Mohammad Reza Kaazempur Mofrad
Professor, Bioengineering
Professor, Mechanical Engineering
Faculty Scientist, Lawrence Berkeley National Lab
Office Address: 208A Stanley Hall
Email: mofrad@berkeley.edu
For more information, see: https://biomechanics.berkeley.edu/
Office hours: Monday 1:30 - 2:30 pm, 208A Stanley Hall
Research areas:
Biomaterials & Nanotechnology, Cell and Tissue Engineering, Computational Biology, Systems and Synthetic Biology
Molecular and Multiscale Biomechanics; Bioinformatics and Computational Biology; Statistical Machine Learning; Computational Precision Health; Microbiome; Personalized Medicine
Education
- 1999 Ph.D., University of Toronto
- 1994 M.A.Sc., University of Waterloo
- 1991 B.A.Sc., Sharif University of Technology
Experience & Training
- 2023-present Core Faculty, UCSF-UC Berkeley Computational Precision Health Graduate Group
- 2014-2015 Faculty Co-Director, Berkeley-UCSF Master of Translational Medicine (MTM) Program
- 2013-present Professor, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley
- 2012-present Faculty Scientist, Molecular Biophysics, Lawrence Berkeley National Lab
- 2012-2014 Faculty Director, UC Berkeley Master of Bioengineering (M.Eng) Program
- 2012-2013 Associate Professor, Department of Mechanical Engineering, University of California, Berkeley
- 2011 Visiting Professor, Department of Bioengineering, EPFL, Lausanne, Switzerland
- 2010-2013 Associate Professor, Department of Bioengineering, University of California, Berkeley
- 2005-2010 Assistant Professor, Department of Bioengineering, University of California, Berkeley
- 2002-2004 Principal Research Scientist, Biological and Mechanical Engineering, MIT
- 2000-2002 Post-Doc, MIT and Harvard Medical School/Mass. General Hospital
- 1999-2000 Post-Doc, Computer Science Department, University of Toronto
Honors & Awards
- 2020 Bill & Melinda Gates Foundation Grantee for the Universal Flu Vaccine Grand Challenge
- 2018 Fellow, Japan Society for Promotion of Science (JSPS)
- 2016 AHA National Innovator Research Award
- 2015 American Institute for Medical and Biological Engineering (AIMBE) Fellow
- 2014 Presidential Chair Fellow (in Curriculum Enrichment)
- 2012 National Academy of Engineering Invitee to ‘Frontiers’ Symposium
- 2012 Minner Faculty Fellow (in Engineering Ethics)
- 2010 National Science Foundation CAREER Award
- 2008 Hellman Faculty Fund Award, UC Berkeley
- 2007 Co-leader of Molecular Biomechanics Group, Summit of Biomechanics
- 2006 University of California Berkeley Futures
- 2005 University of California Regents’ Junior Faculty Fellow
- 2002 Runner-up for American Society of Biomechanics Award, World Congress of Biomechanics
2024
Valiei, Amin; Dickson, Andrew; Aminian-Dehkordi, Javad; Mofrad, Mohammad R. K.
Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities Journal Article
In: NPJ BIOFILMS AND MICROBIOMES, vol. 10, no. 1, 2024.
@article{WOS:001327015700002,
title = {Metabolic interactions shape emergent biofilm structures in a conceptual
model of gut mucosal bacterial communities},
author = {Amin Valiei and Andrew Dickson and Javad Aminian-Dehkordi and Mohammad R. K. Mofrad},
doi = {10.1038/s41522-024-00572-y},
year = {2024},
date = {2024-10-01},
journal = {NPJ BIOFILMS AND MICROBIOMES},
volume = {10},
number = {1},
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Montes, Andre R.; Barroso, Anahi; Wang, Wei; O'Connell, Grace D.; Tepole, Adrian B.; Mofrad, Mohammad R. K.
Integrin mechanosensing relies on a pivot-clip mechanism to reinforce cell adhesion Journal Article
In: BIOPHYSICAL JOURNAL, vol. 123, no. 16, pp. 2443-2454, 2024, ISSN: 0006-3495.
@article{WOS:001313131300001,
title = {Integrin mechanosensing relies on a pivot-clip mechanism to reinforce
cell adhesion},
author = {Andre R. Montes and Anahi Barroso and Wei Wang and Grace D. O'Connell and Adrian B. Tepole and Mohammad R. K. Mofrad},
doi = {10.1016/j.bpj.2024.06.008},
issn = {0006-3495},
year = {2024},
date = {2024-08-01},
journal = {BIOPHYSICAL JOURNAL},
volume = {123},
number = {16},
pages = {2443-2454},
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Dickson, Andrew; Mofrad, Mohammad R. K.
Fine-tuning protein embeddings for functional similarity evaluation Journal Article
In: BIOINFORMATICS, vol. 40, no. 8, 2024, ISSN: 1367-4803.
@article{WOS:001283609500001,
title = {Fine-tuning protein embeddings for functional similarity evaluation},
author = {Andrew Dickson and Mohammad R. K. Mofrad},
doi = {10.1093/bioinformatics/btae445},
issn = {1367-4803},
year = {2024},
date = {2024-08-01},
journal = {BIOINFORMATICS},
volume = {40},
number = {8},
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Gharizadeh, Ali; Abbasi, Karim; Ghareyazi, Amin; Mofrad, Mohammad R. K.; Rabiee, Hamid R.
HGTDR: Advancing drug repurposing with heterogeneous graph transformers Journal Article
In: BIOINFORMATICS, vol. 40, no. 7, 2024, ISSN: 1367-4803.
@article{WOS:001261931800004,
title = {HGTDR: Advancing drug repurposing with heterogeneous graph transformers},
author = {Ali Gharizadeh and Karim Abbasi and Amin Ghareyazi and Mohammad R. K. Mofrad and Hamid R. Rabiee},
doi = {10.1093/bioinformatics/btae349},
issn = {1367-4803},
year = {2024},
date = {2024-07-01},
journal = {BIOINFORMATICS},
volume = {40},
number = {7},
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Talebi, Salmonn; Gai, Siyu; Sossin, Aaron; Zhu, Vivian; Tong, Elizabeth; Mofrad, Mohammad R. K.
Deep Learning for Perfusion Cerebral Blood Flow (CBF) and Volume (CBV) Predictions and Diagnostics Journal Article
In: ANNALS OF BIOMEDICAL ENGINEERING, vol. 52, no. 6, pp. 1568-1575, 2024, ISSN: 0090-6964.
@article{WOS:001170783900001,
title = {Deep Learning for Perfusion Cerebral Blood Flow (CBF) and Volume (CBV)
Predictions and Diagnostics},
author = {Salmonn Talebi and Siyu Gai and Aaron Sossin and Vivian Zhu and Elizabeth Tong and Mohammad R. K. Mofrad},
doi = {10.1007/s10439-024-03471-7},
issn = {0090-6964},
year = {2024},
date = {2024-06-01},
journal = {ANNALS OF BIOMEDICAL ENGINEERING},
volume = {52},
number = {6},
pages = {1568-1575},
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pubstate = {published},
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Talebi, Salmonn; Tong, Elizabeth; Li, Anna; Yamin, Ghiam; Zaharchuk, Greg; Mofrad, Mohammad R. K.
Exploring the performance and explainability of fine-tuned BERT models for neuroradiology protocol assignment Journal Article
In: BMC MEDICAL INFORMATICS AND DECISION MAKING, vol. 24, no. 1, 2024.
@article{WOS:001157510200001,
title = {Exploring the performance and explainability of fine-tuned BERT models
for neuroradiology protocol assignment},
author = {Salmonn Talebi and Elizabeth Tong and Anna Li and Ghiam Yamin and Greg Zaharchuk and Mohammad R. K. Mofrad},
doi = {10.1186/s12911-024-02444-z},
year = {2024},
date = {2024-02-01},
journal = {BMC MEDICAL INFORMATICS AND DECISION MAKING},
volume = {24},
number = {1},
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Khavani, Mohammad; Mehranfar, Aliyeh; Mofrad, Mohammad R. K.
Antimicrobial peptide interactions with bacterial cell membranes Journal Article
In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2024, ISSN: 0739-1102.
@article{WOS:001149820100001,
title = {Antimicrobial peptide interactions with bacterial cell membranes},
author = {Mohammad Khavani and Aliyeh Mehranfar and Mohammad R. K. Mofrad},
doi = {10.1080/07391102.2024.2304683},
issn = {0739-1102},
year = {2024},
date = {2024-01-01},
journal = {JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS},
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2023
Yerima, Ghafar; Domkam, Nya; Ornowski, Jessica; Jahed, Zeinab; Mofrad, Mohammad R. K.
Force transmission and SUN-KASH higher-order assembly in the LINC complex models Journal Article
In: BIOPHYSICAL JOURNAL, vol. 122, no. 23, pp. 4582-4597, 2023, ISSN: 0006-3495.
@article{WOS:001135494800001,
title = {Force transmission and SUN-KASH higher-order assembly in the LINC
complex models},
author = {Ghafar Yerima and Nya Domkam and Jessica Ornowski and Zeinab Jahed and Mohammad R. K. Mofrad},
doi = {10.1016/j.bpj.2023.11.001},
issn = {0006-3495},
year = {2023},
date = {2023-12-01},
journal = {BIOPHYSICAL JOURNAL},
volume = {122},
number = {23},
pages = {4582-4597},
keywords = {},
pubstate = {published},
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Montes, Andre R.; Gutierrez, Gabriela; Tepole, Adrian Buganza; Mofrad, Mohammad R. K.
Multiscale computational framework to investigate integrin mechanosensing and cell adhesion Journal Article
In: JOURNAL OF APPLIED PHYSICS, vol. 134, no. 11, 2023, ISSN: 0021-8979.
@article{WOS:001146149700001,
title = {Multiscale computational framework to investigate integrin
mechanosensing and cell adhesion},
author = {Andre R. Montes and Gabriela Gutierrez and Adrian Buganza Tepole and Mohammad R. K. Mofrad},
doi = {10.1063/5.0164826},
issn = {0021-8979},
year = {2023},
date = {2023-09-01},
journal = {JOURNAL OF APPLIED PHYSICS},
volume = {134},
number = {11},
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Khavani, Mohammad; Mehranfar, Aliyeh; Mofrad, Mohammad R. K.
On the interactions of peptides with gold nanoparticles: effects of sequence and size Journal Article
In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2023, ISSN: 0739-1102.
@article{WOS:001003525400001,
title = {On the interactions of peptides with gold nanoparticles: effects of
sequence and size},
author = {Mohammad Khavani and Aliyeh Mehranfar and Mohammad R. K. Mofrad},
doi = {10.1080/07391102.2023.2220816},
issn = {0739-1102},
year = {2023},
date = {2023-06-01},
journal = {JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS},
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Bajaj, Teena; Wehri, Eddie; Suryawanshi, Rahul K.; King, Elizabeth; Pardeshi, Kundan Singh; Behrouzi, Kamyar; Khodabakhshi, Zahra; Schulze-Gahmen, Ursula; Kumar, G. Renuka; Mofrad, Mohammad R. K.; Nomura, Daniel K.; Ott, Melanie; Schaletzky, Julia; Murthy, Niren
Mercapto-pyrimidines are reversible covalent inhibitors of the papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication Journal Article
In: RSC ADVANCES, vol. 13, no. 26, pp. 17667-17677, 2023.
@article{WOS:001006972100001,
title = {Mercapto-pyrimidines are reversible covalent inhibitors of the
papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication},
author = {Teena Bajaj and Eddie Wehri and Rahul K. Suryawanshi and Elizabeth King and Kundan Singh Pardeshi and Kamyar Behrouzi and Zahra Khodabakhshi and Ursula Schulze-Gahmen and G. Renuka Kumar and Mohammad R. K. Mofrad and Daniel K. Nomura and Melanie Ott and Julia Schaletzky and Niren Murthy},
doi = {10.1039/d3ra01915b},
year = {2023},
date = {2023-06-01},
journal = {RSC ADVANCES},
volume = {13},
number = {26},
pages = {17667-17677},
keywords = {},
pubstate = {published},
tppubtype = {article}
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Han, Hesong; Gracia, Albert Vallejo; Roise, Joachim J.; Boike, Lydia; Leon, Kristoffer; Schulze-Gahmen, Ursula; Stentzel, Michael R.; Bajaj, Teena; Chen, Dake; Li, I. -Che; He, Maomao; Behrouzi, Kamyar; Khodabakhshi, Zahra; Nomura, Daniel K.; Mofrad, Mohammad R. K.; Kumar, G. Renuka; Ott, Melanie; Murthy, Niren
A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication Journal Article
In: RSC ADVANCES, vol. 13, no. 16, pp. 10636-10641, 2023.
@article{WOS:000964370800001,
title = {A covalent inhibitor targeting the papain-like protease from SARS-CoV-2
inhibits viral replication},
author = {Hesong Han and Albert Vallejo Gracia and Joachim J. Roise and Lydia Boike and Kristoffer Leon and Ursula Schulze-Gahmen and Michael R. Stentzel and Teena Bajaj and Dake Chen and I. -Che Li and Maomao He and Kamyar Behrouzi and Zahra Khodabakhshi and Daniel K. Nomura and Mohammad R. K. Mofrad and G. Renuka Kumar and Melanie Ott and Niren Murthy},
doi = {10.1039/d3ra00426k},
year = {2023},
date = {2023-04-01},
journal = {RSC ADVANCES},
volume = {13},
number = {16},
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Sanati, Alireza; Esmaeili, Yasaman; Khavani, Mohammad; Bidram, Elham; Rahimi, Azadeh; Dabiri, Arezou; Rafienia, Mohammad; Jolfaie, Nafise Arbab; Mofrad, Mohammad R. K.; Javanmard, Shaghayegh Haghjooy; Shariati, Laleh; Zarrabi, Ali
Smartphone-assisted lab-in-a-tube device using gold nanocluster-based aptasensor for detection of MUC1-overexpressed tumor cells Journal Article
In: ANALYTICA CHIMICA ACTA, vol. 1252, 2023, ISSN: 0003-2670.
@article{WOS:000954986900001,
title = {Smartphone-assisted lab-in-a-tube device using gold nanocluster-based
aptasensor for detection of MUC1-overexpressed tumor cells},
author = {Alireza Sanati and Yasaman Esmaeili and Mohammad Khavani and Elham Bidram and Azadeh Rahimi and Arezou Dabiri and Mohammad Rafienia and Nafise Arbab Jolfaie and Mohammad R. K. Mofrad and Shaghayegh Haghjooy Javanmard and Laleh Shariati and Ali Zarrabi},
doi = {10.1016/j.aca.2023.341017},
issn = {0003-2670},
year = {2023},
date = {2023-04-01},
journal = {ANALYTICA CHIMICA ACTA},
volume = {1252},
keywords = {},
pubstate = {published},
tppubtype = {article}
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Mehranfar, Aliyeh; Khavani, Mohammad; Mofrad, Mohammad R. K.
Adsorption Process of Various Antimicrobial Peptides on Different Surfaces of Cellulose Journal Article
In: ACS APPLIED BIO MATERIALS, vol. 6, no. 3, pp. 1041-1053, 2023, ISSN: 2576-6422.
@article{WOS:000972878200001,
title = {Adsorption Process of Various Antimicrobial Peptides on Different
Surfaces of Cellulose},
author = {Aliyeh Mehranfar and Mohammad Khavani and Mohammad R. K. Mofrad},
doi = {10.1021/acsabm.2c00905},
issn = {2576-6422},
year = {2023},
date = {2023-03-01},
journal = {ACS APPLIED BIO MATERIALS},
volume = {6},
number = {3},
pages = {1041-1053},
keywords = {},
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Khavani, Mohammad; Mehranfar, Aliyeh; Mofrad, Mohammad R. K.
On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation Journal Article
In: VIRUS RESEARCH, vol. 326, 2023, ISSN: 0168-1702.
@article{WOS:000925000400001,
title = {On the potentials of sialic acid derivatives as inhibitors for the mumps
virus: A molecular dynamics and quantum chemistry investigation},
author = {Mohammad Khavani and Aliyeh Mehranfar and Mohammad R. K. Mofrad},
doi = {10.1016/j.virusres.2023.199050},
issn = {0168-1702},
year = {2023},
date = {2023-03-01},
journal = {VIRUS RESEARCH},
volume = {326},
keywords = {},
pubstate = {published},
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Dickson, Andrew; Asgari, Ehsaneddin; McHardy, Alice C.; Mofrad, Mohammad R. K.
GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations Journal Article
In: BIOINFORMATICS, vol. 39, no. 2, 2023, ISSN: 1367-4803.
@article{WOS:000937000600002,
title = {GO Bench: shared hub for universal benchmarking of machine
learning-based protein functional annotations},
author = {Andrew Dickson and Ehsaneddin Asgari and Alice C. McHardy and Mohammad R. K. Mofrad},
doi = {10.1093/bioinformatics/btad081},
issn = {1367-4803},
year = {2023},
date = {2023-02-01},
journal = {BIOINFORMATICS},
volume = {39},
number = {2},
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Khavani, Mohammad; Mehranfar, Aliyeh; Mofrad, Mohammad R. K.
On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study Journal Article
In: JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2023, ISSN: 1549-9596.
@article{WOS:000928602400001,
title = {On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces
against the SARS-CoV-2 Virus: A Comparative Computational Study},
author = {Mohammad Khavani and Aliyeh Mehranfar and Mohammad R. K. Mofrad},
doi = {10.1021/acs.jcim.2c01378},
issn = {1549-9596},
year = {2023},
date = {2023-02-01},
journal = {JOURNAL OF CHEMICAL INFORMATION AND MODELING},
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2022
Khavani, Mohammad; Mehranfar, Aliyeh; Mofrad, Mohammad R. K.
Effects of Ionic Liquids on the Stabilization Process of Gold Nanoparticles Journal Article
In: JOURNAL OF PHYSICAL CHEMISTRY B, vol. 126, no. 46, pp. 9617-9631, 2022, ISSN: 1520-6106.
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title = {Effects of Ionic Liquids on the Stabilization Process of Gold
Nanoparticles},
author = {Mohammad Khavani and Aliyeh Mehranfar and Mohammad R. K. Mofrad},
doi = {10.1021/acs.jpcb.2c05878},
issn = {1520-6106},
year = {2022},
date = {2022-11-01},
journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
volume = {126},
number = {46},
pages = {9617-9631},
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pubstate = {published},
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Nourani, Esmaeil; Asgari, Ehsaneddin; McHardy, Alice C.; Mofrad, Mohammad R. K.
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks Journal Article
In: IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, vol. 19, no. 6, pp. 3744-3753, 2022, ISSN: 1545-5963.
@article{WOS:000966719600067,
title = {TripletProt: Deep Representation Learning of Proteins Based On Siamese
Networks},
author = {Esmaeil Nourani and Ehsaneddin Asgari and Alice C. McHardy and Mohammad R. K. Mofrad},
doi = {10.1109/TCBB.2021.3108718},
issn = {1545-5963},
year = {2022},
date = {2022-11-01},
journal = {IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS},
volume = {19},
number = {6},
pages = {3744-3753},
keywords = {},
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McKinley, Jonathan P.; Montes, Andre R.; Wang, Maple N.; Kamath, Anuya R.; Jimenez, Gissell; Lim, Jianhua; Marathe, Siddharth A.; Mofrad, Mohammad R. K.; O'Connell, Grace D.
Design of a flexing organ-chip to model in situ loading of the intervertebral disc Journal Article
In: BIOMICROFLUIDICS, vol. 16, no. 5, 2022.
@article{WOS:000878375700001,
title = {Design of a flexing organ-chip to model \textit{in situ} loading of the
intervertebral disc},
author = {Jonathan P. McKinley and Andre R. Montes and Maple N. Wang and Anuya R. Kamath and Gissell Jimenez and Jianhua Lim and Siddharth A. Marathe and Mohammad R. K. Mofrad and Grace D. O'Connell},
doi = {10.1063/5.0103141},
year = {2022},
date = {2022-09-01},
journal = {BIOMICROFLUIDICS},
volume = {16},
number = {5},
keywords = {},
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Zamri, Muhammad Harith Bin; Ujihara, Yoshihiro; Nakamura, Masanori; Mofrad, Mohammad R. K.; Sugita, Shukei
Decoding the Effect of Hydrostatic Pressure on TRPV1 Lower-Gate Conformation by Molecular-Dynamics Simulation Journal Article
In: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 23, no. 13, 2022.
@article{WOS:000824223600001,
title = {Decoding the Effect of Hydrostatic Pressure on TRPV1 Lower-Gate
Conformation by Molecular-Dynamics Simulation},
author = {Muhammad Harith Bin Zamri and Yoshihiro Ujihara and Masanori Nakamura and Mohammad R. K. Mofrad and Shukei Sugita},
doi = {10.3390/ijms23137366},
year = {2022},
date = {2022-07-01},
journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
volume = {23},
number = {13},
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pubstate = {published},
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