Current News: To keep up with lab (and non-lab) news and events, follow @MoKhalilLab on Twitter!
May 19, 2020: Our very own Chris Mancuso is recipient of this year's Best Dissertation Award in the Biomedical Engineering Department. Bravo Chris!
May 12, 2020: Mo was awarded the 2020 Vannevar Bush Faculty Fellowship. Check out the DoD Press Release, and the BU Research story by Jessica Colarossi.
April 1, 2020: Congratulations to Chris Mancuso, who successfully defended his PhD Thesis!
September 20, 2019: Check out the nice feature in Bostonia by Kat McAlpine highlighting our work: "The Transformers: Meet Seven BU Researchers Who are Transforming the Human Experience".
May 23, 2019: Our eVOLVER platform was featured in Nature by Mike May: "Automated Science on a Shoestring".
April 18, 2019: Our paper "Complex Signal Processing in Synthetic Gene Circuits Using Cooperative Regulatory Assemblies" was published online in Science. Congratulations to the whole team! Also check out the accompanying Press Release and BU News story on our work.
March 12, 2019: Our paper "Engineering Epigenetic Regulation Using Synthetic Read-Write Modules" was highlighted in Biochemistry by Theresa Loveless and Chang Liu.
January 30, 2019: Our paper "Engineering Epigenetic Regulation Using Synthetic Read-Write Modules" was highlighted in Nature Methods by Nicole Rusk.
December 18, 2018: Check out the BU Today article highlighting our wonderful undergraduate, Rachel Petherbridge, for being named BU's first Mitchell Scholar!
December 6, 2018: Our paper "Engineering Epigenetic Regulation Using Synthetic Read-Write Modules" was published online in Cell. Congratulations to the whole team! Also check out the BU News story on our work.
October 4-6, 2018: Mo helped organize and gave a talk at the 2nd Epigenetics and Bioengineering Conference (EpiBio 2018) in San Francisco, CA.
September 20-22, 2018: Divya was invited to give a talk at the Cell Therapies and Bioengineering Conference in San Francisco, CA.
September 5-7, 2018: Mo was selected to attend the National Academy of Engineering 2018 Frontiers of Engineering Symposium at MIT Lincoln Laboratory.
June 11, 2018: Our paper "Precise, Automated Control of Conditions for High-Throughput Growth of Yeast and Bacteria with eVOLVER" was published online in Nature Biotechnology. Congratulations to the whole team! Also check out the BU News and BU Research stories on our work.
June 3-7, 2018: Our wonderful graduate students -- Chris, Minhee and Nikit -- presented their work at this year's SEED meeting in Scottsdale, AZ.
May 30, 2018: Congratulations to Nikit Patel, who successfully defended his PhD Thesis! Check out the celebration video!
April 18, 2018: Congratulations to Brandon Wong, who successfully defended his PhD Thesis!
April 4-5, 2018: Mo gave talks in the Department of Chemical & Biological Engineering and Biotechnology Training Program Seminar Series at Northwestern University in Evanston, IL.
March 23-24, 2018: Mo, Nikit and Brandon attended the EBRC Spring 2018 retreat at the University of Washington in Seattle, WA. Mo was invited to give a talk, and Brandon and Nikit presented posters.
March 28, 2018: Congratulations to Szilvia Kiriakov, who successfully defended her PhD Thesis!
March 6, 2018: Mo gave a talk in the Department of Genetics & Development at Columbia University Medical Center in New York, NY.
February 22-25, 2018: Our wonderful graduate students -- Brandon, Minhee and Nikit -- presented their work at this year's Winter Q-Bio meeting in Hawaii.
February 8, 2018: Our paper "Precise, Automated Control of Conditions for High-Throughput Growth of Yeast and Bacteria with eVOLVER" was accepted for publication in Nature Biotechnology. Congratulations to the whole team!
February 2, 2018: Our paper "Hsf1 and Hsp70 Constitute a Two-Component Feedback Loop that Regulates the Yeast Heat Shock Response" was accepted for publication in eLife. Congratulations to the whole team!
January 9, 2018: Mo gave the Keynote address at the Quantitative Biology Bootcamp at Brandeis University in Waltham, MA.
November 10, 2017: Mo gave a talk in the Department of Biomedical Engineering at Cornell University in Ithaca, NY.
November 2, 2017: Our paper "A genetic tool to track protein aggregates and control prion inheritance" was officially published in Cell, and was chosen as the journal cover!
November 2, 2017: Mo gave a talk in The BioTechnology Institute at the University of Minnesota in St Paul, MN.
October 30, 2017: Our paper "A genetic tool to track protein aggregates and control prion inheritance" was recommended by F1000! Also check out the BU Research news story on this work.
October 19, 2017: Our paper "A genetic tool to track protein aggregates and control prion inheritance" was published online in Cell. Congratulations to the whole team!
October 12, 2017: Mo gave a talk at GEARS, the Boston-based monthly Gene Expression and RNA seminar series.
October 1, 2017: Kole Sedlack officially joins the lab as a research associate. Welcome Kole! See all our new members.
September 19-21, 2017: Mo gave a talk at an International Workshop on Synthetic Biology hosted by WISB in Venice, Italy.
September 14-15, 2017: We celebrated the official opening of the Rajen Kilachand Center for Integrated Life Sciences & Engineering! Check out BU Today's pieces on the building and inaugural symposium (featuring our lab). Also check out a wonderful piece in BU Research about communication and language in interdisciplinary research.
August 25 2017: Our paper "A genetic tool to track protein aggregates and control prion inheritance" was accepted in principle at Cell!
August 9, 2017: Mo gave the Green Center for Systems Biology Seminar at UT Southwestern Medical Center in Dallas, Texas.
August 8, 2017: A great piece on epigenetic editing in Nature Medicine that highlights our lab.
July 30-August 4, 2017: Mo and Szilvia attended the Gordon Research Conference on Synthetic Biology. Mo gave a talk and Szilvia presented a poster. Mo was also elected Vice Chair for the next GRC.
June 28, 2017: Congratulations to Dana Braff, who successfully defended her PhD Thesis!
June 22, 2017: Our work on antibiotic resistance was highlighted by Dr. Francis Collins in the NIH Director's Blog.
June 20, 2017: Mo gave a talk at SEED 2017 in Vancouver, British Columbia, Canada.
May 23, 2017: Congratulations to Saloni Jain, who successfully defended her PhD Thesis!
May 22, 2017: Mo gave a talk at the Integrative BioSystems Institute (IBSI) and Department of Biomedical Engineering at Georgia Tech in Atlanta, GA.
May 12, 2017: Mo gave a talk at the Genome Editing and Advances in Transgenic Technology Congress in Boston, MA.
May 10, 2017: Check out the new feature article on BU Research, “Hacking Nature: Mo Khalil Seeks Synthetic-Biology Solutions to the World’s Biggest Problems”.
May 6-7, 2017: We hosted the Fourth International Mammalian Synthetic Biology Workshop (mSBW4.0) at Boston University. Our own Minhee Park was selected to give a talk on her work!
May 2, 2017: Our paper "Prospective isolation of NKX2-1–expressing human lung progenitors derived from pluripotent stem cells" was published in JCI. See Papers for all our papers and commentary.
May 1-2, 2017: Our lab has moved to the Center for Integrated Life Sciences and Engineering (CILSE).
April 21, 2017: Mo gave a talk in the Department of Chemical and Systems Biology at Stanford University in Stanford, CA.
April 19, 2017: Mo gave a talk in the Department of Bioengineering at UC Berkeley in Berkeley, CA.
April 13, 2017: Mo gave a talk in the Department of Bioengineering at UPenn in Philadelphia, PA.
February 24, 2017: Mo gave a talk in the School of Biological and Health Systems Engineering at Arizona State University in Tempe, AZ.
January 9, 2017: President Obama recognized our lab by naming Mo a recipient of the PECASE award! See also the NSF MCB blog post and BU News story.
December 7, 2016: Check out this "Office Artifacts" story on Mo Khalil in BU Today.
December 1, 2016: Haytham Khalil officially joins the lab as a research associate. Welcome Haytham! See all our new members.
November 10, 2016: Our paper "Dynamic Control of Hsf1 During Heat Shock By a Chaperone Switch and Phosphorylation" was published in eLife. See Papers for all our papers and commentary.
November 1, 2016: Giulio Chiesa officially joins the lab as a postdoctoral associate. Welcome Giulio! See all our new members.
September 1, 2016: Our lab received a 2016 NIH New Innovator Award! See the news stories in Bostonia, BU Today, and the BU College of Engineering.
August 31, 2016: See our Review on epigenetic engineering in Genome Biology.
August 24, 2016: See our Preview in Cell Systems highlighting recent work from Jan Skotheim's lab.
August 8-14, 2016: Mo and Brandon are at beautiful Cold Spring Harbor Laboratory, serving as instructors for the 2016 Synthetic Biology Course.
June 24, 2016: Mo gave a lecture in the MBL Physiology Course at Woods Hole.
June 21, 2016: Our preprint "Vibrio natriegens, a new genomic powerhouse" was highlighted in Science and Wired.
June 12, 2016: Our preprint "Vibrio natriegens, a new genomic powerhouse" was published in bioRxiv.
May 21-22, 2016: Mo Co-Chaired another successful International Workshop on Mammalian Synthetic Biology (mSBW3.0) at MIT.
May 14, 2016: Mo is the 2016 College of Engineering Outstanding Professor of the Year. See the BU News story.
May 2, 2016: Mo was chosen as the 2016 Biomedical Engineering Professor of the Year, and will receive the Award For Teaching Excellence.
April 21, 2016: Mo served as a Guest Editor for a special themed issue of Integrative Biology titled Biological Insights from Synthetic Biology. See the Editorial.
April 1, 2016: Mo was selected as a Hartwell Investigator, and will receive a 2015 Hartwell Foundation Individual Biomedical Research Award. See the BU BME announcement.
March 14, 2016: Mo spoke at the 2016 Gene Circuits LabLinks meeting at the Broad Institute. This meeting was co-sponsored by Cell Press and the Broad's Center for Cell Circuits.
March 1, 2016: Ali Beyzavi becomes our first graduate student to successfully defend his PhD thesis! Ali will be a postdoctoral fellow in the Langer Lab at MIT. Congratulations Ali!
February 26, 2016: Mo gave the Systems Biology Theory Lunch at Harvard Medical School.
February 12, 2016: See our Perspective in Science highlighting recent work from Michael Elowitz's lab.
January 27, 2016: The journal Cell Systems asks "What have the principles of engineering taught us about biological systems?" See Mo's "Voices" piece.
January 7, 2016: The 哈利勒实验室 is part of a multi-institutional team that was awarded a National Science Foundation "Expeditions in Computing" grant to advance synthetic biology. See the NSF press release, the AAAS EurekAlert! press release, and the BU News story. For more information on the project, visit the project website.
November 30, 2015: Mo gave a talk in the Department of Biomedical Engineering seminar series at Johns Hopkins University in Baltimore, MD.
October 22, 2015: Mo gave a talk in the Department of Molecular Microbiology and Immunology seminar series at Brown University in Providence, RI.
September 17-18, 2015: Mo co-organized and participated in a B-Debate entitled "Synthetic Biology: From Standard Biological Parts to Artificial Life" in Barcelona. B-Debate is a set of scientific meetings, organized in a debate forum, that bring together international scientific leaders in different sub-disciplines to discuss and exchange ideas.
August 29, 2015: Khalil lab canoe trip on the Concord River! Check out Brandon's video.
June 28-July 3, 2015: Mo attended and served as a Discussion Leader at the Gordon Research Conference on Synthetic Biology in Sunday River, Maine.
June 22, 2015: Our paper "Antibiotic Efficacy is Linked to Bacterial Cellular Respiration" was published in PNAS. See the Wyss Institute news story.
June 3-5, 2015: Mo attended a fantastic workshop entitled "Gene Regulation by the Numbers" at the Radcliffe Institute for Advanced Study at Harvard. See Arjun Raj's blog posts from the meeting!
June 1, 2015: Our work on chromatin was highlighted by the NSF Division of Molecular and Cellular Biosciences blog.
May 4, 2015: The Biological Design Center at Boston University has been officially launched, serving as a focal point for research and education activities focused on the engineering of complex biological systems. Mo was selected to serve as the Associate Director. See the BU News story.
May 1, 2015: Mo was chosen as the 2015 Biomedical Engineering Professor of the Year, and will receive the Award For Teaching Excellence.
February 10, 2015: Our review paper "Chromatin Regulation at the Frontier of Synthetic Biology" was published in Nature Reviews Genetics.
January 26, 2015: The 哈利勒实验室 is awarded a DARPA grant for BAA 14-49 Biological Robustness in Complex Settings (BRICS), entitled "ROBUST: Robust Operation of Bacterial Universes with Synthetic-biology Technologies" (with Tim Lu, Jeff Gore, Farren Isaacs, Daniel Segré, and Jim Collins).
December 12, 2014: Our very own Brandon Wong, caught in action at the new Engineering Product Innovation Center (EPIC). See the BU News story.
November 17, 2014: Mo gave a talk in the Bioengineering Lecture Series at Caltech in Pasadena, California.
November 10, 2014: Mo gave a talk in the Cell Circuits & Epigenomics Seminar Series at the Broad Institute in Cambridge, Massachusetts.
October 26-29, 2014: Mo was selected to attend the National Academy of Engineering's (NAE) Sixth Frontiers of Engineering Education Symposium in Irvine, California. See the BU News story.
October 23-24, 2014: Mo gave a talk at the Annual Meeting for the Mérieux Research Grants in Annecy, France.
September 26, 2014: Mo gave a talk at the Genetics Training Grant Retreat in the Departments of Biology and Biochemistry at Brandeis University in Waltham, Massachusetts.
July 8, 2014: Mo gave a talk at the The World Congress of Biomechanics in Boston, Massachusetts.
April 29, 2014: Our good friend and collaborator, Jim Collins, was elected to the National Academy of Sciences! See the BU Today article.
April 3, 2014: Albert's paper, which is also the Khalil lab's first official paper, was accepted for publication in Cell! Congratulations to Albert and the whole lab.
January 1, 2014: Mo was named a Visiting Scholar at the Wyss Institute for Biologically Inspired Engineering at Harvard University.
December 23, 2013: Mo was named as one of 20 of the most promising Young Investigators in genomics research by GenomeWeb, a leading publication in the field. Nominated by established, high-impact biomedical researchers, individuals on GenomeWeb’s eighth annual Young Investigators list were recognized for original work in developing and applying genomic methods—such as DNA sequencing, assembly and analysis—to everything from cell communication to plant growth to the development of cancer. See the BU News story.
November 20, 2013: Albert Keung received a Ruth L. Kirschstein National Research Service Award Postdoctoral Fellowship from the NIH!
November 1, 2013: Mo received an NSF CAREER Award! See the BU News story.
October 18, 2013: Our paper "A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions" was highlighted in J. Craig Venter's new book: Life at the Speed of Light.
October 16, 2013: The Boston University Center of Synthetic Biology is launched! See the BU News story.
September 15, 2013: Mo was chosen to receive the Innovation Career Development Professorship. He is one of two faculty members at Boston University to be named this endowed professorship. See the BU Today article.
August 26, 2013: Mo was named a 2013 Kern Faculty Fellow at Boston University.
August 1, 2013: Our synthetic biology feature "Engineering Life" was published in The Scientist.
August 1, 2013: The Khalil lab has expanded! Please see all our new members.
June 13, 2013: Mo was interviewed by The Science Coalition as one of its Featured Innovators ( video interview).
June 6, 2013: Mo gave the Materials Research Science and Engineering Center (MRSEC) seminar at Brandeis University.
May 3, 2013: Mo was chosen as the 2013 Biomedical Engineering Professor of the Year, and will receive the Award For Teaching Excellence.
March 19, 2013: Mo gave a talk at the Keystone Symposia on Precision Engineering and Synthetic Biology in Breckenridge, Colorado.
February 5, 2013: Mo and other researchers urge Congress to stop the sequester, the across-the-board cuts to the nation's discretionary spending that would devastate research funding. See his video editorial and the BU Today article.

Please help Mo and the Association of American Universities (AAU) get the word out!
January 13-16, 2013: Mo is a session chair at the 4th International Conference on Biomolecular Engineering in Fort Lauderdale, Forida.
January 2013: A feature highlighting our work: "Streamlined Engineering for Synthetic Biology" in Nature Methods.
December 2012: A feature highlighting our work: "Hot-Wiring Cells" in Biotechniques.
November 12, 2012: Szilvia Kiriakov is awarded a prestigious Boehringer Ingelheim Fonds PhD Fellowship. Congratulations Szilvia!
November 6, 2012: Mo is recipient of a Merieux Research Grant Award.
October 11, 2012: The Khalil lab was highlighted in a feature on Synthetic Biology at Boston University: "Life is Suite" in Bostonia (this includes a great video!).
October 7, 2012: Our paper "Iterative Plug-and-Play Methodology for Constructing and Modifying Synthetic Gene Networks" was published in Nature Methods.
September 25, 2012: Mo gave a talk in the Plenary Symposium at the 12th Congress of the Italian Federation of Life Sciences (FISV) in Rome.
July 1, 2012: Albert Keung officially joins the lab as a postdoctoral associate. Welcome Albert!
June 11, 2012: Mo is awarded a Wallace H. Coulter Translational Partnership Award (with Jim Collins, Mark Klempner, Israel Green-Hopkins).
May 22, 2012: Ali Beyzavi, Szilvia Kiriakov, and Nikit Patel officially join the lab as graduate students.
May 18, 2012: Nikit Patel is awarded an NIH Quantitative Biology & Physiology (QBP) Training Fellowship. Congratulations Nikit!
May 10, 2012: Mo is awarded a Dean's Catalyst Award for "Microfluidic Biocomputing" (with Douglas Densmore). News story.
May 1, 2012: Our artwork for the paper "Signaling-Mediated Bacterial Persister Formation" was chosen as the journal cover!
March 18, 2012: Our paper "Signaling-Mediated Bacterial Persister Formation" was published in Nature Chemical Biology.
February 1, 2012: Albert Keung has decided to join the lab as a postdoctoral associate.
January 15, 2012: The 哈利勒实验室 is officially launched!
August 1, 2011: The 哈利勒实验室 is awarded a DARPA grant for "Synthetic Mammalian Gene Regulatory Circuits for In Vivo Biomedical Applications" (with Jim Collins, Pamela Silver, Timothy Lu, J. Keith Joung, George Church, Harris Wang).
May 27, 2010: Our paper "Synthetic Biology: Applications Come of Age" was highlighted in The New York Times and Folha de S. Paulo (Brazil's leading daily newspaper).
May 1, 2010: Our paper "Synthetic Biology: Applications Come of Age" was chosen for the journal cover!
May 1, 2010: Our paper "Synthetic Biology: Applications Come of Age" was published in Nature Reviews Genetics.

Synthetic Reconstitution of Complex Cellular Behavior

Can we build biological systems that recapitulate complex cellular functions like those seen in nature? Answering this question is the central goal of our research.

This question also forms the basis of reconstitution, an established experimental approach that reimagines how a biological process can be recapitulated outside of its natural context (e.g. outside of the cell and in a test tube) using a reduced set of molecular components. Biochemical reconstitution has been successfully applied to recreate many processes, enabling precise control over molecular parameters and a powerful way to test mechanistic models and establish sufficiency. Our vision is to implement the power and precision afforded by biochemical reconstitution within the complex environment of a living cell. If we can achieve this, then we can understand and predictably control complex cellular functions that have eluded our understanding, such as those that regulate how cells make decisions, execute responses, establish memories, and develop into multicellular organisms.

To do this, our laboratory is developing novel tools at the intersection of synthetic & systems biology, protein & cell engineering, laboratory evolution, genomics, and computation that enable us to recapitulate and control cellular behavior with synthetic circuitry. This enables us to effectively replace biochemistry with genetics. Taking this leap forward is fundamentally important for basic biology, to discover how cellular behaviors and diseases arise from complex networks of interacting molecules. It is also important for engineering and medicine, offering the potential to precisely control cellular function for next-generation therapies and to “teach” cells and organisms to solve the greatest health, climate, and engineering challenges of today.

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Genome Duplication in a Long-Term Multicellularity Evolution Experiment
Kai Tong*†, Sayantan Datta*, Vivian Cheng, Daniella J. Haas, Saranya Gourisetti, Harley L. Yopp, Thomas C. Day, Dung T. Lac, Ahmad S. Khalil, Peter L. Conlin, G. Ozan Bozdag and William C. Ratcliff†
Nature, 639: 691-699 (2025)

Development of Compact Transcriptional Effectors Using High-Throughput Measurements in Diverse Contexts
Josh Tycko*, Mike V. Van*, Aradhana, Nicole DelRosso, Hanrong Ye, David Yao, Raeline Valbuena, Alun Vaughan-Jackson, Xiaoshu Xu, Connor Ludwig, Kaitlyn Spees, Katherine Liu, Mingxin Gu, Venya Khare, Adi Xiyal Mukund, Peter H. Suzuki, Sophia Arana, Catherine Zhang, Peter P. Du, Thea S. Ornstein, Gaelen T. Hess, Roarke A. Kamber, Lei S. Qi, Ahmad S. Khalil, Lacramioara Bintu† and Michael C. Bassik†
Nature Biotechnology, Nov 1 (2024)

Mapping the Dynamics of Epigenetic Adaptation in S. Pombe During Heterochromatin Misregulation
Ajay Larkin*, Colin Kunze*, Melissa Seman, Alexander Levashkevich, Justin Curran, Ahmad S. Khalil† and Kaushik Ragunathan†
Developmental Cell, 59 (2024)

Brainwide Silencing of Prion Protein by AAV-Mediated Delivery of an Engineered Compact Epigenetic Editor
Edwin N. Neumann*, Tessa M. Bertozzi*, Elaine Wu, Fiona Serack, John W. Harvey, Pamela P. Brauer, Catherine P. Pirtle, Alissa Coffey, Michael Howard, Nikita Kamath, Kenney Lenz, Kenia Guzman, Michael H. Raymond, Ahmad S. Khalil, Benjamin E. Deverman, Eric Vallabh Minikel, Sonia M. Vallabh and Jonathan S. Weissman
Science, 384: ado7082 (2024)

A Multiplex MoClo Toolkit for Extensive and Flexible Engineering of Saccharomyces cerevisiae
William M. Shaw, Ahmad S. Khalil and Tom Ellis
ACS Synthetic Biology, 12: 3393-3405 (2023)

Cooperative Assembly Confers Regulatory Specificity and Long-Term Genetic Circuit Stability
Meghan D. J. Bragdon*, Nikit Patel*, James Chuang, Ethan Levien, Caleb J. Bashor* and Ahmad S. Khalil*
Cell, 186: 3810-3825 (2023)

Mapping the Dynamics of Epigenetic Adaptation
Ajay Larkin*, Colin Kunze*, Melissa Seman, Alexander Levashkevich, Justin Curran, Ahmad S. Khalil† and Kaushik Ragunathan†
bioRxiv, doi: 10.1101/2023.07.10.548368 (2023)

Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes
Heidi E. Klumpe*, Jean-Baptiste Lugagne*, Ahmad S. Khalil and Mary J. Dunlop
ACS Synthetic Biology, 12: 2367-2381 (2023)

Long-Term Evolution of Proliferating Yeast Cells Using the eVOLVER Platform
Daniel Garcia-Ruano, Akanksha Jain, Zachary J. Heins, Brandon G. Wong, Ezira Yimer Wolle, Ahmad S. Khalil and Damien Coudreuse
Open Biology, 13: 230118 (2023)

Transcriptional Kinetic Synergy: A Complex Landscape Revealed by Integrating Modelling and Synthetic Biology
Rosa Martinez-Corral, Minhee Park, Kelly M. Biette, Dhana Friedrich, Clarissa Scholes, Ahmad S. Khalil, Jeremy Gunawardena and Angela H. DePace
Cell Systems, 14: 324-339 (2023)

High-Throughput Continuous Evolution of Compact Cas9 Variants Targeting Single-Nucleotide-Pyrimidine PAMs
Tony P. Huang*, Zachary J. Heins*, Shannon M. Miller, Brandon G. Wong, Pallavi A. Balivada, Tina Wang, Ahmad S. Khalil† and David R. Liu†
Nature Biotechnology, 41: 96-107 (2023)

Multidimensional Control of Therapeutic Human Cell Function with Synthetic Gene Circuits
Hui-Shan Li*, Divya V. Israni*, Keith A. Gagnon, Kok Ann Gan, Michael H. Raymond, Jeffry D. Sander, Kole T. Roybal, J. Keith Joung, Wilson W. Wong and Ahmad S. Khalil
Science, 378: 1227-1234 (2022)

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