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Biol., 6, 1519, 10.1016\u002FS0960-9822(96)00757-9\nLiu, 2000, Mutation of a conserved residue (D123) required for oligomerization of human immunodeficiency virus type 1 Nef protein abolishes interaction with human thioesterase and results in impairment of Nef biological functions, J. 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Dis., 1, 179, 10.1034\u002Fj.1399-3062.1999.010306.x\nTanabe, 1997, Comparative study of cytomegalovirus (CMV) antigenemia assay, polymerase chain reaction, serology and shell vial assay in the early diagnosis and monitoring of CMV infection after renal transplantation, Transplantation, 64, 1721, 10.1097\u002F00007890-199712270-00016\nMeyer-Koenig, 2004, Cytomegalovirus infection in organ-transplant recipients: diagnostic value of pp65 antigen test, qualitative polymerase chain reaction (PCR) and quantitative Taqman PCR, Transplantation, 77, 1692, 10.1097\u002F01.tp.0000133992.89191.52\nAquino, 2001, Cytomegalovirus infection in renal transplant recipients diagnosed by nested-PCR, Braz. J. Med. Biol. Res., 34, 93, 10.1590\u002FS0100-879X2001000100011\nHumar, 2004, Clinical utility of cytomegalovirus viral load testing for predicting CMV disease in D+\u002FR– solid organ transplant recipients, Am. J. Transplant., 4, 644, 10.1111\u002Fj.1600-6143.2004.00391.x\nHumar, 2003, Cytomegalovirus (CMV) glycoprotein B genotypes and response to antiviral therapy, in solid-organ-transplant recipients with CMV disease, J. Infect. 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Today, 10, 412, 10.1016\u002F0169-4758(94)90238-0\nSchofield, 1996, J. Immunol, 156, 1886, 10.4049\u002Fjimmunol.156.5.1886\nViebig, 2005, Direct activation of human endothelial cells by Plasmodium falciparum-infected erythrocytes, Infect. Immun, 73, 3271, 10.1128\u002FIAI.73.6.3271-3277.2005\nTripathi, 2006, Plasmodium falciparum-infected erythrocytes increase intercellular adhesion molecule 1 expression on brain endothelium through NF-kappaB, Infect. Immun, 74, 3262, 10.1128\u002FIAI.01625-05\nYipp, 2003, Src-family kinase signaling modulates the adhesion of Plasmodium falciparum on human microvascular endothelium under flow, Blood, 101, 2850, 10.1182\u002Fblood-2002-09-2841\nHo, 2005, Ectophosphorylation of CD36 regulates cytoadherence of Plasmodium falciparum to microvascular endothelium under flow conditions, Infect. Immun, 73, 8179, 10.1128\u002FIAI.73.12.8179-8187.2005\nPouvelle, 2003, Modeling of Plasmodium falciparum-infected erythrocyte cytoadhesion in microvascular conditions: chondroitin-4-sulfate binding, a competitive phenotype, J. Infect. Dis, 187, 292, 10.1086\u002F346050\nGay, 1995, Isolation and characterization of brain microvascular endothelial cells from Saimiri monkeys. An in vitro model for sequestration of Plasmodium falciparum-infected erythrocytes, J. Immunol. Methods, 184, 15, 10.1016\u002F0022-1759(95)00070-Q\nGysin, 1999, Ex vivo desequestration of Plasmodium falciparum-infected erythrocytes from human placenta by chondroitin sulfate A, Infect. Immun, 67, 6596, 10.1128\u002FIAI.67.12.6596-6602.1999\nTrager, 1976, Human malaria parasites in continuous culture, Science, 193, 673, 10.1126\u002Fscience.781840\nPouvelle, 1998, Biological and biochemical characteristics of cytoadhesion of Plasmodium falciparum-infected erythrocytes to chondroitin-4-sulfate, Infect. Immun, 66, 4950, 10.1128\u002FIAI.66.10.4950-4956.1998\nMuanza, 1996, Primary culture of human lung microvessel endothelial cells: a useful in vitro model for studying Plasmodium falciparum-infected erythrocyte cytoadherence, Res. Immunol, 147, 149, 10.1016\u002F0923-2494(96)83167-1\nCrandall, 1991, Plasmodium falciparum: the effect of pH and Ca2+ concentration on the in vitro cytoadherence of infected erythrocytes to amelanotic melanoma cells, Exp. Parasitol, 73, 362, 10.1016\u002F0014-4894(91)90108-9\nBrennan, 1997, CD44 expression by leucocytes in rheumatoid arthritis and modulation by specific antibody: implications for lymphocyte adhesion to endothelial cells and synoviocytes in vitro, Scand. J. Immunol, 45, 213, 10.1046\u002Fj.1365-3083.1997.d01-382.x\nBeeson, 2006, Antigenic differences and conservation among placental Plasmodium falciparum-infected erythrocytes and acquisition of variant-specific and cross-reactive antibodies, J. Infect. 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Chem., 280, 35999, 10.1074\u002Fjbc.M506374200\nSchlaepfer, 1998, Multiple Grb2-mediated integrin-stimulated signaling pathways to ERK2\u002Fmitogen-activated protein kinase: summation of both c-Src- and focal adhesion kinase-initiated tyrosine phosphorylation events, Mol. Cell. Biol., 18, 2571, 10.1128\u002FMCB.18.5.2571\nGerthoffer, 2005, Signal-transduction pathways that regulate visceral smooth muscle function. III. Coupling of muscarinic receptors to signaling kinases and effector proteins in gastrointestinal smooth muscles, Am. J. Physiol. Gastrointest. Liver Physiol, 288, G849, 10.1152\u002Fajpgi.00530.2004\nHai, 2006, Caldesmon phosphorylation in actin cytoskeletal remodeling, Eur. J. Cell Biol., 85, 305, 10.1016\u002Fj.ejcb.2005.08.008\nBodin, 2005, Integrin-dependent interaction of lipid rafts with the actin cytoskeleton in activated human platelets, J. 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2006, 1918 Influenza: the mother of all pandemics, Emerg Infect Dis, 12, 15, 10.3201\u002Feid1209.05-0979\nTaubenberger, 2019, The 1918 influenza pandemic: 100 years of questions answered and unanswered, Sci Transl Med, 11, 10.1126\u002Fscitranslmed.aau5485\nTaubenberger, 1997, Initial genetic characterization of the 1918 \"Spanish\" influenza virus, Science, 275, 1793, 10.1126\u002Fscience.275.5307.1793\nAhmad, 2009, Controlling SARS: a review on China’s response compared with other SARS-affected countries, Trop Med Int Health, 14, 36, 10.1111\u002Fj.1365-3156.2008.02146.x\nTsang, 2003, A cluster of cases of severe acute respiratory syndrome in Hong Kong, N Engl J Med, 348, 1977, 10.1056\u002FNEJMoa030666\nWHO: https:\u002F\u002Fwww.who.int\u002Fcsr\u002Fdon\u002F2003_03_16\u002Fen\u002F.\nWang, 2006, Review of bats and SARS, Emerg Infect Dis, 12, 1834, 10.3201\u002Feid1212.060401\nHu, 2017, Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus, PLoS Pathog, 13, 10.1371\u002Fjournal.ppat.1006698\nFouchier, 2003, Aetiology: Koch’s postulates fulfilled for SARS virus, Nature, 423, 240, 10.1038\u002F423240a\nPang, 2003, Evaluation of control measures implemented in the severe acute respiratory syndrome outbreak in Beijing, 2003, J Am Med Assoc, 290, 3215, 10.1001\u002Fjama.290.24.3215\nParashar, 2004, Severe acute respiratory syndrome: review and lessons of the 2003 outbreak, Int J Epidemiol, 33, 628, 10.1093\u002Fije\u002Fdyh198\nWHO: https:\u002F\u002Fwww.who.int\u002Fcsr\u002Fsars\u002Fcountry\u002F2003_06_30\u002Fen\u002F.\nWHO: http:\u002F\u002Fapplications.emro.who.int\u002Fdocs\u002FEMROPub-MERS-SEP-2019-EN.pdf?ua=1&ua=1.\nMemish, 2013, Middle East respiratory syndrome coronavirus in bats, Saudi Arabia, Emerg Infect Dis, 19, 1819, 10.3201\u002Feid1911.131172\nOmrani, 2015, Middle East respiratory syndrome coronavirus (MERS-CoV): animal to human interaction, Pathog Glob Health, 109, 354, 10.1080\u002F20477724.2015.1122852\nWu, 2020, A new coronavirus associated with human respiratory disease in China, Nature, 10.1038\u002Fs41586-020-2008-3\nZhou, 2020, A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, 10.1038\u002Fs41586-020-2951-z\nWuhan-MHC: http:\u002F\u002Fwjw.wuhan.gov.cn\u002Ffront\u002Fweb\u002FshowDetail\u002F2019123108989.\nKofi Ayittey, 2020, Updates on Wuhan 2019 novel coronavirus epidemic, J Med Virol, 92, 403, 10.1002\u002Fjmv.25695\nChina MHC: http:\u002F\u002Fwww.nhc.gov.cn\u002Fxcs\u002Fyqtb\u002F202001\u002Fc5da49c4c5bf4bcfb320ec2036480627.shtml.\nChina-MHC: http:\u002F\u002Fwww.nhc.gov.cn\u002Fxcs\u002Fyqtb\u002F202001\u002Fa53e6df293cc4ff0b5a16ddf7b6b2b31.shtml.\nWHO: https:\u002F\u002Fwww.who.int\u002Fnews-room\u002Fdetail\u002F30-01-2020-statement-on-the-second-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-outbreak-of-novel-coronavirus-(2019-ncov).\nSinaNews: http:\u002F\u002Fnews.sina.com.cn\u002Fo\u002F2020-01-25\u002Fdoc-iihnzahk6304748.shtml.\nCCTV: http:\u002F\u002Fnews.cctv.com\u002F2020\u002F01\u002F25\u002FARTIj6fo5JL3hCJJuAl3We5C200125.shtml.\nCCTV: http:\u002F\u002Fnews.cctv.com\u002F2020\u002F01\u002F27\u002FARTIMaQ6B6bTGFWXrVvW1Tp6200127.shtml.\nCCTV: http:\u002F\u002Fnews.cctv.com\u002F2020\u002F02\u002F02\u002FARTI4gEc8npt85sZCHx7h7OE200202.shtml. http:\u002F\u002Fnews.cctv.com\u002F2020\u002F02\u002F02\u002FARTI4gEc8npt85sZCHx7h7OE200202.shtml.\nChina-MHC: http:\u002F\u002Fwww.nhc.gov.cn\u002Fxcs\u002Ffkdt\u002F202001\u002F50050057b6fe4a2b90763d95c4273ceb.shtml.\nGeneral Office of the State Council,PRC: http:\u002F\u002Fwww.gov.cn\u002Fxinwen\u002F2020-02\u002F03\u002Fcontent_5474309.htm.\nChina-MHC: http:\u002F\u002Fwww.nhc.gov.cn\u002Fxcs\u002Fyqtb\u002F202002\u002F24a796819bf747bd8b945384517e9a51.shtml.\nChina-MHC: 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http:\u002F\u002Fwww.nhc.gov.cn\u002Fxcs\u002Fxxgzbd\u002F202001\u002Fde5f07afe8054af3ab2a25a61d19ac70.shtml.\nSohu.News: http:\u002F\u002Fwww.sohu.com\u002Fa\u002F367195671_342073.\nChu, 2020, Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia, Clin Chem, 10.1093\u002Fclinchem\u002Fhvaa029\nCorman, 2020, Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR, Euro Surveill, 25, 10.2807\u002F1560-7917.ES.2020.25.3.2000045\nChina-MHC: http:\u002F\u002Fwww.nhc.gov.cn\u002Fxcs\u002Ffkdt\u002F202001\u002Ffdae6ee4724542ba82daa1c9ad06ebf7.shtml.\nGuan, 2003, Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China, Science, 302, 276, 10.1126\u002Fscience.1087139\nPoon, 2003, Early diagnosis of SARS Coronavirus infection by real time RT-PCR, J Clin Virol, 28, 233, 10.1016\u002Fj.jcv.2003.08.004\nShi, 2003, Diagnosis of severe acute respiratory syndrome (SARS) by detection of SARS coronavirus nucleocapsid antibodies in an antigen-capturing enzyme-linked immunosorbent assay, J Clin Microbiol, 41, 5781, 10.1128\u002FJCM.41.12.5781-5782.2003\nMarra, 2003, The genome sequence of the SARS-associated coronavirus, Science, 300, 1399, 10.1126\u002Fscience.1085953\nWuhan-Gov: http:\u002F\u002Fwww.wuhan.gov.cn\u002F2019_web\u002Fwhyw\u002F202001\u002Ft20200123_304083.html.\nHubei-Gov: http:\u002F\u002Fwww.hubei.gov.cn\u002Fzhuanti\u002F2020\u002Fgzxxgzbd\u002Fqfqk\u002F202001\u002Ft20200124_2014612.shtml.\nCAAC: http:\u002F\u002Fwww.caac.gov.cn\u002FXXGK\u002FXXGK\u002FTJSJ\u002F201511\u002Ft20151102_8648.html.\nCAAC: http:\u002F\u002Fwww.caac.gov.cn\u002FXXGK\u002FXXGK\u002FTJSJ\u002F201905\u002Ft20190508_196033.html.\nHubei-Gov: http:\u002F\u002Fwww.hubei.gov.cn\u002Fhbfb\u002Fbmdt\u002F202002\u002Ft20200206_2019987.shtml.\nHubei-MHC: http:\u002F\u002Fwjw.hubei.gov.cn\u002Ffbjd\u002Fdtyw\u002F202002\u002Ft20200204_2018742.shtml.\nWuhan-Gov: 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Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology, Clin Microbiol Infect, 24, 355, 10.1016\u002Fj.cmi.2017.11.001\nGreninger, 2015, Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis, Genome Med, 7, 99, 10.1186\u002Fs13073-015-0220-9\nZmora, 2018, Personalized gut mucosal colonization resistance to empiric probiotics as associated with unique host and microbiome features, Cell, 174, 1388, 10.1016\u002Fj.cell.2018.08.041\nSuez, 2018, Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT, Cell, 174, 1406, 10.1016\u002Fj.cell.2018.08.047\nZeevi, 2015, Personalized nutrition by prediction of glycemic responses, Cell, 163, 1079, 10.1016\u002Fj.cell.2015.11.001\nRouty, 2018, Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors, Science, 359, 91, 10.1126\u002Fscience.aan3706\nRavel, 2011, Vaginal microbiome of reproductive-age women, Proc Natl Acad Sci, 108, 4680, 10.1073\u002Fpnas.1002611107\nGrumaz, 2016, Next-generation sequencing diagnostics of bacteremia in septic patients, Genome Med, 8, 73, 10.1186\u002Fs13073-016-0326-8\nBrenner, 2018, Next-generation sequencing diagnostics of bacteremia in sepsis (Next GeneSiS-Trial): study protocol of a prospective, observational, noninterventional, multicenter, clinical trial, Medicine (Baltimore), 97, e9868, 10.1097\u002FMD.0000000000009868\nMellmann, 2017, High interlaboratory reproducibility and accuracy of next-generation-sequencing-based bacterial genotyping in a ring trial, J Clin Microbiol, 55, 908, 10.1128\u002FJCM.02242-16\nQuainoo, 2017, Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis, Clin Microbiol Rev, 30, 1015, 10.1128\u002FCMR.00016-17\nZankari, 2012, Identification of acquired antimicrobial resistance genes, J Antimicrob Chemother, 67, 2640, 10.1093\u002Fjac\u002Fdks261\nGupta, 2014, ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes, Antimicrob Agents Chemother, 58, 212, 10.1128\u002FAAC.01310-13\nMcArthur, 2013, The comprehensive antibiotic resistance database, Antimicrob Agents Chemother, 57, 3348, 10.1128\u002FAAC.00419-13\nLakin, 2017, MEGARes: an antimicrobial resistance database for high throughput sequencing, Nucleic Acids Res, 45, D574, 10.1093\u002Fnar\u002Fgkw1009\nArango-Argoty, 2018, DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data, Microbiome, 6, 23, 10.1186\u002Fs40168-018-0401-z\nYang, 2016, ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database, Bioinformatics, 32, 2346, 10.1093\u002Fbioinformatics\u002Fbtw136\nTomczyk, 2019, Control of carbapenem-resistant Enterobacteriaceae, Acinetobacter baumannii, and Pseudomonas aeruginosa in healthcare facilities: a systematic review and reanalysis of quasi-experimental studies, Clin Infect Dis, 68, 873, 10.1093\u002Fcid\u002Fciy752\nRuppé, 2017, Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing, Clin Microbiol Infect, 23, 470, 10.1016\u002Fj.cmi.2017.01.015\nMulvey, 2016, Multiple variants of Klebsiella pneumoniae producing carbapenemase in one Patient, N Engl J Med, 375, 2408, 10.1056\u002FNEJMc1511360\nPaulson, 2013, Epidemiology: a mortal foe, Nature, 502, S2, 10.1038\u002F502S2a\nThe Cryptic Consortium, 2018, The 100,000 Genomes Project. Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing, N Engl J Med, 379, 1403, 10.1056\u002FNEJMoa1800474\nCrisan, 2018, Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory, PeerJ, 6, e4218, 10.7717\u002Fpeerj.4218",{"EN":918},"Messages from the third International Conference on Clinical Metagenomics 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1990, Fatal infection with a novel unindentified mycobacterium in a man with the acquired immunodeficiency syndrome, New Engl. 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Microbiol., 24, 2514, 10.1128\u002Fjcm.33.9.2514-2515.1995\nBogdan, 1997, Systemic infection with Mycobacterium genavense following immunosuppressive therapy in a patient who was seronegative for human immunodeficiency virus, Clin. Infect. Dis., 31, 1245, 10.1086\u002F513634\nHoop, 1993, Mycobacteriosis due to Mycobacterium genavense in six pet birds, J. Clin. Microbiol., 34, 990, 10.1128\u002Fjcm.31.4.990-993.1993\nKiehn, 1996, Mycobacterium genavense infection in pet animals, J. Clin. Microbiol., 12, 1840, 10.1128\u002Fjcm.34.7.1840-1842.1996\nSchurr, 1991, Genetic control of innate resistance to mycobacterial infections, Immunol. Today, 73, A42, 10.1016\u002FS0167-5699(05)80012-X\nVidal, 1993, Natural resistance to infection with intracellular parasites: isolation of a candidate for Bcg, Cell, 182, 469, 10.1016\u002F0092-8674(93)90135-D\nVidal, 1995, The Ity\u002FLsh\u002FBcg locus: natural resistance to infection with intracellular parasites is abrogated by disruption of the Nramp1 gene, J. Exp. M, 7, 655, 10.1084\u002Fjem.182.3.655\nCooper, 1995, The protective immune response to Mycobacterium tuberculosis, Curr. Opin. Immunol., 60, 512, 10.1016\u002F0952-7915(95)80096-4\nHubbard, 1992, T-cell immune responses in Mycobacterium avium-infected mice, Infect. Immun., 25, 150, 10.1128\u002Fiai.60.1.150-153.1992\nLadel, 1995, Immune response to Mycobacterium bovis bacille Calmette Guérin infection in major histocompatibility complex class I- and II-deficient knock-out mice: contribution of CD4 and CD8 T cells to acquired resistance, Eur. J. Immunol., 40, 377, 10.1002\u002Feji.1830250211\nPotter, 1983, A BALB\u002Fc congenic strain of mice that carries a genetic locus (ityr) controlling resistance to intracellular parasites, Infect. Immun., 145, 1234, 10.1128\u002Fiai.40.3.1234-1235.1983\nNauciel, 1990, Role of CD4+ T cells and T-independent mechanisms in acquired resistance to Salmonella typhimurium infection, J. Immunol., 183, 1265, 10.4049\u002Fjimmunol.145.4.1265\nMedina, 1996, Evidence inconsistent with a role for the Bcg gene (Nramp1) in resistance of mice to infection with virulent Mycobacterium tuberculosis, J. Exp. M, 62, 1045, 10.1084\u002Fjem.183.3.1045\nAppelberg, 1994, Role of gamma interferon and tumor necrosis factor alpha during T-cell independent and -dependent phases of Mycobacterium avium infection, Infect. Immun., 335, 3962, 10.1128\u002Fiai.62.9.3962-3971.1994\nNewport, 1996, A mutation in the interferon-γ -receptor gene and susceptibility to mycobacterial infection, New Engl. J. 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1982, Selective protection against conidia by mononuclear and against mycelia by polymorphonuclear phagocytes in resistance to Aspergillus. Observations on these two lines of defense in vivo and in vitro with human and mouse phagocytes, J. Clin. Invest., 69, 617, 10.1172\u002FJCI110489\nMorgenstern, 1997, Absence of respiratory burst in X-linked chronic granulomatous disease mice leads to abnormalities in both host defense and inflammatory response to Aspergillus fumigatus, J. Exp. Med., 185, 207, 10.1084\u002Fjem.185.2.207\nMehrad, 1999, CXC chemokine receptor-2 ligands are necessary components of neutrophil-mediated host defense in invasive pulmonary aspergillosis, J. Immunol., 163, 6086, 10.4049\u002Fjimmunol.163.11.6086\nLatge, 1999, Aspergillus fumigatus and aspergillosis, Clin. Microbiol. Rev., 12, 310, 10.1128\u002FCMR.12.2.310\nGil-Lamaignere, 2005, Inteferon gamma and granulocyte-macrophage colony-stimulating factor augment the antifungal activity of human polymorphonuclear leukocytes against Scedosporium spp.: comparison with Aspergillus spp, Med. Mycol., 43, 253, 10.1080\u002F13693780412331271072\nGordon, 2005, Gamma interferon enhances internalization and early nonoxidative killing of Salmonella enterica serovar Typhimurium by human macrophages and modifies cytokine responses, Infect. Immun., 73, 3445, 10.1128\u002FIAI.73.6.3445-3452.2005\nHebart, 2002, Analysis of T-cell responses to Aspergillus fumigatus antigens in healthy individuals and patients with hematologic malignancies, Blood, 100, 4521, 10.1182\u002Fblood-2002-01-0265\nGrazziutti, 1997, Aspergillus fumigatus conidia induce a Th1-type cytokine response, J. Infect. Dis., 176, 1579, 10.1086\u002F514157\nBozza, 2003, A dendritic cell vaccine against invasive aspergillosis in allogeneic hematopoietic transplantation, Blood, 102, 3807, 10.1182\u002Fblood-2003-03-0748\nCenci, 1998, Cytokine- and T helper-dependent lung mucosal immunity in mice with invasive pulmonary aspergillosis, J. Infect. 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Immun., 74, 1480, 10.1128\u002FIAI.74.3.1480-1489.2006\nSerrano-Gomez, 2005, DC-SIGN mediates the binding of Aspergillus fumigatus and keratinophylic fungi by human dendritic cells, Immunobiology, 210, 175, 10.1016\u002Fj.imbio.2005.05.011\nScimone, 2005, Migration of polymorphonuclear leucocytes is influenced by dendritic cells, Immunology, 114, 375, 10.1111\u002Fj.1365-2567.2005.02104.x\nTorosantucci, 1997, Responsiveness of human polymorphonuclear cells (PMNL) to stimulation by a mannoprotein fraction (MP-F2) of Candida albicans; enhanced production of IL-6 and tumour necrosis factor-alpha (TNF-alpha) by MP-F2-stimulated PMNL from HIV-infected subjects, Clin. Exp. 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