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Items: 1 to 50 of 103

1.

Intratumoral heterogeneity and clonal evolution in liver cancer.

Losic B, Craig AJ, Villacorta-Martin C, Martins-Filho SN, Akers N, Chen X, Ahsen ME, von Felden J, Labgaa I, DʹAvola D, Allette K, Lira SA, Furtado GC, Garcia-Lezana T, Restrepo P, Stueck A, Ward SC, Fiel MI, Hiotis SP, Gunasekaran G, Sia D, Schadt EE, Sebra R, Schwartz M, Llovet JM, Thung S, Stolovitzky G, Villanueva A.

Nat Commun. 2020 Jan 15;11(1):291. doi: 10.1038/s41467-019-14050-z.

2.

Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection.

Wang C, Forst CV, Chou TW, Geber A, Wang M, Hamou W, Smith M, Sebra R, Zhang B, Zhou B, Ghedin E.

mBio. 2020 Jan 14;11(1). pii: e02880-19. doi: 10.1128/mBio.02880-19.

3.

Prevalence and disease predisposition of p.A91V perforin in an aged Caucasian population.

Voskoboinik I, Lacaze P, Jang HS, Flinsenberg T, Fernando SL, Kerridge I, Riaz M, Sebra R, Thia K, Noori T, Schadt EE, McNeil JJ, Trapani JA.

Blood. 2020 Jan 13. pii: blood.2019003487. doi: 10.1182/blood.2019003487. [Epub ahead of print] No abstract available.

PMID:
31932842
4.

Tumoral and immune heterogeneity in an anti-PD-1 responsive glioblastoma: a case study.

Restrepo P, Yong R, Laface I, Tsankova N, Nael K, Akturk G, Sebra R, Gnjatic S, Hormigo A, Losic B.

Cold Spring Harb Mol Case Stud. 2020 Jan 6. pii: mcs.a004762. doi: 10.1101/mcs.a004762. [Epub ahead of print]

5.

Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing.

Seiden AH, Richter F, Patel N, Rodriguez OL, Deikus G, Shah H, Smith M, Roberts A, King EC, Sebra RP, Sharp AJ, Gelb BD.

Hum Mutat. 2020 Jan 3. doi: 10.1002/humu.23971. [Epub ahead of print]

PMID:
31898844
6.

Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms.

Lindblad KA, Pathmanathan JS, Moreira S, Bracht JR, Sebra RP, Hutton ER, Landweber LF.

BMC Genomics. 2019 Dec 30;20(1):1037. doi: 10.1186/s12864-019-6189-9.

7.

In Reply: Retention of ATRX and DAXX Expression in Meningiomas.

Gill CM, Loewenstern J, Rutland JW, Arib H, Pain M, Umphlett M, Kinoshita Y, McBride RB, Bederson J, Donovan M, Sebra R, Fowkes M, Shrivastava RK.

Neurosurgery. 2020 Feb 1;86(2):E244-E246. doi: 10.1093/neuros/nyz504. No abstract available.

PMID:
31803910
8.

Neuronal impact of patient-specific aberrant NRXN1α splicing.

Flaherty E, Zhu S, Barretto N, Cheng E, Deans PJM, Fernando MB, Schrode N, Francoeur N, Antoine A, Alganem K, Halpern M, Deikus G, Shah H, Fitzgerald M, Ladran I, Gochman P, Rapoport J, Tsankova NM, McCullumsmith R, Hoffman GE, Sebra R, Fang G, Brennand KJ.

Nat Genet. 2019 Dec;51(12):1679-1690. doi: 10.1038/s41588-019-0539-z. Epub 2019 Nov 29.

PMID:
31784728
9.

Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis.

Oliveira PH, Ribis JW, Garrett EM, Trzilova D, Kim A, Sekulovic O, Mead EA, Pak T, Zhu S, Deikus G, Touchon M, Lewis-Sandari M, Beckford C, Zeitouni NE, Altman DR, Webster E, Oussenko I, Bunyavanich S, Aggarwal AK, Bashir A, Patel G, Wallach F, Hamula C, Huprikar S, Schadt EE, Sebra R, van Bakel H, Kasarskis A, Tamayo R, Shen A, Fang G.

Nat Microbiol. 2020 Jan;5(1):166-180. doi: 10.1038/s41564-019-0613-4. Epub 2019 Nov 25.

PMID:
31768029
10.

The genome of a subterrestrial nematode reveals adaptations to heat.

Weinstein DJ, Allen SE, Lau MCY, Erasmus M, Asalone KC, Walters-Conte K, Deikus G, Sebra R, Borgonie G, van Heerden E, Onstott TC, Bracht JR.

Nat Commun. 2019 Nov 21;10(1):5268. doi: 10.1038/s41467-019-13245-8.

11.

Reprioritization of biofilm metabolism is associated with nutrient adaptation and long-term survival of Haemophilus influenzae.

Harrison A, Hardison RL, Wallace RM, Fitch J, Heimlich DR, Bryan MO, Dubois L, John-Williams LS, Sebra RP, White P, Moseley MA, Thompson JW, Justice SS, Mason KM.

NPJ Biofilms Microbiomes. 2019 Nov 5;5:33. doi: 10.1038/s41522-019-0105-6. eCollection 2019.

12.

Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors.

Vasan N, Razavi P, Johnson JL, Shao H, Shah H, Antoine A, Ladewig E, Gorelick A, Lin TY, Toska E, Xu G, Kazmi A, Chang MT, Taylor BS, Dickler MN, Jhaveri K, Chandarlapaty S, Rabadan R, Reznik E, Smith ML, Sebra R, Schimmoller F, Wilson TR, Friedman LS, Cantley LC, Scaltriti M, Baselga J.

Science. 2019 Nov 8;366(6466):714-723. doi: 10.1126/science.aaw9032.

PMID:
31699932
13.

Blurred Molecular Epidemiological Lines Between the Two Dominant Methicillin-Resistant Staphylococcus aureus Clones.

Dupper AC, Sullivan MJ, Chacko KI, Mishkin A, Ciferri B, Kumaresh A, Berbel Caban A, Oussenko I, Beckford C, Zeitouni NE, Sebra R, Hamula C, Smith M, Kasarskis A, Patel G, McBride RB, van Bakel H, Altman DR.

Open Forum Infect Dis. 2019 Jun 27;6(9):ofz302. doi: 10.1093/ofid/ofz302. eCollection 2019 Sep.

14.

A Complete Genome Screening Program of Clinical Methicillin-Resistant Staphylococcus aureus Isolates Identifies the Origin and Progression of a Neonatal Intensive Care Unit Outbreak.

Sullivan MJ, Altman DR, Chacko KI, Ciferri B, Webster E, Pak TR, Deikus G, Lewis-Sandari M, Khan Z, Beckford C, Rendo A, Samaroo F, Sebra R, Karam-Howlin R, Dingle T, Hamula C, Bashir A, Schadt E, Patel G, Wallach F, Kasarskis A, Gibbs K, van Bakel H.

J Clin Microbiol. 2019 Nov 22;57(12). pii: e01261-19. doi: 10.1128/JCM.01261-19. Print 2019 Dec.

15.

Genetic resilience to Alzheimer's disease in APOE ε4 homozygotes: A systematic review.

Huq AJ, Fransquet P, Laws SM, Ryan J, Sebra R, Masters CL, Winship IM, James PA, Lacaze P.

Alzheimers Dement. 2019 Dec;15(12):1612-1623. doi: 10.1016/j.jalz.2019.05.011. Epub 2019 Sep 7.

PMID:
31506248
16.

High-coverage, long-read sequencing of Han Chinese trio reference samples.

Wang YC, Olson ND, Deikus G, Shah H, Wenger AM, Trow J, Xiao C, Sherry S, Salit ML, Zook JM, Smith M, Sebra R.

Sci Data. 2019 Jun 14;6(1):91. doi: 10.1038/s41597-019-0098-2.

17.

Comparative genomic analysis of driver mutations in matched primary and recurrent meningiomas.

Loewenstern J, Rutland J, Gill C, Arib H, Pain M, Umphlett M, Kinoshita Y, McBride R, Donovan M, Sebra R, Bederson J, Fowkes M, Shrivastava R.

Oncotarget. 2019 May 28;10(37):3506-3517. doi: 10.18632/oncotarget.26941. eCollection 2019 May 28.

18.

A personalized platform identifies trametinib plus zoledronate for a patient with KRAS-mutant metastatic colorectal cancer.

Bangi E, Ang C, Smibert P, Uzilov AV, Teague AG, Antipin Y, Chen R, Hecht C, Gruszczynski N, Yon WJ, Malyshev D, Laspina D, Selkridge I, Rainey H, Moe AS, Lau CY, Taik P, Wilck E, Bhardwaj A, Sung M, Kim S, Yum K, Sebra R, Donovan M, Misiukiewicz K, Schadt EE, Posner MR, Cagan RL.

Sci Adv. 2019 May 22;5(5):eaav6528. doi: 10.1126/sciadv.aav6528. eCollection 2019 May.

19.

Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.

Beh LY, Debelouchina GT, Clay DM, Thompson RE, Lindblad KA, Hutton ER, Bracht JR, Sebra RP, Muir TW, Landweber LF.

Cell. 2019 Jun 13;177(7):1781-1796.e25. doi: 10.1016/j.cell.2019.04.028. Epub 2019 May 16.

PMID:
31104845
20.

Mce3R Stress-Resistance Pathway Is Vulnerable to Small-Molecule Targeting That Improves Tuberculosis Drug Activities.

Yang X, Yuan T, Ma R, Chacko KI, Smith M, Deikus G, Sebra R, Kasarskis A, van Bakel H, Franzblau SG, Sampson NS.

ACS Infect Dis. 2019 Jul 12;5(7):1239-1251. doi: 10.1021/acsinfecdis.9b00099. Epub 2019 May 3.

21.

Dissemination of multiple carbapenem resistance genes in an in vitro gut model simulating the human colon.

Rooney CM, Sheppard AE, Clark E, Davies K, Hubbard ATM, Sebra R, Crook DW, Walker AS, Wilcox MH, Chilton CH.

J Antimicrob Chemother. 2019 Jul 1;74(7):1876-1883. doi: 10.1093/jac/dkz106.

PMID:
30989197
22.

Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing Reveals Novel and Distinct mRNA Isoforms in Human Bone Marrow Cell Subpopulations.

Deslattes Mays A, Schmidt M, Graham G, Tseng E, Baybayan P, Sebra R, Sanda M, Mazarati JB, Riegel A, Wellstein A.

Genes (Basel). 2019 Mar 27;10(4). pii: E253. doi: 10.3390/genes10040253.

23.

Don't overlook the little guy: An evaluation of the frequency of small plasmids co-conjugating with larger carbapenemase gene containing plasmids.

Barry KE, Wailan AM, Sheppard AE, Crook D, Vegesana K, Stoesser N, Parikh HI, Sebra R, Mathers AJ.

Plasmid. 2019 May;103:1-8. doi: 10.1016/j.plasmid.2019.03.005. Epub 2019 Mar 27.

24.

Klebsiella quasipneumoniae Provides a Window into Carbapenemase Gene Transfer, Plasmid Rearrangements, and Patient Interactions with the Hospital Environment.

Mathers AJ, Crook D, Vaughan A, Barry KE, Vegesana K, Stoesser N, Parikh HI, Sebra R, Kotay S, Walker AS, Sheppard AE.

Antimicrob Agents Chemother. 2019 May 24;63(6). pii: e02513-18. doi: 10.1128/AAC.02513-18. Print 2019 Jun.

25.

Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus.

Copin R, Sause WE, Fulmer Y, Balasubramanian D, Dyzenhaus S, Ahmed JM, Kumar K, Lees J, Stachel A, Fisher JC, Drlica K, Phillips M, Weiser JN, Planet PJ, Uhlemann AC, Altman DR, Sebra R, van Bakel H, Lighter J, Torres VJ, Shopsin B.

Proc Natl Acad Sci U S A. 2019 Jan 29;116(5):1745-1754. doi: 10.1073/pnas.1814265116. Epub 2019 Jan 11. Erratum in: Proc Natl Acad Sci U S A. 2019 Feb 25;:.

26.

A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci.

Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H.

Genome Res. 2019 Jan;29(1):146-156. doi: 10.1101/gr.242594.118. Epub 2018 Nov 8.

27.

Ex vivo human HSC expansion requires coordination of cellular reprogramming with mitochondrial remodeling and p53 activation.

Papa L, Zimran E, Djedaini M, Ge Y, Ozbek U, Sebra R, Sealfon SC, Hoffman R.

Blood Adv. 2018 Oct 23;2(20):2766-2779. doi: 10.1182/bloodadvances.2018024273.

28.

Genome organization and DNA accessibility control antigenic variation in trypanosomes.

Müller LSM, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, Otto TD, Saliba AE, Sebra RP, Siegel TN.

Nature. 2018 Nov;563(7729):121-125. doi: 10.1038/s41586-018-0619-8. Epub 2018 Oct 17.

29.

Microevolution in response to transient heme-iron restriction enhances intracellular bacterial community development and persistence.

Hardison RL, Harrison A, Wallace RM, Heimlich DR, O'Bryan ME, Sebra RP, Pinkett HW, Justice SS, Mason KM.

PLoS Pathog. 2018 Oct 17;14(10):e1007355. doi: 10.1371/journal.ppat.1007355. eCollection 2018 Oct.

30.

Detection of endometrial precancer by a targeted gynecologic cancer liquid biopsy.

Martignetti JA, Pandya D, Nagarsheth N, Chen Y, Camacho O, Tomita S, Brodman M, Ascher-Walsh C, Kolev V, Cohen S, Harkins TT, Schadt EE, Reva B, Sebra R, Dottino P.

Cold Spring Harb Mol Case Stud. 2018 Dec 17;4(6). pii: a003269. doi: 10.1101/mcs.a003269. Print 2018 Dec.

31.

A Large, Refractory Nosocomial Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Escherichia coli Demonstrates Carbapenemase Gene Outbreaks Involving Sink Sites Require Novel Approaches to Infection Control.

Decraene V, Phan HTT, George R, Wyllie DH, Akinremi O, Aiken Z, Cleary P, Dodgson A, Pankhurst L, Crook DW, Lenney C, Walker AS, Woodford N, Sebra R, Fath-Ordoubadi F, Mathers AJ, Seale AC, Guiver M, McEwan A, Watts V, Welfare W, Stoesser N, Cawthorne J; TRACE Investigators’ Group.

Antimicrob Agents Chemother. 2018 Nov 26;62(12). pii: e01689-18. doi: 10.1128/AAC.01689-18. Print 2018 Dec.

32.

Influenza virus infection causes global RNAPII termination defects.

Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, Ma Y, Rialdi A, Albrecht R, Fenouil R, Sánchez-Aparicio MT, Ayllon J, Ravisankar S, Haddad B, Ho JSY, Low D, Jin J, Yurchenko V, Prinjha RK, Tarakhovsky A, Squatrito M, Pinto D, Allette K, Byun M, Smith ML, Sebra R, Guccione E, Tumpey T, Krogan N, Greenbaum B, van Bakel H, García-Sastre A, Marazzi I.

Nat Struct Mol Biol. 2018 Sep;25(9):885-893. doi: 10.1038/s41594-018-0124-7. Epub 2018 Sep 3.

PMID:
30177761
33.

High-density single cell mRNA sequencing to characterize circulating tumor cells in hepatocellular carcinoma.

D'Avola D, Villacorta-Martin C, Martins-Filho SN, Craig A, Labgaa I, von Felden J, Kimaada A, Bonaccorso A, Tabrizian P, Hartmann BM, Sebra R, Schwartz M, Villanueva A.

Sci Rep. 2018 Aug 1;8(1):11570. doi: 10.1038/s41598-018-30047-y.

34.

Genome Plasticity of agr-Defective Staphylococcus aureus during Clinical Infection.

Altman DR, Sullivan MJ, Chacko KI, Balasubramanian D, Pak TR, Sause WE, Kumar K, Sebra R, Deikus G, Attie O, Rose H, Lewis M, Fulmer Y, Bashir A, Kasarskis A, Schadt EE, Richardson AR, Torres VJ, Shopsin B, van Bakel H.

Infect Immun. 2018 Sep 21;86(10). pii: e00331-18. doi: 10.1128/IAI.00331-18. Print 2018 Oct.

35.

Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing.

Zhu S, Beaulaurier J, Deikus G, Wu TP, Strahl M, Hao Z, Luo G, Gregory JA, Chess A, He C, Xiao A, Sebra R, Schadt EE, Fang G.

Genome Res. 2018 Jul;28(7):1067-1078. doi: 10.1101/gr.231068.117. Epub 2018 May 15.

36.

Coupling of Single Molecule, Long Read Sequencing with IMGT/HighV-QUEST Analysis Expedites Identification of SIV gp140-Specific Antibodies from scFv Phage Display Libraries.

Han SY, Antoine A, Howard D, Chang B, Chang WS, Slein M, Deikus G, Kossida S, Duroux P, Lefranc MP, Sebra RP, Smith ML, Fofana IBF.

Front Immunol. 2018 Mar 1;9:329. doi: 10.3389/fimmu.2018.00329. eCollection 2018.

37.

Treatment-associated TP53 DNA-binding domain missense mutations in the pathogenesis of secondary gliosarcoma.

Pain M, Wang H, Lee E, Strahl M, Hamou W, Sebra R, Zhu J, Yong RL.

Oncotarget. 2017 Dec 20;9(2):2603-2621. doi: 10.18632/oncotarget.23517. eCollection 2018 Jan 5.

38.

Single-cell profiling of peanut-responsive T cells in patients with peanut allergy reveals heterogeneous effector TH2 subsets.

Chiang D, Chen X, Jones SM, Wood RA, Sicherer SH, Burks AW, Leung DYM, Agashe C, Grishin A, Dawson P, Davidson WF, Newman L, Sebra R, Merad M, Sampson HA, Losic B, Berin MC.

J Allergy Clin Immunol. 2018 Jun;141(6):2107-2120. doi: 10.1016/j.jaci.2017.11.060. Epub 2018 Jan 31.

39.

Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of a Bardet-Biedl Syndrome 9 (BBS9) deletion.

Reiner J, Pisani L, Qiao W, Singh R, Yang Y, Shi L, Khan WA, Sebra R, Cohen N, Babu A, Edelmann L, Jabs EW, Scott SA.

NPJ Genom Med. 2018 Jan 22;3:3. doi: 10.1038/s41525-017-0042-3. eCollection 2018.

40.

Genetic Basis of Emerging Vancomycin, Linezolid, and Daptomycin Heteroresistance in a Case of Persistent Enterococcus faecium Bacteremia.

Chacko KI, Sullivan MJ, Beckford C, Altman DR, Ciferri B, Pak TR, Sebra R, Kasarskis A, Hamula CL, van Bakel H.

Antimicrob Agents Chemother. 2018 Mar 27;62(4). pii: e02007-17. doi: 10.1128/AAC.02007-17. Print 2018 Apr.

41.

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation.

Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen B, Chen XG, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, Sutton GG, Phillippy AM, Piermarini PM, Shabman RS.

Gigascience. 2018 Mar 1;7(3):1-13. doi: 10.1093/gigascience/gix135.

42.

Using single-cell multiple omics approaches to resolve tumor heterogeneity.

Ortega MA, Poirion O, Zhu X, Huang S, Wolfgruber TK, Sebra R, Garmire LX.

Clin Transl Med. 2017 Dec 28;6(1):46. doi: 10.1186/s40169-017-0177-y. Review.

43.

A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells.

Yang J, Hagen J, Guntur KV, Allette K, Schuyler S, Ranjan J, Petralia F, Gesta S, Sebra R, Mahajan M, Zhang B, Zhu J, Houten S, Kasarskis A, Vishnudas VK, Akmaev VR, Sarangarajan R, Narain NR, Schadt EE, Argmann CA, Tu Z.

BMC Genomics. 2017 Dec 22;18(1):987. doi: 10.1186/s12864-017-4359-1.

44.

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.

Beaulaurier J, Zhu S, Deikus G, Mogno I, Zhang XS, Davis-Richardson A, Canepa R, Triplett EW, Faith JJ, Sebra R, Schadt EE, Fang G.

Nat Biotechnol. 2018 Jan;36(1):61-69. doi: 10.1038/nbt.4037. Epub 2017 Dec 11.

45.

Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology.

Chen X, Houten S, Allette K, Sebra RP, Stolovitzky G, Losic B.

Pac Symp Biocomput. 2018;23:8-19.

46.

DNA sequencing at ultra-high fidelity.

Sebra R.

Nat Biotechnol. 2017 Dec;35(12):1143-1144. doi: 10.1038/nbt.4001. Epub 2017 Oct 30. No abstract available.

PMID:
29106409
47.

HIV-1 Infection of Primary CD4+ T Cells Regulates the Expression of Specific Human Endogenous Retrovirus HERV-K (HML-2) Elements.

Young GR, Terry SN, Manganaro L, Cuesta-Dominguez A, Deikus G, Bernal-Rubio D, Campisi L, Fernandez-Sesma A, Sebra R, Simon V, Mulder LCF.

J Virol. 2017 Dec 14;92(1). pii: e01507-17. doi: 10.1128/JVI.01507-17. Print 2018 Jan 1.

48.

Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify.

Komor MA, Pham TV, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA.

Mol Cell Proteomics. 2017 Oct;16(10):1850-1863. doi: 10.1074/mcp.TIR117.000056. Epub 2017 Jul 26.

49.

Resistance to Ceftazidime-Avibactam Is Due to Transposition of KPC in a Porin-Deficient Strain of Klebsiella pneumoniae with Increased Efflux Activity.

Nelson K, Hemarajata P, Sun D, Rubio-Aparicio D, Tsivkovski R, Yang S, Sebra R, Kasarskis A, Nguyen H, Hanson BM, Leopold S, Weinstock G, Lomovskaya O, Humphries RM.

Antimicrob Agents Chemother. 2017 Sep 22;61(10). pii: e00989-17. doi: 10.1128/AAC.00989-17. Print 2017 Oct.

50.

Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli.

Stoesser N, Sheppard AE, Peirano G, Anson LW, Pankhurst L, Sebra R, Phan HTT, Kasarskis A, Mathers AJ, Peto TEA, Bradford P, Motyl MR, Walker AS, Crook DW, Pitout JD.

Sci Rep. 2017 Jul 19;7(1):5917. doi: 10.1038/s41598-017-06256-2.

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