"retraction" problem persists in some bibtex sources,

Sun Oct 29 12:53:32 CET 2023

FYI in case of interest the original PubPeer notice about the paper is here
<https://pubpeer.com/publications/AB642E6CCC495991B3410938D408A8?utm_source=Chrome&utm_medium=BrowserExtension&utm_campaign=Chrome>
.

On Sat, 28 Oct 2023 at 14:51, Mike Marchywka <marchywka at hotmail.com> wrote:

>
> This seems to be a recurring issue with inconsistent retraction
> notice updates. This for example is clearly retracted with big
> read notice on page,
>
> https://pubmed.ncbi.nlm.nih.gov/33953832/
> Zottero webform did not pick it up AFAICT,
>
> @article{ikram_oral_2021,
>         title = {Oral {Administration} of {Gintonin} {Protects} the
> {Brains} of {Mice} against {Aβ}-{Induced} {Alzheimer} {Disease}
> {Pathology}: {Antioxidant} and {Anti}-{Inflammatory} {Effects}},
>         volume = {2021},
>         issn = {1942-0994},
>         shorttitle = {Oral {Administration} of {Gintonin} {Protects} the
> {Brains} of {Mice} against {Aβ}-{Induced} {Alzheimer} {Disease}
> {Pathology}},
>         doi = {10.1155/2021/6635552},
>         abstract = {The study was aimed at analyzing the protective
> effects of gintonin in an amyloid beta- (Aβ-) induced Alzheimer's disease
> (AD) mouse model. For the development of the Aβ-induced AD mouse model, the
> amyloid-β (Aβ 1-42) peptide was stereotaxically injected into the brains of
> mice. Subsequently, gintonin was administered at a dose of 100
> mg/kg/day/per oral (p.o) for four weeks daily, and its effects were
> evaluated by using western blotting, fluorescence analysis of brain
> sections, biochemical tests, and memory-related behavioral evaluations. To
> elucidate the effects of gintonin at the mechanistic level, the activation
> of endogenous antioxidant mechanisms, as well as the activation of
> astrocytes, microglia, and proinflammatory mediators such as nuclear factor
> erythroid 2-related factor 2 (NRF-2) and heme oxygenase-1 (HO-1), was
> evaluated. In addition, microglial cells (BV-2 cells) were used to analyze
> the effects of gintonin on microglial activation and signal!
>  ing mechanisms. Collectively, the results suggested that gintonin reduced
> elevated oxidative stress by improving the expression of NRF-2 and HO-1 and
> thereby reducing the generation of reactive oxygen species (ROS) and lipid
> peroxidation (LPO). Moreover, gintonin significantly suppressed activated
> microglial cells and inflammatory mediators in the brains of Aβ-injected
> mice. Our findings also indicated improved synaptic and memory functions in
> the brains of Aβ-injected mice after treatment with gintonin. These results
> suggest that gintonin may be effective for relieving AD symptoms by
> regulating oxidative stress and inflammatory processes in a mouse model of
> AD. Collectively, the findings of this preclinical study highlight and
> endorse the potential, multitargeted protective effects of gintonin against
> AD-associated oxidative damage, neuroinflammation, cognitive impairment,
> and neurodegeneration.},
>         language = {eng},
>         journal = {Oxidative Medicine and Cellular Longevity},
>         author = {Ikram, Muhammad and Jo, Min Gi and Park, Tae Ju and Kim,
> Min Woo and Khan, Ibrahim and Jo, Myeung Hoon and Kim, Myeong Ok},
>         year = {2021},
>         pmid = {33953832},
>         pmcid = {PMC8068536},
>         keywords = {Administration, Oral, Alzheimer Disease, Animals,
> Anti-Inflammatory Agents, Antioxidants, Disease Models, Animal,
> Glycoproteins, Male, Mice, Oxidative Stress, Plant Extracts},
>         pages = {6635552},
> }
>
> The output of "toobib -all",  which picked up  several different
> ways to get the bibtex, found again medline was updated ( extracted
> with eutils entrez interface to pubmed ) and scraping the webpage
> html pickedup the retracted keyword but only using a
> scraping approach for meta data you might not normally do
> and which Zoterro apparently ignored.
> Below is the bibtex file it generated with the collection methods
> and any mention  of retraction.
>
> cat xxxx | grep -i "mjmhandler\|etract" | grep -v "final_assembl"
> % 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=16 goods=1 )(crossref)
> % mjmhandler: toobib handlepdfstrings(crossref)
> % mjmhandler: toobib handleadhochtml<-citation
> % mjmhandler: toobib handleadhochtml<-og
> % mjmhandler: toobib handleadhochtml<-all
> keywords = {pmid:33953832, PMC8068536, doi:10.1155/2021/6635552, Retracted
> Publication, Muhammad Ikram, Min Gi Jo, Myeong Ok Kim, Administration,
> Oral, Alzheimer Disease / drug therapy*, Alzheimer Disease / prevention \&
> control*, Animals, Anti-Inflammatory Agents / pharmacology,
> Anti-Inflammatory Agents / therapeutic use*, Antioxidants / pharmacology,
> Antioxidants / therapeutic use*, Disease Models, Animal, Glycoproteins /
> therapeutic use*, Male, Mice, Oxidative Stress / drug effects*, Plant
> Extracts / pharmacology, Plant Extracts / therapeutic use*, 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
>
> Toobib may miss a few too but need to keep looking for ways
> to get high confidence result :)
> I'm not sure what the publisher's webpage would contain but
> checking the PMID or PMCID may be helpful as the DOI
> info does not seem to be updated.
>
> --
>
> mike marchywka
> 44 Crosscreek Trail
> Jasper GA 30143
> USA, Earth marchywka at hotmail.com
>  404-788-1216 ORCID: 0000-0001-9237-455X
>
>

-- 
Kaveh Bazargan PhD
Director
River Valley Technologies <http://rivervalley.io> ● Twitter
<https://twitter.com/rivervalley1000> ● LinkedIn
<https://www.linkedin.com/in/bazargankaveh/> ● ORCID
<https://orcid.org/0000-0002-1414-9098> ● @kaveh1000 at mastodon.social
<https://mastodon.social/@kaveh1000>
*Accelerating the Communication of Research*

*
<https://www.linkedin.com/posts/bazargankaveh_ismte-innovation-award-recipient-kaveh-bazargan-activity-7039348552526921728-XAEB/?utm_source=share&utm_medium=member_desktop>
 [image:
https://rivervalley.io/gigabyte-wins-the-alpsp-scholarly-publishing-innovation-award-using-river-valleys-publishing-technology/]
<https://rivervalley.io/gigabyte-wins-the-alpsp-scholarly-publishing-innovation-award-using-river-valleys-publishing-technology/>*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://tug.org/pipermail/texhax/attachments/20231029/af4b3623/attachment.htm>