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The bittersweet world of science publishing

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Improving the replicability of empirical research. Authors retract meningitis paper over permission - but data are in a public database. A study characterizing subtypes of the bacteria that cause bacterial meningitis is being retracted after the authors didn’t have permission to publish the data, even though the data itself remain available in a public database.

Authors retract meningitis paper over permission - but data are in a public database

The paper, in PLOS ONE, relied on a laboratory collection of patient samples. In October, the authors retracted it because they “did not have permission” from the laboratory “to publish the data in their current form.” The data — anonymized — are now available at PubMLST. Here’s the retraction notice, published on October 16: The authors wish to retract this article at the request of the Scottish Haemophilus Legionella Meningococcus Pneumococcus Reference Laboratory (SHLMPRL). The paper, “Clonal Analysis of Meningococci during a 26 Year Period Prior to the Introduction of Meningococcal Serogroup C Vaccines,” examined the prevalence of different subtypes of the bacterium Neisseria meningitides from 1972 to 1998.

Wiley published a biology paper in the wrong journal. Wiley Periodicals is withdrawing a biochemistry paper after mistakenly publishing it in the wrong journal.

Wiley published a biology paper in the wrong journal

The mistake took a few months to sort out. Wiley initially published “Protein Kinase C Is Involved in the Induction of ATP-Binding Cassette Transporter A1 Expression by Liver X Receptor/Retinoid X Receptor Agonist in Human Macrophages” online in Journal of Cellular Physiology in May of last year. The article was posted in the correct journal — Journal of Cellular Biochemistry — in July. At the very end of 2015, the publisher officially withdrew the version it posted in the Journal of Cellular Physiology. We have a new record: 80 years from publication to retraction. We have a new record for the longest time from publication to retraction: 80 years.

We have a new record: 80 years from publication to retraction

It’s for a case report about a 24-year-old man who died after coughing up more than four cups of what apparently looked — and smelled — like pee. According to the case report titled “Een geval van uroptoë” published in 1923, an autopsy revealed that the man had a kidney that was strangely located in his chest cavity. A case of pneumonia caused the kidney to leak urine into the space around his lungs, leading to the perplexing cough. If that sounds too crazy to be true, you’re right: This man never existed. The case was retracted in 2003. The incredible tale of irresponsible chocolate milk research at the University of Maryland. Academic press offices are known to overhype their own research.

The incredible tale of irresponsible chocolate milk research at the University of Maryland

But the University of Maryland recently took this to appalling new heights — trumpeting an incredibly shoddy study on chocolate milk and concussions that happened to benefit a corporate partner. BishopBlog: My collapse of confidence in Frontiers journals. Frontiers journals have become a conspicuous presence in academic publishing since they started in 2007 with the advent of Frontiers in Neuroscience.

BishopBlog: My collapse of confidence in Frontiers journals

When they were first launched, I, like many people, was suspicious. This was an Open Access (OA) online journal where authors paid to publish, raising questions about the academic rigour of the process. However, it was clear that the publishers had a number of innovative ideas that were attractive to authors, with a nice online interface and a collaborative review process that made engagement with reviewers more of a discussion than a battle with anonymous critics. Like many other online OA journals, the editorial decision to publish was based purely on an objective appraisal of the soundness of the study, not on a subjective evaluation of importance, novelty or interest.

The publishing model has been highly successful. With success, however, have come growing rumbles of discontent. You can't make this stuff up: Plagiarism guideline paper retracted for...plagiarism. This could be an April Fools’ joke.

You can't make this stuff up: Plagiarism guideline paper retracted for...plagiarism

But it isn’t. BishopBlog: Editors behaving badly? The H-index is a metric that was devised to identify talented individuals whose published work had made a significant impact on the field (Hirsch, 2005).

BishopBlog: Editors behaving badly?

One of its apparent virtues was that it was relatively difficult to game. However, analysis of publications in a group of journals in the field of developmental disabilities suggest there has been a systematic and audacious attempt at gaming the H-index by a cabal of editors. What's the evidence for this claim? Let's start by briefly explaining what the H-index is. It's computed by rank ordering a set of publications in terms of their citation count, and identifying the point where the rank order exceeds the number of citations. The reason this is reckoned to be relatively impervious to gaming is that authors don't, in general, have much too much control over whether their papers get published in the first place, and how many citations their published papers get: that's down to other people. Reference Hirsch, J. (2005). P. 1. 2. Deux sociologues piègent une revue pour dénoncer la « junk science »

Le Monde.fr | • Mis à jour le | Par Benoît Floc'h.

Deux sociologues piègent une revue pour dénoncer la « junk science »

[34] My Links Will Outlive You. If you are like me, from time to time your papers include links to online references.

[34] My Links Will Outlive You

Because the internet changes so often, by the time readers follow those links, who knows if the cited content will still be there. This blogpost shares a simple way to ensure your links live “forever.” I got the idea from a recent New Yorker article [.html]. Content RotIt is estimated that about 20%-30% of links referenced in papers are already dead and, like you and me, the remaining links aren’t getting any younger.

The shroud of retraction: Virology Journal withdraws paper about whether Christ cured a woman with flu. It takes decades, and even centuries, to overturn the Catholic canon of law, but medical journals move much more quickly: Just three weeks after the Virology Journal published a paper speculating that a woman described in the Bible as being “cured by our Lord Jesus Christ” had flu, the journal has apologized for ever posting it online.

The shroud of retraction: Virology Journal withdraws paper about whether Christ cured a woman with flu

After bemused — to put it mildly — reactions from bloggers Bob O’Hara (who alerted us to the retraction), P.Z. Myers, and Tara C. Smith, as well as questions from a journal reader, the journal’s editor, Robert F. Garry, posted a retraction to O’Hara’s blog, and in his own journal: Nobelist Linda Buck retracts two studies on olfactory networks — and the news is embargoed. Well, it’s happened: The Embargo Watch and Retraction Watch worlds have collided. I had initially figured on two posts here, but it soon became clear that how journals were handling these retractions, using embargoes, was central to both. So this is being cross-posted on both blogs. Linda Buck, who shared the 2004 Nobel Prize in Physiology or Medicine, has retracted two papers published in 2005 and 2006. Paper retractions do not induce citation mutations. Dear Christian Specht, Thank you very much for your detailed response in The Scientist to our previous letter regarding citation mutations.

You clarified several issues that were raised in your original study, particularly that citation mutation rates have dropped significantly in the last 10 years (probably due to the more widespread use of reference management software), and that some citation mutations (e.g. 680→685 in Laemmli 1970) might be introduced not by citing authors, but by the citation database. You rightfully point out that citation mutations indicate a much bigger problem: authors often do not read the publications cited in their work. I am not aware of any available direct data, but in an ongoing study Richard Grant is looking at this question (Do you read the papers you cite?). The preliminary data that Richard kindly made available indicate that more than 85% of authors indeed read the papers they cite.

In another study made aware to us by Noah Gray, Neale et al. Controversial chronic fatigue-virus paper retracted. Andy Coghlan, reporter. For shame! Nature shills for traditional Chinese medicine : Respectful Insolence. Nature is one of the oldest and most respected scientific journals around. It’s been around since 1869 and is said to be the world’s most cited journal. What makes Nature unusual these days is that it’s a general science journal. Astronomy, physics, chemistry, medicine, biology, it publishes it all. Condamnée pour avoir plagié le mémoire de son étudiant. Viewpoint: The spectre of plagiarism haunting Europe. 24 July 2012Last updated at 20:18 ET By Debora Weber-Wulff Professor of Media and Computing, University of Applied Sciences, Berlin Bucharest university says it cannot withdraw the PM's PhD without education ministry approval A spectre is haunting Europe, and this time it is the spectre of plagiarism and scientific misconduct.

Some high-profile politicians have had to resign in the last 18 months - but the revelations are also shaking respected European universities. Many European countries, especially Germany, have long considered it unnecessary to give plagiarism more than a cursory look. Reflections on a foray into post-publication peer review. Recently I posted a comment on a PLOS ONE article for the first time. As someone who had a decent chunk of his career before post-publication peer review came along — and has an even larger chunk of his career left with it around — it was an interesting experience.

It started when a colleague posted an article to his Facebook wall. I followed the link out of curiosity about the subject matter, but what immediately jumped out at me was that it was a 4-study sequence with pretty small samples. Math paper retracted because it “contains no scientific content” A first? Papers retracted for citation manipulation. In what appears to be a first, two papers have been retracted for including citations designed to help another journal improve its impact factor rankings. Mighty molten powder researchers publish paper in journal twice, months apart.

Science publishers don't care about the public : We Beasties. When Peer Review Falters - Room for Debate. Mohamed Gad-el-Hak is the Inez Caudill Eminent Professor of Mechanical & Nuclear Engineering at Virginia Commonwealth University. The peer review system in all fields is not infallible. There are too many submitted manuscripts, and competent reviewers are often overwhelmed. “What I find offensive is not that they plagiarized us, it’s that they did it so badly” Why was that paper retracted? Editor to Retraction Watch: “It’s none of your damn business”

L. Henry Edmunds, photo by University of Pennsylvania. Citation Cartel Journals Denied 2011 Impact Factor. Time out, in the corner by Ken Wilcox via. Plagiarism pinioned : Nature. A paper by Maggie Simpson and Edna Krabappel was accepted by two scientific journals. Publishing: The peer-review scam. Leadership journal to retract five papers from FIU scholar - Retraction Watch at Retraction Watch.

Bogus Journal Accepts Profanity-Laced Anti-Spam Paper. Shit My Reviewers Say — This paper reads like a woman’s diary, not like a... Publishers withdraw more than 120 gibberish papers. On “Kardashians” in science and the general relationship between achievement and fame. Should scientists handle retractions differently? Journal allows authors to update their research. NIH Presses Journals to Focus on Reproducibility of Studies.

Sharing science: Searchability, accessibility, and the future of academic publishing // cogsci.nl. SAGE Publications busts “peer review and citation ring,” 60 papers retracted. The Availability of Research Data Declines Rapidly with Article Age: Current Biology. 9 questions about the new PLoS clarification. [15] Citing Prospect Theory. Flawed sting operation singles out open access journals. Whomp! Using invited editorial commentary to neutralize negative findings. [9] Titleogy: Some facts about titles. How journals like Nature, Cell and Science are damaging science. Thousands of scientific papers uploaded to the Pirate Bay. Are Peer-Reviewers Overloaded? Or Are Their Incentives Misaligned.

Nearer, better. News Desk: More Thoughts on the Decline Effect. Research. National-Academies.org. Do we need an alternative to peer-reviewed journals? A “Consumer Reports” for Academic Journals? (and wouldn’t a Wiki work?) News / Comments / Do you really want to publish in a high-retraction journal? ONE Launches Reproducibility Initiative. Sick of Impact Factors. Open access to research is inevitable, says Nature editor-in-chief. Do peer reviewers get worse with experience? Plus a poll. Publish-or-Perish Culture Promotes Scientific Narcissism. JournalReviewer. Impacting our young — PNAS. The Decline Effect and the Scientific Method. Publishing your science paper is only the half the job.

Harvard University says it can't afford journal publishers' prices.