Dr.
Shiyong Lu's publications
Also see his DBLP
list and Google
scholar citations. Dr. Lu’s students are marked with *.
2008
1. Liqiang Wang, Shiyong Lu, Xubo Fei, Artem Chebotko, H. Victoria Bryant, and
Jeffrey L. Ram, “Atomicity and Provenance Support for Pipelined Scientific
Workflows”, Future Generation Computer Systems, 2008. In press.
2. Claudia Lalancette, Andrian
Platts, Yi Lu, Shiyong Lu, Stephen Krawetz, “Transcription Frameworks of Early
Committed Spermatogenic Genes”, Molecular Genetics and Genomics, 2008.
In press.
3. Cui Lin*, Shiyong Lu, Zhaoqiang Lai, Artem Chebotko*, Xubo Fei*, Jing
Hua, and F. Fotouhi, “Service-Oriented Architecture for VIEW: a Visual
Scientific Workflow Management System”, In Proc. of the IEEE 2008
International Conference on Services Computing (SCC 2008), Honolulu,
Hawaii, USA, July 2008. In press. (Acceptance rate 18%)
4. Yong Zhao and Shiyong Lu, “A Logic Programming Approach to Scientific
Workflow Provenance Querying”, in Proc. of the 2008 International Provenance
and Annotation Workshop (IPAW 2008), Salt Lake City, Utah, 2008. In
press.
5. Xubo Fei*, Shiyong Lu, Thomas Breithaupt, Jörg D. Hardege, and Jeffrey
L. Ram,“Modeling mate-finding behavior of the swarming polychaete, Nereis
succinea, with TangoInSilico, a scientific workflow based simulation system for
sexual searching”, Invertebrate
Reproduction and Development. In press.
6. Cui Lin*, Shiyong Lu, Xuwei Liang, Jing Hua, and Otto Muzik, “Cocluster
Analysis of Thalamo-Cortical Fiber Tracts Extracted from Diffusion Tensor MRI”,
International Journal of Data Mining and Bioinformatics (IJDMB). In
press.
7. Jamal Alhiyafi*, Cavitha Sabesan*, Shiyong Lu, and Jeffrey L. Ram,
“RECOMBFLOW: A scientific workflow environment for intragenomic gene conversion
analysis in bacterial genomes, including the pathogen Streptococcus pyogenes”, International
Journal of Bioinformatics Research and Applications (IJBRA), 2008.
In press.
8. Zijiang Yang, Shiyong Lu, and Ping Yang, “Trustworthy and Dynamic Mobile
Task Scheduling in Data-Intensive Scientific Workflow Environments”. Journal of Autonomic and Trusted
Computing (JoATC), 2008. In press.
9. Zijiang Yang, Shiyong Lu, and Ping Yang, “Model Checking Approach to
Secure Host Access Enforcement of Mobile Tasks in Scientific Workflows”, Journal
of Autonomic and Trusted Computing (JoATC), 2008. In press.
10. Jefferey Ram, Xubo Fei*, Michelle Danaher, Shiyong Lu, Thomas
Breithaupt, and Jörg D. Hardege, “Finding females: Pheromone-guided
reproductive tracking behavior by male Nereis succinea in the marine
environment”, Journal of Experimental Biology (JEB), 211(5), 757-765,
Feb. 2008.
2007
11. Artem Chebotko*, Mustafa Atay*, Shiyong Lu, and Farshad Fotouhi , “XML
Subtree Reconstruction from Relational Storage of XML Documents”, Data and
Knowledge Engineering (DKE), 62(2), pp. 199-218, 2007.
12. Mustafa Atay*, Artem Chebotko*, Dapeng Liu*, Shiyong Lu, Farshad Fotouhi
, “Efficient Schema-Based XML-to-Relational Data Mapping”, Information
Systems (IS), 32(3), pp.458-476, 2007.
13. Otto Muzik, Diane Chugani, Guangyu Zou, Jing Hua, Yi Lu, Shiyong Lu,
Elshi Asano, and Harry Chugani, “Multimodality Data Integration in Epilepsy”, International
Journal of Biomedical Imaging (IJBI), Volume 2007, Article ID 13963, 2007.
14. Artem Chebotko*, Xubo Fei*, Cui Lin*, Shiyong Lu, and Farshad Fotouhi,
“Storing and Querying Scientific Workflow Provenance Metadata Using an RDBMS”,
in Proc. of the 2nd International Workshop on Scientific Workflows and
Business Workflow Standards in e-Science, in conjunction with IEEE
International Conference on e-Science and Grid Computing (e-Science’07 ),
pp.611-618, Bangalore, India, December, 2007.
15. Ping Yang, Zijiang Yang, and Shiyong Lu, “Formal Modeling and Analysis
of Scientific Workflows Using Hierarchical State Machines”, in Proc. of the
2nd International Workshop on Scientific Workflows and Business Workflow
Standards in e-Science, in conjunction with IEEE International Conference
on e-Science and Grid Computing (e-Science’07 ), pp.619-626, Bangalore, India,
December, 2007.
16. Artem Chebotko*, Cui Lin*, Xubo Fei*, Zhaoqiang Lai, Shiyong Lu, Jing
Hua, and Farshad Fotouhi, “VIEW: a VIsual SciEntific Workflow management
system”, in Proc. of the first IEEE International Workshop on Scientific
Workflows (SWF'07), in conjunction with the IEEE 2007 International
Conference on Web Services (ICWS’07), pp.207-208, July 9-13, 2007, Salt Lake
City, Utah, USA.
17. Artem Chebotko*, Mustafa Atay*, Shiyong Lu, and Farshad Fotouhi ,
“Relational Nested Optional Join for Efficient Semantic Web Query Processing”,
Guozhu Dong, Xuemin Lin, Wei Wang, Yun Yang, Jeffrey Xu Yu (Eds.), Lecture
Notes in Computer Science 4505, pp.428-439, Springer-Verlag 2007, ISBN
978-3-540-72483-4.
18. Cui Lin*, Shiyong Lu, Danqing Wu, Jing Hua, and Otto Muzik,
“Coclustering Based Parcellation of Human Brain Cortex Using Diffusion Tensor
MRI Ion I. Mandoiu, Alexander Zelikovsky (Eds.), Lecture Notes in Computer
Science 4463, pp. 539-550, Springer-Verlag 2007, ISBN 978-3-540-72030-0.
19. Mustafa Atay*, Artem Chebotko*, Shiyong Lu, and Farshad Fotouhi,
“XML-to-SQL Query Mapping in the Presence of Multi-valued Schema Mappings and
Recursive XML Schemas”, Roland Wagner, Norman Revell, Günther Pernul (Eds.), Lecture
Notes in Computer Science 4653, pp.603-616, Springer-Verlag 2007, ISBN
978-3-540-74467-2.
20. Xubo Fei*, Shiyong Lu, Horia F. Pop, and Lily R. Liang, “GFBA: A
Biclustering Algorithm for Discovering Value-Coherent Biclusters”, Ion I.
Mandoiu, Alexander Zelikovsky (Eds.), Lecture Notes in Computer Science
4463, pp. 1-12, Springer-Verlag 2007, ISBN 978-3-540-72030-0.
21. Zijiang Yang, Shiyong Lu, and Ping Yang, “Itinerary-based access control
for mobile tasks in scientific workflows”, in Proc. of the 2007 IEEE
International Symposium on Ubisafe Computing (UbiSafe 2007), pages
506–511, Niagara Falls, Ontario, Canada, May 2007.
22. Liqiang Wang, Shiyong Lu, Xubo Fei*, and Jeffrey L. Ram, “A
Dataflow-Oriented Atomicity and Provenance System for Pipelined Scientific
Workflows”, Yong Shi, G. Dick van Albada, Jack Dongarra, Peter M. A. Sloot
(Eds.), Lecture Notes in Computer Science 4489, pp.244-252,
Springer-Verlag 2007, ISBN 978-3-540-72587-9.
23. Seunghan Chang*, Artem Chebotko*, Shiyong Lu, and Farshad Fotouhi,
“Graph Matching Based Authorization Model for Efficient Secure XML Querying”,
in Proc. of the 2007 IEEE International Symposium on Ubisafe Computing
(UbiSafe’07), pp.473-478, Niagara Falls, Ontario, Canada, May 21-23, 2007.
24. Jamal Alhiyafi*, Cavitha Sebesan*, Shiyong Lu, Melphine Harriott,
Deborah Jurczyszyn, Raquel P. Ritchie, Felicitas S. Gonzales, and Jeffrey Ram,
“Computational Methods for Analysis of Cryptic Recombination in the Performance
of Genomic Recombination Detection Software”, in Proc. of the 2007 IEEE
International Symposium on Bioinformatics & Life Science Computing
(BLSC’07), pp.706-712, May 2007, Niagara Falls Canada.
25. Cui Lin, Shiyong Lu, Xuena Liang, and Jing Hua, and Otto Muzik, “Genetic
cocluster analysis of Thalamo-Cortical Connectivity in Human Brain”, MICWIC,
Kellogg Biological Station, 2007.
2006
26. Shiyong Lu, Arthur Bernstein, and Philip Lewis, “Automatic Workflow
Verification and Generation”, Theoretical Computer Science (TCS),
353(1-3), pp. 71-92, 2006.
27. Shiyong Lu, Feng Cao*, and Yi Lu*, “PAMA: a Fast String Matching
Algorithm”. International Journal of Foundations of Computer Science (IJFCS),
17(2), pp.357-378, 2006. Impact
factor in 2003: 0.52. Currently ranked as one of the five top accessed articles
of the journal, see http://www.worldscinet.com/ijfcs/mkt/top.shtml for more
details.
28. Shiyong Lu, Arthur Bernstein, and Philip Lewis, “Completeness and
Realizability: Conditions for Automatic Generation of Workflows”, International
Journal of Foundations of Computer Science (IJFCS), 17(1), pp.
223-245, 2006.
29. Shiyong Lu, Lily R. Liang, Xuena Wang, Yi Lu, Vinay Mandal, Dorrelyn
Patacsil, and Deepak Kumar, “FM-test: A Fuzzy-Set-Theory-Based Approach to
Differential Gene Expression Data Analysis”, BMC Bioinformatics, 7
(Suppl 4): S7. 2006. Impact factor in 2007: 3.62. (First two authors
contributed equally to the paper).
30. Cui Lin*, Shiyong Lu, Xuena Liang, and Jing Hua, “GCA: a Coclustering
Algorithm for Thalamo-Cortico-Thalamic Connectivity Analysis”, in Proc. of
the IEEE International Workshop on Data Mining in Bioinformatics (DMB’2007),
pp.163-168, Hong Kong, December, 2006. Acceptance rate: 27%.
31. Yi Lu*, Shiyong Lu, Adrian Platts, and Stephen Krawetz, “Mining
Correlation between Motifs and Gene Expression”, in Proc. of the IEEE
International Conference on Data Mining (ICDM’2006), pp.986-990, Hong Kong,
December, 2006. Acceptance rate: 19.6%.
32. Artem Chetbotko*, Shiyong Lu, Farshad Fotouhi, and Anthony Aristar,
“Ontology-based Annotation of Multimedia Language Data for the Semantic Web”,
in book “Semantic Web-Based Information Systems: State-of-the-Art
Applications”, Amit Sheth and Miltiadis Lytras (Eds.), Cybertech Publishing,
ISBN 1599044269, November, 2006.
33. Zijiang Yang, Shiyong Lu, and Ping Yang, “Runtime Security Verification
for Itinerary-Driven Mobile Agents”, in Proc. of the 2nd IEEE International
Symposium on Dependable, Autonomic and Secure Computing (DASC'06),
pp.177-186, at Indiana University, Purdue University, Indianapolis, USA,
September 29-October 1, 2006.
34. Yi Lu*, Shiyong Lu, Lily R. Liang, and Deepak Kumar, “FM-test: A Fuzzy
Set Theory Based Approach to Discovering Diabetes Genes”, in Proc. of the
IEEE International Symposium of Computations in Bioinformatics and Bioscience
(SCBB’06), pp.48-55, Hangzhou, Zhejiang, China, June, 2006.
35. Lily R. Liang, Shiyong Lu, Yi Lu*, Puneet Dhawan, and Deepak Kumar,
“CM-test: An Innovative Divergence Measurement and Its Application in Diabetes
Gene Expression Data Analysis”, in Proc. of the IEEE International
Conference on Granular Computing (GrC’06), Atlanta, pp.262-268, GA, USA,
May, 2006. Acceptance rate: 15%.
36. Yi Lu*, Shiyong Lu, Farshad Fotouhi, Yan Sun, Zijiang Yang, and Lily R.
Liang, “PDC: Pattern Discovery with Confidence in DNA Sequences”, in Proc.
of the IASTED International Conference on Advances in Computer Science and
Technology, pp.345-350, Puerto Vallarta, Mexico, 2006.
37. Yi Lu*, Shiyong Lu, and Jeffrey Ram, “Fast Search in DNA Sequence
Databases Using Punctuation and Indexing”, in Proc. of the IASTED
International Conference on Advances in Computer Science and Technology,
pp.351-356, Puerto Vallarta, Mexico, 2006.
2005
38. Shiyong Lu, Yezhou Sun, Mustafa Atay and Farshad Fotouhi, “On the
Consistency of XML DTDs”, Data and Knowledge Engineering, 52(2),
pp.231-247, 2005. Impact factor in 2006: 1.367.
39. Artem Chebotko, Yu Deng, Shiyong Lu, Farshad Fotouhi, Anthony Aristar,
“An Ontology-Based Multimedia Annotator for the Semantic Web of Language
Engineering”. Int. J. Semantic Web Inf. Syst. 1(1): 50-67, 2005.
40. Farhad Mostowfi, Farshad Fotouhi, Shiyong Lu and Anthony Aristar,
“LINGOES: A Linguistic Ontology Management System”, International Journal of
Digital Information Management, 3(4), pp. 231-234, December 2005.
41. Darshan Pai, Jiafeng Jiang, Jing Hua, Ye Duan, Otto Muzik, and Shiyong
Lu, “3D Segmentation of Brain Structures Using PDE-Driven Surface Growing”. In Proc.
of the 2005 NAFIPS Annual Conference on Soft Computing for Real World
Applications, Ann Arbor, MI, USA, June 2005.
42. Shiyong Lu and Cheng-zhong Xu, “A Formal Framework for Mobile Agent
Itinerary Specification, Safety Reasoning, and Logic Analysis”, in Proc. of
the 3rd IEEE International Workshop on Mobile Distributed Computing (MDC’05),
in conjunction with ICDCS’2005, Columbus, OH, USA, 2005.
43. Artem Chebotko*, Dapeng Liu*, Mustafa Atay*, Shiyong Lu, and Farshad
Fotouhi, “Reconstructing XML Subtrees from Relational Storage of XML
Documents”, in Proc. of the 2nd International Workshop on XML Schema and
Data Management (XSDM’05), in conjunction with ICDE’2005, Tokyo, Japan,
April, 2005.
44. Chunxia Zhang*, Shiyong Lu, and Lily R. Liang. “MetaFinder: a
Meta-Search Engine with an Open Architecture”, in Proc. of the 20th
International Conference on Computers and Their Applicaitons (CATA’2005), New
Orleans, Louisiana, USA. March 2005.
2004
45. Yi Lu*, Shiyong Lu, Farshad Fotouhi, Youping Deng, and Susan Brown,
“Incremental Genetic K-means Algorithm and its Application in Gene Expression
Data Analysis”, BMC Bioinformatics, 5(172), 2004. Impact factor in 2007: 3.62.
46. Artem Chebotko*, Yu Deng*, Shiyong Lu, Farshad Fotouhi, Hennie Brugman,
Alexander Klassmann, Han Sloetjes, Albert Russel, and Peter Wittenburg,
“OntoELAN: An Ontology-based Linguistic Multimedia Annotator”, in Proc. of
the IEEE Sixth International Symposium on Multimedia Software Engineering
(MSE’2004), pp. 329-336, Miami, FL, USA, December, 2004.
47. Shiyong Lu, Arthur Bernstein, and Philip Lewis, “Correct Execution of
Transactions at Different Isolation Levels”, IEEE Transactions on Knowledge
and Data Engineering (TKDE). 16(9), pp. 1070-1081, September
2004.
48. Ziyang Duan, Arthur Bernstein, Philip Lewis, and Shiyong Lu, “A Model
for Abstract Process Specification, Verification and Composition”, in Proc.
of the Second ACM International Conference on Service Oriented Computing (ICSOC
2004), pp. 232-241, New York City, NY, USA, November, 2004.
49. Mustafa Atay*, Yezhou Sun*, Dapeng Liu*, Shiyong Lu, and Farshad
Fotouhi, “Mapping XML Data to Relational Data: a DOM-based Approach”, in Proc.
of the 8th IASTED International Conference on Internet and Multimedia Systems
and Applications (IMSA’2004), pp. 59-64, Kauai, Hawaii, USA. August 2004.
50. Lei Chen*, Shiyong Lu, and Jeffrey Ram, “Compressed Pattern Matching in
DNA Sequences”, in Proc. of the IEEE Computational Systems Bioinformatics
Conference (CSB'2004), pp. 62-68, Stanford, CA, USA, August 2004. Acceptance rate: 15%.
51. Ziyang Duan, Arthur Bernstein, Philip Lewis, and Shiyong Lu, “Semantics
Based Verification and Synthesis of BPEL4WS Abstract Processes”, in Proc. of
the IEEE International Conference on Web Services (ICWS 2004),
52. Shiyong Lu, Rong Huang*, Artem Chebotko*, Yu Deng*, and Farshad Fotouhi,
“ImageSpace: An Environment for Image Ontology Management”, International
Journal of Information Theories and Applications, 11(2), pp. 127-134, 2004.
53. Shiyong Lu, Dapeng Liu*, Farshad Fotouhi, Ming Dong, Robert Reynolds,
Anthony Aristar, Martha Ratliff, Geoff Nathan, Joseph Tan, and Ronald Powell,
“Language Engineering for the Semantic Web: a Digital Library for Endangered
Languages”, Information Research, 9(3), April, 2004.
54. Artem Chebotko, Shiyong Lu, Farshad Fotouhi, “Challenges for Information
Systems Towards the Semantic Web”, AIS SIGSEMIS Semantic Web and Information
Systems Newsletter, Volume 1, Number 1, pp. 26-28, April, 2004. Download Full Bulletin
55. Shiyong Lu, Rong Huang*, and Farshad Fotouhi, “Annotating Linguistic
Data with ImageSpace for the Preservation of Endangered Languages”, in Proc.
of the 19th International Conference on Computers and Their Applications
(CATA'2004), pp. 193-196, Seattle, WA, USA, March, 2004.
56. Rong Huang*, Shiyong Lu, and Farshad Fotouhi, “ImageSpace: An Image
Ontology Creation and Annotation Tool”, in Proc. of the 19th International
Conference on Computers and Their Applications (CATA'2004), pp. 340-343,
Seattle, WA, USA, March, 2004.
57. Yi Lu*, Shiyong Lu, Farshad Fotouhi, Youping Deng, and Susan Brown,
“FGKA: A Fast Genetic K-means Algorithm”, in Proc. of the 19th ACM Symposium
on Applied Computing, pp. 162-163, Nicosia, Cyprus, March, 2004.
58. Manjeet Rege*, Izabell Caraconcea*, Shiyong Lu, and Farshad Fotouhi,
“Querying XML Documents from a Relational Database in the Presence of DTDs”, Lecture
Notes in Computer Science, Volume 3347, pp. 168-177, R. K. Ghosh and
Hrushikesha Mohanty (Eds.), Springer-Verlag, ISBN 3-540-24075-6, 2004.
2003
59. Jeffrey Stefan, Robert Reynolds, Farshad Fotouhi, Anthony Aristar,
Shiyong Lu, and Ming Dong, "Evolution Based Approaches to the Preservation
of Endangered Natural Languages", in Proc. of the IEEE International
Congress on Evolutionary Computation (CEC'2003), pp. 1980-1987, Canberra,
Australia, December, 2003.
60. William I. Grosky, Farshad Fotouhi, Anthony Aristar, Shiyong Lu, Ming
Dong, and Robert Reynolds, “A Digital Library for Endangered Languages”, the
Nara Symposium for Digital Silk Roads (DSR), Nara, Japan, December, 2003.
61. Subhra Bose, Ziyang Duan, and Shiyong Lu, “An XML-based Framework for
Rapid Development of Interoperable Trading Systems”, in Proc. of the 7th IASTED
International Conference on Software Engineering and Applications (SEA'2003),
pp. 184--189, Marina del Rey, CA, USA, November 2003.
62. Zongmin Ma*, Shiyong Lu, and Farshad Fotouhi, “Conceptual Data Models
for Engineering Information Modeling and Formal Transformation of EER and
EXPRESS-G”, Lecture Notes in Computer Science, Volume 2813, pp. 573-575,
Il-Yeol Song, Stephen W. Liddle, Tok Wang Ling and Peter Scheuermann (Eds.),
Spinger-Verlag, ISBN 3-540-20299-4, 2003.
63. Shiyong Lu, Yezhou Sun*, Mustafa Atay*, and Farshad Fotouhi, “A New
Inlining Algorithm for Mapping XML DTDs to Relational Schemas”, Lecture
Notes in Computer Science, Volume 2814, pp. 366-377, Manfred A. Jeusfeld
and Oscar Pastor (Eds.), Springer-Verlag, ISBN 3-540-20257-9, 2003.
64. Shiyong Lu, Yezhou Sun*, Mustafa Atay*, and Farshad Fotouhi, “A
Sufficient and Necessary Condition for the Consistency of XML DTDs”, Lecture
Notes in Computer Science, Volume 2814, pp. 250-260, Manfred A. Jeusfeld
and Oscar Pastor (Eds.), Spinger-Verlag, ISBN 3-540-20257-9, 2003.
65. Farshad Fotouhi, Shiyong Lu, Ming Dong and Michael Johnson, “Deriving
Ontologies from Image Databases”, International Workshop on Annotation and
Resource Discovery of Geographic Image Data, Nikko, Japan, March, 2003.
66. Shuyun Xu, Yu Li, and Shiyong Lu, “ERDraw: an XML-based ER-diagram
Drawing and Translation Tool”, in Proc. of the 18th International Conference
on Computers and Their Applications (CATA’2003), pp. 143-146, Honolulu,
Hawaii, USA, March, 2003.
67. Farshad Fotouhi, Shiyong Lu, Ming Dong and Michael Johnson, “Deriving
Ontologies from Web Documents”, International Symposium on Digital Silk
Roads (DSR), Hawaii, USA, March, 2003.
1999-2002
68. Shiyong Lu, Ming Dong and Farshad Fotouhi, “The Semantic Web: Opportunities
and Challenges for Next-Generation Web Applications”, Information Research,
Special Issue on the Semantic Web, 7(4), 2002.
69. Shiyong Lu, “Semantic Correctness of Transactions and Workflows”, Ph.D.
dissertation, Stony Brook University, 2002. Advisor: Arthur J. Bernstein.
70. Shiyong Lu and Steven Skiena, “Filling a Penny Album”, Chance,
13(29), pp. 25-28, 2000.
71. Ziyang Duan, Albert Loo, Biswajit Sarkar, Shiyong Lu, Mark Van Loon and
Subhra Bose, “A Structured Approach to Trade Negotiation Applications”, in Proc.
of the 15th International Conference on Computer Applications in Industry and
Engineering (CAINE’2002), pp. 162—165, San Diego, CA, USA, November, 2002.
72. Shiyong Lu and Ziyang Duan, “EsMS: a Database-driven E-service
Management System”, in Proc. of the 5th International Conference on Computer
Supported Cooperative Work in Design (CSCWD’2000), pp. 106-110, Hong Kong,
November, 2000.
73. Arthur J. Bernstein, Philip M. Lewis, and Shiyong Lu,
“Semantic Conditions for Correctness at Different Isolation Levels”,
in Proc. of the 16th IEEE International Conference on Data
Engineering (ICDE 2000), pp. 57--66, San Diego, CA, USA,
February 28 -
74. Shiyong Lu and Scott Smolka, “Model Checking the Secure Electronic
Transaction (SET) Protocol”, in Proc. of the 7th IEEE International
Symposium on Modeling, Analysis and Simulation of Computer and
Telecommunication Systems (MASCOTS’1999), pp. 358-365, University of
Maryland, College Park, MD, USA, October, 1999.
75. Arthur Bernstein, David Gerstl, Philip Lewis, and Shiyong Lu, “Using
Transaction Semantics to Increase Performance”, in Proc. of the 8th
International Workshop on High Performance Transaction System (HPTS’1999),
Pacific Grove, CA, USA, September, 1999.
76. Shiyong Lu, Xiafeng Yuan, and Sergio Silva, “Collaborative Web Surfing”,
in Proc. of the International Joint Conference on Work Activities
Coordination and Collaboration (WACC’1999), San Francisco, CA, USA,
February, 1999.
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