui Shen, Nan Song, Chunrong Cheng, Chi Song, Naftali Kaminski and George C Tseng*. (2010) Module-based prediction approach for robust inter-study prediction in microarray data. Bioinformatics. 26: 2586-2593. (PMID: 20719761; PMCID: PMC2951088)
  15. Kui Shen and George C Tseng*. (2010) Meta-analysis for pathway enrichment analysis when combining multiple microarray studies. Bioinformatics. 26:1316-1323. (PMID: 20410053; PMCID: PMC2865865) (software download)
  16. Shuya Lu, Jia Li, Chi Song, Kui Shen and George C Tseng*. (2010) Biomarker Detection in the Integration of Multiple Multi-class Genomic Studies. Bioinformatics. 26:333-340. (PMID: 19965884; PMCID: PMC2815659) (software download)
  17. George C. Tseng*. (2010). Visualization of multiple distributions with quantiles and Fisher information with application to tandem mass spectrometry data. Computational Statistics and Data Analysis. 54:1124-1137. (PMID: 20161641; PMCID: PMC2818137) (software download)
  18. Chunrong Cheng, Kui Shen, Chi Song, Jianhua Luo and George C Tseng*. (2009) Ratio Adjustment and Calibration Scheme for Gene-wise Normalization to Enhance Microarray Inter-study Prediction. Bioinformatics. 25:1655-1661. (PMID: 19414534; PMCID: PMC2732320)
  19. George C. Tseng, Chunrong Cheng, Yan Ping Yu, Joel Nelson, George Michalopoulos and Jian-Hua Luo. (2009) Investigating multi-cancer biomarkers and their cross-predictability in the expression profiles of multiple cancer types. Biomarker Insights. 4:57-79. (PMID: 19652763; PMCID: PMC2716681)
  20. Yan Lin, George C. Tseng, Soo Yeon Cheong, Lora J.H. Bean, Stephanie L. Sherman, Eleanor Feingold. (2008) Smarter Clustering Methods for SNP Genotype Calling. Bioinformatics. 24:2665-2671. (PMID: 18826959; PMCID: PMC2732271)
  21. Yu-Shuen Tsai, Chin-Teng Lin, George C. Tseng, I-Fang Chung and Nikhil Ranjan Pal. (2008) Discovery of Dominant and Dormant Genes from Expression Data Using a Novel Generalization of SNR for Multi-class Problems. BMC Bioinformatics. 9:425. (PMID: 18842155; PMCID: PMC2620271)
  22. Guy N. Brock, John R. Shaffer, Richard E. Blakesley-Ball, Meredith J. Lotz, and George C. Tseng*. (2008) Which Missing Value Imputation Method to Use in Expression Profiles: a Comparative Study and Two Selection Schemes. BMC Bioinformatics. 9:12. (PMID: 18186917; PMCID: PMC2253514)
  23. Yingying Huang, George C. Tseng, Shinsheng Yuan, Ljiljana Pasa-Tolic, Mary S. Lipton, Richard D. Smith, Vicki H. Wysocki. (2008). A data mining scheme for identifying peptide structural motifs behind different MS/MS fragmentation intensity patterns. Journal of Proteome Research. 7:70-79. (PMID: 18052120; PMCID: PMC2464298)
  24. George C. Tseng* (2008) Book Review for "Genomic Signal Processing". Biometrics. 64:10-11.
  25. George C. Tseng*. (2007). Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data. Bioinformatics. 23:2247-2255. (PMID: 17597097) (Supplement Material) (software download)
  26. Anbupalam Thalamuthu, Indranil Mukhopadhyay, Xiaojing Zheng and George C. Tseng*. (2006) Evaluation and comparison of gene clustering methods in microarray analysis. Bioinformatics. 22:2405-2412. (PMID: 16882653) (PDF)(simu data) (real data)
  27. Wei Wu, Nilesh Dave, George C. Tseng, Thomas Richards, Eric Xing, Naftali Kaminski. (2005). Comparison of normalization methods for CodeLink Bioarray data. BMC Bioinformatics. 6:309. (PMID: 16381608)
  28. George C. Tseng and Wing H. Wong. (2005) Tight Clustering: A Resampling-based Approach for Identifying Stable and Tight Patterns in Data. Biometrics.61:10-16. (PMID: 15737073) (PDF) (elected in August 2006 as Fast Breaking Paper in Mathematics by Essential Science Indicators) (software download)
  29. George C. Tseng* (2004) A comparative review of gene clustering in expression profile. Proc. 8th International Conference on Control, Automation, Robotics and Vision (ICARCV). 1320-1324.
  30. Xiaotong Shen, George C. Tseng, Xuegong Zhang, and Wing H. Wong. (2003) On psi-Learning. Journal of the American Statistical Association. 98:724-734. (PDF)
  31. George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao, and Wing Hung Wong. (2001) Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Research. 29: 2549-2557. (PMID: 11410663; PMCID: PMC55725) (announced in 2003 as one of the eight most accessed papers in NAR)
Collaborative work:
  1. Yu-Chen Han, Zhong-Liang Zheng, Yan P. Yu, Rui Chen, George C. Tseng, Joel Nelson and Jian-Hua Luo. (2013) Metallothionein 1h Tumor Suppressor Activity in Prostate Cancer Is Mediated By Euchromatin Methyltransferase 1. Journal of Pathology. Accepted.
  2. Kui Shen; Shara D Rice; David A Gingrich; Dakun Wang; Zhibao Mi; Chunqiao Tian; Zhenyu Ding; Stacey L Brower; Paul R Ervin; Michael J Gabrin; George Tseng; Nan Song. (2012) Distinct genes related to drug response identified in ER positive and ER negative breast cancer cell lines by meta-analysis. PLoS ONE. 7(7):e40900.
  3. Jean-Philippe Guilloux, Gaelle Douillard-Guilloux, Rama Kota, Xingbin Wang, Alain Gardier, Keri Martinowich, George C. Tseng, David A. Lewis, Etienne Sibille. (2012) Molecular evidence for BDNF- and GABA-related dysfunctions in the amygdala of female subjects with Major Depression. Molecular Psychiatry. 17(11):1130-42.
  4. Leo A. Niemeier, Haruko Akatsu Kuffner, Chi Song, Sally E. Carty, Steven P. Hodak, Linwah Yip, Robert L. Ferris, George C. Tseng, Marina N. Nikiforova, Raja R. Seethala, Shane O. LeBeau, Michael T. Stang, Christopher Coyne, Jonas T. Johnson, Andrew F. Stewart, and Yuri E. Nikiforov. (2012) A Combined Molecular-Pathological Score to Assess Aggressive Behavior of Thyroid Papillary Microcarcinoma. Cancer. 118: 2069-2077.
  5. Li W, Song C, Bailey DJ, Tseng GC, Coon JJ, Wysocki VH. (2011) Statistical Analysis of Electron Transfer Dissociation Pairwise Fragmentation Patterns. Analytical Chemistry. 83(24):9540-5.
  6. Sunghee OH, George C. Tseng and Etienne Sibille. (2011) Reciprocal Phylogenetic Conservation of Molecular Aging in Mouse and Human Brain. Neurobiology of Aging . 32:1331-1335. (PMID: 19729224; PMCID: PMC2888783)
  7. Marian Rollins-Raval, Mamatha Chivukula, George C. Tseng, Drazen Jukic, and David J. Dabbs. (2011) An Immunohistochemical Panel to Differentiate Metastatic Breast Carcinoma to Skin From Primary Sweat Gland Carcinomas With a Review of the Literature. Arch Pathol Lab Med. 135:975-983.
  8. Shi YK, Yu YP, Tseng GC, Luo JH. (2010) Inhibition of prostate cancer growth and metastasis using small interference RNA specific for minichromosome complex maintenance component 7. Cancer Gene Ther. 17:694-9. (PMID: 20539323)
  9. Gao F, Carter G, Tseng G, Chivukula M. (2010) Clinical importance of histologic grading of lobular carcinoma in situ in breast core needle biopsy specimens: current issues and controversies. Am J Clin Pathol. 133(5):767-71. (PMID: 20395524)
  10. Shirish Paranjpe, William C Bowen, George C. Tseng, Luo, Jian-Hua, Ann Orr and Michalopoulos, George K. (2010) RNA Interference against hepatic EGFR has suppressive effects on liver regeneration in rats. American Journal of Pathology . 176:2669-81. (PMID: 20395437; PMCID: PMC2877830)
  11. Olga L. Bohn, Irem Nasir, Adam Brufsky, George C Tseng, Rohit Bhargava, Kim MacManus, Mamatha Chivukula. (2010) Biomarker profile in breast carcinomas presenting with bone metastasis. Int J Clin Exp Pathol. 3:139-146. (PMID: 20126581; PMCID: PMC2809993)
  12. Etienne Sibille, Yingjie Wang, Jennifer Joeyen-Waldorf, Chris Gaiteri, Alexandre Surget, Sunghee Oh, Catherine Belzung, George C Tseng, and David A Lewis. (2009) A Molecular Signature of Depression in the Amygdala. American Journal of Psychiatry. 166:1011-24. (PMID: 19605536; PMCID: PMC2882057)
  13. Chivukula M, Bhargava R, Tseng GC and Dabbs DJ. (2009) Clinicopathologic Clinicopathologic implications of "flat epithelial atypia" in core needle biopsy specimens of the breast. American Journal of Clinical Pathology. 131:802-808. (PMID: 19461086)
  14. Chivukula M, Domfeh A, Carter G, Tseng GC and Dabbs DJ. (2009) Characterization of High-grade Ductal Carcinoma In Situ With and Without Regressive Changes: Diagnostic and Biologic Implications. Applied Immunohistochemistry & Molecular Morphology. 17(6):495-499. (PMID: 19407654)
  15. Han YC, Yu YP, Tseng GC and Luo JH. (2009) Trypsin and reduction method to prepare DNA from formalin-fixed paraffin-embedded samples for methylation analysis. Histopathology. 54:773-775. (PMID: 19438756)
  16. Hamm JT, Wilson JW, Rastogi P, Lembersky BC, Tseng GC, Song YK, Kim W, Robidoux A, Raymond JM, Kardinal CG, Shalaby IA, Ansari R, Paik S, Geyer CE, Wolmark N. (2008) Gemcitabine/Epirubicin/Paclitaxel as Neoadjuvant Chemotherapy in Locally Advanced Breast Cancer: A Phase II Trial of the NSABP Foundation Research Group. Clinical Breast Cancer. 8:257-263. (PMID: 18650156)
  17. Marina N. Nikiforova, George C. Tseng, David Steward, Donna Diorio, and Yuri E. Nikiforov. (2008) MicroRNA Expression Profiling of Thyroid Tumors: Biological Significance and Diagnostic Utility. Journal of Clinical Endocrinology & Metabolism 93:1600-1608. (PMID: 18270258; PMCID: PMC2386678)
  18. P Limaye, W Bowen, J Luo, GC Tseng, G Michalopoulos.(2008) Mechanisms of HGF and EGF mediated signaling in Transdifferentiation of Rat Hepatocytes to Biliary Epithelium. Hepatology 47:1702-1713. (PMID: 18398918; PMCID: PMC2615562)
  19. Alfred Guirguis, Esther Elishaev, Sung-hee Oh, George C. Tseng, Kristin Zorn, Julie A. DeLoia. (2008). Use of Gene Expression Profiles to Stage Concurrent Endometrioid Tumors for the Endometrium and Ovary. Gynecologic Oncology 108:370-376. (PMID: 18083218)
  20. Yan Yu, Guoying Yu, George C Tseng, Kathleen Cieply, Joel Nelson, Marie Defrances, Reza Zarnegar, George Michalopoulos and Jianhua Luo. (2007). Glutathione peroxidase 3, deleted or methylated in prostate cancer, suppresses prostate cancer growth and metastasis. Cancer Research. 67:8043-50. (PMID: 17804715)
  21. E.Sibille, J.Su, S.Leman, A.M.Le Guisquet, Y.Ibarguen-Vargas, J.Joeyen-Waldorf, C.A. Glorioso, G.C.Tseng, M.Pezzone, R.Hen, C.Belzung. (2007) Lack of serotonin1B receptor expression leads to age-related motor dysfunction, early onset of brain molecular aging and reduced longevity. Molecular Psychiatry. 12:1042-1056. (PMID: 17420766)
  22. Baoguo Ren, Yan Yu, George C. Tseng, Chuanyue Wu, Ka Chen, Uma Rao, Joel Nelson, George Michalopoulos, and Jian-Hua Luo. (2007). Analysis of Integrin alpha-7 Mutations in Prostate Cancer, Liver Cancer, Glioblastoma Multiforme, and Leiomyosarcoma. JNCI. 99:868-80. (PMID: 17551147) (news release: ScienceDaily)
  23. C.E. Lagoa, J. Bartels, A. Barratt, G.C. Tseng , G. Clermont, M.P. Fink, T.R. Billiar, Y. Vodovotz. (2006) The role of initial trauma in the host's response to injury and hemorrhage: insights from a correlation of mathematical simulations and hepatic transcriptomic analysis. Shock. 6:592-600. (PMID: 17117135)
  24. Yu YP, Tseng GC, Luo JH. (2006) Inactivation of myopodin expression associated with prostate cancer relapse. Urology. 68:578-582. (PMID: 16979744)
  25. Jian-Hua Luo, Baoguo Ren, Sergei Keryanov, George C. Tseng, Uma N.M. Rao, Satdarshan P. Monga, Steven Strom, Anthony J. Demetris, Michael Nalesnik, Yan P. Yu, Sarangarajan Ranganathan and George K. Michalopoulos. (2006) Transcriptomic and Genomic analysis of Human Hepatocellular Carcinomas and Hepatoblastomas. Hepatology 44:1012-1024. (PMID: 17006932)
  26. Alejandro Sweet-Cordero, George C. Tseng, Han You, Margaret Douglass, Bing Huey, Todd Golub, Donna Albertson and Tyler Jacks. (2006) Comparison of Gene Expression and Copy Number Changes in a Murine Model of Lung Cancer. Genes, Chromosomes and Cancer. 45:338-348. (PMID: 16323170)
  27. Baoguo Ren, Guoying Yu, George C. Tseng, Kathleen Cieply, Tim Gavel, Joel Nelson, George Michalopoulos, Yan Ping Yu and Jian-Hua Luo. (2006) MCM7 amplification and overexpression are associated with prostate cancer progression. Oncogene. 25:1090-1098. (PMID: 16247466)
  28. Guoying Yu, George C. Tseng, Yan Ping Yu, Tim Gavel, Joel Nelson, Alan Wells, George Michalopoulos, Demetrius Kokkinakis, and Jian-Hua Luo. (2006) CSR1 Suppresses Tumor Growth and Metastasis of Prostate Cancer. American Journal of Pathology. 168:597-607. (PMID: 16436673)
  29. Yingying Huang, Joseph M. Triscari, George C. Tseng, Ljiljana Pasa-Tolic, Mary S. Lipton, Richard D. Smith, Vicki H. Wysocki. (2005) Statistical Characterization of Charge State and Residue Dependence of Low Energy CID Peptide Dissociation Patterns. Analytical Chemistry. 77:5800-5813. (PMID: 16159109)
  30. Juey-Jen Hwang, Paul D. Allen, George C. Tseng, Ching-Wan Lam, Lameh Fananapazir, Victor J. Dzau, and Choong-Chin Liew. (2002) Microarray gene expression profiles in dilated and hypertrophic cardiomyopathic end-stage heart failure. Physiological Genomics. 10:31-44. (PMID: 12118103)
Papers under preparation, under review or under revision:
    Major:
  1. Shaowu Tang and George C. Tseng*. (2012). Imputation of truncated p-values for meta-analysis methods and its genomic application. in revision. (This paper won 2012 ENAR student award)
  2. Dongwan Kang and George C. Tseng* (2012) A meta-analysis framework for principal component analysis: with applications to combining multiple transcriptomic studies.
  3. Lunching Chang, George C. Tseng* and Etienne Sibille*. (2012) Synergizing transcriptome and genome-wide association studies in depression and other neuropsychiatric disorders.
  4. Lunching Chang, Huimin Lin and George C. Tseng*. (2012) Characterization and comparison of microarray meta-analysis methods.
  5. Ying Ding, Shaowu Tang, Serena Liao, Jia Jia, Yan Lin* and George C. Tseng*. (2012) Bias correctioin in the selection of minimal-error classifier from many machine learning models.
  6. Serena Liao, Dongwan Kang, Naftali Kaminski, Frank Sciurba, George C. Tseng*. (2012) Missing value imputation in phenomic data: applications in lung diseases.
    7. Collaborative:
  7. Maya JH, Noth I, Richards T, Ma SF, Guardela BJ, Tseng GC, Lussie Y, Huang Y, Lindell KO, Duncan S, Gibson K, Shapiro S, Garcia JGN and Naftali Kaminski N. (2012) Peripheral blood monuclear cells gene expression patterns predict survival in patients with idiopathic pulmonary fibrosis. submitted.
  8. Arion D, ..... Lewis D. (2013) Transcriptome alteration in layer 3 and layer 5 pyramidal cells in human DLPFC and schizophrenia.
  9. Ying Ding^, Lun-Ching Chang^, Xingbin Wang^, Jean-Philippe Guilloux, Jenna Parrish, Hyunjung Oh, David A. Lewis, George C. Tseng* and Etienne Sibille*. (2013) Molecular Evidence for a Dimensional Basis of Depression. (^ joint first author)
  10. Dongwan D. Kang^, SungHwan Kim^, John Tedrow, T. Richards, D.A. Schwartz, M.I. Schwarz, F.J. Martinez, A.H. Limper, J. Quackenbush, M.W. Geraci, B. Bartholmai, A. Spira, F.C. Sciurba, G.C. Tseng* and Naftali Kaminski*. (2013) Integrative Framework for Phenomic and Transcriptomic Data Identifies Novel Disease Phenotypes. (^ joint first author)
  11. Yan P. Yu^, Ying Ding^, Rui Chen, Serena Liao, Bao-Guo Ren, Amantha Michalopoulos, George Michalopoulos, Joel Nelson, George C. Tseng*, and Jian-Hua Luo*. (2013) Whole genome methylation sequencing reveals impact of differential methylation on gene transcription in prostate cancer.
Journal Editorial:
  • Associate editor, BMC Medical Genomics, 2010-2013. (This journal has an impact factor of 3.77 and is a well-established open access journal focused on all aspects of functional genomics, genome structure, genome-scale population genetics, epigenomics, proteomics, systems analysis, and pharmacogenomics in relation to human health and disease.)
  • Associate editor, Journal of Computational and Graphical Statistics (JCGS). 2011-
Study section/grant review:
  • Komen for the Cure Breast Cancer Foundation; ad hoc member, Endocrine Therapies study section. 2008/11
  • Review for intramural grants in NIOSH, CDC. (2008/09, 2008/11)
  • Komen for the Cure Breast Cancer Foundation; review committee member, Endocrine Therapies study section. 2009-2011
  • NIH Challenge Grants in Health and Science Research, stage 1 expert reviewer. 2009/05
  • NIH; ad hoc member, Genomics, Computational Biology and Technology Study Section (GCAT). 2009/10/14-15
  • DOD DMRDP; ad hoc member, REHAB Panel. 2010/2/7-9
Honors and awards:
  • UCLA Chancellor’s Fellowship, CA. 1999-2000.
  • “Tight clustering” paper (published in Biometrics 2005) elected as a “Fast Breaking Paper” in Mathematics by Essential Science Indicators. 2006.
  • Clinical Research Scholar (K12) Award, Clinical and Translational Science Institute (CTSI), NIH. 2007-2009.
  • Elected for “Senior Vice Chancellor’s Seminar Series”, University of Pittsburgh. 2010.
  • Elected member, International Statistical Institute (ISI). 2012.
Patents:
  • METHODS FOR DIAGNOSING PROSTATE CANCER AND PREDICTING PROSTATE CANCER RELAPSE. Inventors: Jianhua Luo; George Michalopoulos; Joel B. Nelson; Chi Song; Chien-Cheng Tseng; Yanping Yu. (patent pending).
Books and Book Chapters:

  • George C. Tseng. (2006) "Support Vector Machines" and "Classification and Regression Trees". Entries in Encyclopedia of Measurement and Statistics. Sage Publications. (Amazon)
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  • Cheng Li, George C. Tseng, and Wing H. Wong (2003) Model-based analysis of oligonucleotide arrays and issues in cDNA microarray analysis. Book chapter in Statistical analysis of gene expression microarray data. Edited by Terry Speed. CRC Press. 1-34. (Amazon)
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