任务一

install.packages("jsonlite")

install.packages("httr")

install.packages("xml2")

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"

任务二

baseUrl2="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"

 pubmedid="29275861,29275860"

 searchArticleParam$total_num=esearchresult$count

searchArticleParam$querykey=esearchresult$querykey

searchArticleParam$webenv=esearchresult$webenv

r2 <- POST(postFetchUrl, 

body = list(

db='pubmed',

id=pubmedidStr,

retmode='xml', 

usehistory=searchArticleParam$usehistory,

querykey=searchArticleParam$querykey,

webenv=searchArticleParam$webenv)) 

stop_for_status(r2)

library(xml2)

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