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Turner","year":"2003","journal-title":"Infect Immun"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1016\/j.clim.2009.01.002","article-title":"Comparisons of affinities, avidities, and complement activation of adalimumab, infliximab, and etanercept in binding to soluble and membrane tumor necrosis factor.","volume":"131","author":"Z Kaymakcalan","year":"2009","journal-title":"Clin Immunol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.1016\/j.jmb.2007.10.034","article-title":"Comparative analyses of complex formation and binding sites between human tumor necrosis factor-alpha and its three antagonists elucidate their different neutralizing mechanisms.","volume":"374","author":"MS Kim","year":"2007","journal-title":"J Mol Biol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1086\/517519","article-title":"Neutralization of tumor necrosis factor (TNF) by antibody but not TNF receptor fusion molecule exacerbates chronic murine tuberculosis.","volume":"195","author":"HL Plessner","year":"2007","journal-title":"J Infect Dis"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.semarthrit.2005.01.009","article-title":"Tumor necrosis factor and granuloma biology: Explaining the differential infection risk of etanercept and infliximab.","volume":"34","author":"RS Wallis","year":"2005","journal-title":"Semin Arthritis Rheum"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1111\/j.1600-065X.2007.00490.x","article-title":"Toward a multiscale model of antigen presentation in immunity.","volume":"216","author":"DE Kirschner","year":"2007","journal-title":"Immunol Rev"},{"key":"ref88","first-page":"238","article-title":"Extravascular diffusion in normal and neoplastic tissues.","volume":"44","author":"LJ Nugent","year":"1984","journal-title":"Cancer Res"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"4628","DOI":"10.1073\/pnas.081626898","article-title":"Role of tumor-host interactions in interstitial diffusion of macromolecules: Cranial vs. subcutaneous tumors.","volume":"98","author":"A Pluen","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1002\/(SICI)1097-0290(19990305)62:5<562::AID-BIT8>3.0.CO;2-4","article-title":"Coupled cellular trafficking and diffusional limitations in delivery of immunotoxins to multicell tumor spheroids.","volume":"62","author":"LA Wenning","year":"1999","journal-title":"Biotechnol Bioeng"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1007\/s10439-007-9425-4","article-title":"Modeling recombinant immunotoxin efficacies in solid tumors.","volume":"36","author":"KC Chen","year":"2008","journal-title":"Ann Biomed Eng"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"3668","DOI":"10.1128\/IAI.73.6.3668-3676.2005","article-title":"Differential effects of total and partial neutralization of tumor necrosis factor on cell-mediated immunity to mycobacterium bovis BCG infection.","volume":"73","author":"R Guler","year":"2005","journal-title":"Infect Immun"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1002\/(SICI)1096-9896(200002)190:2<211::AID-PATH530>3.0.CO;2-3","article-title":"Apoptosis in mycobacterium tuberculosis infection in mice exhibiting varied immunopathology.","volume":"190","author":"VE Watson","year":"2000","journal-title":"J Pathol"},{"key":"ref94","first-page":"5838","article-title":"Pharmacokinetic analysis of the perivascular distribution of bifunctional antibodies and haptens: Comparison with experimental data.","volume":"52","author":"LT Baxter","year":"1992","journal-title":"Cancer Res"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"2645","DOI":"10.1002\/jps.20178","article-title":"Antibody pharmacokinetics and pharmacodynamics.","volume":"93","author":"ED Lobo","year":"2004","journal-title":"J Pharm Sci"}],"container-title":["PLoS Computational 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