c759619f687d6ff12fa1a083ad3b922d 252433.pdf 61255d689e7ffb4f89a0fbcd17d42dae7f56aa11 252433.pdf 0ac00c42d674dd828a6d2659913a5fa14a2b98a3ac55ce2d2803f9234a86ca58 252433.pdf Title: Permanent control of HIV-1 pathogenesis in exceptional elite controllers: a model of spontaneous cure Subject: Scientific Reports, doi:10.1038/s41598-020-58696-y Keywords: Author: Concepcion Casado Creator: Springer Producer: iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) CreationDate: Wed Jan 29 06:45:55 2020 CET ModDate: Thu Jan 30 16:34:45 2020 CET Tagged: no UserProperties: no Suspects: no Form: AcroForm JavaScript: no Pages: 11 Encrypted: no Page size: 595.276 x 782.362 pts Page rot: 0 File size: 2615008 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- VNJEVX+Corbel-Bold CID TrueType Identity-H yes yes yes 125 0 QPMPOS+Corbel-BoldItalic Type 1C WinAnsi yes yes yes 525 0 EuclidSymbol-Bold Type 1C Custom yes no yes 526 0 CKPWKD+Corbel-Bold2 Type 1C WinAnsi yes yes yes 64 0 MinionPro-Regular Type 1C Custom yes no yes 63 0 NFFRXQ+Corbel2 Type 1C WinAnsi yes yes yes 66 0 ZVNHZP+Corbel CID TrueType Identity-H yes yes yes 67 0 MyriadPro-It Type 1C WinAnsi yes no yes 68 0 EuclidSymbol Type 1C Custom yes no yes 62 0 MinionPro-It Type 1C Custom yes no yes 65 0 CIDZKJ+STIXGeneral-Regular Type 1C Custom yes yes yes 126 0 MinionPro-Bold Type 1C WinAnsi yes no yes 159 0 EuclidSymbol-Italic Type 1C Custom yes no yes 188 0 RPZXMF+TimesNewRomanPSMT Type 1C WinAnsi yes yes yes 352 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-09-13 02:32:20 CEST RepresentationInformation: 252433.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-09-05 11:03:45 CEST Size: 2615008 Format: PDF Version: 1.4 Status: Well-Formed, but not valid SignatureMatches: PDF-hul ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: 13. Salgado, M. et al. Mechanisms That Contribute to a Profound Reduction of the HIV-1 Reservoir After Allogeneic Stem Cell Transplant. Ann. Intern. Med. 169, 674–683, https://doi.org/10.7326/M18-0759 (2018). :55' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: 10. Pernas, M. et al. Factors Leading to the Loss of Natural Elite Control of HIV-1 Infection. J. Virol. 92, 1805–1817, https://doi.org/10.1128/JVI.01805-17 (2018). :62' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: Table 1. Clinical, epidemiological and host-genetic characteristics. aViral dating performed in the last sample and estimated according to17. bNo further expositions after HIV-1 diagnosis. c“1” indicates the mo:69' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 1. Clinical characteristics and HIV-1 reservoir quantification. (A–C) Plasma RNA viral load, absolute CD4+ and CD4+ T cell percentage over time in the individuals studied. Grey symbols for viral load indicate values below the detect:70' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: Table 1. Clinical, epidemiological and host-genetic characteristics. aViral dating performed in the last sample and estimated according to17. bNo further expositions after HIV-1 diagnosis. c“1” indicates the m:71' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: 9. Casado, C. et al. Host and viral genetic correlates of clinical definitions of HIV-1 disease progression. PLoS One 5, e11079 (2010). :74' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: Table 1. Clinical, epidemiological and host-genetic characteristics. aViral dating performed in the last sample and estimated according to17. bNo further expositions after HIV-1 diagnosis. c“1” indicates the :76' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: Table 1. Clinical, epidemiological and host-genetic characteristics. aViral dating performed in the last sample and estimated according to17. bNo further expositions after HIV-1 diagnosis. c“1” indicates the:78' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: 25. Pereyra, F. et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Sci. 330, 1551–1557 (2010). :80' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 1. Clinical characteristics and HIV-1 reservoir quantification. (A–C) Plasma RNA viral load, absolute CD4+ and CD4+ T cell percentage over time in the individuals studied. Grey symbols for viral load indicate values below the detec:82' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 1. Clinical characteristics and HIV-1 reservoir quantification. (A–C) Plasma RNA viral load, absolute CD4+ and CD4+ T cell percentage over time in the individuals studied. Grey symbols for viral load indicate values below the dete:83' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 1. Clinical characteristics and HIV-1 reservoir quantification. (A–C) Plasma RNA viral load, absolute CD4+ and CD4+ T cell percentage over time in the individuals studied. Grey symbols for viral load indicate values below the det:84' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 1. Clinical characteristics and HIV-1 reservoir quantification. (A–C) Plasma RNA viral load, absolute CD4+ and CD4+ T cell percentage over time in the individuals studied. Grey symbols for viral load indicate values below the de:85' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: 17. Bello, G. et al. Co-existence of recent and ancestral nucleotide sequences in viral quasispecies of human immunodeficiency virus type 1 patients. J. Gen. Virol. 85, 399–407 (2004). :89' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: Table 1. Clinical, epidemiological and host-genetic characteristics. aViral dating performed in the last sample and estimated according to17. bNo further expositions after HIV-1 diagnosis. c“1” indicates th:90' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 2. Genetic variability and evolutionary dynamics of viral populations (A) Phylogenetic trees with env gene sequences of the individuals during follow-up. The evolutionary history was inferred in trees by using the Maximum Likelihood :94' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 2. Genetic variability and evolutionary dynamics of viral populations (A) Phylogenetic trees with env gene sequences of the individuals during follow-up. The evolutionary history was inferred in trees by using the Maximum Likelihood:95' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 3. Cellular Immune responses. (A) Total CD8+ T-cell Gag-specific response from EEC and HIV-1-infected individuals on suppressive ART. (B) INDEX of polyfuncionality (pINDEX) of Gag-specific total CD8+ T-cells from EEC and HIV-1-infe:97' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 3. Cellular Immune responses. (A) Total CD8+ T-cell Gag-specific response from EEC and HIV-1-infected individuals on suppressive ART. (B) INDEX of polyfuncionality (pINDEX) of Gag-specific total CD8+ T-cells from EEC and HIV-1-inf:99' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 3. Cellular Immune responses. (A) Total CD8+ T-cell Gag-specific response from EEC and HIV-1-infected individuals on suppressive ART. (B) INDEX of polyfuncionality (pINDEX) of Gag-specific total CD8+ T-cells from EEC and HIV-1-in:100' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 2. Genetic variability and evolutionary dynamics of viral populations (A) Phylogenetic trees with env gene sequences of the individuals during follow-up. The evolutionary history was inferred in trees by using the Maximum Likelihoo:102' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 4. Inflammation biomarkers and antibody titers. (A–E) Different inflammatory markers were analyzed including (A) hsCPR, (B) β2-microglobulin, (C) D-dimer, (D) IL-6 and (E) sCD163. EEC individuals were compared with HIV-1-in:104' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 4. Inflammation biomarkers and antibody titers. (A–E) Different inflammatory markers were analyzed including (A) hsCPR, (B) β2-microglobulin, (C) D-dimer, (D) IL-6 and (E) sCD163. EEC individuals were compared with HIV-1-i:105' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: 26. Moron-Lopez, S. et al. Short-term Treatment With Interferon Alfa Diminishes Expression of HIV-1 and Reduces CD4+ T-Cell Activation in Patients Coinfected With HIV and Hepatitis C Virus and Receiving Antiretroviral Therapy. J. Infect. D:106' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 1. Clinical characteristics and HIV-1 reservoir quantification. (A–C) Plasma RNA viral load, absolute CD4+ and CD4+ T cell percentage over time in the individuals studied. Grey symbols for viral load indicate values below the d:111' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: 15. Sandonis, V. et al. A combination of defective DNA and protective host factors are found in a set of HIV-1 ancestral LTNPs. Virology 391, 73–82 (2009). :112' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 2. Genetic variability and evolutionary dynamics of viral populations (A) Phylogenetic trees with env gene sequences of the individuals during follow-up. The evolutionary history was inferred in trees by using the Maximum Likeliho:120' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: 4. Gupta, R. K. et al. HIV-1 remission following CCR5Delta32/Delta32 haematopoietic stem-cell transplantation. Nat. 568, 244–248, https://doi.org/10.1038/s41586-019-1027-4 (2019). :128' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 3. Cellular Immune responses. (A) Total CD8+ T-cell Gag-specific response from EEC and HIV-1-infected individuals on suppressive ART. (B) INDEX of polyfuncionality (pINDEX) of Gag-specific total CD8+ T-cells from EEC and HIV-1-:130' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd: 10. Pernas, M. et al. Factors Leading to the Loss of Natural Elite Control of HIV-1 Infection. J. Virol. 92, 1805–1817, https://doi.org/10.1128/JVI.01805-17 (2018). :131' cannot be found Offset: 2263336 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_58696.indd:Figure 4. Inflammation biomarkers and antibody titers. (A–E) Different inflammatory markers were analyzed including (A) hsCPR, (B) β2-microglobulin, (C) D-dimer, (D) IL-6 and (E) sCD163. EEC individuals were compared with HIV-1-:133' cannot be found Offset: 2263336 MIMEtype: application/pdf PDFMetadata: Objects: 633 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseOutlines Language: EN Outlines: Item: Title: Permanent control of HIV-1 pathogenesis in exceptional elite controllers: a model of spontaneous cure Children: Item: Title: Materials and Methods Children: Item: Title: Individuals, samples and clinical characteristics. Item: Title: Viral persistence. Children: Item: Title: Total proviral HIV-1 DNA. Item: Title: Quantitative Viral Outgrowth Assay (qVOA). Item: Title: Plasma viral load and residual viremia. Item: Title: Cell-Associated HIV-1 RNA. Item: Title: Genetic studies. Children: Item: Title: Nucleotide sequence and phylogenetic analysis in env gene. Item: Title: Quasispecies diversity analysis. Item: Title: Immune responses. Children: Item: Title: Cell stimulation. Item: Title: Immunophenotyping and intracellular cytokine staining. Item: Title: Susceptibility and viral inhibition assay. Item: Title: Assay of soluble biomarkers. Item: Title: HIV-1 antibody determination. Item: Title: Statistical analysis. Item: Title: Results Children: Item: Title: Clinical characteristics of the individuals. Item: Title: Viral persistence. Item: Title: Sequence analysis, genetic variability and evolutionary dynamics of viral populations. Item: Title: Evolution of immune responses. Children: Item: Title: HIV-1-specific T-cell responses and poly-functionality. Item: Title: CD4+ susceptibility and CD8+ viral inhibition. Item: Title: Myeloid cell quantification. Item: Title: Inflammation biomarkers. Item: Title: HIV-1-specific antibody levels. Item: Title: Discussion Item: Title: Acknowledgements Item: Title: Figure 1 Clinical characteristics and HIV-1 reservoir quantification. Item: Title: Figure 2 Genetic variability and evolutionary dynamics of viral populations (A) Phylogenetic trees with env gene sequences of the individuals during follow-up. Item: Title: Figure 3 Cellular Immune responses. Item: Title: Figure 4 Inflammation biomarkers and antibody titers. Item: Title: Table 1 Clinical, epidemiological and host-genetic characteristics. 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-239, 1155, 952 FontFile2: true XMP: application/pdf doi:10.1038/s41598-020-58696-y Springer US Scientific Reports, doi:10.1038/s41598-020-58696-y Permanent control of HIV-1 pathogenesis in exceptional elite controllers: a model of spontaneous cure Concepcion Casado Cristina Galvez Maria Pernas Laura Tarancon-Diez Carmen Rodriguez Vamp#x000ED;ctor Sanchez-Merino Mar Vera Isabel Olivares Rebeca De Pablo-Bernal Alberto Merino-Mansilla Jorge Del Romero Ramon Lorenzo-Redondo Ezequiel Ruiz-Mateos Maramp#x000ED;a Salgado Javier Martinez-Picado Cecilio Lopez-Galindez 10.1038/s41598-020-58696-y http://dx.doi.org/10.1038/s41598-020-58696-y journal Scientific Reports © 2020, The Author(s) 2045-2322 10.1038/s41598-020-58696-y Springer 2020-01-30T16:34:45+01:00 2020-01-29T11:15:55+05:30 2020-01-30T16:34:45+01:00 True iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) VoR uuid:89f4b834-d0af-42a2-945a-8fc948878eaf uuid:c69af50b-6887-46e7-b8ee-69202248a2cc default 1 converted 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OriginalDocumentID URI http://ns.adobe.com/pdf/1.3/ pdf Adobe PDF Schema internal A name object indicating whether the document has been modified to include trapping information Trapped Text http://ns.adobe.com/pdfx/1.3/ pdfx pdfx internal ID of PDF/X standard GTS_PDFXVersion Text internal Conformance level of PDF/X standard GTS_PDFXConformance Text internal Company creating the PDF Company Text internal Date when document was last modified SourceModified Text internal Mirrors crossmark:DOI doi Text http://www.aiim.org/pdfa/ns/id/ pdfaid PDF/A ID Schema internal Part of PDF/A standard part Integer internal Amendment of PDF/A standard amd Text internal Conformance level of PDF/A standard conformance Text http://prismstandard.org/namespaces/basic/2.0/ prism Prism external The aggregation type specifies the unit of aggregation for a content collection. Comment PRISM recommends that the PRISM Aggregation Type Controlled Vocabulary be used to provide values for this element. 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PRISM recommends that a subset of the PCV platform values, namely “mobile” and “web”, be used in conjunction with this element. NOTE: PRISM recommends against the use of the #other value allowed in the PRISM Platform controlled vocabulary. In lieu of using #other please reach out to the PRISM group at prism-wg@yahoogroups.com to request addition of your term to the Platform Controlled Vocabulary. url Text http://www.niso.org/schemas/jav/1.0/ jav NISO external Values for Journal Article Version are one of the following: AO = Author’s Original SMUR = Submitted Manuscript Under Review AM = Accepted Manuscript P = Proof VoR = Version of Record CVoR = Corrected Version of Record EVoR = Enhanced Version of Record journal_article_version Closed Choice of Text Pages: Page: Sequence: 1 Annotations: Annotation: Subtype: Link Rect: 223, 25, 370, 16 Flags: Print AppearanceDictionary: true Annotation: Subtype: Link Rect: 449, 245, 452, 233 Flags: Print AppearanceDictionary: true Destination: 286 Annotation: Subtype: Link Rect: 454, 245, 457, 233 Flags: Print AppearanceDictionary: true Destination: 286 Annotation: Subtype: Link Rect: 498, 235, 500, 223 Flags: Print AppearanceDictionary: true Destination: 286 Annotation: Subtype: Link 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