Mary Dunlop | Profiles RNS

Mary Dunlop, PhD

Associate Professor

Boston University College of Engineering

Biomedical Engineering

PhD, California Institute of Technology
MS, California Institute of Technology
BS, Princeton University

Websites

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	Dunlop Lab
	BU College of Engineering

ORCID : 0000-0002-9261-8216

Mary Dunlop is an Associate Professor of Biomedical Engineering at Boston University with additional appointments in Molecular Biology, Cell Biology & Biochemistry and Bioinformatics. She graduated from Princeton University with a B.S.E. in Mechanical and Aerospace Engineering and a minor in Computer Science. She then received her Ph.D. from the California Institute of Technology, where she studied synthetic biology with a focus on dynamics and feedback in gene regulation. As a postdoctoral scholar, she conducted research on biofuel production at the Department of Energy’s Joint BioEnergy Institute. Her lab engineers novel synthetic feedback control systems and also studies naturally occurring examples of feedback in gene regulation. In recognition of her outstanding research and service contributions, she has received many honors including a Department of Energy Early Career Award, a National Science Foundation CAREER Award, and the ACS Synthetic Biology Young Investigator Award.

BU Research
NIH RePORTER Research

NRT-URoL: A Convergent Training Program on Biological Control
08/01/2023 - 07/31/2028 (Multi-PI)
PI: Mary Dunlop, PhD
National Science Foundation
DGE-2244366

Optogenetic selection for dynamic phenotypes in bacteria
08/01/2023 - 07/31/2026 (PI)
National Science Foundation
MCB-2324909

Clare Boothe Luce Fellowship for Madison Fletcher
09/01/2023 - 08/31/2025 (PI)
The Henry Luce Foundation, Inc.

Transitions: Deep learning models for microbial image analysis and time-series predictions
01/01/2022 - 12/31/2024 (PI)
National Science Foundation
MCB-2143289

Single-cell feedback, optogenetics, and deep learning to control gene expression in bacteria
08/15/2020 - 07/31/2024 (PI)
National Science Foundation
MCB-2032357

Cell-to-cell heterogeneity and the emergence of antibiotic resistance
06/05/2019 - 05/31/2024 (PI)
NIH/National Institute of Allergy & Infectious Diseases
3R01AI102922-010S1

High-throughput chemical imaging for optimizing biofuel synthesis using synthetic biology
09/15/2018 - 09/14/2023 (Multi-PI)
PI: Mary Dunlop, PhD
Department of Energy
DE-SC0019387

Quantifying Clostridioides difficile single-cell growth dynamics using time-lapse microscopy
01/15/2021 - 06/30/2023 (Subcontract PI)
Trustees of Tufts College Inc NIH NIAID
1R21AI153853-01A1

Exploiting dynamics and cell-to-cell variation in metabolic engineering
07/01/2018 - 06/30/2022 (PI)
National Science Foundation
CBET-1804096

Efflux pumps and the emergence of antibiotic resistance in single cells
02/01/2018 - 01/31/2021 (PI)
NIH/National Institute of Allergy & Infectious Diseases
5R21AI137843-02

Showing 10 of 13 results. Show All Results

Title

Yr	Title	Project-Sub Proj	Pubs
2023	Cell-to-cell heterogeneity and the emergence of antibiotic resistance	5R01AI102922-10
2023	Cell-to-cell heterogeneity and the emergence of antibiotic resistance	3R01AI102922-10S1
2023	Cell-to-cell heterogeneity and the emergence of antibiotic resistance	3R01AI102922-09S1
2022	Cell-to-cell heterogeneity and the emergence of antibiotic resistance	5R01AI102922-09
2021	Cell-to-cell heterogeneity and the emergence of antibiotic resistance	5R01AI102922-08	12
2020	Cell-to-cell heterogeneity and the emergence of antibiotic resistance	5R01AI102922-07	12
2019	Efflux pumps and the emergence of antibiotic resistance in single cells	5R21AI137843-02	2
2019	Cell-to-cell heterogeneity and the emergence of antibiotic resistance	2R01AI102922-06	12
2018	Efflux pumps and the emergence of antibiotic resistance in single cells	1R21AI137843-01	2
2018	Feedback and Noise in a Multiple Antibiotic Resistance Circuit	5R01AI102922-05	12

Showing 10 of 14 results. Show All Results

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Lugagne JB, Blassick CM, Dunlop MJ. Deep model predictive control of gene expression in thousands of single cells. Nat Commun. 2024 Mar 08; 15(1):2148. PMID: 38459057; PMCID: PMC10923782; DOI: 10.1038/s41467-024-46361-1;

Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light-inducible protein degradation in E. coli with the LOVdeg tag. Elife. 2024 Jan 25; 12. PMID: 38270583; PMCID: PMC10945698; DOI: 10.7554/eLife.87303;

Andreani V, South EJ, Dunlop MJ. Generating information-dense nucleotide sequences with optimal string packing. bioRxiv. 2023 Nov 03.View Related Profiles.

Dunlop, Mary
Andreani, Virgile

PMID: 37961203; PMCID: PMC10635063; DOI: 10.1101/2023.11.01.565124;

Tague N, Andreani V, Fan Y, Timp W, Dunlop MJ. Comprehensive Screening of a Light-Inducible Split Cre Recombinase with Domain Insertion Profiling. ACS Synth Biol. 2023 Oct 20; 12(10):2834-2842.View Related Profiles.

Dunlop, Mary
Andreani, Virgile

PMID: 37788288

Klumpe HE, Lugagne JB, Khalil AS, Dunlop MJ. Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes. ACS Synth Biol. 2023 Aug 18; 12(8):2367-2381.View Related Profiles.

Khalil, Ahmad
Dunlop, Mary

PMID: 37467372

Tague N, Lin H, Lugagne JB, O'Connor OM, Burman D, Wong WW, Cheng JX, Dunlop MJ. Longitudinal Single-Cell Imaging of Engineered Strains with Stimulated Raman Scattering to Characterize Heterogeneity in Fatty Acid Production. Adv Sci (Weinh). 2023 Jul; 10(20):e2206519. PMID: 37288534; PMCID: PMC10369233; DOI: 10.1002/advs.202206519;

Tague N, Andreani V, Fan Y, Timp W, Dunlop MJ. Comprehensive screening of a light-inducible split Cre recombinase with domain insertion profiling. bioRxiv. 2023 May 26.View Related Profiles.

Dunlop, Mary
Andreani, Virgile

PMID: 37293111; PMCID: PMC10245967; DOI: 10.1101/2023.05.26.542511;

Tague EP, McMahan JB, Tague N, Dunlop MJ, Ngo JT. Controlled Protein Activities with Viral Proteases, Antiviral Peptides, and Antiviral Drugs. ACS Chem Biol. 2023 May 19; 18(5):1228-1236.View Related Profiles.

Ngo, John
Dunlop, Mary

PMID: 37140437; PMCID: PMC10501127; DOI: 10.1021/acschembio.3c00138;

Tague EP, McMahan JB, Tague N, Dunlop MJ, Ngo JT. Controlled protein activities with viral proteases, antiviral peptides, and antiviral drugs. bioRxiv. 2023 Feb 27.View Related Profiles.

Ngo, John
Dunlop, Mary

PMID: 36909459; PMCID: PMC10002686; DOI: 10.1101/2023.02.27.530290;

Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light inducible protein degradation in E. coli with LOVtag. bioRxiv. 2023 Feb 26. PMID: 36865169; PMCID: PMC9980293; DOI: 10.1101/2023.02.25.530042;

Showing 10 of 59 results. Show More

Sheets MB, Tague N, Dunlop MJ. An optogenetic toolkit for light-inducible antibiotic resistance. Nat Commun. 2023 Feb 23; 14(1):1034. PMID: 36823420; PMCID: PMC9950086; DOI: 10.1038/s41467-023-36670-2;

Alnahhas RN, Dunlop MJ. Advances in linking single-cell bacterial stress response to population-level survival. Curr Opin Biotechnol. 2023 Feb; 79:102885. PMID: 36641904; PMCID: PMC9899315; DOI: 10.1016/j.copbio.2022.102885;

Zhang J, Shin J, Tague N, Lin H, Zhang M, Ge X, Wong W, Dunlop MJ, Cheng JX. Visualization of a Limonene Synthesis Metabolon Inside Living Bacteria by Hyperspectral SRS Microscopy. Adv Sci (Weinh). 2022 Nov; 9(32):e2203887.View Related Profiles.

Dunlop, Mary
Wong, Wilson

PMID: 36169112; PMCID: PMC9661820; DOI: 10.1002/advs.202203887;

Beardall WAV, Stan GB, Dunlop MJ. Deep Learning Concepts and Applications for Synthetic Biology. GEN Biotechnol. 2022 Aug 01; 1(4):360-371. PMID: 36061221; PMCID: PMC9428732; DOI: 10.1089/genbio.2022.0017;

Shin J, South EJ, Dunlop MJ. Transcriptional Tuning of Mevalonate Pathway Enzymes to Identify the Impact on Limonene Production in Escherichia coli. ACS Omega. 2022 Jun 07; 7(22):18331-18338. PMID: 35694509; PMCID: PMC9178717; DOI: 10.1021/acsomega.2c00483;

Sampaio NMV, Blassick CM, Andreani V, Lugagne JB, Dunlop MJ. Dynamic gene expression and growth underlie cell-to-cell heterogeneity in Escherichia coli stress response. Proc Natl Acad Sci U S A. 2022 Apr 05; 119(14):e2115032119.View Related Profiles.

Dunlop, Mary
Andreani, Virgile

PMID: 35344432; PMCID: PMC9168488; DOI: 10.1073/pnas.2115032119;

Lugagne JB, Dunlop MJ. Anticipating antibiotic resistance. Science. 2022 02 25; 375(6583):818-819. PMID: 35201873; DOI: 10.1126/science.abn9969;

O'Connor OM, Alnahhas RN, Lugagne JB, Dunlop MJ. DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics. PLoS Comput Biol. 2022 01; 18(1):e1009797. PMID: 35041653; PMCID: PMC8797229; DOI: 10.1371/journal.pcbi.1009797;

Lin H, Lee HJ, Tague N, Lugagne JB, Zong C, Deng F, Shin J, Tian L, Wong W, Dunlop MJ, Cheng JX. Microsecond fingerprint stimulated Raman spectroscopic imaging by ultrafast tuning and spatial-spectral learning. Nat Commun. 2021 05 24; 12(1):3052.View Related Profiles.

Cheng, Ji-Xin
Dunlop, Mary
Wong, Wilson

PMID: 34031374; PMCID: PMC8144602; DOI: 10.1038/s41467-021-23202-z;

Wang T, Tague N, Whelan SA, Dunlop MJ. Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites. Nucleic Acids Res. 2021 01 25; 49(2):1163-1172. PMID: 33367820; PMCID: PMC7826281; DOI: 10.1093/nar/gkaa1234;

Langevin AM, El Meouche I, Dunlop MJ. Mapping the Role of AcrAB-TolC Efflux Pumps in the Evolution of Antibiotic Resistance Reveals Near-MIC Treatments Facilitate Resistance Acquisition. mSphere. 2020 12 16; 5(6). PMID: 33328350; PMCID: PMC7771234; DOI: 10.1128/mSphere.01056-20;

Sheets MB, Wong WW, Dunlop MJ. Correction to Light-Inducible Recombinases for Bacterial Optogenetics. ACS Synth Biol. 2020 Oct 16; 9(10):2857-2859.View Related Profiles.

Dunlop, Mary
Wong, Wilson

PMID: 33001633; DOI: 10.1021/acssynbio.0c00477;

Sampaio NMV, Dunlop MJ. Functional roles of microbial cell-to-cell heterogeneity and emerging technologies for analysis and control. Curr Opin Microbiol. 2020 10; 57:87-94. PMID: 32919307; PMCID: PMC7722170; DOI: 10.1016/j.mib.2020.08.002;

Lugagne JB, Lin H, Dunlop MJ. DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning. PLoS Comput Biol. 2020 04; 16(4):e1007673. PMID: 32282792; PMCID: PMC7153852; DOI: 10.1371/journal.pcbi.1007673;

White JA, Gaver DP, Butera RJ, Choi B, Dunlop MJ, Grande-Allen KJ, Grosberg A, Hitchcock RW, Huang-Saad AY, Kotche M, Kyle AM, Lerner AL, Linehan JH, Linsenmeier RA, Miller MI, Papin JA, Setton L, Sgro A, Smith ML, Zaman M, Lee AP. Core Competencies for Undergraduates in Bioengineering and Biomedical Engineering: Findings, Consequences, and Recommendations. Ann Biomed Eng. 2020 Mar; 48(3):905-912.View Related Profiles.

White, John
Dunlop, Mary
Smith, Michael
Zaman, Muhammad

PMID: 32026231

Sheets MB, Wong WW, Dunlop MJ. Light-Inducible Recombinases for Bacterial Optogenetics. ACS Synth Biol. 2020 02 21; 9(2):227-235.View Related Profiles.

Dunlop, Mary
Wong, Wilson

PMID: 31961670; PMCID: PMC7393974; DOI: 10.1021/acssynbio.9b00395;

Rossi NA, El Meouche I, Dunlop MJ. Erratum: Author Correction: Forecasting cell fate during antibiotic exposure using stochastic gene expression. Commun Biol. 2019; 2:330. PMID: 31482144; PMCID: PMC6717196; DOI: 10.1038/s42003-019-0584-2;

Rossi NA, El Meouche I, Dunlop MJ. Forecasting cell fate during antibiotic exposure using stochastic gene expression. Commun Biol. 2019; 2:259. PMID: 31312728; PMCID: PMC6624276; DOI: 10.1038/s42003-019-0509-0;

Wang T, Kunze C, Dunlop MJ. Salicylate Increases Fitness Cost Associated with MarA-Mediated Antibiotic Resistance. Biophys J. 2019 08 06; 117(3):563-571. PMID: 31349991; PMCID: PMC6697527; DOI: 10.1016/j.bpj.2019.07.005;

Westbrook A, Tang X, Marshall R, Maxwell CS, Chappell J, Agrawal DK, Dunlop MJ, Noireaux V, Beisel CL, Lucks J, Franco E. Distinct timescales of RNA regulators enable the construction of a genetic pulse generator. Biotechnol Bioeng. 2019 05; 116(5):1139-1151. PMID: 30636320; DOI: 10.1002/bit.26918;

Lugagne JB, Dunlop MJ. Cell-machine interfaces for characterizing gene regulatory network dynamics. Curr Opin Syst Biol. 2019 Apr; 14:1-8. PMID: 31579842; PMCID: PMC6774389; DOI: 10.1016/j.coisb.2019.01.001;

Rossi NA, Mora T, Walczak AM, Dunlop MJ. Active degradation of MarA controls coordination of its downstream targets. PLoS Comput Biol. 2018 12; 14(12):e1006634. PMID: 30589845; PMCID: PMC6307708; DOI: 10.1371/journal.pcbi.1006634;

El Meouche I, Dunlop MJ. Heterogeneity in efflux pump expression predisposes antibiotic-resistant cells to mutation. Science. 2018 11 09; 362(6415):686-690. PMID: 30409883; PMCID: PMC6343669; DOI: 10.1126/science.aar7981;

Wen X, Langevin AM, Dunlop MJ. Antibiotic export by efflux pumps affects growth of neighboring bacteria. Sci Rep. 2018 10 11; 8(1):15120. PMID: 30310093; PMCID: PMC6181935; DOI: 10.1038/s41598-018-33275-4;

Wang T, Dunlop MJ. Controlling and exploiting cell-to-cell variation in metabolic engineering. Curr Opin Biotechnol. 2019 06; 57:10-16. PMID: 30261323; DOI: 10.1016/j.copbio.2018.08.013;

Agrawal DK, Tang X, Westbrook A, Marshall R, Maxwell CS, Lucks J, Noireaux V, Beisel CL, Dunlop MJ, Franco E. Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression. ACS Synth Biol. 2018 05 18; 7(5):1219-1228. PMID: 29709170; DOI: 10.1021/acssynbio.8b00040;

Rossi NA, Dunlop MJ. Making Waves with Synthetic Oscillators. Cell Syst. 2018 04 25; 6(4):406-407. PMID: 29698647; DOI: 10.1016/j.cels.2018.04.001;

Langevin AM, Dunlop MJ. Stress Introduction Rate Alters the Benefit of AcrAB-TolC Efflux Pumps. J Bacteriol. 2018 01 01; 200(1). PMID: 29038251; PMCID: PMC5717160; DOI: 10.1128/JB.00525-17;

Siu Y, Fenno J, Lindle JM, Dunlop MJ. Design and Selection of a Synthetic Feedback Loop for Optimizing Biofuel Tolerance. ACS Synth Biol. 2018 01 19; 7(1):16-23. PMID: 29022700; DOI: 10.1021/acssynbio.7b00260;

Tomko TA, Dunlop MJ. Expression of Heterologous Sigma Factor Expands the Searchable Space for Biofuel Tolerance Mechanisms. ACS Synth Biol. 2017 07 21; 6(7):1343-1350. PMID: 28319371; DOI: 10.1021/acssynbio.6b00375;

Wang T, El Meouche I, Dunlop MJ. Bacterial persistence induced by salicylate via reactive oxygen species. Sci Rep. 2017 03 10; 7:43839. PMID: 28281556; PMCID: PMC5345018; DOI: 10.1038/srep43839;

Rossi NA, Dunlop MJ. Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA. PLoS Comput Biol. 2017 01; 13(1):e1005310. PMID: 28060821; PMCID: PMC5257004; DOI: 10.1371/journal.pcbi.1005310;

Garcia-Bernardo J, Dunlop MJ. Phenotypic Diversity Using Bimodal and Unimodal Expression of Stress Response Proteins. Biophys J. 2016 08 09; 111(3):675. PMID: 27508450; PMCID: PMC5405226; DOI: 10.1016/j.bpj.2016.07.030;

Garcia-Bernardo J, Dunlop MJ. Phenotypic Diversity Using Bimodal and Unimodal Expression of Stress Response Proteins. Biophys J. 2016 05 24; 110(10):2278-87. PMID: 27224492; PMCID: PMC4881231; DOI: 10.1016/j.bpj.2016.04.012;

Lindle JM, Dunlop MJ. Performing selections under dynamic conditions for synthetic biology applications. Integr Biol (Camb). 2016 Apr 18; 8(4):556-63. PMID: 26758547; PMCID: PMC5778442; DOI: 10.1039/c5ib00286a;

El Meouche I, Siu Y, Dunlop MJ. Stochastic expression of a multiple antibiotic resistance activator confers transient resistance in single cells. Sci Rep. 2016 Jan 13; 6:19538. PMID: 26758525; PMCID: PMC4725842; DOI: 10.1038/srep19538;

Tomko TA, Dunlop MJ. Engineering improved bio-jet fuel tolerance in Escherichia coli using a transgenic library from the hydrocarbon-degrader Marinobacter aquaeolei. Biotechnol Biofuels. 2015; 8:165. PMID: 26448785; PMCID: PMC4596283; DOI: 10.1186/s13068-015-0347-3;

Garcia-Bernardo J, Dunlop MJ. Noise and low-level dynamics can coordinate multicomponent bet hedging mechanisms. Biophys J. 2015 Jan 06; 108(1):184-93. PMID: 25564865; PMCID: PMC4286610; DOI: 10.1016/j.bpj.2014.11.048;

Turner WJ, Dunlop MJ. Trade-Offs in Improving Biofuel Tolerance Using Combinations of Efflux Pumps. ACS Synth Biol. 2015 Oct 16; 4(10):1056-63. PMID: 25496359; DOI: 10.1021/sb500307w;

Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A. Development of a native Escherichia coli induction system for ionic liquid tolerance. PLoS One. 2014; 9(7):e101115. PMID: 24983352; PMCID: PMC4077768; DOI: 10.1371/journal.pone.0101115;

Garcia-Bernardo J, Dunlop MJ. Tunable stochastic pulsing in the Escherichia coli multiple antibiotic resistance network from interlinked positive and negative feedback loops. PLoS Comput Biol. 2013; 9(9):e1003229. PMID: 24086119; PMCID: PMC3784492; DOI: 10.1371/journal.pcbi.1003229;

Harrison ME, Dunlop MJ. Synthetic feedback loop model for increasing microbial biofuel production using a biosensor. Front Microbiol. 2012; 3:360. PMID: 23112794; PMCID: PMC3481154; DOI: 10.3389/fmicb.2012.00360;

Koh RS, Dunlop MJ. Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network. BMC Syst Biol. 2012 May 20; 6:47. PMID: 22607777; PMCID: PMC3434061; DOI: 10.1186/1752-0509-6-47;

Dunlop MJ. Engineering microbes for tolerance to next-generation biofuels. Biotechnol Biofuels. 2011 Sep 21; 4:32. PMID: 21936941; PMCID: PMC3189103; DOI: 10.1186/1754-6834-4-32;

Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A. Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol. 2011 May 10; 7:487. PMID: 21556065; PMCID: PMC3130554; DOI: 10.1038/msb.2011.21;

Cox RS, Dunlop MJ, Elowitz MB. A synthetic three-color scaffold for monitoring genetic regulation and noise. J Biol Eng. 2010 Jul 21; 4:10. PMID: 20646328; PMCID: PMC2918530; DOI: 10.1186/1754-1611-4-10;

Dunlop MJ, Keasling JD, Mukhopadhyay A. A model for improving microbial biofuel production using a synthetic feedback loop. Syst Synth Biol. 2010 Jun; 4(2):95-104. PMID: 20805930; PMCID: PMC2923299; DOI: 10.1007/s11693-010-9052-5;

Dunlop MJ, Cox RS, Levine JH, Murray RM, Elowitz MB. Regulatory activity revealed by dynamic correlations in gene expression noise. Nat Genet. 2008 Dec; 40(12):1493-8. PMID: 19029898; PMCID: PMC2829635; DOI: 10.1038/ng.281;

Wall ME, Dunlop MJ, Hlavacek WS. Multiple functions of a feed-forward-loop gene circuit. J Mol Biol. 2005 Jun 10; 349(3):501-14. PMID: 15890368; DOI: 10.1016/j.jmb.2005.04.022;

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 59 publications over 17 distinct years, with a maximum of 10 publications in 2023

Bar chart showing 59 publications over 17 distinct years, with a maximum of 10 publications in 2023

Year	Publications
2005	1
2008	1
2010	2
2011	2
2012	2
2013	1
2014	2
2015	2
2016	4
2017	5
2018	6
2019	5
2020	6
2021	2
2022	6
2023	10
2024	2

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2022 National Science Foundation: Transitions Award

2020 College of Engineering: Teaching Excellence Award

2019 Biomedical Engineering: Professor of the Year

2017 ACS: Synthetic Biology Young Investigator

2015 University of Vermont, Graduate Student Senate: Nominee for Outstanding Faculty Advisor Award

2014 National Science Foundation : CAREER Award

2013 University of Vermont, College of Engineering and Mathematical Sciences: Outstanding Junior Faculty Award

2011 Department of Energy: Early Career Award

2008 California Institute of Technology: Dean’s Award for Community Service

2004 American Control Conference: Best Student Paper

2002-2006 Department of Energy: Computational Science Graduate Fellowship

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