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Farhat M, Greenaway C, Pai M, Menzies D. False-positive tuberculin skin tests: what is the absolute effect of BCG and non-tuberculous mycobacteria?. Int J Tuberc Lung Dis. 2006 Nov;10(11):1192-204. Review. PubMed PMID: 17131776.
Bazari H, Jaff MR, Mannstadt M, Yan S. Case records of the Massachusetts General Hospital. Case 7-2007. A 59-year-old woman with diabetic renal disease and nonhealing skin ulcers. N Engl J Med. 2007 Mar 8;356(10):1049-57. doi: 10.1056/NEJMcpc069038. PubMed PMID: 17347459.
Cobelens FG, Menzies D, Farhat M. False-positive tuberculin reactions due to non-tuberculous mycobacterial infections. Int J Tuberc Lung Dis. 2007 Aug;11(8):934-5;author reply 935. PubMed PMID: 17705966.
Menzies D, Gardiner G, Farhat M, Greenaway C, Pai M. Thinking in three dimensions: a web-based algorithm to aid the interpretation of tuberculin skin test results. Int J Tuberc Lung Dis. 2008 May;12(5):498-505. PubMed PMID: 18419884.
Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol. 2009 Aug;5(8):e1000489. doi: 10.1371/journal.pcbi.1000489. Epub 2009 Aug 28. PubMed PMID: 19714220; PubMed Central PMCID: PMC2726785.
Karvellas CJ, Farhat MR, Sajjad I, Mogensen SS, Leung AA, Wald R, Bagshaw SM. A comparison of early versus late initiation of renal replacement therapy in critically ill patients with acute kidney injury: a systematic review and meta-analysis. Crit Care. 2011;15(1):R72. doi: 10.1186/cc10061. Epub 2011 Feb 25. Review. PubMed PMID: 21352532; PubMed Central PMCID: PMC3222005.
Farhat MR, Loring SH, Riskind P, Weinhouse G. Disturbance of respiratory muscle control in a patient with early-stage multiple sclerosis. Eur Respir J. 2013 Jun;41(6):1454-6. doi: 10.1183/09031936.00172312. PubMed PMID: 23728406.
Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013 Oct;45(10):1183-9. doi: 10.1038/ng.2747. Epub 2013 Sep 1. PubMed PMID: 23995135; PubMed Central PMCID: PMC3887553.
Nebenzahl-Guimaraes H, Jacobson KR, Farhat MR, Murray MB. Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis. J Antimicrob Chemother. 2014 Feb;69(2):331-42. doi: 10.1093/jac/dkt358. Epub 2013 Sep 20. Review. PubMed PMID: 24055765; PubMed Central PMCID: PMC3886931.
Farhat MR, Shapiro BJ, Sheppard SK, Colijn C, Murray M. A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens. Genome Med. 2014;6(11):101. doi: 10.1186/s13073-014-0101-7. eCollection 2014. PubMed PMID: 25484920; PubMed Central PMCID: PMC4256898.
Farhat MR, Mitnick CD, Franke MF, Kaur D, Sloutsky A, Murray M, Jacobson KR. Concordance of Mycobacterium tuberculosis fluoroquinolone resistance testing: implications for treatment. Int J Tuberc Lung Dis. 2015 Mar;19(3):339-41. doi: 10.5588/ijtld.14.0814. PubMed PMID: 25686144; PubMed Central PMCID: PMC4486051.
Farhat MR, Jacobson KR, Franke MF, Kaur D, Sloutsky A, Mitnick CD, Murray M. Gyrase Mutations Are Associated with Variable Levels of Fluoroquinolone Resistance in Mycobacterium tuberculosis. J Clin Microbiol. 2016 Mar;54(3):727-33. doi: 10.1128/JCM.02775-15. Epub 2016 Jan 13. PubMed PMID: 26763957; PubMed Central PMCID: PMC4767988.
Ramly EP, Bohnen JD, Farhat MR, Razmdjou S, Mavros MN, Yeh DD, Lee J, Butler K, De Moya M, Velmahos GC, Kaafarani HM. The nature, patterns, clinical outcomes, and financial impact of intraoperative adverse events in emergency surgery. Am J Surg. 2016 Jul;212(1):16-23. doi: 10.1016/j.amjsurg.2015.07.023. Epub 2015 Oct 24. PubMed PMID: 26601649.
Andre E, Isaacs C, Affolabi D, Alagna R, Brockmann D, de Jong BC, Cambau E, Churchyard G, Cohen T, Delmee M, Delvenne JC, Farhat M, Habib A, Holme P, Keshavjee S, Khan A, Lightfoot P, Moore D, Moreno Y, Mundade Y, Pai M, Patel S, Nyaruhirira AU, Rocha LE, Takle J, Trébucq A, Creswell J, Boehme C. Connectivity of diagnostic technologies: improving surveillance and accelerating tuberculosis elimination. Int J Tuberc Lung Dis. 2016 Aug;20(8):999-1003. doi: 10.5588/ijtld.16.0015. PubMed PMID: 27393530; PubMed Central PMCID: PMC4937753.
Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am J Respir Crit Care Med. 2016 Sep 1;194(5):621-30. doi: 10.1164/rccm.201510-2091OC. PubMed PMID: 26910495; PubMed Central PMCID: PMC5027209.
Nebenzahl-Guimaraes H, van Laarhoven A, Farhat MR, Koeken VACM, Mandemakers JJ, Zomer A, van Hijum SAFT, Netea MG, Murray M, van Crevel R, van Soolingen D. Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes. Am J Respir Crit Care Med. 2017 Jun 1;195(11):1519-1527. doi: 10.1164/rccm.201605-1042OC. PubMed PMID: 27997216; PubMed Central PMCID: PMC5803666.
Farhat MR, Jacobson KR, Franke MF, Kaur D, Murray M, Mitnick CD. Fluoroquinolone Resistance Mutation Detection Is Equivalent to Culture-Based Drug Sensitivity Testing for Predicting Multidrug-Resistant Tuberculosis Treatment Outcome: A Retrospective Cohort Study. Clin Infect Dis. 2017 Oct 15;65(8):1364-1370. doi: 10.1093/cid/cix556. PubMed PMID: 29017248; PubMed Central PMCID: PMC5850426.
Pollock N, Dhiman R, Daifalla N, Farhat M, Campos-Neto A. Discovery of a unique Mycobacterium tuberculosis protein through proteomic analysis of urine from patients with active tuberculosis. Microbes Infect. 2018 Apr;20(4):228-235. doi: 10.1016/j.micinf.2017.12.011. Epub 2018 Jan 3. PubMed PMID: 29306028; PubMed Central PMCID: PMC5946903.
Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. N Engl J Med. 2018 Oct 11;379(15):1403-1415. doi: 10.1056/NEJMoa1800474. Epub 2018 Sep 26. PubMed PMID: 30280646; PubMed Central PMCID: PMC6121966.
Schubert B, Maddamsetti R, Nyman J, Farhat MR, Marks DS. Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings. Nat Microbiol. 2019 Feb;4(2):328-338. doi: 10.1038/s41564-018-0309-1. Epub 2018 Dec 3. PubMed PMID: 30510172; PubMed Central PMCID: PMC6663919.
Dixit A, Freschi L, Vargas R, Calderon R, Sacchettini J, Drobniewski F, Galea JT, Contreras C, Yataco R, Zhang Z, Lecca L, Kolokotronis SO, Mathema B, Farhat MR. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Sci Rep. 2019 Apr 3;9(1):5602. doi: 10.1038/s41598-019-41967-8. PubMed PMID: 30944370; PubMed Central PMCID: PMC6447560.
Chen ML, Doddi A, Royer J, Freschi L, Schito M, Ezewudo M, Kohane IS, Beam A, Farhat M. Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction. EBioMedicine. 2019 May;43:356-369. doi: 10.1016/j.ebiom.2019.04.016. Epub 2019 Apr 29. PubMed PMID: 31047860; PubMed Central PMCID: PMC6557804.
Farhat MR, Freschi L, Calderon R, Ioerger T, Snyder M, Meehan CJ, de Jong B, Rigouts L, Sloutsky A, Kaur D, Sunyaev S, van Soolingen D, Shendure J, Sacchettini J, Murray M. GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nat Commun. 2019 May 13;10(1):2128. doi: 10.1038/s41467-019-10110-6. PubMed PMID: 31086182; PubMed Central PMCID: PMC6513847.
Farhat MR, Sixsmith J, Calderon R, Hicks ND, Fortune SM, Murray M. Rifampicin and rifabutin resistance in 1003 Mycobacterium tuberculosis clinical isolates. J Antimicrob Chemother. 2019 Jun 1;74(6):1477-1483. doi: 10.1093/jac/dkz048. PubMed PMID: 30793747; PubMed Central PMCID: PMC6524487.
Andersen SB, Shapiro BJ, Vandenbroucke-Grauls C, de Vos MGJ. Microbial evolutionary medicine: from theory to clinical practice. Lancet Infect Dis. 2019 Aug;19(8):e273-e283. doi: 10.1016/S1473-3099(19)30045-3. Epub 2019 Apr 30. Review. PubMed PMID: 31053492.
Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, Farhat MR, Guthrie JL, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton PM, Brites D, Cabibbe AM, de Jong BC, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo DM, Niemann S, Comas I, Van Rie A. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol. 2019 Sep;17(9):533-545. doi: 10.1038/s41579-019-0214-5. Review. PubMed PMID: 31209399.
Yang Y, Walker TM, Walker AS, Wilson DJ, Peto TEA, Crook DW, Shamout F, Zhu T, Clifton DA. DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis. Bioinformatics. 2019 Sep 15;35(18):3240-3249. doi: 10.1093/bioinformatics/btz067. PubMed PMID: 30689732; PubMed Central PMCID: PMC6748723.
Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, van Soolingen D, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook DW, Iqbal Z. Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe. Wellcome Open Res. 2019;4:191. doi: 10.12688/wellcomeopenres.15603.1. eCollection 2019. PubMed PMID: 32055708; PubMed Central PMCID: PMC7004237.
Vargas R Jr, Farhat MR. Antibiotic treatment and selection for glpK mutations in patients with active tuberculosis disease. Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):3910-3912. doi: 10.1073/pnas.1920788117. Epub 2020 Feb 19. PubMed PMID: 32075922; PubMed Central PMCID: PMC7049102.
Gröschel MI, Meehan CJ, Barilar I, Diricks M, Gonzaga A, Steglich M, Conchillo-Solé O, Scherer IC, Mamat U, Luz CF, De Bruyne K, Utpatel C, Yero D, Gibert I, Daura X, Kampmeier S, Rahman NA, Kresken M, van der Werf TS, Alio I, Streit WR, Zhou K, Schwartz T, Rossen JWA, Farhat MR, Schaible UE, Nübel U, Rupp J, Steinmann J, Niemann S, Kohl TA. The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nat Commun. 2020 Apr 27;11(1):2044. doi: 10.1038/s41467-020-15123-0. PubMed PMID: 32341346; PubMed Central PMCID: PMC7184733.
Bonde A, Gaitanidis A, Breen K, El Hechi M, Nederpelt C, Christensen M, Kokoroskos N, Mendoza A, Velmahos G, Sillesen M, Farhat MR, Kaafarani HMA. Identification of a new genetic variant associated with cholecystitis: A multicenter genome-wide association study. J Trauma Acute Care Surg. 2020 Jul;89(1):173-178. doi: 10.1097/TA.0000000000002647. PubMed PMID: 32118827.
Wilson DJ. GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes. Mol Biol Evol. 2020 Aug 1;37(8):2450-2460. doi: 10.1093/molbev/msaa069. PubMed PMID: 32167543; PubMed Central PMCID: PMC7403622.
Kadura S, King N, Nakhoul M, Zhu H, Theron G, Köser CU, Farhat M. Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid. J Antimicrob Chemother. 2020 Aug 1;75(8):2031-2043. doi: 10.1093/jac/dkaa136. PubMed PMID: 32361756; PubMed Central PMCID: PMC7825472.
Rankin NA, Gröschel MI, Farhat MR. Mentorship at a distance. Science. 2020 Oct 23;370(6515):494. doi: 10.1126/science.370.6515.494. PubMed PMID: 33093113.
El Moheb M, Naar L, Christensen MA, Kapoen C, Maurer LR, Farhat M, Kaafarani HMA. Gastrointestinal Complications in Critically Ill Patients With and Without COVID-19. JAMA. 2020 Nov 10;324(18):1899-1901. doi: 10.1001/jama.2020.19400. PubMed PMID: 32970139; PubMed Central PMCID: PMC7516799.
Vargas R, Freschi L, Marin M, Epperson LE, Smith M, Oussenko I, Durbin D, Strong M, Salfinger M, Farhat MR. In-host population dynamics of Mycobacterium tuberculosis complex during active disease. Elife. 2021 Feb 1;10. doi: 10.7554/eLife.61805. PubMed PMID: 33522489; PubMed Central PMCID: PMC7884073.
Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, DeRuff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Lin AE, Carter A, Myhrvold C, Kemball ME, Chaluvadi S, Cusick C, Flowers K, Neumann A, Cerrato F, Farhat M, Slater D, Harris JB, Branda JA, Hooper D, Gaeta JM, Baggett TP, O'Connell J, Gnirke A, Lieberman TD, Philippakis A, Burns M, Brown CM, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ, MacInnis BL. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science. 2021 Feb 5;371(6529). doi: 10.1126/science.abe3261. Epub 2020 Dec 10. PubMed PMID: 33303686; PubMed Central PMCID: PMC7857412.
Ektefaie Y, Dixit A, Freschi L, Farhat MR. Globally diverse Mycobacterium tuberculosis resistance acquisition: a retrospective geographical and temporal analysis of whole genome sequences. Lancet Microbe. 2021 Mar;2(3):e96-e104. doi: 10.1016/s2666-5247(20)30195-6. Epub 2021 Jan 27. PubMed PMID: 33912853; PubMed Central PMCID: PMC8078851.
Marin M, Vargas R, Harris M, Jeffery B, Epperson E, Durbin D, Strong M, Salfinger M, Iqbal Z, Akhundova I, Vashakidze S, Rosenthal A, Farhat MR. Genomic sequence characteristics and the empiric accuracy of short-read sequencing. [preprint]. 2021 April. Available from: https://www.biorxiv.org/content/10.1101/2021.04.08.438862v1. doi: https://doi.org/10.1101/2021.04.08.438862.
Alser O, Mokhtari A, Naar L, Langeveld K, Breen KA, El Moheb M, Kapoen C, Gaitanidis A, Christensen MA, Maurer LR, Mashbari H, Bankhead-Kendall B, Parks J, Fawley J, Saillant N, Mendoza A, Paranjape C, Fagenholz P, King D, Lee J, Farhat MR, Velmahos GC, Kaafarani HMA. Multisystem outcomes and predictors of mortality in critically ill patients with COVID-19: Demographics and disease acuity matter more than comorbidities or treatment modalities. J Trauma Acute Care Surg. 2021 May 1;90(5):880-890. doi: 10.1097/TA.0000000000003085. PubMed PMID: 33891572.
El Halabi J, Palmer N, McDuffie M, Golub JJ, Fox K, Kohane I, Farhat MR. Measuring health-care delays among privately insured patients with tuberculosis in the USA: an observational cohort study. Lancet Infect Dis. 2021 Aug;21(8):1175-1183. doi: 10.1016/S1473-3099(20)30732-5. Epub 2021 Mar 23. PubMed PMID: 33770534; NIHMSID:NIHMS1696383.
Gröschel MI, Owens M, Freschi L, Vargas R Jr, Marin MG, Phelan J, Iqbal Z, Dixit A, Farhat MR. GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. Genome Med. 2021 Aug 30;13(1):138. doi: 10.1186/s13073-021-00953-4. PubMed PMID: 34461978; PubMed Central PMCID: PMC8407037.
Dixit A, Freschi L, Roger V, Groeschel M, Tahseen S, SM Masud A, SM Mostofa K, Skrahina A, Basilio RP, Lim DR, Ismail NA, Farhat MR. Estimation of country-specific tuberculosis antibiograms using genomic data. medRxiv. 2021 September.
Gaitanidis A, Kaafarani HMA, Christensen MA, Breen K, Mendoza A, Fagenholz PJ, Velmahos GC, Farhat MR. Association Between NEDD4L Variation and the Genetic Risk of Acute Appendicitis: A Multi-institutional Genome-Wide Association Study. JAMA Surg. 2021 Oct 1;156(10):917-923. doi: 10.1001/jamasurg.2021.3303. PubMed PMID: 34319380; PubMed Central PMCID: PMC8319828.
Malatesta S, Rooney J, Bouton T, Carney T, Meyers B, Horsburgh CR, Warren RM, Jacobson KR, White LF. Handling Missing Data in Serially Sampled Sputum Specimens for Mycobacterial Culture Conversion Calculation. The Union World Conference on Lung Health. 2021 October.
Vargas R Jr, Freschi L, Spitaleri A, Tahseen S, Barilar I, Niemann S, Miotto P, Cirillo DM, Köser CU, Farhat MR. Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex. Antimicrob Agents Chemother. 2021 Oct 18;65(11):e0116421. doi: 10.1128/AAC.01164-21. Epub 2021 Aug 30. PubMed PMID: 34460306; PubMed Central PMCID: PMC8522733.
Freschi L, Vargas R Jr, Husain A, Kamal SMM, Skrahina A, Tahseen S, Ismail N, Barbova A, Niemann S, Cirillo DM, Dean AS, Zignol M, Farhat MR. Population structure, biogeography and transmissibility of Mycobacterium tuberculosis. Nat Commun. 2021 Oct 20;12(1):6099. doi: 10.1038/s41467-021-26248-1. PubMed PMID: 34671035; PubMed Central PMCID: PMC8528816.
Taaffe J, Croda J, Moultrie H, Silva DS, Rosenthal A, Farhat M. Advancing TB research using digitized programmatic data. Int J Tuberc Lung Dis. 2021 Nov 1;25(11):890-895. doi: 10.5588/ijtld.21.0325. PubMed PMID: 34686230; PubMed Central PMCID: PMC8544923.
Yang Y, Walker TM, Kouchaki S, Wang C, Peto TEA, Crook DW, Clifton DA. An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction. Brief Bioinform. 2021 Nov 5;22(6). doi: 10.1093/bib/bbab299. PubMed PMID: 34414415; PubMed Central PMCID: PMC8575050.
El Halabi J, Palmer N, Fox K, Kohane I, Farhat MR. Fecal microbiota transplantation and Clostridioides difficile infection among privately insured patients in the United States. J Gastroenterol. 2022 Jan;57(1):10-18. doi: 10.1007/s00535-021-01822-y. Epub 2021 Sep 8. PubMed PMID: 34495400.
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