A very strange & annoying Google Scholar / Biomed Central "glitch" #GamingMetrics

So I discovered a few days ago I had dozens of new publications in 2015.  Cool right?  Here is a screengrab:



And here is another


Until I realized, well, those were published years ago.  WTF are they doing being listed as 2015?  Clearly some glitch. And then I saw a few Tweets that pointed me to figuring out what was going on.

.





So I responded


And some discussion followed





Fascinating. But I knew my papers were not published as preprints. And that they were published years before Google Scholar was not listing them as being published.

So - what happened? I think I now. These papers were all published in one journal - Standards in Genomic Sciences. The journal used to be published semi-independently by the Genomics Standards Consortium. Then they were transferred to / bout.
ht by / merged with Biomed Central and even the web address was forwarded to BMC where they host the archive of articles from before the transfer.  Then there is a new site with articles from after the transfer.

So when I click on the articles from the Google Scholar site I get to a strange thing.  The articles published before the transfer are also listed on the new site http://standardsingenomics.biomedcentral.com/.

For example - the Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T) is shown here with a 2015 publication date:



Although note the Copyright 2010 little bit.  Which is interesting since this paper was in fact published in 2010.  And you can find it on the other site http://standardsingenomics.org with a 2010 publication data here.



And also in Pubmed and Pubmed Central.





So - even though Biomed Central says the new papers will be in the new site and the old papers will be ket in a separate site that is not what is happening.



For some reasons some of the older papers are now being listed in the new site with a new publication date.  And I assume because Google Scholar scrapes from the journal sites, it found the "new" papers and has now added them to it's clustering collection and has fed them into my publication list.  And despite trying I am not sure how to fix this.

I tried to "unmerge" the new publications to see if somehow the old publications showed up.  But they did not.  So .. am not sure what to do here other than to send this to BMC and Google Scholar, which I will do.  Ahh - the perils of automated systems ...

I note -  this does seem to have possibly temporarily increased my total number of citations since it seems like some of these papers are now being considered twice by Google Scholar but not sure about that.  More digging.




Beware of mimicry in #OpenAccess journals

Wow - just got this email from a new journal soliciting papers:

Dear colleagues,
we are pleased to announce that the call for papers for the Special Issue “Molecular Phylogenetics 2016” is now open with the BioMed Research International
journal.
The scope of the Special Issue covers:
•  Evolutionary genomics
•  Molecular phylogenetics and systematics
•  Molecular dating, inferring complex scenarios of coevolution, reconstruction of complex ancestral traits and events in genome evolution
•  Development and phylogeny (evo-devo)
•  Models and algorithms for molecular evolution
•  Applied phylogenetics: genotyping and barcoding of biological objects, molecular anthropology, molecular epidemiology, forensic science, etc.
•  Molecular ecology, biodiversity, and biogeography
All submissions go through the peer-review process. The journal publishes research and review articles with no page limit. It is an Open Access journal, and
fixed article processing charges apply to accepted manuscripts (www.hindawi.com/journals/bmri/apc). The journal is indexed by all major abstracting and
citation systems.
Important deadlines:
Manuscript due: 26 February 2016
First round of reviews: 20 May 2016
Publication date: 15 July 2016
Earlier manuscripts will be processed for review upon submission date. The Editors team is making all effort to provide for a fast and friendly review
process.
Detailed information on the Call-for-Papers is available online at www.hindawi.com/journals/bmri/si/295862/cfp.
Contents of the Special Issues 2013 and 2014 are available online at www.hindawi.com/journals/bmri/si/585782 and
www.hindawi.com/journals/bmri/si/392635.
We welcome all contributors interested in submitting their research.

With best regards,
the Editors team of “Molecular Phylogenetics 2016”
Whatever you think of Hindawi as a publisher (I am skeptical) the name "BioMed Research International journal." struck me as very strange.  It seems like a mimic of Biomed Central.  So I googled around and found others who also think it is a mimic (and not in a good way).  For example see Jeffrey Beale from Sept 2014: New Predatory Publisher Copies Look and Feel of BioMed Central.

Yuck.  The name appears to be a clear attempt to confuse authors that they are affiliated with Biomed Central.  And the format and look appears to be doing the same too.  So thus Hindawi has moved from my "maybe a spammy predatory publisher" to "definitely a spammy predatory publisher" list.


Are companies selling fake peer reviews to help papers get published?

Faked peer reviews — a subject about which we’ve been writing more and more recently — are concerning enough to a number of publishers that they’ve approached the Committee on Publication Ethics (COPE) to work together on a solution. In the past, we have reported on a number of cases in which authors were able […]

The post Are companies selling fake peer reviews to help papers get published? appeared first on Retraction Watch.

Publisher discovers 50 manuscripts involving fake peer reviewers

BioMed Central has uncovered about fifty manuscripts in their editorial system that involved fake peer reviewers, Retraction Watch has learned. Most of the cases were not published because they were discovered by a manuscript editor on a final pre-publication check. The five or so that have been published will go through some sort of re-review, […]

Lost from translation(al) medicine: Publisher error leads to retraction

jrntransmedA technical hiccup led the Journal of Translational Medicine to double publish a 2012 paper by a pair of researchers from China and the United States, leading to a retraction.

The article is/was titled “Opportunities and challenges of disease biomarkers: a new section in the journal of translational medicine,” and it was written by Xiangdong Wang and Peter Ward — both members of the journal’s editorial board. It appeared in the Nov. 7, 2012 issue of the JTM. And it appeared less than a month later, on Dec. 5.

As the retraction notice explains:

The publisher has retracted this article [1] because it was republished in error [2] due to technical reasons. BioMed Central apologize to the authors and readers for the error and any inconvenience caused.

In case you’re wondering, here’s what the article has to say:

Disease biomarkers are defined to diagnose various phases of diseases, monitor severities of diseases and responses to therapies, or predict prognosis of patients. Disease-specific biomarkers should benefit drug discovery and development, integrate multidisciplinary sciences, be validated by molecular imaging. The opportunities and challenges in biomarker development are emphasized and considered. The Journal of Translational Medicine opens a new Section of Disease Biomarkers to bridge identification and validation of gene or protein-based biomarkers, network biomarkers, dynamic network biomarkers in human diseases, patient phenotypes, and clinical applications. Disease biomarkers are also important for determining drug effects, target specificities and binding, dynamic metabolism and pharmacological kinetics, or toxicity profiles.

This is the second double publication retraction we’ve seen from BioMed Central in a month. But since they’re an open access publisher, at least they didn’t charge $37 for the privilege of reading any of the notices.


Giving thanks for plagiarism detection software: Catching up on retractions for the sincerest form of flattery

Today, on Thanksgiving in the U.S., Retraction Watch is taking a bit of a holiday as we dig into some turkey — not to be confused with retractions from Turkey. We’d like to give thanks for the thousands of Retraction Watch readers all over the world who’ve helped us shine a spotlight on the scientific process, warts and all.

And we imagine that journal editors around the globe are giving thanks to plagiarism detection software such as iThenticate, so today’s post is a roundup of some recent retractions for plagiarism:

1. BMC Complementary & Alternative Medicine, “In Vitro antioxidant and anticancer activity of young Zingiber officinale against human breast carcinoma cell lines,” by Shahedur Rahman, Faizus Salehin and Asif Iqbal:

The journal has retracted this article (Rahman, S et al., BMC Complementary and Alternative Medicine 2011, 11:76) because it contains large portions of text that were duplicated from articles previously published in The Journal of Medicinal Plants Research (Ghasemzadeh A, et al, Journal of Medicinal Plants Research 2011, 5(14):3247-3255) and Molecules (Ghasemzadeh A, et al., Molecules 2010, (15):7907-7922).

2. Molecular Cancer, “Application of cytology and molecular biology in diagnosing premalignant or malignant oral lesions,” by Ravi Mehrotra, Anurag Gupta, Mamta Singh,and Rahela Ibrahim:

The authors would like to retract the article “Application of cytology and molecular biology in diagnosing premalignant or malignant oral lesions” [1]. After publication of the article it came to light that large portions of the article are duplicated from a previously published article [2]. The authors apologize to the readers, reviewers, and Editors of Molecular Cancer for the inconvenience caused.

3. Photonic Network Communications,An approach to evaluate the effects of virtual topology on in-band crosstalk attack propagation in transparent optical networks,” by Yonghua Xiao, Yunfeng Peng, Zeyu Sun, Changming Zhao, and Keping Long:

This paper has been retracted because it is copied, in parts, from the publication of another author without permission or justification.

4. Renewable Energy, “Comparison of Chemical and Biological Pretreatment of Corn Straw for Biogas Production by Anaerobic Digestion,” by Weizhang Zhong, Zhongzhi Zhang, Wei Qiao, Pengcheng Fu, and Man Liu:

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).

This article has been retracted at the request of the Editor-in-Chief.

The authors have plagiarized part of a paper that had already appeared in ‘Improving biogas production of cornstalk through chemical and biological pretreatment: a preliminary comparison study’; Transactions of the CSAE, 19, (2003) 209–213.

One of the conditions of submission of a paper for publication is that authors declare explicitly that their work is original and has not appeared in a publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

Noteworthy: We can’t find the 2003 paper this allegedly plagiarized, so it’s not clear if this was actually duplication of the authors’ previous work — in which case plagiarism is an, um….straw man.

5. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, “Experimental FT-IR, FT-Raman spectra and quantum chemical studies of optimized molecular structures, conformers and vibrational characteristics of nicotinic acid and thio-nicotinic acid,” by Priyanka Singh, T.K. Yadav, M. Karabacak, R.A. Yadav, and N.P. Singh:

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).

This article has been retracted at the request of the Editor-in-Chief.

This article has been retracted because the authors have copied several parts of the following already published paper without permission of the authors: Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Volume 79, Issue 5, September 2011, Pages 1316–1325. http://dx.doi.org/10.1016/j.saa.2011.04.062.

Noteworthy: R.A. Yadav is an author on both papers, and both studies appeared in the same journal. So this could have been called duplication, too.

We’ll leave you with the words of Thorakkal Shamim, who writes in the Saudi Journal of Anesthesia:

I had reported a case of pemphigus vulgaris in oral cavity in May-Aug 2007 issue ofSaudi Dental Journal. The article was plagiarized by Indian authors and they published the same article in July-Sept 2010 issue of Journal of Indian Society of Pedodontics and Preventive Dentistry.The authors copied the entire text (introduction, case report, discussion, conclusion, photomicrograph [Figure 4], and direct immunofluorescence photograph) from the original article. They changed the department and presented the case as if it occurred in a pediatric patient.

Here’s what Shamim would like to see in future cases:

The authors should inform the editor of a journal where a plagiarized article is published. Both original and plagiarized articles should be produced in hard and soft copy, with the plagiarized part highlighted. The author should also ask the editor to form a disciplinary committee to investigate the case of plagiarism. If the evidence of plagiarism is convincing, the editor should refer the case to the chief editor and other staff members with a request to arrange a disciplinary meeting. The editor of the journal where the plagiarized article is published should communicate with the editor of the journal containing the original article to rectify the matter. The allegedly plagiarized article has to be temporarily retracted from publication and a notice should be published in the journal. The plagiarist should provide an explanation. In case of non-response in the stipulated time or an unsatisfactory explanation, the article should be permanently retracted, and the author blacklisted and debarred for submitting an article to a particular journal for at least 5 years. The concerned head of the institution and head of the department of the author’s institute have to be notified. Even though there are setbacks from the higher authorities, it is the prime duty of the author and the editor to take strong decisions to tackle plagiarism at the earliest to avoid unethical publishing.


You’ve been dupe’d: Catching up on authors who liked their work enough to use it again

photo by Mark Turnauckas via Flickr http://www.flickr.com/photos/marktee/

As we’ve noted before, we generally let duplication retractions make their way to the bottom of our to-do pile, since there’s often less of an interesting story behind them, duplication is hardly the worst of publishing sins, and the notices usually tell the story. (These are often referred to — imprecisely — as “self-plagiarism.”)

But that skews what’s represented here — boy, are there a lot of duplication retractions we haven’t covered! — and we might as well be more comprehensive. Plus, our eagle-eyed readers may find issues that we won’t see on a quick scan.

So with this post, we’re inaugurating a new feature here at Retraction Watch, “You’ve been dupe’d.” Every now and then, we’ll gather five of these duplication retractions at a time, and post them so they get into the mix, and into our category listing (see drop-down menu in right-hand column if you haven’t already). Here are the first five:

1. The AAPS Journal, “Recent advances for the treatment of cocaine abuse: central nervous system immunopharmacotherapy,” by Tobin J. Dickerson and Kim D. Janda, cited by 25 other papers:

“Recent advances for the treatment of cocaine abuse: central nervous system immunopharmacotherapy. AAPS Journal. 2005; 07(03): E579-E586” has been retracted because of a substantial degree of duplication with “Bacteriophage-mediated protein delivery into the central nervous system and its application in immunopharmacotherapy. Expert Opin Biol Ther. 2005 Jun;5(6) 773–781.”

Noteworthy: This is referred to on the journal’s site as an erratum as well as a retraction.

2. Biophysical Journal, “Funneled Landscape Leads to Robustness of Cellular Networks: MAPK Signal Transduction,” by Jin Wang, Bo Huang, Xuefeng Xia, and Zhirong Sun, cited 33 times:

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).

This article has been retracted at the request of the Editor-in-Chief.

The editors have noted that there is a substantial overlap of text and content between this Biophysical Journal article and the following article: Wang, J., Huang, B., Xia, X., and Sun, Z., Funneled landscape leads to robustness of cell networks: yeast cell cycle. PLoS Comput. Biol., 2 (2006) e147, http://dx.doi.org/10.1371/journal.pcbi.0020147.

The submission of this paper was inconsistent with Biophysical Journal policy, which states: “Manuscripts submitted to Biophysical Journal(BJ) must be original; papers that have already been published or are concurrently submitted elsewhere for publication are not acceptable for submission. This includes manuscripts previously submitted to (BJ), as well as material that has been submitted to other journals while (BJ) is considering the manuscript. If some part of the work has appeared or will appear elsewhere, the authors must give the specific details of such appearances in the cover letter accompanying the (BJ) submission. If previously published illustrative material, such as figures or tables, must be included, the authors are responsible for obtaining the appropriate permissions from the publisher(s) before the material may be published in (BJ).”

We are therefore retracting the publication of the Biophysical Journal article.

The authors do not agree with this decision.

Noteworthy: Authors are usually either absent from duplication notices, or they apologize. These authors apparently wanted to take a stand.

3. International Journal of Surgery Case Reports, “Nipple adenoma in a man: An unusual case report,” by S. Boutayeb, S. Benomar, Y. Sbitti, T. Harroudi, B. Hassam, and H. Errihani:

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).

This article has been retracted at the request of the Editor-in-Chief.

This article is a duplicate of a paper that has already been published in WebmedCentral Cancer, 1 (2010) WMC00605 (Boutayeb, S., Benomar, S., Hassam, B., Errihani, H., Adenoma of The Nipple in a Man: Case Report). One of the conditions of submission of a paper for publication is that the authors declare explicitly that the paper has not previously been published and is not under consideration for publication elsewhere. As no such declaration was made and the article did not refer to the earlier paper it is being withdrawn in line with journal policy.

4. Journal of Diabetes & Metabolic Disorders, “Mobile phone text messaging and telephone followup in type 2 diabetic patients for 3 months: a comparative study,” by Mirta Zolfaghari, Seyedeh A Mousavifar and Hamid Haghani:

This article (Zolfaghari M, et al., Metabolic Disorders 2012, 11:7) has been retracted as it has already been published in the Iranian Journal of Diabetes and Obesity (Zolfaghari M, et al., Iranian Journal of Diabetes and Obesity 2009, 1(1):45-51).

5. Nonlinear Analysis: Theory, Methods & Applications, “Approximation of solutions of generalized equations of Hammerstein type,” by C.E. Chidume and Y. Shehu:

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).

This article has been retracted at the request of the Editors-in-Chief.

The authors have plagiarized part of a paper that had already appeared in Comp. Math. Appl., 63 (2012) 966–974, http://dx.doi.org/10.1016/j.camwa.2011.12.001. One of the conditions of submission of a paper for publication is that authors declare explicitly that their work is original and has not appeared in a publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

Noteworthy: The journal calls this “plagiarism,” even though it’s duplication.