Rewrite the narrative review with at least 100 reference
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fluoroquinolone resistance narrative review mechanisms epidemiology clinical impact 2024
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python3 -c "from docx import Document; p='/tmp/workspace/attachments/1e192d2a-7972-4af2-9dd8-09d8b09a6561/FQ_Resistance_Review.docx'; d=Document(p); print('PARAGRAPHS',len(d.paragraphs),'TABLES',len(d.tables)); [print(f'[{x.style.name}] {x.text}') for x in d.paragraphs if x.text.strip()]"
fluoroquinolone resistance
fluoroquinolone resistance mechanisms
fluoroquinolone resistance Enterobacterales
fluoroquinolone resistance urinary tract infection
fluoroquinolone resistance tuberculosis
fluoroquinolone resistance gonorrhea
fluoroquinolone adverse events
fluoroquinolone antimicrobial stewardship
fluoroquinolone resistance food animals Campylobacter
gepotidacin zoliflodacin gonorrhea
mkdir -p "/tmp/workspace/fq-resistance-review/src" "/tmp/workspace/fq-resistance-review/output" && python3 - <<'PY' from docx import Document p='/tmp/workspace/attachments/1e192d2a-7972-4af2-9dd8-09d8b09a6561/FQ_Resistance_Review.docx' d=Document(p) for ti,t in enumerate(d.tables,1): print('\nTABLE',ti) for row in t.rows: print(' | '.join(c.text.replace('\n',' / ') for c in row.cells)) PY
python3 - <<'PY' import requests, xml.etree.ElementTree as ET, json, os queries=[ 'fluoroquinolone resistance mechanisms', 'fluoroquinolone resistance urinary tract infections', 'fluoroquinolone resistance tuberculosis', 'fluoroquinolone resistance gonorrhea', 'fluoroquinolone antimicrobial stewardship', 'fluoroquinolone adverse effects', 'fluoroquinolone resistance Campylobacter animals', 'gepotidacin zoliflodacin', 'fluoroquinolone resistance plasmid qnr', 'fluoroquinolone pharmacodynamics mutant prevention concentration' ] pmids=[] for q in queries: r=requests.get('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',params={'db':'pubmed','term':q,'retmax':20,'sort':'relevance','retmode':'json'},timeout=30) r.raise_for_status(); pmids += r.json()['esearchresult']['idlist'] seen=[] for x in pmids: if x not in seen: seen.append(x) # Fetch 115 to allow filtering later ids=seen[:115] r=requests.get('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',params={'db':'pubmed','id':','.join(ids),'rettype':'medline','retmode':'text'},timeout=60); r.raise_for_status() os.makedirs('/tmp/workspace/fq-resistance-review/src',exist_ok=True) open('/tmp/workspace/fq-resistance-review/src/pubmed_records.txt','w').write(r.text) open('/tmp/workspace/fq-resistance-review/src/pmids.json','w').write(json.dumps(ids,indent=2)) print('UNIQUE',len(seen),'FETCHED',len(ids),'BYTES',len(r.text)) PY
python3 - <<'PY' p='/tmp/workspace/fq-resistance-review/src/pubmed_records.txt' text=open(p).read() print(text[:3000]) PY
python3 - <<'PY' import re s=open('/tmp/workspace/fq-resistance-review/src/pubmed_records.txt').read(); recs=re.split(r'\n\n(?=PMID-)',s.strip()) for i,r in enumerate(recs,1): pmid=re.search(r'^PMID-\s+(.*)',r,re.M).group(1); ti=re.search(r'^TI\s+-\s+(.*(?:\n\s+.*)*)',r,re.M) title=' '.join(ti.group(1).split()) if ti else '' print(i,pmid,title[:100]) PY
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