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intestinal cell apoptosis is the underlying mechanism of the regenerative enteropathy of early infection","volume":"197","author":"Q Li","year":"2008","journal-title":"J Infect Dis"},{"key":"ppat.1008333.ref094","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/j.crohns.2008.05.009","article-title":"Intestinal fibrosis in inflammatory bowel disease\u2014current knowledge and future perspectives","volume":"2","author":"F Rieder","year":"2008","journal-title":"J Crohns Colitis"},{"key":"ppat.1008333.ref095","doi-asserted-by":"crossref","first-page":"734","DOI":"10.5009\/gnl14155","article-title":"Changes in the expression and distribution of claudins, increased epithelial apoptosis, and a mannan-binding lectin-associated immune response lead to barrier dysfunction in dextran sodium sulfate-induced rat colitis","volume":"9","author":"B Yuan","year":"2015","journal-title":"Gut 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Silvestri","year":"2003","journal-title":"Immunity"},{"key":"ppat.1008333.ref106","doi-asserted-by":"crossref","first-page":"7913","DOI":"10.1128\/JVI.00281-07","article-title":"Virus subtype-specific features of natural simian immunodeficiency virus SIVsmm infection in sooty mangabeys","volume":"81","author":"C Apetrei","year":"2007","journal-title":"J Virol"},{"key":"ppat.1008333.ref107","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1038\/nm.2013","article-title":"Toward an AIDS vaccine: lessons from natural simian immunodeficiency virus infections of African nonhuman primate hosts","volume":"15","author":"DL Sodora","year":"2009","journal-title":"Nat Med"},{"key":"ppat.1008333.ref108","doi-asserted-by":"crossref","first-page":"S58","DOI":"10.1093\/infdis\/jiw258","article-title":"Gut mucosal barrier dysfunction, microbial dysbiosis, and their role in HIV-1 disease progression","volume":"214","author":"JC Mudd","year":"2016","journal-title":"J Infect 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Wang","year":"2018","journal-title":"Cell Tissue Res"},{"key":"ppat.1008333.ref117","doi-asserted-by":"crossref","first-page":"5145","DOI":"10.1128\/JVI.02433-07","article-title":"Plasmacytoid dendritic cell dynamics and alpha interferon production during simian immunodeficiency virus infection with a nonpathogenic outcome","volume":"82","author":"OM Diop","year":"2008","journal-title":"J Virol"},{"key":"ppat.1008333.ref118","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004311","article-title":"Early mucosal sensing of SIV infection by paneth cells induces IL-1\u03b2 production and initiates gut epithelial disruption","volume":"10","author":"LA Hirao","year":"2014","journal-title":"PLoS Pathog"},{"key":"ppat.1008333.ref119","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1016\/j.virol.2014.07.010","article-title":"Virus-host mucosal interactions during early SIV rectal transmission","volume":"464\u2013465","author":"W Lu","year":"2014","journal-title":"Virology"},{"key":"ppat.1008333.ref120","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/S0042-6822(02)00045-4","article-title":"The C-X-C chemokine IP-10 stimulates HIV-1 replication","volume":"307","author":"BR Lane","year":"2003","journal-title":"Virology"},{"key":"ppat.1008333.ref121","doi-asserted-by":"crossref","first-page":"e1000296","DOI":"10.1371\/journal.ppat.1000296","article-title":"Transcriptional profiling in pathogenic and non-pathogenic SIV infections reveals significant distinctions in kinetics and tissue compartmentalization","volume":"5","author":"S Lederer","year":"2009","journal-title":"PLOS Pathog"},{"key":"ppat.1008333.ref122","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1016\/j.jaci.2015.08.007","article-title":"Hematopoietic prostaglandin D synthase defines a proeosinophilic pathogenic effector human TH2 cell subpopulation with enhanced function","volume":"137","author":"A Mitson-Salazar","year":"2016","journal-title":"J Allergy Clin Immunol"},{"key":"ppat.1008333.ref123","doi-asserted-by":"crossref","first-page":"1886","DOI":"10.4049\/jimmunol.180.3.1886","article-title":"The myeloid differentiation factor 88 (MyD88) is required for CD4+ T cell effector function in a murine model of inflammatory bowel disease","volume":"180","author":"M Fukata","year":"2008","journal-title":"J Immunol"},{"key":"ppat.1008333.ref124","first-page":"1832","article-title":"Regulation of wound healing and organ fibrosis by toll-like receptors","author":"P Huebener","year":"2013","journal-title":"Biochim Biophys Acta"},{"key":"ppat.1008333.ref125","doi-asserted-by":"crossref","first-page":"1774","DOI":"10.2353\/ajpath.2007.061048","article-title":"Wound healing is impaired in myd88-deficient mice","volume":"171","author":"L Macedo","year":"2007","journal-title":"Am J Pathol"},{"key":"ppat.1008333.ref126","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.cbi.2008.10.036","article-title":"Human and zebrafish hydroxysteroid dehydrogenase like 1 (HSDL1) proteins are inactive enzymes but conserved among species","volume":"178","author":"M Meier","year":"2009","journal-title":"Chem Biol Interact"},{"key":"ppat.1008333.ref127","doi-asserted-by":"crossref","first-page":"748","DOI":"10.4049\/jimmunol.178.2.748","article-title":"The extra domain A from fibronectin targets antigens to TLR4-expressing cells and induces cytotoxic T cell responses in vivo","volume":"178","author":"JJ Lasarte","year":"2007","journal-title":"J Immunol"},{"key":"ppat.1008333.ref128","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.1096\/fj.201801176R","article-title":"Stat3 is indispensable for damage-induced crypt regeneration but not for Wnt-driven intestinal tumorigenesis","volume":"33","author":"H Oshima","year":"2018","journal-title":"FASEB J"},{"key":"ppat.1008333.ref129","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1084\/jem.20082683","article-title":"STAT3 links IL-22 signaling in intestinal epithelial cells to mucosal wound healing","volume":"206","author":"G Pickert","year":"2009","journal-title":"J Exp Med"},{"key":"ppat.1008333.ref130","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1097\/MIB.0b013e31828028ad","article-title":"Deletion of intestinal epithelial cell STAT3 promotes T-lymphocyte STAT3 activation and chronic colitis following acute dextran sodium sulfate injury in mice","volume":"19","author":"TA Willson","year":"2013","journal-title":"Inflamm Bowel Dis"},{"key":"ppat.1008333.ref131","doi-asserted-by":"crossref","first-page":"2959","DOI":"10.4049\/jimmunol.1202319","article-title":"Rate of AIDS progression is associated with gastrointestinal dysfunction in simian immunodeficiency virus\u2013infected pigtail macaques","volume":"190","author":"LA Canary","year":"2013","journal-title":"J Immunol"},{"key":"ppat.1008333.ref132","doi-asserted-by":"crossref","first-page":"7962","DOI":"10.1128\/JVI.00543-14","article-title":"Deep transcriptional sequencing of mucosal challenge compartment from rhesus macaques acutely infected with simian immunodeficiency virus implicates loss of cell adhesion preceding immune activation","volume":"88","author":"F Barrenas","year":"2014","journal-title":"J Virol"},{"key":"ppat.1008333.ref133","doi-asserted-by":"crossref","DOI":"10.1097\/QAD.0000000000000636","article-title":"Role of intestinal myofibroblasts in HIV-associated intestinal collagen deposition and immune reconstitution following combination antiretroviral therapy","volume":"29","author":"D M Asmuth","year":"2015","journal-title":"AIDS Lond Engl"},{"key":"ppat.1008333.ref134","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1093\/infdis\/jiu519","article-title":"Antifibrotic therapy in simian immunodeficiency virus infection preserves CD4+ T-cell populations and improves immune reconstitution with antiretroviral therapy","volume":"211","author":"JD Estes","year":"2015","journal-title":"J Infect Dis"},{"key":"ppat.1008333.ref135","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1172\/JCI200519229","article-title":"Human intestinal macrophages display profound inflammatory anergy despite avid phagocytic and bacteriocidal activity","volume":"115","author":"LE Smythies","year":"2005","journal-title":"J Clin Invest"},{"key":"ppat.1008333.ref136","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1093\/intimm\/dxq449","article-title":"Commensal microbiota induce LPS hyporesponsiveness in colonic macrophages via the production of IL-10","volume":"22","author":"Y Ueda","year":"2010","journal-title":"Int Immunol"},{"key":"ppat.1008333.ref137","doi-asserted-by":"crossref","first-page":"8838","DOI":"10.1128\/JVI.02663-06","article-title":"Low immune activation despite high levels of pathogenic human immunodeficiency virus type 1 results in long-term asymptomatic disease","volume":"81","author":"SK Choudhary","year":"2007","journal-title":"J Virol"},{"key":"ppat.1008333.ref138","doi-asserted-by":"crossref","first-page":"e1004345","DOI":"10.1371\/journal.ppat.1004345","article-title":"Limited HIV infection of central memory and stem cell memory CD4+ T cells is associated with lack of progression in viremic individuals","volume":"10","author":"NR Klatt","year":"2014","journal-title":"PLOS Pathog"},{"key":"ppat.1008333.ref139","unstructured":"National Research Council (US) Committee for the Update of the Guide for the Care and Use of Laboratory Animals. Guide for the care and use of laboratory animals. 8th ed. Washington (DC): National Academies Press (US); 2011. Available: http:\/\/www.ncbi.nlm.nih.gov\/books\/NBK54050\/"},{"key":"ppat.1008333.ref140","author":"AW Regulations","year":"2013","journal-title":"Animal Welfare Act"},{"key":"ppat.1008333.ref141","unstructured":"Sir David Weatherall Working Group. The Weatherall report on the use of non-human primates in research. A working group report chaired by Sir David Weatherall FRS FMedSci. 12 Dec 2006 [cited 12 Feb 2018]. Available: https:\/\/royalsociety.org\/topics-policy\/publications\/2006\/weatherall-report\/"},{"key":"ppat.1008333.ref142","doi-asserted-by":"crossref","first-page":"3288","DOI":"10.1128\/JVI.02423-08","article-title":"High specific infectivity of plasma virus from the pre-ramp-up and ramp-up stages of acute simian immunodeficiency virus infection","volume":"83","author":"Z-M Ma","year":"2009","journal-title":"J Virol"},{"key":"ppat.1008333.ref143","doi-asserted-by":"crossref","first-page":"e1004440","DOI":"10.1371\/journal.ppat.1004440","article-title":"Vaginal challenge with an SIV-based dual reporter system reveals that infection can occur throughout the upper and lower female reproductive tract","volume":"10","author":"DJ Stieh","year":"2014","journal-title":"PLOS Pathog"},{"key":"ppat.1008333.ref144","doi-asserted-by":"crossref","first-page":"9616","DOI":"10.1128\/JVI.01196-15","article-title":"Critical role for the adenosine pathway in controlling simian immunodeficiency virus-related immune activation and inflammation in gut mucosal tissues","volume":"89","author":"T He","year":"2015","journal-title":"J Virol"},{"key":"ppat.1008333.ref145","doi-asserted-by":"crossref","first-page":"6687","DOI":"10.4049\/jimmunol.181.10.6687","article-title":"Cutting edge: experimentally induced immune activation in natural hosts of simian immunodeficiency virus induces significant increases in viral replication and CD4+ T cell depletion","volume":"181","author":"I Pandrea","year":"2008","journal-title":"J Immunol"},{"key":"ppat.1008333.ref146","doi-asserted-by":"crossref","first-page":"e1002170","DOI":"10.1371\/journal.ppat.1002170","article-title":"Functional cure of SIVagm infection in rhesus macaques results in complete recovery of CD4+ T cells and is reverted by CD8+ cell depletion","volume":"7","author":"I Pandrea","year":"2011","journal-title":"PLoS Pathog"},{"key":"ppat.1008333.ref147","doi-asserted-by":"crossref","first-page":"6249","DOI":"10.1128\/JVI.79.10.6249-6259.2005","article-title":"Impact of viral factors on very early in vivo replication profiles in simian immunodeficiency virus SIVagm-infected african green monkeys","volume":"79","author":"I Pandrea","year":"2005","journal-title":"J Virol"},{"key":"ppat.1008333.ref148","doi-asserted-by":"crossref","first-page":"e1005879","DOI":"10.1371\/journal.ppat.1005879","article-title":"Multi-dose romidepsin reactivates replication competent SIV in post-antiretroviral rhesus macaque controllers","volume":"12","author":"BB Policicchio","year":"2016","journal-title":"PLOS Pathog"},{"key":"ppat.1008333.ref149","doi-asserted-by":"crossref","first-page":"6155","DOI":"10.1128\/JVI.00256-15","article-title":"Simian Immunodeficiency Virus SIVsab Infection of Rhesus Macaques as a Model of Complete Immunological Suppression with Persistent Reservoirs of Replication-Competent Virus: Implications for Cure Research","volume":"89","author":"D Ma","year":"2015","journal-title":"J Virol"},{"key":"ppat.1008333.ref150","first-page":"1","article-title":"Guidelines for performing single-platform absolute CD4+ T-cell determinations with CD45 gating for persons infected with human immunodeficiency virus. Centers for Disease Control and Prevention","volume":"52","author":"CDC","year":"2003","journal-title":"MMWR Recomm Rep Morb Mortal Wkly Rep Recomm Rep"},{"key":"ppat.1008333.ref151","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1097\/SLA.0b013e3181d778c4","article-title":"Non-invasive markers for early diagnosis and determination of the severity of necrotizing enterocolitis","volume":"251","author":"G Thuijls","year":"2010","journal-title":"Ann Surg"},{"key":"ppat.1008333.ref152","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1093\/bioinformatics\/btp184","article-title":"Globally optimal stitching of tiled 3D microscopic image acquisitions","volume":"25","author":"S Preibisch","year":"2009","journal-title":"Bioinformatics"},{"key":"ppat.1008333.ref153","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"J Schindelin","year":"2012","journal-title":"Nat Methods"},{"key":"ppat.1008333.ref154","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1186\/s12859-017-1934-z","article-title":"ImageJ2: ImageJ for the next generation of scientific image data","volume":"18","author":"CT Rueden","year":"2017","journal-title":"BMC Bioinformatics"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1008333","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T00:00:00Z","timestamp":1584403200000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1008333","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T17:43:58Z","timestamp":1584467038000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1008333"}},"subtitle":[],"editor":[{"given":"David T.","family":"Evans","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,3,2]]},"references-count":154,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,3,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1008333","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.ppat.1008333","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,2]]}}}