The Open Bioinformatics Journal




ISSN: 1875-0362 ― Volume 14, 2021

Note: Average publication time is 18 days between the final acceptance of revised manuscript and its publication

Editor-in-Chief:

Feng Cheng (Biography
Feng Cheng

Dr. Cheng is a computational biologist. He received systematic training in bioinformatics at Chinese Academy of Science, University of Illinois, Rice University, University of Virginia and Yale University. His researches mainly focus on applications of bioinformatics methods for the identifications of drug-drug interactions and for drug repositioning by analyzing Big Data from public resources. He is also interested in computer-aided drug design. He has published over 50 research papers in prestigious journals. Presently, He is an editor board member of Scientific Reports, Journal of Biomedical Science and Engineering, Journal of Proteomics and Bioinformatics, and the Open Biological Sciences Journal. He has been serving as a peer reviewer for more than ten journals.

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Department of Pharmaceutical Science
University of South Florida
Tampa, FL
USA



Editorial Board Members:

Maciej Antczak (Biography
Maciej Antczak

Dr. Maciej Antczak is assistant professor in Institute of Computing Science at Poznan University of Technology and Department of Bioinformatics, Institute of Bioorganic Chemistry, PAS. He is also member of European Centre for Bioinformatics and Genomics. His research focuses on the development of computational methods and tools for modeling and evaluation of RNA 3D structures. He has published over 35 articles, including peer-reviewed papers in leading, high-impact journals, book chapters, and conference papers. Two of them were classified as highly cited papers in Web of Science. He co-authored several publicly available servers/tools providing novel computational methods to the scientific community.

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Polish Academy of Sciences
Poznan University of Technology
Poznan
Poland

Daniele D'Agostino (Biography
Daniele D'Agostino

Dr. Daniele D'Agostino, Ph.D., is member of the Computing Architectures and High Performance Computing at the Institute for Applied Mathematics and Information Technologies - E. Magenes (IMATI) of the National Research Council of Italy (CNR) since October, 2001. The diffusion of parallel and distributed computing puts the activity of the research group at the forefront of many initiatives in the bioinformatics, hydrometeorological and astrophysical research fields. In 2014, he was a co-chair of the 22nd Euromicro International Conference on Parallel, Distributed and network based Processing. He has co-authored more than 80 papers in international journals, books and conference proceedings. He also acted as co-guest editor of several special issues of ISI international.

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Institute for Applied Mathematics and Information Technology
Italian National Research Council
Genoa
Italy

Oxana V. Galzitskaya (Biography
Oxana V. Galzitskaya

Dr. Oxana V. Galzitskaya obtained her Ph.D. in Biophysics from the Institute of Theoretical and Experimental Biophysics, Pushchino (1996), from where she also received the title of Doctor of Science (2006). Dr. Oxana V. Galzitskaya is head of the Bioinformatics group at the Institute of Protein Research Russian Academy of Sciences (since 2008). She was awarded for Outstanding Russian Young Scientists, 1997, and for Doctor of Science of Russian Science Support Foundation. Her areas of expertise involve protein physics, theoretical and experimental investigations of protein folding, molecular biology, biochemistry, bioinformatics, and search for factors triggering induction of amyloidosis in Alzheimer’s disease. She is an author/co-author of more than 160 peer-reviewed publications, with more than 2,320 total citations.

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Group of Bioinformatics
Institute of Protein Research
Russian Academy of Sciences
Pushchino, Moscow
Russia

Bhaskar D. Gupta (Biography
Bhaskar D. Gupta

Dr. Bhaskar DasGupta is a Professor of Computer Science at University of Illinois at Chicago (UIC) with a joint courtesy appointment with the Bioengineering department. He did his PhD from University of Minnesota in 1995, was a post-doctoral fellow at DIMACS and jointly at University of Waterloo and McMaster University in Canada before he joined the computer science department of the Camden campus of Rutgers University; in 2001 he moved to UIC. His current research interests include application of combinatorial/geometric techniques to design efficient algorithms for computational problems in bioinformatics, systems biology and hybrid systems; his broader research interests include designing efficient combinatorial algorithms for computationally hard problems in diverse areas in addition to bioinformatics such as computational geometry, parallel computing, and combinatorial auctions. His research works have been supported by numerous NSF grants, including an NSF CAREER award.

)

Department of Computer Science
University of Illinois
Chicago, IL
USA

Eugene Korotkov (Biography
Eugene Korotkov

Eugene Korotkov is a Professor at the Department of Applied Mathematics in Moscow Engineering Physics Institute and Principal Investigator in Bioinformatics Department of Bioengineering Centre, Russian Academy of Sciences. He graduated from the National Nuclear Research University (MEPI), Department of Experimental and Theoretical Physics in 1974. PhD thesis was completed in radiobiology. Then, from 1980 to 1995 Korotkov EV worked at the Institute of Chemical Physics, NN Semenov and began work on the development of mathematical algorithms to study the symbolic sequences. Since 1995, Korotkov EV working with the Center "Bioengineering", Russian Academy of Sciences. His research interests are in developing new methods for the analysis of symbolical sequences and time series and application of it for study of various sequences, such as DNA, protein and linguistic sequences.

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Department of Applied Mathematics
National Research Nuclear University (MEPhI)
Moscow
Russia

Dhirendra Kumar (Biography
Dhirendra Kumar

Dr. Kumars research interests lie in systems biology, approaches to understanding regulation of biological processes governing human health and diseases. Particularly, in developing computational methods and tools to integrate multiple high-throughput “-omics” datasets to provide a holistic understanding of cellular processes like transcription and protein translation. He has developed algorithms to integrate epigenomic datasets with other omics technologies and applied these methods to study bivalent chromatin, an epigenetic feature of embryonic stem cells. In his current role at NIEHS as a staff scientist, he is studying epigenetic regulation of gene expression through integrative multi-omics data analysis.

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National Institute of Environmental Health Sciences (NIEHS)
Durham, NC
United States
Email:dhirendra.kumar@nih.gov

Marco Tutone (Biography
Marco Tutone

Marco Tutone graduated in Chemistry and Technologies with summa cum laudae in 2001 In 2006 PhD in Pharmaceutical Science with the dissertation "Chemometrics methods in the study of HIV-1 inhibitors: multivariate statistical techniques and molecular docking" Since 2008 to date he is researcher at the University of Palermo The scientific activity of Marco Tutone was molecular modeling in the field of Medicinal Chemistry (Molecular Dynamics, QSAR and 3D-QSAR, Pharmacophore Modeling, Molecular Docking, HTVS of compounds with potential antiviral, antitumor, anti-protozoarian activity).

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Department of Biological
Chemical and Pharmaceutical Sciences and Technologies
University of Palermo, Palermo
Italy

Ka-Chun Wong (Biography
Ka-Chun Wong

Dr. Ka-Chun Wong finished his PhD degree in Department of Computer Science at University of Toronto within 3.5 years, after his RGC-funded MPhil degree. He is merited as the first associate editor outside USA and Germany for the open-access and open-peer-review journal, BioData Mining, in 2016. He is also on the editorial board of Applied Soft Computing since 2016. Dr. Wong was invited as the plenary/keynote speaker for ICBCB 2017 and ISACIT 2018. In addition, Dr. Wong has solely edited 2 books published by Springer and CRC Press, attracting 30 peer-reviewed book chapters around the world (i.e. Argentina, Australia, Belgium, Brazil, China, Egypt, France, Germany, Hong Kong, India, Japan, Spain, and USA).

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Department of Computer Science
City University of Hong Kong
Kowloon Tong
Hong Kong

S.M. Gupta
Defence Institute of Bio-Energy research
Haldwani
India

Fabio Baselice (Biography
Fabio Baselice

Dr. Fabio Baselice was born in Castellammare di Stabia, Italy, in 1982. He received the BS and MS degrees (summa cum laude) in Telecommunication Engineering and the PhD degree in Information Engineering from the Università di Napoli Parthenope in 2004, 2007, and 2010 respectively. Actually he works as Assistant Professor at the Università di Napoli Parthenope. He is author of more than 70 scientific papers published in International Journals and in Conference Proceedings. His main research interests deal with statistical signal and image processing on different kinds of signals.

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Engineering Department
Università degli Studi di Napoli Parthenope
Naples
Italy

Satchidananda Dehuri (Biography
Satchidananda Dehuri

Dr. Satchidananda Dehuri received his M.Tech. and Ph.D. degrees in Computer Science from Utkal University, Vani Vihar, Odisha, in 2001 and 2006 respectively. He is working as an Associate Professor in the Department of Information and Communication Technology, Fakir Mohan University, Balasore, Odisha, India. His research interests include Evolutionary Computation, Neural Networks, Pattern Recognition, Data Warehousing and Mining, Object Oriented Programming and its Applications and Bioinformatics. He has already published about 220 research papers in reputed journals and referred conferences, has published five textbooks for undergraduate and post-graduate students, and has edited more than ten books of contemporary relevance.

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Department of Information and Communication Technology
Fakir Mohan University
Balasore, Odisha
India

Nuno M. Garcia
Computer Science Department
Universidade da Beira Interior
Covilhã
Portugal

Seongho Kim (Biography
Seongho Kim

Dr. Kim's research interests lie in the data analysis and the methodology development for biological and clinical cancer data. He has participated in various research projects, including pattern recognitions, decision support systems, comparative genomics, metabolomics, proteomics, pharmacokinetics/pharmacodynamics, biomarker discovery, high-dimensional data analysis, pathway analysis, clinical trial design and cancer screening.

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Department of Oncology
Wayne State University
Detroit, MI
USA

Igor Kotenko (Biography
Igor Kotenko

Dr. Igor Kotenko is Professor of computer science and Head of the Laboratory of Computer Security Problems of St.Petersburg Institute for Informatics and Automation. He is the author of more than 320 refereed publications, including 12 textbooks and monographs. Igor Kotenko has a high experience in the research and participated in several projects on developing new information technologies. For example, he was a project leader in the research projects from the US Air Force research department, via its EOARD (European Office of Aerospace Research and Development) branch, EU FP7 and FP6 Projects, HP, Intel, F-Secure, etc. The research results of Igor Kotenko were tested and implemented in more than fifty Russian research and development projects.

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Laboratory of Computer Security Problems
St.Petersburg Institute for Informatics and Automation of the Russian Academy of Sciences (SPIIRAS)
St.Petersburg
Russia

Carlotta Orsenigo (Biography
Carlotta Orsenigo

Carlotta Orsenigo is Assistant Professor of Computer Science at Politecnico di Milano, where she teaches courses in Machine learning and Optimization and is the Co-Director of the International Master in Business Analytics and Big Data. Formerly, she was Assistant Professor at Università degli Studi di Milano and the Scientific Responsible of the Observatory on Big Data Analytics and Business Intelligence at Politecnico di Milano. Her research interests focus on the development of novel models and methods for pattern recognition and dimensionality reduction and their use in several application domains ranging from biolife sciences to marketing.

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Department of Management, Economics and Industrial Engineering
Politecnico di Milano
Milan
Italy

Shibiao Wan (Biography
Shibiao Wan

Dr. Shibiao Wan is currently a Research Scientist at St. Jude Children's Research Hospital. With more than 10 years of experience in bioinformatics, machine learning and computational biology, Dr. Wan is particularly interested in single-cell analysis, sequence analysis, transcriptomics, proteomics, genomics, epigenetics, metabolism, cardiovascular biology, neurobiology, etc. Before joining St. Jude, Dr. Wan received his postdoctoral training from University of Pennsylvania and Princeton University. So far, Dr. Wan has published >30 articles in prestigious journals like Genome Research, Circulation Research, Bioinformatics, Journal of Proteome Research, etc. Dr. Wan is a guest associate editor for Frontiers in Genetics and an academic editor for BioMed Research International.

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St. Jude Children’s Research Hospital
Memphis, TN
USA
Email:Shibiao.Wan@STJUDE.ORG

Xuan Xiao (Biography
Xuan Xiao

Dr Xuan Xiao has received his PhD in Donghua University during the period of Mar. 2003 to Dec.2006. Currently, he is working as full professor in Jingdezhen Ceramic Institute. He has successfully completed his Administrative responsibilities as college principal. His research has included Bioinformatics and Pattern recognition. Based on this research and fellowship training he has received several awards and honors, such as “2010 The Second SCOUPS Young Researcher Award”, “2009 National Outstanding teacher” and “Top 100 Most Cited Chinese Papers Published in International Journals”. He is serving as an expert Reviewers for 20 journals. He has authored 150 research articles.

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Department of Computer
Jingdezhen Ceramic Institute
Jingdezhen
China

Yusen Zhang (Biography
Yusen Zhang

Yusen Zhang received PhD degree in Computational Mathematics from Dalian University of Technology, China, in 2003. He is a professor at School of Mathematics and Statistics in the Shandong University, China. During 2004-2006, He was a postdoctoral fellow in Bioinformatics and Computer Applications at Graduate University of Chinese Academy of Science. His research is in the algorithms in computational biology, bioinformatics and statistical genetics. He has contributed his valuable publications in different national and international journals.

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School of Mathematics and Statistics,
Shandong University
Weihai
China


Associate Editorial Board Members:

Salman Akhtar (Biography
Salman Akhtar

Dr. Salman Akhtar serving as an Associate Professor in the Department of Bioengineering, Integral University, India has an academic and research experience of more than 10 years. With PhD. in Bioinformatics in area of Cancer Biology he has published more than 35 peer reviewed SCI covered high impact factor research papers. Also been awarded with Young scientist research project from UPCST India and been nominated as Editor/Reviewers in International Journals of repute Dr. Salman has organized and attended several national and international conferences, workshops and seminars with an active national and international research collaborations namely with NGCEF, Australia.

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Department of Bioengineering
Integral University
Lucknow
India

Payam Behzadi (Biography
Payam Behzadi

Dr. Payam BEHZADI (BSC and MSC in Microbiology; PhD in Molecular Biology), the Assistant Professor of Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran-Iran teaches students from undergraduate to PhD levels. He has been a faculty member of the above mentioned university since 2004 and he has led some graduate (Master of Science) students as supervisor and adviser. His primary research fields are: Infectious Diseases (in particular Urinary Tract Infections), Molecular biology, Gene profiling, Genetics and Bioinformatics. Dr. Payam Behzadi has authored, edited and refereed many books and papers. 60 papers and 20 books and chapters are the outcomes of his scientific activities.

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Microbiology Department
Islamic Azad University
Tehran
Iran

Ertuğrul Filiz (Biography
Ertuğrul Filiz

Dr. E. Filiz works at the Department of Crop and Animal Production, Duzce University. His research interests include plant science, ranging from theoretical application to wet-lab studies. In recent years, he has focused on bioinformatics applications in plant genomes. Dr. Filiz has mined gene members in plant genomes and comparative analyses among plant species. Also he worked on 3D protein modeling, gene co-expression network, protein-protein interaction (PPIs), in silico gene expression profiles and protein docking.

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Department of Crop and Animal Production
Duzce University
Duzce
Turkey
Email:ertugrulfiliz@gmail.com

Rajarshi K. Gaur (Biography
Rajarshi K. Gaur

Dr. Rajarshi Kumar Gaur earned his PhD in 2005, Professor, Department of Biotechnology, Deen Dayal Upadhyaya Gorakhur University, Gorakhpur, Uttar Pradesh, India. His PhD was on molecular characterization of sugarcane viruses, viz., mosaic, streak mosaic, and yellow luteovirus. He received MASHAV Fellowship in 2004 from the Israel Government for his postdoctoral studies and joined The Volcani Centre, Israel, and BenGurion University, Negev, Israel. In 2007, he received the Visiting Scientist Fellowship from Swedish Institute Fellowship, Sweden, for 1 year to work in the Umeå University, Umeå, Sweden. He has made significant contributions on sugarcane viruses and published 130 national/international papers and edited more than 10 books published by Springer, CRC press, Elsevier, Nova Science Publisher presented nearly about 50 papers in the national and international conferences. He was awarded as Fellow of Linnean Society, London. Currently, he is handling many national and international grants and international collaborative projects on plant viruses and disease management.

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Department of Biotechnology
Deen Dayal Upadhyaya Gorakhpur University
Gorakhpur
India
Email:gaurrajarshi@hotmail.com

Vinayakumar Ravi (Biography
Vinayakumar Ravi

Dr. Vinayakumar Ravi is working as a Postdoctoral research fellow in developing and implementing novel computational and machine learning algorithms and applications for big data integration and data mining with Jegga Lab at Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. His research interests include application of data mining, machine learning (including deep learning), natural language processing and image processing for cyber security, big security data analytics, disease gene discovery/prioritization, computational drug discovery and drug repositioning. Dr. Ravi has more than 50 research publications in reputed IEEE conferences and Transactions and Journals. Ravi's publications include prestigious conferences in the area of Cyber Security, like IEEE S&P and IEEE Infocom.

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Division of Biomedical Informatics
Cincinnati Children’s Hospital Medical Center
Cincinnati, OH
United States
Email:vinayakumarr77@gmail.com

Yuanliang Yan (Biography
Yuanliang Yan

I am a Cancer Researcher. I have received systematic training in cancer research and treatment at Xiangya Hospital, Central South University. My research mainly focuses on the cancer research and treatment in glioma and lung cancer, especially the roles of non-coding RNA in glioma and lung cancer. I have published over 30 SCI-indexed papers in prestigious journals. Presently, I am an editor board member of Traditional Medicine Research, Journal of Clinical and Pathological Research, Chinese Journal of General Surgery, et al. I have been serving as a peer reviewer for about 10 journals, including J Exp Clin Cancer Res.

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Xiangya Hospital
Central South University
Hunan
China

Ravi P. Barnwal (Biography
Ravi P. Barnwal

Dr. Barnwal earned his Ph.D. at Tata Institute of Fundamental Research (TIFR), Mumbai with Prof. Kandala VR Chary. Subsequently, he worked as an acting instructor/ postdoctoral fellow in the laboratory of Prof. Gabriele Varani, Department of Chemistry, University of Washington, Seattle, USA. His research interests encompass the studies of proteins and nucleic acids in solution using NMR and other analytical/biophysical techniques.

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Department of Biophysics
Panjab University
Chandigarh
India

Alexander E. Berezin (Biography
Alexander E. Berezin

Dr. Alexander E. Berezin has received PhD in 1994 in the State Medical University of Zaporozhye (Ukraine). He is currently working as Senior Consultant, Lecturer and Professor of Medicine in the State Medical University of Zaporozhye (Ukraine). His research goals are fundamental study of biological markers, the development of cardiovascular prevention and rehabilitation. Based on this research and training in heart failure he has received several awards and honors. He has published 1050 papers and more in reputed journals, 57 books/chapters and has been serving as an editorial board member of repute

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Internal Medicine Department
Zaporozhye State Medical University
Zaporozhye
Ukraine

Antonio Muñoz Gallego (Biography
Antonio Muñoz Gallego

Antonio Muñoz is currently professor at University of Málaga. He cooperates as security expert for Ericsson. He has more than 15 years or experience as Secutiry Engineer. He part of research GISUM group at the University of Malaga since 2003. His principal research interests include Agent technology, Digital Content Protection, Cryptographic Hardware based Systems, Security Patterns and Security Engineering and BioComputing.

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Languages and Computer Science Department
University of Málaga
Málaga
Spain

Ivan Izonin (Biography
Ivan Izonin

Dr. Ivan Izonin is a lecturer at the Institute of Computer Science and Information Technology of Lviv Polytechnic National University, Ukraine. He received his MSc degree in Computer science from the Lviv Polytechnic National University in 2011 and his MSc degree in Economic cybernetics from the Ivan Franko National University of Lviv in 2012. He received a Ph.D. in Artificial Intelligence from the Lviv Polytechnic National University in 2016. Ivan has authored more than 125 publications, including 11 patents for inventions and 2 tutorials.

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Department of Publishing Information Technologies
Institute of Computer Science and Information Technologies
Lviv Polytechnic National University
Lviv
Ukraine
Email:ivanizonin@gmail.com

Swapnil G. Sanmukh (Biography
Swapnil G. Sanmukh

Dr. Swapnil Ganesh Sanmukh is presently Marie Curie Postdoctoral fellow funded by MSCA-COFUND at Institute of Bioengineering of Catalonia (IBEC), Barcelona, Spain, and he is currently working on chronic bacterial infections and antibacterial therapies. Dr. Sanmukh completed his Ph.D. degree in Applied General Biology from State University of Sao Paulo, Brazil. His skills and expertise mainly lie in the subject areas/fields of PCR, Cell Culture, Protein Purification, RNA, Genomics, Biotechnology, Microbiology, Enzymes, Genetic Engineering, Bioinformatics, Protein Biochemistry, Applied Microbiology, Protein Structure, Proteomics, etc. Dr. Sanmukh has published numerous manuscripts in various national/international journals.

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IBEC Institute for Bioengineering of Catalonia
Barcelona
Spain

Jiapu Zhang (Biography
Jiapu Zhang

Dr Jiapu Zhang (1971– ) received excellent educations from universities and research organizations. He got his bachelor degree in 1993 and first master degree in research in 1996, both from Qufu Normal University, P.R. China; second master degree in research in 2000 from National University of Singapore, Republic of Singapore; a PhD degree in 2005 from Federation University, Australia; and then a formal postdoctoral fellowship training from CSIRO (Commonwealth Scientific and Industrial Research Organisation), Australia. Dr Zhang also received honors in Australia and worldwide for his prion research. In 2011, the report of MIT (Massachusetts Institute of Technology) Technology Review on his prion results caused worldwide impacts so that several organizations (e.g., the Physics Society of Iran) published his prion results in seven languages. NHMRC (National Health and Medical Research Council) of Australia assigned him review tasks on prion projects. CSIRO once conferred him an award (together with Drs. Varghese JN and Epa VC) for rabbit prion protein research. Springer published two volumes of his monographs on neurodegenerative diseases. He has been a reviewer for many top academic journals. All these made Dr. Zhang feel honored for his neuroscience research.

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Centre of Informatics and Applied Optimization
Federation University
Victoria
Australia
Email:j.zhang@federation.edu.au












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