Strange India All Strange Things About India and world


  • 1.

    Roden, M. & Shulman, G. I. The integrative biology of type 2 diabetes. Nature 576, 51–60 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 2.

    Friedman, S. L., Neuschwander-Tetri, B. A., Rinella, M. & Sanyal, A. J. Mechanisms of NAFLD development and therapeutic strategies. Nat. Med. 24, 908–922 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 3.

    Hotamisligil, G. S. Inflammation, metaflammation and immunometabolic disorders. Nature 542, 177–185 (2017).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 4.

    Wolf, M. J. et al. Metabolic activation of intrahepatic CD8+ T cells and NKT cells causes nonalcoholic steatohepatitis and liver cancer via cross-talk with hepatocytes. Cancer Cell 26, 549–564 (2014).

    CAS 
    Article 

    Google Scholar 

  • 5.

    Malehmir, M. et al. Platelet GPIbα is a mediator and potential interventional target for NASH and subsequent liver cancer. Nat. Med. 25, 641–655 (2019).

    CAS 
    Article 

    Google Scholar 

  • 6.

    Clapper, J. R. et al. Diet-induced mouse model of fatty liver disease and nonalcoholic steatohepatitis reflecting clinical disease progression and methods of assessment. Am. J. Physiol. Gastrointest. Liver Physiol. 305, G483–G495 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 7.

    Ma, C. et al. NAFLD causes selective CD4+ T lymphocyte loss and promotes hepatocarcinogenesis. Nature 531, 253–257 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 8.

    Fernandez-Ruiz, D. et al. Liver-resident memory CD8+ T cells form a front-line defense against malaria liver-stage infection. Immunity 45, 889–902 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 9.

    Topham, D. J. & Reilly, E. C. Tissue-resident memory CD8+ T cells: from phenotype to function. Front. Immunol. 9, 515 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 10.

    Böttcher, J. P. et al. Functional classification of memory CD8+ T cells by CX3CR1 expression. Nat. Commun. 6, 8306 (2015).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 11.

    Gerlach, C. et al. The chemokine receptor CX3CR1 defines three antigen-experienced CD8 T cell subsets with distinct roles in immune surveillance and homeostasis. Immunity 45, 1270–1284 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 12.

    Olson, J. A., McDonald-Hyman, C., Jameson, S. C. & Hamilton, S. E. Effector-like CD8+ T cells in the memory population mediate potent protective immunity. Immunity 38, 1250–1260 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 13.

    Khan, O. et al. TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature 571, 211–218 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 14.

    Alfei, F. et al. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature 571, 265–269 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 15.

    Mackay, L. K. et al. Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes. Science 352, 459–463 (2016).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 16.

    Veldhoen, M. Interleukin 17 is a chief orchestrator of immunity. Nat. Immunol. 18, 612–621 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 17.

    Man, K. & Kallies, A. Synchronizing transcriptional control of T cell metabolism and function. Nat. Rev. Immunol. 15, 574–584 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 18.

    Wang, Z. et al. BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. Bioinformatics 34, 2867–2869 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 19.

    Leonard, W. J., Lin, J. X. & O’Shea, J. J. The γc family of cytokines: basic biology to therapeutic ramifications. Immunity 50, 832–850 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 20.

    Hedrick, S. M., Hess Michelini, R., Doedens, A. L., Goldrath, A. W. & Stone, E. L. FOXO transcription factors throughout T cell biology. Nat. Rev. Immunol. 12, 649–661 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 21.

    Cepero-Donates, Y. et al. Interleukin-15-mediated inflammation promotes non-alcoholic fatty liver disease. Cytokine 82, 102–111 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 22.

    Chirifu, M. et al. Crystal structure of the IL-15–IL-15Rα complex, a cytokine-receptor unit presented in trans. Nat. Immunol. 8, 1001–1007 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 23.

    Balmer, M. L. et al. Memory CD8+ T cells require increased concentrations of acetate induced by stress for optimal function. Immunity 44, 1312–1324 (2016).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 24.

    Qiu, J. et al. Acetate promotes T cell effector function during glucose restriction. Cell Rep. 27, 2063–2074 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 25.

    Liu, X. et al. Acetate production from glucose and coupling to mitochondrial metabolism in mammals. Cell 175, 502–513 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 26.

    Bachem, A. et al. Microbiota-derived short-chain fatty acids promote the memory potential of antigen-activated CD8+ T cells. Immunity 51, 285–297 (2019).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 27.

    Voskoboinik, I., Whisstock, J. C. & Trapani, J. A. Perforin and granzymes: function, dysfunction and human pathology. Nat. Rev. Immunol. 15, 388–400 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 28.

    Chang, C. H. et al. Posttranscriptional control of T cell effector function by aerobic glycolysis. Cell 153, 1239–1251 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 29.

    Linden, J., Koch-Nolte, F. & Dahl, G. Purine release, metabolism, and signaling in the inflammatory response. Annu. Rev. Immunol. 37, 325–347 (2019).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 30.

    Chekeni, F. B. et al. Pannexin 1 channels mediate ‘find-me’ signal release and membrane permeability during apoptosis. Nature 467, 863–867 (2010).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 31.

    Stark, R. et al. TRM maintenance is regulated by tissue damage via P2RX7. Sci. Immunol. 3, eaau1022 (2018).

    PubMed 
    Article 

    Google Scholar 

  • 32.

    Borges da Silva, H. et al. The purinergic receptor P2RX7 directs metabolic fitness of long-lived memory CD8+ T cells. Nature 559, 264–268 (2018).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 33.

    Zhao, J. et al. Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human. Cell Discov. 6, 22 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 34.

    Setoguchi, R. IL-15 boosts the function and migration of human terminally differentiated CD8+ T cells by inducing a unique gene signature. Int. Immunol. 28, 293–305 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 35.

    Lampl, S. et al. Reduced mitochondrial resilience enables non-canonical induction of apoptosis after TNF receptor signaling in virus-infected hepatocytes. J. Hepatol. 73, 1347–1359 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 36.

    Chen, H. et al. Cytofkit: a Bioconductor package for an integrated mass cytometry data analysis pipeline. PLoS Comput. Biol. 12, e1005112 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 37.

    Mackay, L. K. et al. T-box transcription factors combine with the cytokines TGF-β and IL-15 to control tissue-resident memory T cell fate. Immunity 43, 1101–1111 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 38.

    Li, M. Z. & Elledge, S. J. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat. Methods 4, 251–256 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 39.

    Guillot, A. & Tacke, F. The unexpected role of neutrophils for resolving liver inflammation by transmitting microRNA-223 to macrophages. Hepatology 71, 749–751 (2020).

    PubMed 
    Article 

    Google Scholar 

  • 40.

    Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 41.

    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 42.

    Zhou, Q. et al. A mouse tissue transcription factor atlas. Nat. Commun. 8, 15089 (2017).

    ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 43.

    Dreos, R., Ambrosini, G., Groux, R., Cavin Périer, R. & Bucher, P. The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. Nucleic Acids Res. 45, D51–D55 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 44.

    Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46, D260–D266 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 45.

    Kulakovskiy, I. V. et al. HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-seq analysis. Nucleic Acids Res. 46, D252–D259 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 46.

    Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 47.

    Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91–100 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 48.

    Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411–420 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 49.

    Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 50.

    Zappia, L. & Oshlack, A. Clustering trees: a visualization for evaluating clusterings at multiple resolutions. Gigascience 7, (2018).

  • 51.

    Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 52.

    Mahi, N. A., Najafabadi, M. F., Pilarczyk, M., Kouril, M. & Medvedovic, M. GREIN: an interactive web platform for re-analyzing GEO RNA-seq data. Sci. Rep. 9, 7580 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 53.

    Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).

    ADS 
    CAS 
    Article 

    Google Scholar 



  • Source link

    Leave a Reply

    Your email address will not be published.