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Publications

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2019
Yang, Yuchen, Ruth Huh, Houston W. Culpepper, Yuan Lin, Michael I. Love, and Yun Li. "SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data." Bioinformatics 35, no. 8 (2019): 1269-1277.
Gao, Fei, Donglin Zeng, David Couper, and D Y. Lin. "Semiparametric Regression Analysis of Multiple Right- and Interval-Censored Events." J Am Stat Assoc 114, no. 527 (2019): 1232-1240.
Lin, Dan-Yu. "A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet Epidemiol 43, no. 4 (2019): 365-372.
Yang, Yanyan, Jinchuan Hu, Christopher P. Selby, Wentao Li, Askar Yimit, Yuchao Jiang, and Aziz Sancar. "Single-nucleotide resolution analysis of nucleotide excision repair of ribosomal DNA in humans and mice." J Biol Chem 294, no. 1 (2019): 210-217.
Shi, Chengchun, Rui Song, and Wenbin Lu. "ON TESTING CONDITIONAL QUALITATIVE TREATMENT EFFECTS." Ann Stat 47, no. 4 (2019): 2348-2377.
Olby, Natasha J., Ji-Hey Lim, Nikki Wagner, Natalia Zidan, Peter J. Early, Christopher L. Mariani, Karen R. Muñana, and Eric Laber. "Time course and prognostic value of serum GFAP, pNFH, and S100β concentrations in dogs with complete spinal cord injury because of intervertebral disc extrusion." J Vet Intern Med 33, no. 2 (2019): 726-734.
Olby, Natasha J., Ji-Hey Lim, Nikki Wagner, Natalia Zidan, Peter J. Early, Christopher L. Mariani, Karen R. Muñana, and Eric Laber. "Time course and prognostic value of serum GFAP, pNFH, and S100β concentrations in dogs with complete spinal cord injury because of intervertebral disc extrusion." J Vet Intern Med 33, no. 2 (2019): 726-734.
Zhou, Jie, Jiajia Zhang, Alexander C. Mclain, Wenbin Lu, Xuemei Sui, and James W. Hardin. "A varying-coefficient generalized odds rate model with time-varying exposure: An application to fitness and cardiovascular disease mortality." Biometrics 75, no. 3 (2019): 853-863.
2018
Fu, Sheng, Sanguo Zhang, and Yufeng Liu. "Adaptively weighted large-margin angle-based classifiers." J Multivar Anal 166 (2018): 282-299.
Burbank, Allison J., Krista Todoric, Pamela Steele, Jonathan Rosen, Haibo Zhou, Marcia Frye, Ceila E. Loughlin, Sally Ivins, Katherine Mills, Lauren Dembnicki Massey et al. "Age and African-American race impact the validity and reliability of the asthma control test in persistent asthmatics." Respir Res 19, no. 1 (2018): 152.
Zhu, Anqi, Joseph G. Ibrahim, and Michael I. Love. apeglm: Approximate posterior estimation for GLM coefficients (R)., 2018.
Zhao, Junlong, Guan Yu, and Yufeng Liu. "ASSESSING ROBUSTNESS OF CLASSIFICATION USING ANGULAR BREAKDOWN POINT." Ann Stat 46, no. 6B (2018): 3362-3389.
Liu, Yang, Qianchuan He, and Wei Sun. "Association analysis using somatic mutations." PLoS Genet 14, no. 11 (2018): e1007746.
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Liu, Ying, Yuanjia Wang, Michael R. Kosorok, Yingqi Zhao, and Donglin Zeng. "Augmented outcome-weighted learning for estimating optimal dynamic treatment regimens." Stat Med 37, no. 26 (2018): 3776-3788.
Li, Wenqing, Ming-Hui Chen, Xiaojing Wangy, and Dipak K. Dey. "Bayesian Design of Non-Inferiority Clinical Trials via the Bayes Factor." Stat Biosci 10, no. 2 (2018): 439-459.
Lin, Jiaxing, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S. Damrauer, Scott Floyd, Joshua Granek, Andrew Allen, Cliburn Chan et al. "bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens." Bioinformatics 34, no. 20 (2018): 3581-3583.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. "Computationally Efficient Estimation for the Generalized Odds Rate Mixture Cure Model with Interval-Censored Data." J Comput Graph Stat 27, no. 1 (2018): 48-58.
Liang, Shuhan, Wenbin Lu, and Rui Song. "Deep advantage learning for optimal dynamic treatment regime." Stat Theory Relat Fields 2, no. 1 (2018): 80-88.
Liang, Shuhan, Wenbin Lu, and Rui Song. "Deep advantage learning for optimal dynamic treatment regime." Stat Theory Relat Fields 2, no. 1 (2018): 80-88.
Lawson, Michael T., Hunyong Cho, Arkopal Choudhury, Yifan Cui, Xiaotong Jiang, Teeranan Pokaprakarn, and Michael R. Kosorok. "Discussion of Laber et al. "Optimal treatment allocations in space and time for on-line control of an emerging infectious disease"." J R Stat Soc Ser C Appl Stat 67, no. 4 (2018): 779-780.
Lin, D Y.. "Discussion of the Paper by R. L. Prentice and Y. Huang - Optimal Designs and Efficient Inference for Biomarker Studies." Stat Theory Relat Fields 2, no. 1 (2018): 21-22.
Chen, Jingxiang, Chong Zhang, Michael R. Kosorok, and Yufeng Liu. "Double Sparsity Kernel Learning with Automatic Variable Selection and Data Extraction." Stat Interface 11, no. 3 (2018): 401-420.
Liu, Ying, Yuanjia Wang, and Donglin Zeng. DTRlearn: Learning Algorithms for Dynamic Treatment Regimes (R). 1.3 ed., 2018.
Wong, Kin Yau, Donglin Zeng, and D Y. Lin. "Efficient Estimation for Semiparametric Structural Equation Models With Censored Data." J Am Stat Assoc 113, no. 522 (2018): 893-905.
Gong, Siliang, Kai Zhang, and Yufeng Liu. "Efficient test-based variable selection for high-dimensional linear models." J Multivar Anal 166 (2018): 17-31.
Chen, Jingxiang, Haoda Fu, Xuanyao He, Michael R. Kosorok, and Yufeng Liu. "Estimating individualized treatment rules for ordinal treatments." Biometrics 74, no. 3 (2018): 924-933.
Kang, Suhyun, Wenbin Lu, and Jiajia Zhang. "ON ESTIMATION OF THE OPTIMAL TREATMENT REGIME WITH THE ADDITIVE HAZARDS MODEL." Stat Sin 28, no. 3 (2018): 1539-1560.
Sibley, Alexander, Zhiguo Li, Yu Jiang, Yi-Ju Li, Cliburn Chan, Andrew Allen, and Kouros Owzar. "Facilitating the Calculation of the Efficient Score Using Symbolic Computing." Am Stat 72, no. 2 (2018): 199-205.
Sibley, Alexander, Zhiguo Li, Yu Jiang, Yi-Ju Li, Cliburn Chan, Andrew Allen, and Kouros Owzar. "Facilitating the Calculation of the Efficient Score Using Symbolic Computing." Am Stat 72, no. 2 (2018): 199-205.
Xie, Jichun, and Ruosha Li. "False discovery rate control for high dimensional networks of quantile associations conditioning on covariates." J R Stat Soc Series B Stat Methodol 80, no. 5 (2018): 1015-1034.
Kong, Dehan, Joseph G. Ibrahim, Eunjee Lee, and Hongtu Zhu. "FLCRM: Functional linear cox regression model." Biometrics 74, no. 1 (2018): 109-117.
Li, Tengfei, Fengchang Xie, Xiangnan Feng, Joseph G. Ibrahim, and Hongtu Zhu. "Functional Linear Regression Models for Nonignorable Missing Scalar Responses." Stat Sin 28, no. 4 (2018): 1867-1886.
Innocenti, Federico, Chen Jiang, Alexander B. Sibley, Amy S. Etheridge, Ace J. Hatch, Stefanie Denning, Donna Niedzwiecki, Ivo D. Shterev, Jiaxing Lin, Yoichi Furukawa et al. "Genetic variation determines VEGF-A plasma levels in cancer patients." Sci Rep 8, no. 1 (2018): 16332.
Lin, Jiaxing, Alexander Sibley, Tracy Truong, Kouros Owzar, and Zhiguo Li. groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R). 1.0.0 ed., 2018.
Lin, Jiaxing, Alexander Sibley, Tracy Truong, Kouros Owzar, and Zhiguo Li. groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R). 1.0.0 ed., 2018.
Shi, Chengchun, Alin Fan, Rui Song, and Wenbin Lu. "HIGH-DIMENSIONAL A-LEARNING FOR OPTIMAL DYNAMIC TREATMENT REGIMES." Ann Stat 46, no. 3 (2018): 925-957.
X Jeng, Jessie, Wenbin Lu, and Huimin Peng. "High-Dimensional Inference for Personalized Treatment Decision." Electron J Stat 12, no. 1 (2018): 2074-2089.
Laber, Eric B., Fan Wu, Catherine Munera, Ilya Lipkovich, Salvatore Colucci, and Steve Ripa. "Identifying optimal dosage regimes under safety constraints: An application to long term opioid treatment of chronic pain." Stat Med 37, no. 9 (2018): 1407-1418.
Laber, Eric B., Fan Wu, Catherine Munera, Ilya Lipkovich, Salvatore Colucci, and Steve Ripa. "Identifying optimal dosage regimes under safety constraints: An application to long term opioid treatment of chronic pain." Stat Med 37, no. 9 (2018): 1407-1418.
Butler, Emily L., Eric B. Laber, Sonia M. Davis, and Michael R. Kosorok. "Incorporating Patient Preferences into Estimation of Optimal Individualized Treatment Rules." Biometrics 74, no. 1 (2018): 18-26.
Lin, Jiaxing, Yuan Wu, Xiaofei F. Wang, and Kouros Owzar. intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R). 0.1.1 ed., 2018.
Pietryk, Edward W., Kiristin Clement, Marwa Elnagheeb, Ryan Kuster, Kayla Kilpatrick, Michael I. Love, and Folami Y. Ideraabdullah. "Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme." Reprod Toxicol 78 (2018): 9-19.
Zhang, Yichi, Eric B. Laber, Marie Davidian, and Anastasios A. Tsiatis. "Interpretable Dynamic Treatment Regimes." J Am Stat Assoc 113, no. 524 (2018): 1541-1549.
Shi, Chengchun, Wenbin Lu, and Rui Song. "A Massive Data Framework for M-Estimators with Cubic-Rate." J Am Stat Assoc 113, no. 524 (2018): 1698-1709.
Shi, Chengchun, Rui Song, Wenbin Lu, and Bo Fu. "Maximin Projection Learning for Optimal Treatment Decision with Heterogeneous Individualized Treatment Effects." J R Stat Soc Series B Stat Methodol 80, no. 4 (2018): 681-702.
Isogai, Yoh, Zheng Wu, Michael I. Love, Michael Ho- Young Ahn, Dhananjay Bambah-Mukku, Vivian Hua, Karolina Farrell, and Catherine Dulac. "Multisensory Logic of Infant-Directed Aggression by Males." Cell 175, no. 7 (2018): 1827-1841.e17.
Wang, Yu-Bo, Ming-Hui Chen, Lynn Kuo, and Paul O. Lewis. "A New Monte Carlo Method for Estimating Marginal Likelihoods." Bayesian Anal 13, no. 2 (2018): 311-333.
Van den Berge, Koen, Fanny Perraudeau, Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit, and Lieven Clement. "Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications." Genome Biol 19, no. 1 (2018): 24.
Laber, Eric B., Nick J. Meyer, Brian J. Reich, Krishna Pacifici, Jaime A. Collazo, and John M. Drake. "Optimal treatment allocations in space and time for on-line control of an emerging infectious disease." J R Stat Soc Ser C Appl Stat 67, no. 4 (2018): 743-770.
Laber, Eric B., E Rose, Marie Davidian, and Anastasios A. Tsiatis. Q-Learning. In Wiley StatsRef: Statistics Reference Online. Wiley, 2018.
Zhang, Chong, Minh Pham, Sheng Fu, and Yufeng Liu. "Robust Multicategory Support Vector Machines using Difference Convex Algorithm." Math Program 169, no. 1 (2018): 277-305.
Liu, Yang, Wei Sun, and Qianchuan He. SAME: Somatic mutation Association test with Measurement Errors (R)., 2018.
Li, Zhiguo, Xiaofei Wang, Yuan Wu, and Kouros Owzar. "Sample size calculation for studies with grouped survival data." Stat Med 37, no. 27 (2018): 3904-3917.
Pan, Yinghao, Jianwen Cai, Matthew P. Longnecker, and Haibo Zhou. "Secondary outcome analysis for data from an outcome-dependent sampling design." Stat Med 37, no. 15 (2018): 2321-2337.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. "Semiparametric regression analysis of interval-censored data with informative dropout." Biometrics 74, no. 4 (2018): 1213-1222.
Hao, Botao, Will Wei Sun, Yufeng Liu, and Guang Cheng. "Simultaneous Clustering and Estimation of Heterogeneous Graphical Models." J Mach Learn Res 18 (2018).
Liu, Leo Yu- Feng, Yufeng Liu, and Hongtu Zhu. "SMAC: Spatial multi-category angle-based classifier for high-dimensional neuroimaging data." Neuroimage 175 (2018): 230-245.
Liu, Leo Yu- Feng, Yufeng Liu, and Hongtu Zhu. "SMAC: Spatial multi-category angle-based classifier for high-dimensional neuroimaging data." Neuroimage 175 (2018): 230-245.
Liang, Shuhan, Wenbin Lu, Rui Song, and Lan Wang. "Sparse concordance-assisted learning for optimal treatment decision." J Mach Learn Res 18 (2018).
Liang, Shuhan, Wenbin Lu, Rui Song, and Lan Wang. "Sparse concordance-assisted learning for optimal treatment decision." J Mach Learn Res 18 (2018).
Jung, Sin-Ho, Ho Yun Lee, and Shein-Chung Chow. "Statistical Methods for Conditional Survival Analysis." J Biopharm Stat 28, no. 5 (2018): 927-938.
Luo, Yiwen, Arnab Maity, Michael C. Wu, Chris Smith, Qing Duan, Yun Li, and Jung-Ying Tzeng. "On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol 42, no. 3 (2018): 276-287.
Luo, Yiwen, Arnab Maity, Michael C. Wu, Chris Smith, Qing Duan, Yun Li, and Jung-Ying Tzeng. "On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol 42, no. 3 (2018): 276-287.
Love, Michael I., Charlotte Soneson, and Rob Patro. "Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification." F1000Res 7 (2018): 952.
2017
Leão, William L., Carlos A. Abanto-Valle, and Ming-Hui Chen. "Bayesian analysis of stochastic volatility-in-mean model with leverage and asymmetrically heavy-tailed error using generalized hyperbolic skew Student's t-distribution." Stat Interface 10 (2017): 529-541.
Lu, Zhao-Hua, Zakaria Khondker, Joseph G. Ibrahim, Yue Wang, and Hongtu Zhu. "Bayesian longitudinal low-rank regression models for imaging genetic data from longitudinal studies." Neuroimage 149 (2017): 305-322.
Fan, Ailin, Rui Song, and Wenbin Lu. "Change-Plane Analysis for Subgroup Detection and Sample Size Calculation." J Am Stat Assoc 112, no. 518 (2017): 769-778.
Li, Zhiguo. "Comparison of adaptive treatment strategies based on longitudinal outcomes in sequential multiple assignment randomized trials." Stat Med 36, no. 3 (2017): 403-415.
Chen, Yong, Yulun Liu, Jing Ning, Lei Nie, Hongjian Zhu, and Haitao Chu. "A composite likelihood method for bivariate meta-analysis in diagnostic systematic reviews." Stat Methods Med Res 26, no. 2 (2017): 914-930.
Fan, Caiyun, Wenbin Lu, Rui Song, and Yong Zhou. "Concordance-Assisted Learning for Estimating Optimal Individualized Treatment Regimes." J R Stat Soc Series B Stat Methodol 79, no. 5 (2017): 1565-1582.
Chiuzan, Cody, Jonathan Shtaynberger, Gulam A. Manji, Jimmy K. Duong, Gary K. Schwartz, Anastasia Ivanova, and Shing M. Lee. "Dose-finding designs for trials of molecularly targeted agents and immunotherapies." J Biopharm Stat 27, no. 3 (2017): 477-494.
Jiang, Runchao, Wenbin Lu, Rui Song, Michael G. Hudgens, and Sonia Naprvavnik. "DOUBLY ROBUST ESTIMATION OF OPTIMAL TREATMENT REGIMES FOR SURVIVAL DATA-WITH APPLICATION TO AN HIV/AIDS STUDY." Ann Appl Stat 11, no. 3 (2017): 1763-1786.
Laber, Eric B., and Marie Davidian. "Dynamic treatment regimes, past, present, and future: A conversation with experts." Stat Methods Med Res 26, no. 4 (2017): 1605-1610.
Holloway, Shannon T., Eric B. Laber, Kristin A. Linn, Baqun Zhang, Marie Davidian, and Anastasios A. Tsiatis. DynTxRegime: A comprehensive package for analysis of dynamic treatment regimes (R).. v3.1 ed., 2017.
Holloway, Shannon T., Eric B. Laber, Kristin A. Linn, Baqun Zhang, Marie Davidian, and Anastasios A. Tsiatis. DynTxRegime: A comprehensive package for analysis of dynamic treatment regimes (R).. v3.1 ed., 2017.
Kang, Suhyun, Wenbin Lu, and Mengling Liu. "Efficient estimation for accelerated failure time model under case-cohort and nested case-control sampling." Biometrics 73, no. 1 (2017): 114-123.
Kang, Suhyun, Wenbin Lu, and Mengling Liu. "Efficient estimation for accelerated failure time model under case-cohort and nested case-control sampling." Biometrics 73, no. 1 (2017): 114-123.
Mao, Lu, and D Y. Lin. "Efficient Estimation of Semiparametric Transformation Models for the Cumulative Incidence of Competing Risks." J R Stat Soc Series B Stat Methodol 79, no. 2 (2017): 573-587.
Tao, Ran, Donglin Zeng, and Dan-Yu Lin. "Efficient Semiparametric Inference Under Two-Phase Sampling, With Applications to Genetic Association Studies." J Am Stat Assoc 112, no. 520 (2017): 1468-1476.
Liu, Ying, Yuanjia Wang, Chaorui Huang, and Donglin Zeng. "Estimating personalized diagnostic rules depending on individualized characteristics." Stat Med 36, no. 7 (2017): 1099-1117.
Jiang, Runchao, Wenbin Lu, Rui Song, and Marie Davidian. "On Estimation of Optimal Treatment Regimes For Maximizing -Year Survival Probability." J R Stat Soc Series B Stat Methodol 79, no. 4 (2017): 1165-1185.
Laber, Eric B., and Min Qian. "Evaluating personalized treatment regimes." In Methods in Comparative Effectiveness Research. New York: Chapman and Hall/CRC, 2017.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. "An Expectation Maximization algorithm for fitting the generalized odds-rate model to interval censored data." Stat Med 36, no. 7 (2017): 1157-1171.
Lin, Jiaxing, Alexander Sibley, Ivo D. Shterev, and Kouros Owzar. fastJT: Efficient Jonckheere-Terpstra Test Statistics for Robust Machine Learning and Genome-Wide Association Studies (R). 1.0.4 ed., 2017.
Laber, Eric B., and Ana-Maria Staicu. "Functional feature construction for individualized treatment regimes." J Am Stat Assoc 113, no. 523 (2017): 1219-1227.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. GORCure: Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data (R)., 2017.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. ICGOR: Fit Generalized Odds Rate Hazards Model with Interval Censored Data (R). 2.0 ed., 2017.
Linn, Kristin A., Eric B. Laber, and Leonard A. Stefanski. "Interactive Q-learning for Quantiles." J Am Stat Assoc 112, no. 518 (2017): 638-649.
Linn, Kristin A., Eric B. Laber, and Leonard A. Stefanski. "Interactive Q-learning for Quantiles." J Am Stat Assoc 112, no. 518 (2017): 638-649.
Zeng, Donglin, Fei Gao, and D Y. Lin. "Maximum likelihood estimation for semiparametric regression models with multivariate interval-censored data." Biometrika 104, no. 3 (2017): 505-525.
Abanto-Valle, Carlos A., Roland Langrock, Ming-Hui Chen, and Michel V. Cardoso. "Maximum likelihood estimation for stochastic volatility in mean models with heavy-tailed distributions." Appl Stoch Models Bus Ind 33, no. 4 (2017): 394-408.
Bai, Xiaofei, Anastasios A. Tsiatis, Wenbin Lu, and Rui Song. "Optimal treatment regimes for survival endpoints using a locally-efficient doubly-robust estimator from a classification perspective." Lifetime Data Anal 23, no. 4 (2017): 585-604.
Kelleher, Sarah A., Caroline S. Dorfman, Jen C. Plumb Vilardaga, Catherine Majestic, Joseph Winger, Vicky Gandhi, Christine Nunez, Alyssa Van Denburg, Rebecca A. Shelby, Shelby D. Reed et al. "Optimizing delivery of a behavioral pain intervention in cancer patients using a sequential multiple assignment randomized trial SMART." Contemp Clin Trials 57 (2017): 51-57.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. PICAFT: Semiparametric Estimation of the Accelerated Failure Time Model With Partly Interval-Censored Data (R)., 2017.
Tang, Zheng-Zheng, Paul Bunn, Ran Tao, Zhouwen Liu, and Dan-Yu Lin. "PreMeta: a tool to facilitate meta-analysis of rare-variant associations." BMC Genomics 18, no. 1 (2017): 160.
Tang, Zheng-Zheng, Paul Bunn, Ran Tao, Zhouwen Liu, and Dan-Yu Lin. "PreMeta: a tool to facilitate meta-analysis of rare-variant associations." BMC Genomics 18, no. 1 (2017): 160.
Tang, Zheng-Zheng, Paul Bunn, Ran Tao, Z Liu, and Dan-Yu Lin. PreMeta: Facilitates the Exchange of Information Between Software Packages for Meta-Analysis (C++)., 2017.
Tang, Zheng-Zheng, Paul Bunn, Ran Tao, Z Liu, and Dan-Yu Lin. PreMeta: Facilitates the Exchange of Information Between Software Packages for Meta-Analysis (C++)., 2017.

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