Friday Foolery #49: The Shortest Abstract Ever! [2]

30 03 2012

In a previous Friday Foolery post I mentioned what I thought was the shortest abstract ever.

 “Probably not”.

But a reader (Trollface”pointed out in a comment that there was an even shorter (and much older) abstract of a paper in the Bulletin of the Seismological Society of America. It was published in 1974.

The abstract simply says: Yes.

It could only be beaten by an abstract saying: “No”, “!”, “?” or a blank one.





Friday Foolery #44. The Shortest Abstract Ever?

2 12 2011

This is the shortest abstract I’ve ever seen:

“probably not”

With many thanks to Michelynn McKnight, PhD, AHIP, Associate Professor, School of Library and Information Science, Louisiana State University, who put it on the MEDLIB-L listserv, saying :  “Not exactly structured …. but a great laugh!”

According to Zemanta (articles related to this post) Future Twit also blogged about it.

Related articles





FUTON Bias. Or Why Limiting to Free Full Text Might not Always be a Good Idea.

8 09 2011

ResearchBlogging.orgA few weeks ago I was discussing possible relevant papers for the Twitter Journal Club  (Hashtag #TwitJC), a succesful initiative on Twitter, that I have discussed previously here and here [7,8].

I proposed an article, that appeared behind a paywall. Annemarie Cunningham (@amcunningham) immediately ran the idea down, stressing that open-access (OA) is a pre-requisite for the TwitJC journal club.

One of the TwitJC organizers, Fi Douglas (@fidouglas on Twitter), argued that using paid-for journals would defeat the objective that  #TwitJC is open to everyone. I can imagine that fee-based articles could set a too high threshold for many doctors. In addition, I sympathize with promoting OA.

However, I disagree with Annemarie that an OA (or rather free) paper is a prerequisite if you really want to talk about what might impact on practice. On the contrary, limiting to free full text (FFT) papers in PubMed might lead to bias: picking “low hanging fruit of convenience” might mean that the paper isn’t representative and/or doesn’t reflect the current best evidence.

But is there evidence for my theory that selecting FFT papers might lead to bias?

Lets first look at the extent of the problem. Which percentage of papers do we miss by limiting for free-access papers?

survey in PLOS by Björk et al [1] found that one in five peer reviewed research papers published in 2008 were freely available on the internet. Overall 8,5% of the articles published in 2008 (and 13,9 % in Medicine) were freely available at the publishers’ sites (gold OA).  For an additional 11,9% free manuscript versions could be found via the green route:  i.e. copies in repositories and web sites (7,8% in Medicine).
As a commenter rightly stated, the lag time is also important, as we would like to have immediate access to recently published research, yet some publishers (37%) impose an access-embargo of 6-12 months or more. (these papers were largely missed as the 2008 OA status was assessed late 2009).

PLOS 2009

The strength of the paper is that it measures  OA prevalence on an article basis, not on calculating the share of journals which are OA: an OA journal generally contains a lower number of articles.
The authors randomly sampled from 1.2 million articles using the advanced search facility of Scopus. They measured what share of OA copies the average researcher would find using Google.

Another paper published in  J Med Libr Assoc (2009) [2], using similar methods as the PLOS survey examined the state of open access (OA) specifically in the biomedical field. Because of its broad coverage and popularity in the biomedical field, PubMed was chosen to collect their target sample of 4,667 articles. Matsubayashi et al used four different databases and search engines to identify full text copies. The authors reported an OA percentage of 26,3 for peer reviewed articles (70% of all articles), which is comparable to the results of Björk et al. More than 70% of the OA articles were provided through journal websites. The percentages of green OA articles from the websites of authors or in institutional repositories was quite low (5.9% and 4.8%, respectively).

In their discussion of the findings of Matsubayashi et al, Björk et al. [1] quickly assessed the OA status in PubMed by using the new “link to Free Full Text” search facility. First they searched for all “journal articles” published in 2005 and then repeated this with the further restrictions of “link to FFT”. The PubMed OA percentages obtained this way were 23,1 for 2005 and 23,3 for 2008.

This proportion of biomedical OA papers is gradually increasing. A chart in Nature’s News Blog [9] shows that the proportion of papers indexed on the PubMed repository each year has increased from 23% in 2005 to above 28% in 2009.
(Methods are not shown, though. The 2008 data are higher than those of Björk et al, who noticed little difference with 2005. The Data for this chart, however, are from David Lipman, NCBI director and driving force behind the digital OA archive PubMed Central).
Again, because of the embargo periods, not all literature is immediately available at the time that it is published.

In summary, we would miss about 70% of biomedical papers by limiting for FFT papers. However, we would miss an even larger proportion of papers if we limit ourselves to recently published ones.

Of course, the key question is whether ignoring relevant studies not available in full text really matters.

Reinhard Wentz of the Imperial College Library and Information Service already argued in a visionary 2002 Lancet letter[3] that the availability of full-text articles on the internet might have created a new form of bias: FUTON bias (Full Text On the Net bias).

Wentz reasoned that FUTON bias will not affect researchers who are used to comprehensive searches of published medical studies, but that it will affect staff and students with limited experience in doing searches and that it might have the same effect in daily clinical practice as publication bias or language bias when doing systematic reviews of published studies.

Wentz also hypothesized that FUTON bias (together with no abstract available (NAA) bias) will affect the visibility and the impact factor of OA journals. He makes a reasonable cause that the NAA-bias will affect publications on new, peripheral, and under-discussion subjects more than established topics covered in substantive reports.

The study of Murali et al [4] published in Mayo Proceedings 2004 confirms that the availability of journals on MEDLINE as FUTON or NAA affects their impact factor.

Of the 324 journals screened by Murali et al. 38.3% were FUTON, 19.1%  NAA and 42.6% had abstracts only. The mean impact factor was 3.24 (±0.32), 1.64 (±0.30), and 0.14 (±0.45), respectively! The authors confirmed this finding by showing a difference in impact factors for journals available in both the pre and the post-Internet era (n=159).

Murali et al informally questioned many physicians and residents at multiple national and international meetings in 2003. These doctors uniformly admitted relying on FUTON articles on the Web to answer a sizable proportion of their questions. A study by Carney et al (2004) [5] showed  that 98% of the US primary care physicians used the Internet as a resource for clinical information at least once a week and mostly used FUTON articles to aid decisions about patient care or patient education and medical student or resident instruction.

Murali et al therefore conclude that failure to consider FUTON bias may not only affect a journal’s impact factor, but could also limit consideration of medical literature by ignoring relevant for-fee articles and thereby influence medical education akin to publication or language bias.

This proposed effect of the FFT limit on citation retrieval for clinical questions, was examined in a  more recent study (2008), published in J Med Libr Assoc [6].

Across all 4 questions based on a research agenda for physical therapy, the FFT limit reduced the number of citations to 11.1% of the total number of citations retrieved without the FFT limit in PubMed.

Even more important, high-quality evidence such as systematic reviews and randomized controlled trials were missed when the FFT limit was used.

For example, when searching without the FFT limit, 10 systematic reviews of RCTs were retrieved against one when the FFT limit was used. Likewise when searching without the FFT limit, 28 RCTs were retrieved and only one was retrieved when the FFT limit was used.

The proportion of missed studies (appr. 90%) is higher than in the studies mentioned above. Possibly this is because real searches have been tested and that only relevant clinical studies  have been considered.

The authors rightly conclude that consistently missing high-quality evidence when searching clinical questions is problematic because it undermines the process of Evicence Based Practice. Krieger et al finally conclude:

“Librarians can educate health care consumers, scientists, and clinicians about the effects that the FFT limit may have on their information retrieval and the ways it ultimately may affect their health care and clinical decision making.”

It is the hope of this librarian that she did a little education in this respect and clarified the point that limiting to free full text might not always be a good idea. Especially if the aim is to critically appraise a topic, to educate or to discuss current best medical practice.

References

  1. Björk, B., Welling, P., Laakso, M., Majlender, P., Hedlund, T., & Guðnason, G. (2010). Open Access to the Scientific Journal Literature: Situation 2009 PLoS ONE, 5 (6) DOI: 10.1371/journal.pone.0011273
  2. Matsubayashi, M., Kurata, K., Sakai, Y., Morioka, T., Kato, S., Mine, S., & Ueda, S. (2009). Status of open access in the biomedical field in 2005 Journal of the Medical Library Association : JMLA, 97 (1), 4-11 DOI: 10.3163/1536-5050.97.1.002
  3. WENTZ, R. (2002). Visibility of research: FUTON bias The Lancet, 360 (9341), 1256-1256 DOI: 10.1016/S0140-6736(02)11264-5
  4. Murali NS, Murali HR, Auethavekiat P, Erwin PJ, Mandrekar JN, Manek NJ, & Ghosh AK (2004). Impact of FUTON and NAA bias on visibility of research. Mayo Clinic proceedings. Mayo Clinic, 79 (8), 1001-6 PMID: 15301326
  5. Carney PA, Poor DA, Schifferdecker KE, Gephart DS, Brooks WB, & Nierenberg DW (2004). Computer use among community-based primary care physician preceptors. Academic medicine : journal of the Association of American Medical Colleges, 79 (6), 580-90 PMID: 15165980
  6. Krieger, M., Richter, R., & Austin, T. (2008). An exploratory analysis of PubMed’s free full-text limit on citation retrieval for clinical questions Journal of the Medical Library Association : JMLA, 96 (4), 351-355 DOI: 10.3163/1536-5050.96.4.010
  7. The #TwitJC Twitter Journal Club, a new Initiative on Twitter. Some Initial Thoughts. (laikaspoetnik.wordpress.com)
  8. The Second #TwitJC Twitter Journal Club (laikaspoetnik.wordpress.com)
  9. How many research papers are freely available? (blogs.nature.com)




To Retract or Not to Retract… That’s the Question

7 06 2011

In the previous post I discussed [1] that editors of Science asked for the retraction of a paper linking XMRV retrovirus to ME/CFS.

The decision of the editors was based on the failure of at least 10 other studies to confirm these findings and on growing support that the results were caused by contamination. When the authors refused to retract their paper, Science issued an Expression of Concern [2].

In my opinion retraction is premature. Science should at least await the results of two multi-center studies, that were designed to confirm or disprove the results. These studies will continue anyway… The budget is already allocated.

Furthermore, I can’t suppress the idea that Science asked for a retraction to exonerate themselves for the bad peer review (the paper had serious flaws) and their eagerness to swiftly publish the possibly groundbreaking study.

And what about the other studies linking the XMRV to ME/CFS or other diseases: will these also be retracted?
And what happens in the improbable case that the multi-center studies confirm the 2009 paper? Would Science republish the retracted paper?

Thus in my opinion, it is up to other scientists to confirm or disprove findings published. Remember that falsifiability was Karl Popper’s basic scientific principle. My conclusion was that “fraud is a reason to retract a paper and doubt is not”. 

This is my opinion, but is this opinion shared by others?

When should editors retract a paper? Is fraud the only reason? When should editors issue a letter of concern? Are there guidelines?

Let first say that even editors don’t agree. Schekman, the editor-in chief of PNAS, has no direct plans to retract another paper reporting XMRV-like viruses in CFS [3].

Schekman considers it “an unusual situation to retract a paper even if the original findings in a paper don’t hold up: it’s part of the scientific process for different groups to publish findings, for other groups to try to replicate them, and for researchers to debate conflicting results.”

Back at the Virology Blog [4] there was also a vivid discussion about the matter. Prof. Vincent Ranciello gave the following answer in response to a question of a reader:

I don’t have any hard numbers on how often journals ask scientists to retract a paper, only my sense that it is very rare. Author retractions are more frequent, but I’m only aware of a handful of those in a year. I can recall a few other cases in which the authors were asked to retract a paper, but in those cases scientific fraud was involved. That’s not the case here. I don’t believe there is a standard policy that enumerates how such decisions are made; if they exist they are not public.

However, there is a Guideline for editors, the Guidance from the Committee on Publication Ethics (COPE) (PDF) [5]

Ivanoranski, of the great blog Retraction Watch, linked to it when we discussed reasons for retraction.

With regard to retraction the COPE-guidelines state that journal editors should consider retracting a publication if:

  1. they have clear evidence that the findings are unreliable, either as a result of misconduct (e.g. data fabrication) or honest error (e.g. miscalculation or experimental error)
  2. the findings have previously been published elsewhere without proper crossreferencing, permission or justification (i.e. cases of redundant publication)
  3. it constitutes plagiarism
  4. it reports unethical research

According to the same guidelines journal editors should consider issuing an expression of concern if:

  1. they receive inconclusive evidence of research or publication misconduct by the authors 
  2. there is evidence that the findings are unreliable but the authors’ institution will not investigate the case 
  3. they believe that an investigation into alleged misconduct related to the publication either has not been, or would not be, fair and impartial or conclusive 
  4. an investigation is underway but a judgement will not be available for a considerable time

Thus in the case of the Science XMRV/CSF paper an expression of concern certainly applies (all 4 points) and one might even consider a retraction, because the results seem unreliable (point 1). But it is not 100%  established that the findings are false. There is only serious doubt……

The guidelines seem to leave room for separate decisions. To retract a paper in case of plain fraud is not under discussion. But when is an error sufficiently established ànd important to warrant retraction?

Apparently retractions are on the rise. Although still rare (0.02% of all publications by the late 2000s) there has been a tenfold increase in retractions compared to the early 1980s (see review at Scholarly Kitchen [6] about two papers: [7] and [8]). However it is unclear whether increasing rates of retraction reflect more fraudulent or erroneous papers or a better diligence. The  first paper [7] also highlights that, out of fear of litigation, editors are generally hesitant to retract an article without the author’s permission.

At the blog Nerd Alert they give a nice overview [9] (based on Retraction Watch, but then summarized in one post ;) ) . They clarify that papers are retracted for “less dastardly reasons then those cases that hit the national headlines and involve purposeful falsification of data”, such as the fraudulent papers of Andrew Wakefield (autism caused by vaccination). Besides the mistaken publication of the same paper twice, data over-interpretation, plagiarism and the like, the reason can also be more trivial: ordering the wrong mice or using an incorrectly labeled bottle.

Still, scientist don’t unanimously agree that such errors should lead to retraction.

Drug Monkey blogs about his discussion [10] with @ivanoransky over a recent post at Retraction Watch, which asks whether a failure to replicate a result justifies a retraction [11]“. Ivanoransky presents a case, where a researcher (B) couldn’t reproduce the findings of another lab (A) and demonstrated mutations in the published protein sequence that excluded the mechanism proposed in A’s paper. This wasn’t retracted, possibly because B didn’t follow the published experimental protocols of A in all details. (reminds me of the XMRV controversy). 

Drugmonkey says (quote):  (cross-posted at Scientopia here — hmmpf isn’t that an example of redundant publication?)

“I don’t give a fig what any journals might wish to enact as a policy to overcompensate for their failures of the past.
In my view, a correction suffices” (provided that search engines like Google and PubMed make clear that the paper was in fact corrected).

Drug Monkey has a point there. A clear watermark should suffice.

However, we should note that most papers are retracted by authors, not the editors/journals, and that the majority of “retracted papers” remain available. Just 13.2% are deleted from the journal’s website. And 31% are not clearly labelled as such.

Summary of how the naïve reader is alerted to paper retraction (from Table 2 in [7], see: Scholarly Kitchen [6])

  • Watermark on PDF (41.1%)
  • Journal website (33.4%)
  • Not noted anywhere (31.8%)
  • Note appended to PDF (17.3%)
  • PDF deleted from website (13.2%)

My conclusion?

Of course fraudulent papers should be retracted. Also papers with obvious errors that invalidate the conclusions.

However, we should be extremely hesitant to retract papers that can’t be reproduced, if there is no undisputed evidence of error.

Otherwise we should retract almost all published papers at one point or another. Because if Professor Ioannides is right (and he probably is) “Much of what medical researchers conclude in their studies is misleading, exaggerated, or flat-out wrong”. ( see previous post [12],  “Lies, Damned Lies, and Medical Science” [13])  and Ioannides’ crushing article “Why most published research findings are false [14]”)

All retracted papers (and papers with major deficiencies and shortcomings) should be clearly labeled as such (as Drugmonkey proposed, not only at the PDF and at the Journal website, but also by search engines and biomedical databases).

Or lets hope, with Biochembelle [15], that the future of scientific publishing will make retractions for technical issues obsolete (whether in the form of nano-publications [16] or otherwise):

One day the scientific community will trade the static print-type approach of publishing for a dynamic, adaptive model of communication. Imagine a manuscript as a living document, one perhaps where all raw data would be available, others could post their attempts to reproduce data, authors could integrate corrections or addenda….

NOTE: Retraction Watch (@ivanoransky) and @laikas have voted in @drugmonkeyblog‘s poll about what a retracted paper means [here]. Have you?

References

  1. Science Asks to Retract the XMRV-CFS Paper, it Should Never Have Accepted in the First Place. (laikaspoetnik.wordpress.com 2011-06-02)
  2. Alberts B. Editorial Expression of Concern. Science. 2011-05-31.
  3. Given Doubt Cast on CFS-XMRV Link, What About Related Research? (blogs.wsj.com)
  4. XMRV is a recombinant virus from mice  (Virology Blog : 2011/05/31)
  5. Retractions: Guidance from the Committee on Publication Ethics (COPE) Elizabeth Wager, Virginia Barbour, Steven Yentis, Sabine Kleinert on behalf of COPE Council:
    http://www.publicationethics.org/files/u661/Retractions_COPE_gline_final_3_Sept_09__2_.pdf
  6. Retract This Paper! Trends in Retractions Don’t Reveal Clear Causes for Retractions (scholarlykitchen.sspnet.org)
  7. Wager E, Williams P. Why and how do journals retract articles? An analysis of Medline retractions 1988-2008. J Med Ethics. 2011 Apr 12. [Epub ahead of print] 
  8. Steen RG. Retractions in the scientific literature: is the incidence of research fraud increasing? J Med Ethics. 2011 Apr;37(4):249-53. Epub 2010 Dec 24.
  9. Don’t touch that blot. (nerd-alert.net/blog/weeklies/ : 2011/02/25)
  10. What_does_a_retracted_paper_mean? (scienceblogs.com/drugmonkey: 2011/06/03)
  11. So when is a retraction warranted? The long and winding road to publishing a failure to replicate (retractionwatch.wordpress.com : 2011/06/03/)
  12. Much Ado About ADHD-Research: Is there a Misrepresentation of ADHD in Scientific Journals? (laikaspoetnik.wordpress.com 2011-06-02)
  13. “Lies, Damned Lies, and Medical Science” (theatlantic.com :2010/11/)
  14. Ioannidis, J. (2005). Why Most Published Research Findings Are False. PLoS Medicine, 2 (8) DOI: 10.1371/journal.pmed.0020124
  15. Retractions: What are they good for? (biochembelle.wordpress.com : 2011/06/04/)
  16. Will Nano-Publications & Triplets Replace The Classic Journal Articles? (laikaspoetnik.wordpress.com 2011-06-02)

NEW* (Added 2011-06-08):

 





Twitter Lists of Medical and other Scientific Journals

6 11 2009

In the previous two posts (“Biomedical Journals on Twitter” and List(s) of Tweeting Journals: Your Votes Please!) I introduced the Google-spreadsheet of (Bio-)medical Journals, manually compiled by the concerted effort of many people on Twitter. At a certain point other non-biomedical scientific journals were added, which made the list more complete, but less useful for most health care people, for whom the list was designed. In the last post I therefore asked people whether they preferred one complete list (as it was), one lists with different tabs for each discipline or different spreadsheets.

The results of the poll:

5-11-2009 17-51-47 results poll

Twenty-seven people responded. Although this is a small sample, it is clear that people either preferred one separate medical or biomedical list (30% and 26%) or one spreadsheet with all types of journals on separate tabs (33%). There was little or no interest in separate lists or all journals on one lists (without separation in tabs).

Discussion about the design of the spreadsheet has become somewhat superfluous by the recent roll out of Twitter Lists. The Twitter List feature is designed to make following and suggesting groups of tweeters easier. Everyone on Twitter can make up 20 lists of maximal 500 Twitter/people each. On the web you can easily add each account you like to your lists.

I have created 3 Twitter Journal List. In line with the outcome of the poll, I made  completely overlapping sets, where the Medical journal set is part of the Biomedical journal set, which belongs to the All/Science set.

If you’re on Twitter you can follow these three journal lists:

The spreadsheet still forms the basis. You can make adjustments here and if you mark them (color) or let me know, I will include them in the Twitter lists.
Found any new journals/magazines? Please feel free to add them.

If you’re interested in following (bio-)medical and/or scientific journals you can follow the list(s) you want, or your own selection from the journals in the lists.

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List(s) of Tweeting Journals: Your Votes Please!

8 08 2009

In the previous post “Biomedical Journals on Twitter” I showed a spreadsheet of biomedical Journals

This list was made on request of and for doctors, hence the original list name: Medical Journals.

As this Google-spreadsheet serves as a wiki, anyone (having g-mail) can edit the list. This was quite successful, as there were many additions made.

However, some of the journal titles I would not regard as biomedical. For instance purely (analytical) chemistry, physics, social sciences or history Journals. To me, Medical Biology is Medicine, Biology and disciplines on the interface (histology, anatomy, etc).

But let’s not discuss semantics and be practical. How would you like to see it?

Just like it is (see here) , with all disciplines mixed, all disciplines in a different spreadsheet or one spreadsheet with different tabs (per discipline).
In case of the latter two options, we could also add humanities/social sciences, such as suggested by Dean Giustini

7-8-2009 0-38-37 giustini spreadsheet journals

I made a (non-editable)* sample of a spreadsheet with different tabs per discipline to see what it looks like: see here
Below is only a Figure (showing the Medical Tab). Click to enlarge.

4-8-2009 17-57-28 spreadsheet twitter journals with tabs

The choice is yours.

*The alternative spreadsheet is not editable, because it is not manageable to have two spreadsheets. Data might get lost.

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Met losse handen publicaties scoren

29 03 2008

losse handen

(naar Bericht in “Status”, maart 2008, Ernst Koelman)

De UvA is doorgedrongen tot de top 50 van ‘s werelds meest productieve universiteiten. Dat komt mede doordat de ‘output’ van het AMC voor het eerst is meegeteld.

Dit heeft alles te maken met de nieuwe electronische registratie van onze Medische Bibliotheek.

Voorheen moesten afdelingen elk jaar zelf een lijst met publicaties aanleveren. Dat gebeurde ‘handmatig’ door Pubmed af te struinen. Overzichten waren zelden compleet of werden soms niet eens ingeleverd. Een volledige registratie is belangrijk, omdat aan de hand van die gegevens in- en extern de wetenschappelijke output bepaald wordt.

Sinds 2007 verzamelt de bibliotheek de gegevens zelf. Met een programma worden automatisch publicaties met het AMC-adres uit PubMed en Web of Science gevist. 85% van de 3000 publicaties wordt daarmee gevangen. De publicaties die gemist zijn, kunnen door de afdeling handmatig worden toegevoegd. Op de bibliotheek-homepage (intern) zijn de recente publicaties te vinden, te rangschikken per auteur of afdeling.

Hulde aan mijn collega’s Cees, Geert en Lieuwe!








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