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Items: 1 to 50 of 69

1.

The cost of insecurity: from flare-up to control of a major Ebola virus disease hotspot during the outbreak in the Democratic Republic of the Congo, 2019.

Jombart T, Jarvis CI, Mesfin S, Tabal N, Mossoko M, Mpia LM, Abedi AA, Chene S, Forbin EE, Belizaire MRD, de Radiguès X, Ngombo R, Tutu Y, Finger F, Crowe M, Edmunds WJ, Nsio J, Yam A, Diallo B, Gueye AS, Ahuka-Mundeke S, Yao M, Fall IS.

Euro Surveill. 2020 Jan;25(2). doi: 10.2807/1560-7917.ES.2020.25.2.1900735.

2.

Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N, Harris D, Chieu TTB, Van Vinh Chau N, Campbell J, Schultsz C, Parkhill J, Bentley SD, Langford PR, Rycroft AN, Wren BW, Farrar J, Baker S, Hoa NT, Holden MTG, Tucker AW, Maskell DJ; BRaDP1T Consortium.

Nat Commun. 2019 Nov 22;10(1):5326. doi: 10.1038/s41467-019-13138-w.

3.

Improved inference of time-varying reproduction numbers during infectious disease outbreaks.

Thompson RN, Stockwin JE, van Gaalen RD, Polonsky JA, Kamvar ZN, Demarsh PA, Dahlqwist E, Li S, Miguel E, Jombart T, Lessler J, Cauchemez S, Cori A.

Epidemics. 2019 Dec;29:100356. doi: 10.1016/j.epidem.2019.100356. Epub 2019 Aug 26.

4.

epiflows: an R package for risk assessment of travel-related spread of disease.

Moraga P, Dorigatti I, Kamvar ZN, Piatkowski P, Toikkanen SE, Nagraj VP, Donnelly CA, Jombart T.

Version 3. F1000Res. 2018 Aug 31 [revised 2019 Jan 1];7:1374. doi: 10.12688/f1000research.16032.3. eCollection 2018.

5.

epicontacts: Handling, visualisation and analysis of epidemiological contacts.

Nagraj VP, Randhawa N, Campbell F, Crellen T, Sudre B, Jombart T.

Version 2. F1000Res. 2018 May 10 [revised 2018 Jan 1];7:566. doi: 10.12688/f1000research.14492.2. eCollection 2018.

6.

A systematic review of MERS-CoV seroprevalence and RNA prevalence in dromedary camels: Implications for animal vaccination.

Dighe A, Jombart T, Van Kerkhove MD, Ferguson N.

Epidemics. 2019 Dec;29:100350. doi: 10.1016/j.epidem.2019.100350. Epub 2019 Jun 5.

7.

Population substructure and signals of divergent adaptive selection despite admixture in the sponge Dendrilla antarctica from shallow waters surrounding the Antarctic Peninsula.

Leiva C, Taboada S, Kenny NJ, Combosch D, Giribet G, Jombart T, Riesgo A.

Mol Ecol. 2019 Jul;28(13):3151-3170. doi: 10.1111/mec.15135. Epub 2019 Jun 25.

PMID:
31125991
8.

Epidemic curves made easy using the R package incidence.

Kamvar ZN, Cai J, Pulliam JRC, Schumacher J, Jombart T.

F1000Res. 2019 Jan 31;8:139. doi: 10.12688/f1000research.18002.1. eCollection 2019.

9.

Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus.

Sewell TR, Zhu J, Rhodes J, Hagen F, Meis JF, Fisher MC, Jombart T.

mBio. 2019 May 21;10(3). pii: e00392-19. doi: 10.1128/mBio.00392-19.

10.

Outbreak analytics: a developing data science for informing the response to emerging pathogens.

Polonsky JA, Baidjoe A, Kamvar ZN, Cori A, Durski K, Edmunds WJ, Eggo RM, Funk S, Kaiser L, Keating P, de Waroux OLP, Marks M, Moraga P, Morgan O, Nouvellet P, Ratnayake R, Roberts CH, Whitworth J, Jombart T.

Philos Trans R Soc Lond B Biol Sci. 2019 Jul 8;374(1776):20180276. doi: 10.1098/rstb.2018.0276.

11.

Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data.

Campbell F, Cori A, Ferguson N, Jombart T.

PLoS Comput Biol. 2019 Mar 29;15(3):e1006930. doi: 10.1371/journal.pcbi.1006930. eCollection 2019 Mar.

12.

A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies.

Cori A, Nouvellet P, Garske T, Bourhy H, Nakouné E, Jombart T.

PLoS Comput Biol. 2018 Dec 17;14(12):e1006554. doi: 10.1371/journal.pcbi.1006554. eCollection 2018 Dec.

13.

outbreaker2: a modular platform for outbreak reconstruction.

Campbell F, Didelot X, Fitzjohn R, Ferguson N, Cori A, Jombart T.

BMC Bioinformatics. 2018 Oct 22;19(Suppl 11):363. doi: 10.1186/s12859-018-2330-z.

14.

A fast likelihood solution to the genetic clustering problem.

Beugin MP, Gayet T, Pontier D, Devillard S, Jombart T.

Methods Ecol Evol. 2018 Apr;9(4):1006-1016. doi: 10.1111/2041-210X.12968. Epub 2018 Jan 30.

15.

When are pathogen genome sequences informative of transmission events?

Campbell F, Strang C, Ferguson N, Cori A, Jombart T.

PLoS Pathog. 2018 Feb 8;14(2):e1006885. doi: 10.1371/journal.ppat.1006885. eCollection 2018 Feb.

16.

An Eigenvalue test for spatial principal component analysis.

Montano V, Jombart T.

BMC Bioinformatics. 2017 Dec 16;18(1):562. doi: 10.1186/s12859-017-1988-y.

17.

mvmapper: Interactive spatial mapping of genetic structures.

Dupuis JR, Bremer FT, Jombart T, Sim SB, Geib SM.

Mol Ecol Resour. 2018 Mar;18(2):362-367. doi: 10.1111/1755-0998.12724. Epub 2017 Oct 23.

18.

Key data for outbreak evaluation: building on the Ebola experience.

Cori A, Donnelly CA, Dorigatti I, Ferguson NM, Fraser C, Garske T, Jombart T, Nedjati-Gilani G, Nouvellet P, Riley S, Van Kerkhove MD, Mills HL, Blake IM.

Philos Trans R Soc Lond B Biol Sci. 2017 May 26;372(1721). pii: 20160371. doi: 10.1098/rstb.2016.0371. Review.

19.

Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013-2016.

Garske T, Cori A, Ariyarajah A, Blake IM, Dorigatti I, Eckmanns T, Fraser C, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Newton E, Nouvellet P, Perkins D, Riley S, Schumacher D, Shah A, Van Kerkhove MD, Dye C, Ferguson NM, Donnelly CA.

Philos Trans R Soc Lond B Biol Sci. 2017 May 26;372(1721). pii: 20160308. doi: 10.1098/rstb.2016.0308.

20.

treespace: Statistical exploration of landscapes of phylogenetic trees.

Jombart T, Kendall M, Almagro-Garcia J, Colijn C.

Mol Ecol Resour. 2017 Nov;17(6):1385-1392. doi: 10.1111/1755-0998.12676. Epub 2017 May 15.

21.

A simple approach to measure transmissibility and forecast incidence.

Nouvellet P, Cori A, Garske T, Blake IM, Dorigatti I, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Van Kerkhove MD, Fraser C, Donnelly CA, Ferguson NM, Riley S.

Epidemics. 2018 Mar;22:29-35. doi: 10.1016/j.epidem.2017.02.012. Epub 2017 Feb 24.

22.

Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network.

Dallman T, Inns T, Jombart T, Ashton P, Loman N, Chatt C, Messelhaeusser U, Rabsch W, Simon S, Nikisins S, Bernard H, le Hello S, Jourdan da-Silva N, Kornschober C, Mossong J, Hawkey P, de Pinna E, Grant K, Cleary P.

Microb Genom. 2016 Aug 25;2(8):e000070. doi: 10.1099/mgen.0.000070. eCollection 2016 Aug.

23.

Climate forcing of an emerging pathogenic fungus across a montane multi-host community.

Clare FC, Halder JB, Daniel O, Bielby J, Semenov MA, Jombart T, Loyau A, Schmeller DS, Cunningham AA, Rowcliffe M, Garner TW, Bosch J, Fisher MC.

Philos Trans R Soc Lond B Biol Sci. 2016 Dec 5;371(1709). pii: 20150454. doi: 10.1098/rstb.2015.0454.

24.

Phylogeography of Toxoplasma gondii points to a South American origin.

Bertranpetit E, Jombart T, Paradis E, Pena H, Dubey J, Su C, Mercier A, Devillard S, Ajzenberg D.

Infect Genet Evol. 2017 Mar;48:150-155. doi: 10.1016/j.meegid.2016.12.020. Epub 2016 Dec 24.

25.

Towards an integrated ecosystem of R packages for the analysis of population genetic data.

Paradis E, Gosselin T, Grünwald NJ, Jombart T, Manel S, Lapp H.

Mol Ecol Resour. 2017 Jan;17(1):1-4. doi: 10.1111/1755-0998.12636. No abstract available.

PMID:
27860406
26.

Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study.

International Ebola Response Team, Agua-Agum J, Ariyarajah A, Aylward B, Bawo L, Bilivogui P, Blake IM, Brennan RJ, Cawthorne A, Cleary E, Clement P, Conteh R, Cori A, Dafae F, Dahl B, Dangou JM, Diallo B, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Fallah M, Ferguson NM, Fiebig L, Fraser C, Garske T, Gonzalez L, Hamblion E, Hamid N, Hersey S, Hinsley W, Jambei A, Jombart T, Kargbo D, Keita S, Kinzer M, George FK, Godefroy B, Gutierrez G, Kannangarage N, Mills HL, Moller T, Meijers S, Mohamed Y, Morgan O, Nedjati-Gilani G, Newton E, Nouvellet P, Nyenswah T, Perea W, Perkins D, Riley S, Rodier G, Rondy M, Sagrado M, Savulescu C, Schafer IJ, Schumacher D, Seyler T, Shah A, Van Kerkhove MD, Wesseh CS, Yoti Z.

PLoS Med. 2016 Nov 15;13(11):e1002170. doi: 10.1371/journal.pmed.1002170. eCollection 2016 Nov.

27.

Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis.

Inns T, Ashton PM, Herrera-Leon S, Lighthill J, Foulkes S, Jombart T, Rehman Y, Fox A, Dallman T, DE Pinna E, Browning L, Coia JE, Edeghere O, Vivancos R.

Epidemiol Infect. 2017 Jan;145(2):289-298. doi: 10.1017/S0950268816001941. Epub 2016 Oct 26.

PMID:
27780484
28.

After Ebola in West Africa--Unpredictable Risks, Preventable Epidemics.

WHO Ebola Response Team, Agua-Agum J, Allegranzi B, Ariyarajah A, Aylward R, Blake IM, Barboza P, Bausch D, Brennan RJ, Clement P, Coffey P, Cori A, Donnelly CA, Dorigatti I, Drury P, Durski K, Dye C, Eckmanns T, Ferguson NM, Fraser C, Garcia E, Garske T, Gasasira A, Gurry C, Hamblion E, Hinsley W, Holden R, Holmes D, Hugonnet S, Jaramillo Gutierrez G, Jombart T, Kelley E, Santhana R, Mahmoud N, Mills HL, Mohamed Y, Musa E, Naidoo D, Nedjati-Gilani G, Newton E, Norton I, Nouvellet P, Perkins D, Perkins M, Riley S, Schumacher D, Shah A, Tang M, Varsaneux O, Van Kerkhove MD.

N Engl J Med. 2016 Aug 11;375(6):587-96. doi: 10.1056/NEJMsr1513109. No abstract available.

29.

Linking genomics and population genetics with R.

Paradis E, Gosselin T, Goudet J, Jombart T, Schliep K.

Mol Ecol Resour. 2017 Jan;17(1):54-66. doi: 10.1111/1755-0998.12577. Epub 2016 Aug 29.

30.

Unraveling the drivers of MERS-CoV transmission.

Cauchemez S, Nouvellet P, Cori A, Jombart T, Garske T, Clapham H, Moore S, Mills HL, Salje H, Collins C, Rodriquez-Barraquer I, Riley S, Truelove S, Algarni H, Alhakeem R, AlHarbi K, Turkistani A, Aguas RJ, Cummings DA, Van Kerkhove MD, Donnelly CA, Lessler J, Fraser C, Al-Barrak A, Ferguson NM.

Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):9081-6. doi: 10.1073/pnas.1519235113. Epub 2016 Jul 25.

31.

apex: phylogenetics with multiple genes.

Jombart T, Archer F, Schliep K, Kamvar Z, Harris R, Paradis E, Goudet J, Lapp H.

Mol Ecol Resour. 2017 Jan;17(1):19-26. doi: 10.1111/1755-0998.12567. Epub 2016 Aug 12.

32.

EpiJSON: A unified data-format for epidemiology.

Finnie TJ, South A, Bento A, Sherrard-Smith E, Jombart T.

Epidemics. 2016 Jun;15:20-6. doi: 10.1016/j.epidem.2015.12.002. Epub 2015 Dec 29.

33.

Estimating the Severity and Subclinical Burden of Middle East Respiratory Syndrome Coronavirus Infection in the Kingdom of Saudi Arabia.

Lessler J, Salje H, Van Kerkhove MD, Ferguson NM, Cauchemez S, Rodriquez-Barraquer I, Hakeem R, Jombart T, Aguas R, Al-Barrak A, Cummings DA; MERS-CoV Scenario and Modeling Working Group.

Am J Epidemiol. 2016 Apr 1;183(7):657-63. doi: 10.1093/aje/kwv452. Epub 2016 Feb 4.

34.

Ebola Virus Disease among Male and Female Persons in West Africa.

WHO Ebola Response Team, Agua-Agum J, Ariyarajah A, Blake IM, Cori A, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Ferguson NM, Fraser C, Garske T, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Newton E, Nouvellet P, Perkins D, Riley S, Schumacher D, Shah A, Thomas LJ, Van Kerkhove MD.

N Engl J Med. 2016 Jan 7;374(1):96-8. doi: 10.1056/NEJMc1510305. No abstract available.

35.

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water.

Karkey A, Jombart T, Walker AW, Thompson CN, Torres A, Dongol S, Tran Vu Thieu N, Pham Thanh D, Tran Thi Ngoc D, Voong Vinh P, Singer AC, Parkhill J, Thwaites G, Basnyat B, Ferguson N, Baker S.

PLoS Negl Trop Dis. 2016 Jan 6;10(1):e0004346. doi: 10.1371/journal.pntd.0004346. eCollection 2016 Jan.

36.

The role of rapid diagnostics in managing Ebola epidemics.

Nouvellet P, Garske T, Mills HL, Nedjati-Gilani G, Hinsley W, Blake IM, Van Kerkhove MD, Cori A, Dorigatti I, Jombart T, Riley S, Fraser C, Donnelly CA, Ferguson NM.

Nature. 2015 Dec 3;528(7580):S109-16. doi: 10.1038/nature16041.

37.

Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N, Harris D, Chieu TT, Chau NV, Campbell J, Schultsz C, Parkhill J, Bentley SD, Langford PR, Rycroft AN, Wren BW, Farrar J, Baker S, Hoa NT, Holden MT, Tucker AW, Maskell DJ; BRaDP1T Consortium.

Nat Commun. 2015 May 12;6:7272. doi: 10.1038/ncomms8272. No abstract available.

38.

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N, Harris D, Chieu TT, Van Vinh Chau N, Campbell J, Schultsz C, Parkhill J, Bentley SD, Langford PR, Rycroft AN, Wren BW, Farrar J, Baker S, Hoa NT, Holden MT, Tucker AW, Maskell DJ; BRaDP1T Consortium.

Nat Commun. 2015 Mar 31;6:6740. doi: 10.1038/ncomms7740. Erratum in: Nat Commun. 2015;6:7272. Nat Commun. 2019 Nov 22;10(1):5326.

39.

Ebola virus disease among children in West Africa.

WHO Ebola Response Team, Agua-Agum J, Ariyarajah A, Blake IM, Cori A, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Ferguson NM, Fowler RA, Fraser C, Garske T, Hinsley W, Jombart T, Mills HL, Murthy S, Nedjati Gilani G, Nouvellet P, Pelletier L, Riley S, Schumacher D, Shah A, Van Kerkhove MD.

N Engl J Med. 2015 Mar 26;372(13):1274-7. doi: 10.1056/NEJMc1415318. No abstract available.

40.

A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae.

Chung The H, Karkey A, Pham Thanh D, Boinett CJ, Cain AK, Ellington M, Baker KS, Dongol S, Thompson C, Harris SR, Jombart T, Le Thi Phuong T, Tran Do Hoang N, Ha Thanh T, Shretha S, Joshi S, Basnyat B, Thwaites G, Thomson NR, Rabaa MA, Baker S.

EMBO Mol Med. 2015 Mar;7(3):227-39. doi: 10.15252/emmm.201404767.

41.

West African Ebola epidemic after one year--slowing but not yet under control.

WHO Ebola Response Team, Agua-Agum J, Ariyarajah A, Aylward B, Blake IM, Brennan R, Cori A, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Ferguson NM, Formenty P, Fraser C, Garcia E, Garske T, Hinsley W, Holmes D, Hugonnet S, Iyengar S, Jombart T, Krishnan R, Meijers S, Mills HL, Mohamed Y, Nedjati-Gilani G, Newton E, Nouvellet P, Pelletier L, Perkins D, Riley S, Sagrado M, Schnitzler J, Schumacher D, Shah A, Van Kerkhove MD, Varsaneux O, Wijekoon Kannangarage N.

N Engl J Med. 2015 Feb 5;372(6):584-7. doi: 10.1056/NEJMc1414992. Epub 2014 Dec 24. No abstract available.

42.

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting.

Tong SY, Holden MT, Nickerson EK, Cooper BS, Köser CU, Cori A, Jombart T, Cauchemez S, Fraser C, Wuthiekanun V, Thaipadungpanit J, Hongsuwan M, Day NP, Limmathurotsakul D, Parkhill J, Peacock SJ.

Genome Res. 2015 Jan;25(1):111-8. doi: 10.1101/gr.174730.114. Epub 2014 Dec 9.

43.

High levels of antimicrobial resistance among escherichia coli isolates from livestock farms and synanthropic rats and shrews in the Mekong Delta of Vietnam.

Nhung NT, Cuong NV, Campbell J, Hoa NT, Bryant JE, Truc VN, Kiet BT, Jombart T, Trung NV, Hien VB, Thwaites G, Baker S, Carrique-Mas J.

Appl Environ Microbiol. 2015 Feb;81(3):812-20. doi: 10.1128/AEM.03366-14. Epub 2014 Nov 14.

44.

Patterns and dynamics of genetic diversity in Plasmodium falciparum: what past human migrations tell us about malaria.

Mita T, Jombart T.

Parasitol Int. 2015 Jun;64(3):238-43. doi: 10.1016/j.parint.2014.09.007. Epub 2014 Oct 8. Review.

PMID:
25305418
45.

Ebola virus disease in West Africa--the first 9 months of the epidemic and forward projections.

WHO Ebola Response Team, Aylward B, Barboza P, Bawo L, Bertherat E, Bilivogui P, Blake I, Brennan R, Briand S, Chakauya JM, Chitala K, Conteh RM, Cori A, Croisier A, Dangou JM, Diallo B, Donnelly CA, Dye C, Eckmanns T, Ferguson NM, Formenty P, Fuhrer C, Fukuda K, Garske T, Gasasira A, Gbanyan S, Graaff P, Heleze E, Jambai A, Jombart T, Kasolo F, Kadiobo AM, Keita S, Kertesz D, Koné M, Lane C, Markoff J, Massaquoi M, Mills H, Mulba JM, Musa E, Myhre J, Nasidi A, Nilles E, Nouvellet P, Nshimirimana D, Nuttall I, Nyenswah T, Olu O, Pendergast S, Perea W, Polonsky J, Riley S, Ronveaux O, Sakoba K, Santhana Gopala Krishnan R, Senga M, Shuaib F, Van Kerkhove MD, Vaz R, Wijekoon Kannangarage N, Yoti Z.

N Engl J Med. 2014 Oct 16;371(16):1481-95. doi: 10.1056/NEJMoa1411100. Epub 2014 Sep 22.

46.

OutbreakTools: a new platform for disease outbreak analysis using the R software.

Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X, Fraser C, Frost S, Hens N, Hugues J, Höhle M, Opatowski L, Rambaut A, Ratmann O, Soubeyrand S, Suchard MA, Wallinga J, Ypma R, Ferguson N.

Epidemics. 2014 Jun;7:28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18.

47.

Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data.

Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N.

PLoS Comput Biol. 2014 Jan;10(1):e1003457. doi: 10.1371/journal.pcbi.1003457. Epub 2014 Jan 23.

48.

Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin.

Tanabe K, Jombart T, Horibe S, Palacpac NM, Honma H, Tachibana S, Nakamura M, Horii T, Kishino H, Mita T.

Mitochondrion. 2013 Nov;13(6):630-6. doi: 10.1016/j.mito.2013.08.008. Epub 2013 Sep 1.

PMID:
24004956
49.

Deciphering the complex: methodological overview of statistical models to derive OMICS-based biomarkers.

Chadeau-Hyam M, Campanella G, Jombart T, Bottolo L, Portengen L, Vineis P, Liquet B, Vermeulen RC.

Environ Mol Mutagen. 2013 Aug;54(7):542-57. doi: 10.1002/em.21797. Epub 2013 Aug 5. Review.

PMID:
23918146
50.

Regular treatments of praziquantel do not impact on the genetic make-up of Schistosoma mansoni in Northern Senegal.

Huyse T, Van den Broeck F, Jombart T, Webster BL, Diaw O, Volckaert FA, Balloux F, Rollinson D, Polman K.

Infect Genet Evol. 2013 Aug;18:100-5. doi: 10.1016/j.meegid.2013.05.007. Epub 2013 May 15.

PMID:
23684792

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