R2-22第二期第一次作业

LIUUU 2018-01-22 20:48:27 阅读: 1277

library(httr)

baseUrl="https://eutils.ncbi.nlm.nih.gov/"

pubmedACTION=list(base="entrez/eutils/index.fcgi",search="entrez/eutils/esearch.fcgi",fetch="entrez/eutils/efetch.fcgi",summary="entrez/eutils/esummary.fcgi")

searchArticleParam=list(retstart=0,retmax=20,usehistory='Y',querykey='',webenv='',term='(cell[TA]) AND 2017[DP]',total_num=0,total_page=1,page_size=20,current_page=1)

postSearchUrl=paste(baseUrl,pubmedACTION$search,sep="")

r=POST(postSearchUrl,body=list(db='pubmed',term=searchArticleParam$term,retmode='json',retstart=searchArticleParam$retstart,retmax=searchArticleParam$retmax,usehistory=searchArticleParam$usehistory,rettype='uilist'))

stop_for_status(r)

data=content(r,"parsed","application/json")

esearchresult=data$esearchresult

count=esearchresult$count

print(count)

[1] "563"

install.packages("xml2")

library(xml2)

searchArticleParam$total_num=esearchresult$count
searchArticleParam$querykey=esearchresult$querykey
searchArticleParam$webenv=esearchresult$webenv
pubmedidStr="29275861,29275860";postFetchUrl=paste(baseUrl,pubmedACTION$fetch,sep="")
r2=POST(postFetchUrl,body=list(db='pubmed',id=pubmedidStr,retmode='xml',usehistory=searchArticleParam$usehistory,querykey=searchArticleParam$querykey,webenv=searchArticleParam$webenv))
r2
stop_for_status(r2)
data2=content(r2,"parsed","application/xml")
article=xml_children(data2)
count=length(article)
cnt=1
while(cnt<=count){
title=xml_find_first(article[cnt],".//ArticleTitle")
abstract=xml_find_first(article[cnt],".//AbstractText")
print(xml_text(title))
print(xml_text(abstract))
cnt = cnt + 1
}

[1] "Natural Killer Cells Control Tumor Growth by Sensing a Growth Factor."
[1] "Many tumors produce platelet-derived growth factor (PDGF)-DD, which promotes cellular proliferation, epithelial-mesenchymal transition, stromal reaction, and angiogenesis through autocrine and paracrine PDGFRβ signaling. By screening a secretome library, we found that the human immunoreceptor NKp44, encoded by NCR2 and expressed on natural killer (NK) cells and innate lymphoid cells, recognizes PDGF-DD. PDGF-DD engagement of NKp44 triggered NK cell secretion of interferon gamma (IFN)-γ and tumor necrosis factor alpha (TNF-α) that induced tumor cell growth arrest. A distinctive transcriptional signature of PDGF-DD-induced cytokines and the downregulation of tumor cell-cycle genes correlated with NCR2 expression and greater survival in glioblastoma. NKp44 expression in mouse NK cells controlled the dissemination of tumors expressing PDGF-DD more effectively than control mice, an effect enhanced by blockade of the inhibitory receptor CD96 or CpG-oligonucleotide treatment. Thus, while cancer cell production of PDGF-DD supports tumor growth and stromal reaction, it concomitantly activates innate immune responses to tumor expansion."
[1] "Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes."
[1] "The immune system can mount T cell responses against tumors; however, the antigen specificities of tumor-infiltrating lymphocytes (TILs) are not well understood. We used yeast-display libraries of peptide-human leukocyte antigen (pHLA) to screen for antigens of \"orphan\" T cell receptors (TCRs) expressed on TILs from human colorectal adenocarcinoma. Four TIL-derived TCRs exhibited strong selection for peptides presented in a highly diverse pHLA-A∗02:01 library. Three of the TIL TCRs were specific for non-mutated self-antigens, two of which were present in separate patient tumors, and shared specificity for a non-mutated self-antigen derived from U2AF2. These results show that the exposed recognition surface of MHC-bound peptides accessible to the TCR contains sufficient structural information to enable the reconstruction of sequences of peptide targets for pathogenic TCRs of unknown specificity. This finding underscores the surprising specificity of TCRs for their cognate antigens and enables the facile indentification of tumor antigens through unbiased screening."

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