Experimental design good, results discouraging

Well, I tested whether competence helps cells survive treatment with hydroxyurea, and the answer appears to be 'No'.

First a reminder of why I did this experiment: For years I've been hypothesizing that the function of at least some cytoplasmic genes in the H. influenzae competence regulon is to stabilize replication forks that have stalled because of a shortage of nucleotides.  Because the simple chemical hydroxyurea specifically inhibits the enzyme ribonucleotide reductase, which is needed to convert NTPs to dNTPs for DNA synthesis, the most important experimental question is whether competence protects cells from the harmful effects of hydroxyurea, with or without DNA uptake. - See more in this post.

What I did:  Cells with different levels of competence, in exponential growth in rich medium, were transferred to the same medium with and without 50 mM hydroxyurea, and growth and survival were followed by plating and by measurement of OD600.

What I observed:  Over a 3 hr period where DNA replication was arrested by hydroxyurea, cultures that were constitutively or partially competent did not exhibit increased growth or survival.

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

The cells:

1. K: Wildtype strain KW20.  Not competent in exponential growth but inducible by starvation.
2. KC: Wildtype strain KW20 with 1 mM cAMP added 45 min earlier to induce moderate competence
3. 5: Mutant strain RR563.  Has a hypercompetence mutation in sxy so is moderaately competent in exponential growth.  Similar transformation frequency to KC.
4. 6: Mutant strain RR648.  Has a knockout of sxy so cannot become competent at all.
5. 7: Mutant strain RR749.  Has a hypercompetence mutation in murE.  Competence is fully induced in exponential growth.

The results:  

Cell growth:  These cells were diluted at t = 0 into medium ± hydroxyurea, and their growth was followed by measuring the turbidity of the culture. Cells with arrested replication are expected to continue growing but to cease division (the cells form filaments), and that's what these cells did - growth was slowed only slightly by 50 mM hydroxyurea.

Cell division:  The same initial cultures were diluted 1:50,000 into medium ± hydroxyurea and their numbers were followed by plating and counting colonies.  Now we see that hydroxyurea did arrest cell division; the cells with hydroxyurea doubled only once or twice in the time that the control cells doubled more than seven times. 

Cell survival:  This is the same data as the above graph, with the addition of cfu counts after the very dilute cultures continued incubating overnight.  Ignore the '300 min' label on the X-axis; this was really after another 16 hr of incubation.  Cells in some of the hydroxyurea cultures divided a few more times, one culture kept the same cfu, and the cfu of the cells with cAMP decreased about 10-fold, probably due to the cAMP's general perturbation of gene expression.  There's no correlation with level of competence - the most competent cells increased only a bit more than the cells unable to become competent.  (The cells in the control cultures grew overnight to the expected 10^9 cfu/ml.)

Complications and plans:  One weakness of this experiment is that many (perhaps most) of the cells in a competent culture are not transformable, so many may not be expressing the cytoplasmic proteins that I hypothesize are protective.  This could reduce the sensitivity of the experiment by a lot.  

One way to clarify this would be to also assess survival of the transformable cells, by adding novR transforming DNA to the cultures and plating cells on novobiocin plates as well as plain plates.  This will make the experiment more complicated, largely because I'd have to work with less dilute cultures and do some dilutions for all the cells on plain plates.On the other hand, having the results of the experiment I've just done will let me streamline the plating, partly making up for the extra work and the uncertainty of survival and transformation frequency on the nov plates.  This strategy won't work for cultures that aren't competent at all (there will be no novR transformants), so I'd leave out the KW20 and RR648 cultures.  But it should work nicely for KW20+cAMP, and for RR563 and RR749. 

Could I also leave out most or all of the no-hydroxyurea controls?  Do I expect the number of transformants to parallel the total numbers of cellsIn the absence of hydroxyurea?  Perhaps not, since new competent cells will continue to become transformed over the time of the experiment.  So I'd better retain these controls.

Unexpected discovery: Cells grow faster when they're very very dilute.  The control cells in the top graph (blue lines) appear to be growing exponentially as expected; the log-scale lines are straight until the second-last time point.  The doubling time is about 35 minutes, which is typical for our cultures.  But when the cells were at a very low density in the same medium (second graph), they grew with a doubling time of about 24 minutes, faster than I've ever seen!  So I should do a separate experiment, following change in cfu of wildtype cells from from very dilute to more dense.  

Survey results by author's number of publications

A Twitter discussion got us wondering whether author's opinions about CC-BY editing and republication would depend on the seniority of the author.  Perhaps authors who had spent decades building their reputations would feel they had more at risk.  Or maybe authors just starting out would feel that their reputations were more vulnerable.

My $25 one-month Survey Monkey upgrade lets me filter the data for graphing, but doesn't make it easy to export the numbers to Excel.  So here are the charts for each publication category.

I haven't bothered labelling the answer choices because the different publication categories gave very similar results.  Respondents who have yet to publish their first paper feel the same as those with more than 20 publications.

I also tried filtering by whether or not the respondent had published any open-access papers.  This didn't affect the results either.

Later:  I figured out how to get the data into Excel, so here's a graph that allows more direct comparison:

And here are the questions again:

Survey results: what should be done about CC-BY reuse?

(As indicated in places below, I've later added points to this post as a result of ongoing Twitter discussions.)

 My first posts on this new problem reported that a for-profit publisher is editing and republishing open access articles as if they were new contributions to special-topic books (here), and described concerns raised by authors I had spoken with (here).  These concerns were largely dismissed by some advocates of open access, who commented that (i) authors should have realized that this is permitted by the obligatory CC-BY license, and (ii) authors should not complain since this is additional exposure for their work and ideas.

I felt that it's unreasonable to expect authors to have anticipated this particular form of reuse, especially since there's no evidence that open access advocates anticipated it.  And I thought most of the concerns authors raised in discussion with me were very reasonable (here).  So I circulated a short survey to get solid data on how authors feel about this new practice.

The survey responses (here) make it clear that authors are seriously concerned about the ways this reuse could harm their reputations.  This is to be expected - I think most scientists see their scientific reputation as even more important than their funding.  The many comments also make it clear that most authors had no idea this republication was happening, even though most of them had published open access articles.

More than 40% of authors in the survey said that they would not have accepted the CC-BY license if they had known this republication could happen.  If nothing is done, these concerns will seriously hinder the spread of open access publishing.

What should be done?  Open access advocates and publishers (the honourable ones, not the predatory ones) could just keep quiet and hope that the problem doesn't become generally known.  That probably won't work out well.  The present problem may be limited to one publisher (Apple Academic Press) but the explosive increase in predatory publishers of open-access journals suggests that it will grow; see the more than 300 publishers (not just journals) on Jeffrey Beall's list.  And awareness of the problem will spread each time authors discuss where to send their next paper.

Open access publishers could also work behind the scenes to ensure that CC-BY articles republished under the authors names are conspicuously labeled as having been previously published and, if appropriate, as having been edited without the authors' participation.  If this effort was successful I think it would eliminate most of the authors' concerns about their reputations.  Enforcing it would probably require expensive and ongoing legal actions, but (added later) I think any journal that requires CC-BY should accept the responsibility of legally protecting their authors' interests in this license.

(Added later)  Although CC-BY doesn't explicitly specify that the journal citation must be included along with the authors' names (not being designed for journal articles), K. Fortino (@kennypeanuts) pointed me to PLOS's very clear statement that full citation of the article is the required form of attribution.  All CC licenses prohibit 'implied endorsement'; that is, the reuse must not imply that the original source approves the reuse.  The offending books I've looked at typically describe all of the article authors as 'contributors' in a list at the beginning of the book; this is clearly a form of implied endorsement.

Because open access articles are a major user of CC licenses, OA advocates and publishers could also work together to develop a specific CC license that better meets the needs of authors and publishers.  It might allow everything that CC-BY does, but also require (i) prominent listing of the journal citation with the authors' names and (i) if the article had been edited from the original publication, whether the authors have approved this editing.  Maybe call it 'CC-OA'.

Finally, open access publishers could actively inform authors about these issues and their efforts to control them.  There are many ways to do this, but the strongest point of contact is when the author agrees to the CC-BY license.  Open access publishers already use this access point to provide authors with information about the benefits of this license.  Now that this problem and the reasonable author concerns have been identified, I think it would be disingenuous of publishers to not also give authors this information.

Open access publishers and advocates have enthusiastically promoted the benefits of CC-BY publication to authors (the BMC text is typical).  In a previous post I drew an analogy with informed consent in clinical trials, suggesting that OA publishers would be negligent if, in promoting the common good of CC-BY licensing, they did not inform authors of the personal risks as well as the personal benefits.

Remember, I'm an advocate of open access, not an enemy. In the short term, increasing awareness of this problem may scare off authors who might otherwise remain ignorant of it.  But if we do nothing about it, in the long term we risk losing many authors who would otherwise invest their limited grant funds to make their articles open.

Survey results

Here are the results of my survey on concerns about republication of CC-BY articles.  I've put a screenshot of the survey questions below the graphs of the results.  I discuss the implications in a separate post.

The survey link was emailed to the Evoldir and Ecolog-L mailing lists and posted to the SSE and CSEE facebook sites (reaching ~20,000 evolutionary biologists and ecologists), and emailed to four UBC departmental faculty lists.  It was also posted on this blog.  The text of the email is provided at the end of this post.

Survey participants:

Survey opinions:

I would be happy to have the quality of my paper recognized. I would be happy that my scientific contribution is being widely disseminated. I would welcome this as another entry in my publication list. I would want to have received a share of the profits. I would want the collection to be freely available. I would want the collection to be a high-quality contribution to the field. I would want the paper's original publication to be conspicuously credited. I would want the paper to be unaltered. I would worry about editing errors. I would worry that the editing has changed my interpretations. I would worry that the book's goals may conflict with mine. I would worry that my citation record will be confused. I would worry that colleagues will think I've self-plagiarized by publishing the same article twice. I would want to learn more about copyright options. I would not have accepted the CC-BY license if I'd known this could happen. In future I would not publish in journals that require the CC-BY license. In future I would not publish in open-access journals. - See more at: http://rrresearch.fieldofscience.com/2013/08/why-authors-are-concerned.html#sthash.l1d0a9eh.dpuf

I would be happy to have the quality of my paper recognized. I would be happy that my scientific contribution is being widely disseminated. I would welcome this as another entry in my publication list. I would want to have received a share of the profits. I would want the collection to be freely available. I would want the collection to be a high-quality contribution to the field. I would want the paper's original publication to be conspicuously credited. I would want the paper to be unaltered. I would worry about editing errors. I would worry that the editing has changed my interpretations. I would worry that the book's goals may conflict with mine. I would worry that my citation record will be confused. I would worry that colleagues will think I've self-plagiarized by publishing the same article twice. I would want to learn more about copyright options. I would not have accepted the CC-BY license if I'd known this could happen. In future I would not publish in journals that require the CC-BY license. In future I would not publish in open-access journals. - See more at: http://rrresearch.fieldofscience.com/2013/08/why-authors-are-concerned.html#sthash.l1d0a9eh.dpuf

The survey choices:

(A thread on Twitter claimed that this survey was very biased.  However, all of the negative choices were ones authors had raised with me; the positive ones I added to give balance.  Perhaps the tweeters mistakenly thought this was a general survey about open access instead of a very narrowly focused survey about one particular form of CC-BY reuse.)

Comments/concerns from survey participants:

• In future it will be obligatory in the UK to publish in an open access format (Green or Gold)
• Frustrating but an acceptable by product of the shifting landscape of publishing
• I would want to be contacted before publication and have the right to decline
• I would want to be consulted first and appropriately recognized for the original contribution and if being sold for profit the authors should receive a share of profits
• Editing of published manuscripts should be illegal.
• In addition to accurate citation of my original publication, I would want the citation to clearly indicate if the paper was copied exactly or adapted.
• always assumed OA was so people could read freely only
• I got my book!! republished this way! I guess that a intermediate (no commercial use) CC license should be required.
• I would be infuriated that I was not notified that they stole my work. I have published in PLOS and this would make me seriously reconsider doing so ever again - especially since I paid $1350 to PLoS so the work would be freely available to everyone and anyone having to pay $100 for this book is being ripped off
• is there a different license, still making freely available / disseminable, but restricting this kind of republishing?
• I would want a disclaimer on the book that clearly states that the individual articles are free on the web.
• The whole idea offends me
• I believe authors are bound by the agreements they make.
• I know these are not mutually compatible responses but its a complicated problem!
• Some of the above seem to conflict with the explicit wording of the CC-BY. Seems like if you agree to CC-BY, you can't really argue some of these.
• I would like to be asked and it should be after a number of years
• I should be able to expect nothing less than ethical conduct by publishers, regardless of what is legal
• I would like the licensing to be more transparent
• Who is making money off of this? It is creepy that they don't have to ask.
• This is truly frightening. Surely profiting from this is in violation, no?
• I don't think it would put me off publishing entirely using CC-BY, but it has certainly made me think twice!
• The CC-BY license should proscribe for-profit use by individuals other than the author(s).
• I would want them to let me know before they do any changes and ask me if these changes are correct!
• I think this would be fine, if proper attribution were clearly given for original work
• It is not clear from the situation description whether the original authors are listed as authors of the paper in the volume. If so, I would also have checked 1-3
• While I know that the CC BY requires only attribution, I think this scenario presents some outcomes that are potentially unintended by many parties who publish in OA journals. I worry that this scenario is essentially duplication of the original work in a way that is anathema in academia. I'm very happy to allow someone to profit by using the CC BY licenses as long as such reuse was actually transformative. As it is, it appears that the CC BY license essentially allows plagiarism to be carried out for profit. In my opinion, such works should not be treated as citable literature in academics, and perhaps the open access licenses should be modified to reflect this goal.
• I would want them to make clear the origins of the work and original context
• I would be absolutely furious if my work was used without my explicit permission. How dare someone attempt to profit off my without doing anything.
• The point is we pay extra to make an article open to the public. No one should be profiting from the information later. Also the book will be somewhat out of date by publication time and may not be that cohesive since it wouldn't include subscription articles. In other words I would worry about the overall quality of the book.
• I do not want people to make money from my work which is published OA. The idea behind OA is to disseminate science freely for everybody!
• I would be angry that others are making a profit of my work while I paid extra to have it FREELY available
• This practice is clearly unethical and violates normative publication standards of the scientific community
• In the future I would publish with the CC-BY-NC-ND license, which would legally prevent abuse by publishers: http://creativecommons.org/licenses/by-nc-nd/3.0/
• I would like to have at least been contacted, even though probably not required under the cc license terms
• I would prefer to be contacted about this before they edit my paper, as a courtesy.
• I'd prefer the CC non-commercial share alike license.
• I don't care because my colleagues are smarter than that.
• Either the paper should be unaltered, or it should be marked clearly as a derivative work with a different set of authors, citing the original from which it was derived conspicuously.
• Regarding the answers to the last two I will try not to publish in these type of journal unless absolutely necessary
• I would not be happy to have the work reprinted for profit. Science should be not for profit: the main objection is that others are making profit from something that they ethically should not be selleing even though it is currently legal.
• I'd be furious!
• I would be surprised and annoyed I was never told that my work would be re-published somewhere else (I should have the option to decline).
• My main concern is that it is scientific plagiarism, whether it is legal or not. It would be inappropriate to publish the same data twice without clearly referencing it, therefore it is inappropriate that anyone can do this to our work.
• If I agreed to the copyright contract, then this is acceptable. An author has an obligation to understand these things.
• It certainly makes me think twice about publishing in OA journals, but I will probably continue to do so.
• You are doing massive harm to the OA cause by trying to scare the children
• Above all, they need to actually notify authors when this happens
• authors should definitely be notified of this possibility and preferable be given an option to opt in or out
• Once someone alters text in the paper- the editors should get approval for that. I have no problem with someone bundling papers (similar to Amazon reading lists) and selling that "value added service". However, they shouldn't change the underlying articles. Perhaps provide an introduction to the volume and then introductions for each paper and why it is significant / ties into the theme of the volume. It should also be made perfectly clear in these volumes what the original citation should be. Also, authors of the original papers could be offered a page or two for commentary - how their paper fits into the theme of the volume and relates to other research.
• I would have liked to be asked for permission
• Except for reediting, which is unacceptable, this practice is entirely legal, and not necessarily directly against the spirit of open access. Two points are important: (1) insisting that a book chapter is clearly labeled as available for free, and (2) educating researches about these kinds of phenomena so that they know they don't have to pay for access.
• if you have research council funding in the UK, then you must publish open access.
• I would want notification my paper was being reprinted
• There are several aspects that seem highly unethical, but the least ambiguous is the publication under my name of words that are not my own.
• I would want to be warned that my paper should be used
• I don't find the major difference from people just printing my papers. Then money goes to the manufacturer of the printer, ink and paper.
• I believe altering the text and putting my name on it would be against the license, so I would demand a copy of the chapter to check if it is altered in any way. If not I would accept it because I accept the license agreement I have signed (and checked before signing).
• I don't think distribution per se is a problem at all, as long as the source is cited and correctly reproduced. Actually, I would like being asked for an "update" of a previous paper
• I would want authors to contact primary authors as a professional courtesy; however, I still support open access publishing
• I would opt for CC-BY-SA as I do for open source code
• I would worry that the work may no longer be up to date, and may be incorrect in light of more recent findings.
• I'd prefer a CC-BY-NC license to stop this
• In the future I'd license under the Creative Commons Attribution-NoDerivs 3.0 United States License (CC BY-ND 3.0 US)
• I wish I knew before this was done
• I would like to be asked if I agree with the re-publication and the alterations by the publisher of the multi-author book!
• I feel that this violates the spirit of open-access publication and may discourage other authors from publishing open-access
• Maybe shifting to CC-BY-ND in future would help to avoid these issues...
• If the original paper isn't being cited, it's breaking the terms of CC-BY and should be disallowed
• For the first two... it would really depend on the book. What if it's a creationist book that's re-using my work, with or without editing, to trash evolution? I wouldn't be happy!
• My feelings are mixed. Communication with the authors should be required and authors should have a say in the editorial process
• I would want to have given permission or been made aware of the book
• I would be angry that this practice might confuse and weaken the peer-review and merit-based foundation of research science publication.

Here's the full text of the email:

Dear Colleagues,

I've recently discovered that some commercial publishers are re-editing articles from open-access journals and publishing them as multi-author books, without the authors' knowledge (example here).  Although most authors I've spoken with find this objectionable it's quite legal, since open-access articles are usually published under Creative Commons attribution-only (CC-BY) licenses. 

Before pressing for any changes I'd like to get a broad set of researchers' opinions on this, so I've prepared a short (3 question) survey.  Here's the link: http://www.surveymonkey.com/s/5SFQSG2.

Please feel free to pass this survey link on to other researchers or scientific email lists (I've already sent it to Evoldir and Ecolog-L).

Thanks,

Rosie

p.s.  If you'd like more information I've also discussed this issue on my blog:

• http://rrresearch.fieldofscience.com/2013/07/apple-academic-press-predatory.html
• http://rrresearch.fieldofscience.com/2013/07/informing-authors-of-real-consequences.html
• http://rrresearch.fieldofscience.com/2013/08/how-many-for-profit-publishers-are.html
• http://rrresearch.fieldofscience.com/2013/08/who-edits-books-for-apple-academic-press.html

Dr. Rosemary J. Redfield     redfield@interchange.ubc.ca  

  Professor, Dept. of Zoology    Univ. of British Columbia                             
  Rm. 2551 Life Sciences Centre, Vancouver, B.C. V6T 1Z3 Canada  
  Office: (604) 822-3744   Lab: (604) 822-6323
  Cell: (778) 960-4950   Fax:    (604) 822-2416 
                 
  Web site:  http://www.zoology.ubc.ca/~redfield
  Research blog:  http://rrresearch.blogspot.com

Citing and being cited

One of the problems we work on is the sequence specificity of the H. influenzae DNA uptake system.  Over the past 10 years we've published 5 major studies of the uptake sequences in H. influenzae and related genomes, and of the bias of the DNA uptake machinery, and several other papers that also included some work on the topic.

Uptake specificity is known in only one other group of bacteria, where it has been extensively studied by another lab.  Our approaches have been similar; they have more funding and a larger molecular biology team but we have a better understanding of evolutionary processes and analysis.  Although we differ in our conclusions about the evolutionary function of uptake specificity, much of what they see in their system closely parallels what we see in ours, and the two systems are clearly convergent responses to very similar evolutionary forces.

We have been meticulous about discussing and citing their work, building an integrated picture of the two systems, and we have published one detailed bioinformatics paper that analyzed both systems, finding very strong similarities in the effects of uptake sequences on proteomes.

However they rarely cite our work. Until now I've just muttered under my breath about this, but their latest paper has me furious. It reports analyses in their system that closely parallel analyses we have reported in ours, and the results are strikingly similar in almost all points.  It's a very nice piece of work, published in a high-impact journal.  But the only mention of all our results is a single sentence in the Introduction, with the same paper later cited in the Methods for a trivial Perl script.  Some of their analyses are novel, but most are asking questions we've already answered in our system, often using more sophisticated methods than they used.

This failure to cite us must be deliberate -it's far too sweeping to be an oversight, and they certainly know that we're the other major group doing work on this problem.  The reviewers also should have caught this - the field is so small that any search for uptake sequences would put our work on the first page.

What's really a shame is that their paper is weaker for its neglect of ours.  They've thrown away the opportunity to extend their result into a unified picture of what happens in both systems.  Taking advantage of this lapse, we're now hard at work on a review that integrates findings from the two systems.

Why authors are concerned

Most of the authors I've spoken with are quite concerned that their open-access articles might be edited and re-published in 'edited' books.  To get a better handle on what authors are concerned about, I'm about to distribute a survey asking for feedback.  I'll post the results and discuss them here.

(August 16:  Here's a link to the results of the survey: http://rrresearch.fieldofscience.com/2013/08/survey-results.html)

Here's the main question of the survey:

Consider this situation, which other researchers are experiencing: Several years ago you published a paper in an open-access journal published by PLOS or BioMed Central. Now you discover that, without your knowledge, your paper has been included as a chapter in a multi-author book. The author list is correct but the paper's title and text have been lightly reedited. You and your co-authors are prominently listed as 'contributors' to the volume, but the original journal citation for the paper is not given or is buried in an 'Authors' Notes appendix. The book looks like a typical multi-author work; it includes a brief Introduction that describes how the chapters contribute to the field but does not mention that some or all of them have been previously published as journal papers. The book is being sold for about $100 through Amazon.

On checking with the original journal you discover that this re-publication is legal because you agreed to the required Creative Commons-Attribution (CC-BY) copyright license when you published the paper.

Which of the following statements would describe your reactions? (Choose all that apply.)

• I would be happy to have the quality of my paper recognized.
• I would be happy that my scientific contribution is being widely disseminated.
• I would welcome this as another entry in my publication list.
• I would want to have received a share of the profits.
• I would want the collection to be freely available.
• I would want the collection to be a high-quality contribution to the field.
• I would want the paper's original publication to be conspicuously credited.
• I would want the paper to be unaltered.
• I would worry about editing errors.
• I would worry that the editing has changed my interpretations.
• I would worry that the book's goals may conflict with mine.
• I would worry that my citation record will be confused.
• I would worry that colleagues will think I've self-plagiarized by publishing the same article twice.
• I would want to learn more about copyright options.
• I would not have accepted the CC-BY license if I'd known this could happen.
• In future I would not publish in journals that require the CC-BY license.
• In future I would not publish in open-access journals.

The other questions just ask how many papers the person has published and if any of them were open access.

(I won't post the link to the survey here or on Twitter because I want to get survey results mainly from authors who have little experience with open-access.  But I'm happy to have discussion of these points in the comments here.)  I've changed my mind; here's the survey link: http://www.surveymonkey.com/s/5SFQSG2.

(Picture below is just for the Field-of-Science header.)

How many for-profit publishers are repackaging CC-BY articles into books?

Note added October 7, 2017:  Apple Academic Press has fully addressed the concerns raised in my July 13 post (http://rrresearch.fieldofscience.com/2013/07/apple-academic-press-predatory.html).  Their practices now ensure that authors are appropriately consulted and credited when their open-access articles are republished. 

As I and others have recently noted, Apple Academic Press is selling what appear to be ordinary multi-author collections of specially written chapters on a scientific topic but actually consist mainly of articles repackaged from open-access journals.  Although this usually comes as an unpleasant surprise to the authors involved, it's quite legal under the CC-BY license used by most open-access journals.

Although I've been a supporter of open access publishing since 2000, when I signed the original Public Library of Science petition, I'm far from being an expert.  I'm only now reading about the Budapest and Bethesda agreements and their strong consensus for CC-BY licensing.  I don't think the authors of these statements anticipated that commercial publishers would repackage CC-BY articles into books that are superficially indistinguishable from the multi-author volumes many of us have contributed specially-written articles to.  I'll do separate posts on the problems this raises for authors (see here and here); in this post I just want to consider how big this phenomenon is or is likely to become.

The only publisher I'm aware of that's doing this is Apple Academic Press.  I discovered them through a colleague whose article they had repackaged.  Further poking around revealed that the book in question consisted entirely of republished articles (not all open access) tied together by an editors' Introduction.  I then found other posts about other volumes from the same publisher, with similar problems. 

I now want to find out how widespread this phenomenon is, but I can't think of an easy way to find out how many other Apple Academic Press books are collections of repackaged articles (some appear to be original material), nor to check books from other publishers.

Even checking the one article I originally learned about from my colleague was surprisingly difficult. Since I know the title had been altered, I searched Google Scholar for the combination of authors of the article.  There were 5 authors; the combination of names was not unique - they've published another article together, with another author.  This search found the original publication but not the new book chapter.  So I clicked on 'Related articles' and the fifth article on the list was the repackaged book chapter, probably missed by the first search because it misspells one of the author's names!  If I had started with the misspelled author list I wouldn't have found the original publication at all.  Similar searches for other articles from the same book worked better - I quickly found the source articles for authors with unusual names or combinations of names.

This one-by-one approach is OK for checking a few chapters from one suspicious publisher, but it would be very inefficient for a general survey.  Unfortunately I can't think of a search strategy to identify other publishers that repackage CC-BY articles into books, or to identify articles that have been republished into books by unspecified publishers.

Suggestions?







.

Who edits books for Apple Academic Press

Note added October 7, 2017:  Apple Academic Press has fully addressed the concerns raised in my July 13 post (http://rrresearch.fieldofscience.com/2013/07/apple-academic-press-predatory.html).  Their practices now ensure that authors are appropriately consulted and credited when their open-access articles are republished. 

More poking around in the Apple Academic Press 2011-12 catalog, now focusing on the editors.  Consider Harold H. Trimm.  He's Chair of the Chemistry Dept. at Broome Community College and an adjunct at Binghamton College SUNY, and although Google Scholar finds that he hasn't published a paper since 1986, Amazon lists 9 collections of articles edited by him, all published in 2011 by Apple Academic Press!  Even better is A. K. Haghi, who has edited 106 scholarly books for Apple Academic Press in the past few years.

Browsing the editors of Apple Academic Press books, a surprising number of them are, like H. H. Trimm, affiliated with Broome Community College and/or Binghamton College.  And AK Haghi, usually listed as a Professor of Textile Engineering at the University of Guilan in Iran, has somehow become an Associate Member (sic) of the University of Ottawa and a free-lance science editor in Montreal!   And is William Hunter III, who edited four chemistry books with Trimm (as Researcher, National Science Foundation, USA) and three more on his own in the same year, the son of William Hunter Jr, of Olean Hospital, who co-edited a book with Sabine Globig, who edited or co-edited six other books that year?


I think we can safely conclude that Apple Academic Press is a shady operation.  The next post considers the thorny problem of whether they are an isolated case or the tip of an iceberg.

Hydroxyurea stalls DNA replication; does competence help cells survive?

In a post a couple of weeks ago I wrote:

Stalled replication forks:  We have been hypothesizing that one function of the competence regulon's proteins is to stabilize replication forks that have stalled because of a shortage of nucleotides.  One way to test this is to see if hydroxyurea induces either the regulon or competence, because hydroxyurea inhibits the enzyme ribonucleotide reductase, which is needed to convert NTPs to dNTPs for DNA synthesis.  I'm told that hydroxyurea is known to cause stalling of replication forks, though I haven't looked for this yet - See more at: http://rrresearch.fieldofscience.com/#sthash.IQAAtROv.dpuf

• Stalled replication forks:  We have been hypothesizing that one function of the competence regulon's proteins is to stabilize replication forks that have stalled because of a shortage of nucleotides.  One way to test this is to see if hydroxyurea induces either the regulon or competence, because hydroxyurea inhibits the enzyme ribonucleotide reductase, which is needed to convert NTPs to dNTPs for DNA synthesis. 

I've now dug up the evidence that hydrozyurea inhibits synthesis of dTPs and blocks DNA replication.  It's partly very old but solid E. coli biochemistry papers and partly new molecular biology in both E. coli and mammalian cells.  The E. coli papers have useful information about kinetics and concentrations.

Stalled replication forks:  We have been hypothesizing that one function of the competence regulon's proteins is to stabilize replication forks that have stalled because of a shortage of nucleotides.  One way to test this is to see if hydroxyurea induces either the regulon or competence, because hydroxyurea inhibits the enzyme ribonucleotide reductase, which is needed to convert NTPs to dNTPs for DNA synthesis.  I'm told that hydroxyurea is known to cause stalling of replication forks, though I haven't looked for this yet - See more at: http://rrresearch.fieldofscience.com/#sthash.IQAAtROv.dpuf

Stalled replication forks:  We have been hypothesizing that one function of the competence regulon's proteins is to stabilize replication forks that have stalled because of a shortage of nucleotides.  One way to test this is to see if hydroxyurea induces either the regulon or competence, because hydroxyurea inhibits the enzyme ribonucleotide reductase, which is needed to convert NTPs to dNTPs for DNA synthesis.  I'm told that hydroxyurea is known to cause stalling of replication forks, though I haven't looked for this yet - See more at: http://rrresearch.fieldofscience.com/#sthash.IQAAtROv.dpuf

I think the most important experimental question is not whether hydroxyurea induces competence but whether competence protects cells from the harmful effects of hydroxyurea, with or without DNA uptake.

I've only done one experiment so far, a preliminary test of the kinetics of growth inhibition (really, cell division inhibition) and killing of wildtype cells.  Over the 2 hr incubation period, 10 mM had no effect, 30 mM slowed the increase in cell numbers only for the first hour, 100 mM prevented cell division but didn't kill the cells, and 200 mM killed most cells in the second hour.   

The next step will be to measure effects of hydroxyurea on cells with different levels of competence.  Rather than artificially inducing competence, I'll mostly rely on mutants, a sxy knockout that can't turn on competence genes at all and two hypercompetent mutants, sxy-1 (moderately competent) and murE749 (very competent even during exponential growth).  But I'll also test wildtype cells with added cyclic AMP, which induces a similar  hypercompetence as the sxy-1 mutation.

I'll try two complementary ways to do these tests.  In both I will get the cells exponentially growing in rich medium and follow growth after adding different concentrations of hydroxyurea.  

Test A will use the same viable-count method I used for the first experiment, plating the cells at different times after hydroxyurea addition to see how much growth/cell division slows or stops and the extent of cell killing. Because I dilute the cells down to about 2000 cfu/ml when I add the hydroxyurea I can just plate the cultures directly, without having to dilute them further at the time of sampling.  This makes it possible to test multiple concentrations and lots of time points.

Test B will make use of the Bioscreen incubator belonging to the lab next door.  This lets me follow detailed growth curves for up to 200 samples at once.  The disadvantage is that it measures growth by changes in optical density, with a fairly narrow range (only a few doublings); it can't measure viability changes at all.

The combination of the two tests should give nicely complementary information about the effects of hydroxyurea on growth and viability.  The trickiness will be getting the initial cell concentrations for each test right - 2000 cfu/ml for Test A and about 10^8 cfu/ml for Test B.

Papers: 

Neuhard 1967. Studies on the acid-soluble nucleotide pool in Escherichia coli: IV. Effects of hydroxyurea.  Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis 145:1–6

Sinha and Snustad. 1972? Mechanism of Inhibition of Deoxyribonucleic Acid Synthesis in Escherichia coli by Hydroxyurea.  J. Bacteriol. 112 :1321-1334

Davies et al. 2009 Hydroxyurea Induces Hydroxyl Radical-Mediated Cell Death in Escherichia coli.   Molecular Cell, Volume 36, Issue 5, 845-860
 (toxin-antitoxin systems involved!  Microarray data!!!)

Making the hemin stock/solving a chemical puzzle

Yesterday I tried, and failed, to make a new lab stock of the hemin that Haemophilus influenzae needs as an iron source. 

Hemin comes as a fine black powder; it's not really soluble in aqueous solutions or even miscible in water.   For our culture media it's prepared as a sterile suspension by mixing 100 mg of hemin with 100 ml of a solution of 4% triethanolamine (a surfactant), and incubating this at 65°C in a waterbath for 30 min.  The hemin forms a black suspension that's, rather surprisingly, both sterile and chemically stable.  Sterility is surprising because 30 min at 65°C isn't expected to kill spores, and stability is surprising because, once the hemin is added to culture media it goes off within 48 hr.

Anyway, we're down to our last 100 ml bottle of hemin stock, and it's my turn to make up lab stock solutions, so yesterday I tried to make more.  We've always used triethanolamine that came as a viscous liquid, but recently we accidentally purchased triethanolamine hydrochloride, which comes as a white powder.  So I made up a 4% solution (nicely soluble) and mixed it with the hemin.  NO SUSPENSION, even after heating.  No different than hemin in pure water.

What to do?  Was the problem the triethanolamine or the hemin, which was also a new bottle (well, a bottle of uncertain age that had never been opened).  The new and old hemins were both from Sigma and had identical labels (the old one in a brown glass bottle, the new one in a white plastic bottle), so that's probably not the problem.  Our ancient CRC handbook (the 'rubber bible') recently disappeared, so I looked triethanolamine up in the Merck Index.  Not much help, so I just left the problem for the next day, thinking I'd email the building to see if anyone had any liquid triethanolamine.

But this morning I've done some Google searching and discovered that liquid triethanolamine is mildly alkaline, but solutions of the hydrochloride are quite acidic.  Triethanolamine hydrochloride is used in various molecular biology and microscopy protocols, always with the pH adjusted to 8.0.  So this morning I'm going to try adjusting the pH of the 4% triethanolamine before I add it to the hemin.

Later:  And here's the result!  Raising the pH caused the hemin to form a nice evenly black suspension (bottle on left).  The bottle on right has its original low pH and all the hemin has settled to the bottom of the bottle.

Informing authors of the real consequences of CC-BY open-access publication

Thanks to comments on the previous post, I now realize that there have been extensive discussions of the merits of different CC licenses for open-access publishing.  See for example: http://oaspa.org/why-cc-by/. These discussion explain that the most open licenses are best for the dissemination and utilization of scientific information. That's probably why both PLOS One and BioMed Central use only the CC-BY license, which allows unlimited use and modification, including commercial uses, provided the source is attributed.  At a minimum the attribution requires listing the names of the authors.  It should also require citing the journal where the article appeared, although this isn't always clearly spelled out.

 

But, as the previous post and a related post describe, the CC-BY license creates new problems for authors, because some for-profit publishers have begun aggregating CC-BY papers into high-priced edited books without the authors' knowledge.  The authors I've discussed this with are quite upset.  They trusted the journals to offer licensing arrangements that were in the authors' best interests, but now they feel that they have relinquished control of their scientific reputations.  (Note that these weren't predatory publishers, but PLOS One and BioMed Central.)

Most of the discussions of open access licenses haven't considered the exploitation of these licenses by for-profit publishers, probably because this niche opened only very recently, once open-access papers became widely available.  I and others discovered this problem by accident.  I don't know how widespread it is, but I expect it will only grow.  (I'd like to do a survey of its prevalence, but I can't figure out any way to distinguish between such repackaged books and traditional multi-author volumes without having to contact individual authors - any suggestions?)

So far, open access publishing has been presented as both a public and a private good.  Science benefits from barrier-free dissemination and reuse, and authors benefit from wider readership. The only cost under discussion has been the transfer of publication expenses from the reader to the authors or their institution.  Opposition has come mainly from the publishers of subscription-access journals whose profits are threatened.

But for-profit republication of open-access articles is a cost that most advocates of open access didn't anticipate and that most authors are unaware of.  It's time for open-access advocates and especially publishers to take on the responsibility of informing authors of all the consequences, not just the good ones.

In some ways the ethical issues are like those of a clinical trial.   Participation generates a public benefit (medical research) and may be directly beneficial to the participant (better medical care, access to new therapies).  But the researchers directing a clinical trial are obliged to make sure that potential participants also understand the risks and costs.  They can't assume that the participants have thought the implications through, but must spell these out in clear and simple language.

Similarly, advocates of open access need to honestly inform authors about the consequences of the CC-BY license.  The onus shouldn't be on the authors to research the implications and consequences of different licenses, but on those with expert knowledge to communicate this to the authors. 

So, two questions:

Should authors in open-access journals be allowed to choose between different CC licenses?  Publishers agree that CC-BY is best for science, but authors may think it is not best for them. The major publishers don't give authors any choice, but I think they should.

How should open-access journals inform authors about license consequences?  This is particularly important when CC-BY is the only or default license.  Most scientists I've talked to are unaware that the CC-BY licenses of their open-access papers allow commercial publishers to alter and republish their papers without consulting them.  And they are very unhappy to learn that this is actually happening, often saying that they'll have to rethink their use of open-access.

Here's what the authors are told at present.  Note the emphasis on benefits and no discussion of risks:

PLOS One:
"Upon submitting an article, authors are asked to indicate their agreement to abide by an open access Creative Commons license (CC-BY). Under the terms of this license, authors retain ownership of the copyright of their articles. However, the license permits any user to download, print out, extract, reuse, archive, and distribute the article, so long as appropriate credit is given to the authors and the source of the work. The license ensures that the article will be available as widely as possible and that the article can be included in any scientific archive."

BioMed Central:

"You retain copyright, licensing the article under a Creative Commons license: This means that articles can be freely redistributed and reused as long as the article is correctly attributed. For example, a published article can be posted on a personal or institutional homepage, emailed to friends and colleagues, printed and sent to people, archived in a collection, distributed on CD-ROM, included in course-packs, quoted in the press, translated and further distributed as often and widely as possible. Read the full Creative Commons license."

When is it ethical to re-publish open-access scholarly articles?

Note added October 7, 2017:  Apple Academic Press has fully addressed the concerns raised below.  Their practices now ensure that authors are appropriately consulted and credited when their open-access articles are republished. 

A colleague just discovered that an article she published in the BioMed Central journal Epigenetics and Chromatin has been republished, without her knowledge or consent, in a book, Epigenetics, Environment and Genes, 'edited' by Sun Woo Kang and published by Apple Academic Press.  You can buy it on Amazon for $104.26 (Can).  

On checking the details of the BioMed Central publication agreement, we discovered that this commercial reuse is permitted.  It's also permitted by the PLOS One agreement, though that is CC-BY which I think requires that the original publisher be credited as well as the authors.

At first we thought that all the reprinted articles were from open-access journals, but at least one isn't.  I've contacted the author of that article to find out if permission was obtained for its republication.

Apple Academic Press sent this reply to an email from the authors:

I am answering the concerns over the reuse of your article in Epigenetic, Environment and Genes book published by AAP. 

This book was contracted through "Harding house publishing services" based out of Vestal, New York. The editor and contractor were responsible for the selection of articles in the book and to our knowledge this article was used under Creative commons license. By allowing your article to be printed by open access journal that lists the Creative Commons license, you as the author are agreeing to those conditions. The rationale for doing so would be to allow your work to be distributed in as many ways possible, which is common practice in the world of academic publishing.  http://creativecommons.org/licenses/by/2.0

However, that said, at Apple Academic Press we agree that authors should be notified whenever their work appears in a new publication. It is our current policy to contact all authors before including their work in any of our books. We apologize that this policy had not yet gone into effect when the edition of Epigenetic, Environment and Genes  was in production, but we have rectified that now. We would be happy to send you a copy of Epigenetic, Environment and Genes.
I have copied Ellyn Sanna (President and CEO) of Harding House publishing, So that she also gets aware of your concerns. I am sure if you have any more questions, she will be happy to take this further with you. 

Also, Our product line is growing rapidly, and we are looking to work with new authors in the STEM subjects. If you have any book concepts for your field (whether originally authored or compilations of recent research), we would be very interested in working with you in that capacity as well. Our authors and editors receive generous royalty contracts.

I particularly like their brazen invitation at the end and the offer of 'generous royalty contracts'.

My colleague and her co-authors are outraged; they had no idea that this commercial reuse was permitted by the standard agreements.  In principle the authors should have read the fine print, but as advocates of open-access publishing I think the onus is on us to make sure that the copyright agreements are in accord with authors' reasonable expectations and wishes.

At a minimum the open-access journals should inform their authors that unscrupulous publishers are standing ready to exploit their work.

We're not the first to note Apple Academic Press's sleazy work.  Read this post written by Mike Taylor a couple of weeks ago, complete with a nasty response from a former employee of the publisher.  And this post by Christopher Schadt from a few days before that, which has a long comment thread about who has the rights to do what.

My turn to do lab meeting

I've been so absorbed in my Useful Genetics course that I've let our weekly lab meetings lapse over the last few months.  But I've set up a new schedule and today it's my turn to present.  Of course I haven't done any experiments lately, but I've done one tiny analysis and I'll also talk about plans for the CIHR proposal.

The tiny analysis was the first step in addressing a question I've been wondering about for a while now- the phylogenetic distribution of the rec2/comEC gene.  In H. influenzae the  Rec2 protein sits in the inner membrane and translocates a single strand of DNA from the periplasm to the cytoplasm.  Its Bacillus subtilis homolog ComEC does the same thing at the one cytoplasmic membrane. 

Homologs of these proteins are present in all known competent species, and the appropt=riate experiments have been done they have the same DNA-translocation function, are competence-regulated, and do not have any other obvious function in the cell.  This distinguishes them from all the other proteins consistently required for DNA uptake, which are members of the type 4 pilus complex and known to also function in other pilus-associated processes.

Thus the phylogenetic distribution of rec2/comEC might be expected to reflect the phylogenetic distribution of competence.  But as far as I know nobody has examined this.

Before I describe what I found, I should bring up the distribution of another competence-induced gene, dprA.  I've written about dprA here and here; it doesn't contribute to DNA uptake but protects incoming DNA from nuclease degradation and promotes homologous recombination with the chromosome.  I previously discussed the phylogenetic distribution of dprA; it's very widespread and highly conserved across a wide range of bacteria not known to be competent, so I argued that it must have another function that's independent of promoting homologous recombination of incoming DNA in competent cells.  I was leaning to the idea that 'competence-regulons' include not only DNA uptake machinery but machinery to mitigate other harmful consequences of nucleotide scarcity, especially stalling of replication forks.

Back to rec2.  My tiny analysis was to take a first look at the distribution of rec2.  All I did was ask Gen Bank to search for rec2 and for comEC.  As controls I used dprA and recA.  GenBank helpfully provides a tree-view summary of what it finds, and that's all I've looked at.  Here are the results of the four searches:

 

First conclusion:  rec2/comEC homologs are present in many many bacterial genomes than there is any evidence of competence for, including some that have been shown to not take up DNA.  This could have one of two interpretations.  First, it could mean that many many more bacteria are naturally competent, and that competence is likely ancestral to all bacteria.  Or, it could mean that rec2/comEC has another function in the cell, one that's independent of the ability to take up DNA.  

Note the similarlty of the comEC and dprA distributions.  (I suspect that most of the rec2 hits are also included in the comEC results.)  I had only been thinking of the first interpretation for rec2/comEC, but had previously taken the second interpretation for dprA. But now I think I need to consider both interpretations for both genes.

Reclaiming my explainer energy (from MOOCing back to blogging)

My Useful Genetics MOOC (massive open online course) isn't really over yet, but almost all the work is done so I'm finally able to think about research.  And it's high time, because we have two research visitors in the lab for the next few months, the post-doc and I have two reviews to write, and I need to write a grant proposal for a Sept. 15 deadline.

I'd better start with the proposal.  We've had 5 (or is it 6?) unsuccessful tries to get CIHR funding for work on the mechanism of DNA uptake so, even though one of our visitors brings expertise that would help with this, I've given up hope of ever getting serious funding for this work.  We then made one try to get funding for a new project, aiming to predict recombination in natural populations.  This was solidly rejected.  So now I'm going to go back to our funded strength, the regulation of competence.
We have several papers in this area recently, and lots of directions to investigate.

Here I've pasted directions onto our standard diagram of competence regulation - all the blue boxes are regulatory problems in serious need of investigation.  I won't necessarily include them all in the proposal, and there are probably other problems I've forgotten about, but here are the basics:

1. Fructose:  Competence is regulated by cAMP levels which are elevated by the H. influenzae phosphotransferase system (PTS) in response to depletion of the sugars that the PTS would otherwise transport.  In H. influenzae the only such sugar is fructose.  Regulation by fructose levels in the host environment makes no regulatory sense.
2. Sxy-CRP interactions: We've done a lot of work on these, and by we I mean the former RA (she has a great new job in a high-powered lab across the street) and former grad student/postdoc (he has a great new job at the University of Regina).  But we still don't know what's going on.
3. Hfq:  Hfq is important for the activities of small regulatory RNAs. Knocking out Hfq reduces competence 10-fold, by an unknown mechanism that's independent of the purine-repression effect described below.
4. Toxin-antitoxin system: One pair of genes regulated by competence turns out to encode a probable toxin-antitoxin system, with the antitoxin preventing the toxin from preventing DNA uptake and transformation.  We have no idea  whether this futile combination has any biological function.
5. Regulation by purines: We have a nice new paper out about the purine regulation, showing that it acts by stabilizing the sxy mRNA secondary structure that blocks translation.  But we have only very indirect evidence of how it does this.
6. Effect of PRPP on sxy mRNA translation:  The indirect evidene suggests that purines may regulate sxy mRNA translatability by changing the intracellular level of the intermediate PRPP (phosphoribosyl pyrophosphate).  We probably can't investigate this biochemically, because PRPP is not something you can buy (probably very unstable?).  But maybe we can investigate its role genetically, by making more mutants.
7. Stalled replication forks:  We have been hypothesizing that one function of the competence regulon's proteins is to stabilize replication forks that have stalled because of a shortage of nucleotides.  One way to test this is to see if hydroxyurea induces either the regulon or competence, because hydroxyurea inhibits the enzyme ribonucleotide reductase, which is needed to convert NTPs to dNTPs for DNA synthesis.  I'm told that hydroxyurea is known to cause stalling of replication forks, though I haven't looked for this yet.
8. murE mutants: Point mutations in the cell wall biosynthesis gene murE cause constitutive expression of the competence regulon.  We have no idea why.

Formatting figures for PLOS journals

A tweet by Jon Eisen last night reminded me what a pain it is to format figures so they are acceptable to the PLOS journals' system.

Kate Stafford was particularly annoyed at the idea that she'd have to spend hundreds of dollars on Adobe Illustrator, just to carry out the required format conversion.

Then I remembered that my excellent postdoc has figured out how to do this using only free software.  Here's his method:


WHAT PLOS RECOMMENDS:

Here (slightly edited for clarity) are the PLoS guidelines for converting PNG-format files to TIFFs using GIMP, an open-source version of Photoshop (similar instructions are provided for PDFs and some other file types.):

In GIMP:    

1. Open the PNG from the File menu. You will need to do this one page at a time.    

2. Crop the image: Use the Crop Tool (third row, second from the right, looks like a knife blade) to select an area close to the borders of your image. Hit Enter to apply the crop. 

3.Resize the image: Under the Image menu choose Scale Image (see screenshot below).  In the pull down menu next to Height (RR: red oval on right), set the units of measurement,to millimeters. If the Width is over 173.5mm, type 173.5 in the Width box (RR: red oval with an X in it) (17.35cm is our maximum allowable width for figures) and hit Tab. The new Height of the figure will appear, scaled proportionately to the change in Width. The Width cannot be below 83.0mm, and the height cannot be more than 233.5mm. If the Height and Width are within these prescribed limits, no adjustment to your figure size needs to be made. 

4. From the File menu: choose Save As. Click the + sign next to "Select File Type (By Extension)". From the menu that appears, select TIFF. Click Save. Set Compression set to LZW. If you're prompted about layers in the file, select Flatten Image.

But it doesn't work!

THE PROBLEM:

Step 3 of the recommended process above tries to shrink the image by adjusting its size in mm to below 173.5.  Resizing this way massively downgrades image quality.  

THE IMMEDIATE SOLUTION:

The work-around is to use the lower set of controls to  increase pixels/mm instead of decreasing mm.  This causes a correlated change in the size of the images, so doesn't degrade image quality. 

First do use the upper drop-down menu to set the image size units to millimeters as instructed above (red oval on right).  Don't change the numbers in the box in the other red oval.

Instead use the lower drop-down menu to change the resolution units to pixels/mm (green oval on the right), and use the box beside it (other green oval) to increase pixels/mm until the image size (in the other red oval) falls to ≤173.5 mm.  

A DESIRABLE LONG-TERM SOLUTION:

This ought to be fixed in PLoS's instructions to authors, so that people can use open-source software to get their images to PLoS's specifications.