Matt Harmon
Chapter four 91 20 Gautier, L., Cope, L., Bolstad, B. M. & Irizarry, R. A. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20 , 307-315, doi:10.1093/bioinformatics/btg405 (2004). 21 Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E. & Storey, J. D. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28 , 882- 883, doi:10.1093/bioinformatics/bts034 (2012). 22 Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43 , e47, doi:10.1093/nar/gkv007 (2015). 23 Cheng, S. C. et al. Broad defects in the energy metabolism of leukocytes underlie immunoparalysis in sepsis. Nat Immunol 17 , 406-413, doi:10.1038/ni.3398 (2016). 24 Zhou, Y. et al. The Cold-Inducible RNA-Binding Protein (CIRP) Level in Peripheral Blood Predicts Sepsis Outcome. PloS one 10 , e0137721, doi:10.1371/journal.pone.0137721 (2015). 25 Zhang, F., Brenner, M., Yang, W. L. & Wang, P. A cold-inducible RNA-binding protein (CIRP)- derived peptide attenuates inflammation and organ injury in septic mice. Sci Rep 8 , 3052, doi:10.1038/ s41598-017-13139-z (2018). 26 Qiang, X. et al. Cold-inducible RNA-binding protein (CIRP) triggers inflammatory responses in hemorrhagic shock and sepsis. Nat Med 19 , 1489-1495, doi:10.1038/nm.3368 (2013). 27 Bruemmer-Smith, S., Stuber, F. & Schroeder, S. Protective functions of intracellular heat-shock protein (HSP) 70-expression in patients with severe sepsis. Intensive care medicine 27 , 1835-1841, doi:10.1007/s00134-001-1131-3 (2001). 28 Asea, A. et al. HSP70 stimulates cytokine production through a CD14-dependant pathway, demonstrating its dual role as a chaperone and cytokine. Nat Med 6 , 435-442, doi:10.1038/74697 (2000). 29 Martine, P. et al. HSP70 is a negative regulator of NLRP3 inflammasome activation. Cell Death & Disease 10 , 256, doi:10.1038/s41419-019-1491-7 (2019). 30 Wirthgen, E. & Hoeflich, A. Endotoxin-Induced Tryptophan Degradation along the Kynurenine Pathway: The Role of Indolamine 2,3-Dioxygenase and Aryl Hydrocarbon Receptor-Mediated Immunosuppressive Effects in Endotoxin Tolerance and Cancer and Its Implications for Immunoparalysis. J Amino Acids 2015 , 973548, doi:10.1155/2015/973548 (2015). 31 Mandi, Y. & Vecsei, L. The kynurenine system and immunoregulation. J Neural Transm (Vienna) 119 , 197-209, doi:10.1007/s00702-011-0681-y (2012). 32 Darcy, C. J. et al. An observational cohort study of the kynurenine to tryptophan ratio in sepsis: association with impaired immune and microvascular function. PloS one 6 , e21185, doi:10.1371/ journal.pone.0021185 (2011). 33 Fallarino, F. et al. T cell apoptosis by tryptophan catabolism. Cell Death Differ 9 , 1069-1077, doi:10.1038/ sj.cdd.4401073 (2002). 34 Hodges, M. R. et al. Defects in breathing and thermoregulation in mice with near-complete absence of central serotonin neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience 28 , 2495-2505, doi:10.1523/JNEUROSCI.4729-07.2008 (2008). 35 Li, Y. et al. Sepsis-induced elevation in plasma serotonin facilitates endothelial hyperpermeability. Sci Rep 6 , 22747, doi:10.1038/srep22747 (2016). 36 Troche, G. et al. Tryptophan pathway catabolites (serotonin, 5-hydroxyindolacetic acid, kynurenine) and enzymes (monoamine oxidase and indole amine 2,3 dioxygenase) in patients with septic shock: A prospective observational study versus healthy controls. Medicine (Baltimore) 99 , e19906, doi:10.1097/ MD.0000000000019906 (2020). 37 Soulet, D. & Rivest, S. Polyamines play a critical role in the control of the innate immune response in the mouse central nervous system. J Cell Biol 162 , 257-268, doi:10.1083/jcb.200301097 (2003). 38 Neugebauer, S. et al. Metabolite Profiles in Sepsis: Developing Prognostic Tools Based on the Type of Infection. Crit Care Med 44 , 1649-1662, doi:10.1097/CCM.0000000000001740 (2016).
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