in praise of hacking, retraction still missed by Zotero

[Mike Marchywka]

On a pubmed serch update this AM, I got a retraction
notice for this,

https://pubmed.ncbi.nlm.nih.gov/33880367/

and of course decided to check bibtex for a warning.
Note that this is pretty new and this may just reflect
the speed of notirication although article is from 2021.


Toobib continued to find the notice only in the entrez eutils
medline output and as a keyword in the pubmed webpage in
a place you, or zoterro, would not normally look.
I also noted the zotero output has an unusual entry
for "pages" ( part of the DOI )  which apparently was only 
found by Toobib in the medline output which is really odd. 

fwiw.

grep -i "retract\|mjmhandler"  xxxx
% mjmhandler: toobib guesspubmed
%PT = {Retracted Publication},
pubtype = {Journal Article Retracted Publication},
% mjmhandler: toobib handledoi(crossref)
% mjmhandler: toobib handledoi(crossref)
% mjmhandler: toobib handledoi(crossref)
% mjmhandler: toobib handledoixml ( quality i=0 szr=10 goods=1 )(crossref)
% mjmhandler: toobib handlepdfstrings(crossref)
% mjmhandler: toobib handleadhochtml<-citation
% mjmhandler: toobib handleadhochtml<-og
% mjmhandler: toobib handleadhochtml<-all
keywords = {pmid:33880367, PMC8046533, doi:10.1155/2021/5532864, Retracted Publication, Maryam Javed, Syed Ahmed Raza, Khalid Mehmood, Animals, Buffaloes / genetics*, Buffaloes / immunology*, Cattle, Gene Frequency / genetics, Gene Regulatory Networks, Genome, Haplotypes / genetics, Heterozygote, Interferon-gamma / chemistry, Interferon-gamma / genetics*, Odds Ratio, Protein Structure, Secondary, Tuberculosis, Bovine / genetics*, Tuberculosis, Bovine / immunology*, PubMed Abstract, NIH, NLM, NCBI, National Institutes of Health, National Center for Biotechnology Information, National Library of Medicine, MEDLINE},
% mjmhandler: toobib handlegsmeta(scraper)
% mjmhandler: toobib handlegsmeta(html)
% mjmhandler: toobib handleheadless<-handledoi
% mjmhandler: toobib handleheadless<-handlepdfstrings
marchywka at happy:/home/documents/latex/proj/qq$ vi zotero.txt
marchywka at happy:/home/documents/latex/proj/qq$ grep -i retra zotero.txt 



cat zotero.txt 

@article{javed_exploring_2021,
	title = {Exploring the {Potential} of {Interferon} {Gamma} {Gene} as {Major} {Immune} {Responder} for {Bovine} {Tuberculosis} in {River} {Buffalo}},
	volume = {2021},
	issn = {2314-6141},
	doi = {10.1155/2021/5532864},
	abstract = {Bovine tuberculosis (bTB) is a widespread zoonotic infection targeting the livestock sector, especially in developing countries, and posing a risk to humans and animal populations. Its recent prevalence in river buffaloes has been estimated as higher as 33.7\%. In emergent countries like Pakistan, there is likeliness of human-livestock interfaces extensively and lacking of effective preventive measures that illustrate the risk of spreading the infection at a remarkable rate. The river buffalo (Bubalus bubalis) is an upkeep host of Mycobacterium bovis and is responsible for disease transmission among buffaloes and other livestock species. In this study, potential molecular biomarkers in the Interferon-gamma gene (IFNg) were identified after genomic screening of river buffaloes. Unique genomic loci in river buffalo proved the novelty of the genomic structure of this phenomenal animal but also highlighted its significance in natural immunity against the Mycobacterium. A total of eight single nucleotide polymorphisms were identified in the coding region of IFNg. The SNPs in the exonic region were all transitions, i.e., the conversion of purines to purines. These SNPs were analyzed for Hardy Weinberg Equilibrium, chi2 test, gene diversity, and protein structural conformation. Pathway analysis in tuberculosis revealed that IFNg inhibits the antigen-presenting cells (APC) through JAK and STAT pathways. Network analysis of IFNg proteins in both species showed strong associations among the immunity-related proteins (interleukins, tissue necrosis factors) and receptors of interferons. The identified polymorphic sites might be novel-potentiated markers for the selection of animals with superior immune response against bTB and can be exploited as promising genomic sites for breeding the resistant animal herds to combat Mycobacterium infection in a long run.},
	language = {eng},
	journal = {BioMed Research International},
	author = {Javed, Maryam and Raza, Syed Ahmed and Nadeem, Asif and Ali, Muhammad Muddassir and Shehzad, Wasim and Mehmood, Khalid},
	year = {2021},
	pmid = {33880367},
	pmcid = {PMC8046533},
	keywords = {Animals, Buffaloes, Cattle, Gene Frequency, Gene Regulatory Networks, Genome, Haplotypes, Heterozygote, Interferon-gamma, Odds Ratio, Protein Structure, Secondary, Tuberculosis, Bovine},
	pages = {5532864},
}

-- 

mike marchywka
44 Crosscreek Trail
Jasper GA 30143
USA, Earth marchywka at hotmail.com
 404-788-1216 ORCID: 0000-0001-9237-455X