Great OpenScience news today

Lots of fantastic OpenScience happenings in the news today:

  • The G8 Science ministers support open data in science with one of the strongest statements I’ve seen: “To the greatest extent and with the fewest constraints possible publicly funded scientific research data should be open…”    See more on this at the Open Knowledge Foundation blog.
  • Mozilla has opened the Mozilla Science Lab, and appointed two great people to run it.  Kaitlin Thaney managed the science program at Creative Commons and has been named the director, and Greg Wilson, who has been involved in Software Carpentry from the beginning has also been appointed to the team.
  • Yesterday’s US Supreme Court ruling that genes cannot be patented is a clear Open Science victory.   I’m not sure how to parse the cDNA portion of the ruling, however. More details on the decision here.

Comments on DOAJ proposed new selection criteria

The Directory of Open Access Journals has posted a draft of their new selection criteria and is requesting comments by July 15, 2013. Kudos to DOAJ for taking this open, transparent approach to their process. Following are my comments.

DOAJ proposed criteria and my comments in bold

We have tried to construct objective criteria that can facilitate compliance verification easily. In order to be listed in the DOAJ, a journal must meet the following criteria:

  • Journal will be asked to provide basic information (title, ISSN, etc.), contact information, and information about journal policies

Comment: make sense!

  • Journal is registered with SHERPA/RoMEO

Comment: this should be a recommended good practice, not a criteria for inclusion in DOAJ. The reason is that registering with SHERPA/RoMEO is controlled by SHERPA/RoMEO, not the journal.  SHERPA/RoMEO is an important service, but it is UK-based and focuses on UK priorities. Few Canadian scholarly journals are listed, for example. Before considering such a suggestion, someone should ask SHERPA/RoMEO if they are prepared to take on the task of including all of the world’s journals on request, including journals from every language used by scholars around the world.

  • Journal has an editorial board with clearly identifiable members (including affiliation information)

Comment: not every high-quality journal has an editorial board; some small journals are managed very well by a single managing editor.  Including a criterion like this may have the unfortunate effect of changing the way that journals are published, and not necessarily for the best. Suggested change to: Journal has a transparent and academically appropriate editorial practice.

  • Journal publishes a minimum of five articles per year (does not apply for new journals)

Comment: this should be struck, for several reasons. This criteria would discriminate against smaller journals. For example, last night in my scholarly communication class a student raised a point about a journal produced by a small community that one year declined to publish any articles, as no submitted articles were seen as meeting the journal’s standards. As open access becomes the default and inclusion in DOAJ essential to marketing, this criteria could end up defining what constitutes a journal. Houghton and colleagues found that the most cost-effective means of providing open access in the long term would involve a peer review overlay over articles deposited in repositories. To facilitate this development we need to allow creativity in how this work is done. Eliminating small journals would not be a good idea!

Another important point is that journals that have ceased to publish should still be made available. DOAJ should work towards noting that the journals are inactive, rather than eliminating them from DOAJ. Otherwise, authors who choose to publish in a journal in part because it is listed in DOAJ may find their work eliminated from DOAJ simply because the journal ceased to exist – a common occurrence even in the print / subscription world. Also, libraries use the DOAJ list to include open access works in library catalogues and serials lists, and dropping ceased journals is a loss of valuable content.

Finally, as may be obvious from the example above of the journal that refused to publish one year, a requirement of a minimum of 5 articles per year may drive journals to publish articles that they would otherwise decline. In other words, this will sometimes be an incentive to publish lower quality articles.

  • Allows use and reuse at least at the following levels (as specified in the Open Access Spectrum, http://www.plos.org/about/open-access/howopenisit/ ): 

Comment: please strike any reference to the Open Access Spectrum. This is a conceptual framework for open access that is not shared by the whole open access community. For example, the website points to PLOS journals using the OAS grid and Assess a Publisher or Publication with the OAS grid. This very much reflects a gold or open access publishing perspective which does not entirely leave out green or open access archives, but places it at a much lower priority level. Another consideration is that is open access definitions are opened up to a spectrum approach, there is no reason why others could not propose alternate spectra. For example, in recent discussions in Canada it appears that there are those who confuse national free access with open access. If we entertain a spectrum approach, why not a continuum from free access to a few people to global free access? Not all alternative possible spectra are negative examples like this. For example, a scholar-centered open access spectrum (which would appeal much more to me, as a scholar) might focus on the continuum of time of sharing, from when a research idea first occurs to you through to publication. Similarly, why not a spectrum from immediate open access to perpetual copyright with extremely limited rights – something that we should all remember is the real closed access.

  • Full text, metadata, and citations of articles can be crawled and accessed with permission (Machine Readability Level 4)
  • Provides free readership rights to all articles immediately upon publication (Reader Rights Level 1)
  • Reuse is subject to certain restrictions; no remixing (Reuse Rights Level 3)
  • Allow authors to retain copyright in their article with no restrictions (Copyrights Level 1)
  • Author can post the final, peer-reviewed manuscript version (postprint) to any repository or website (Author Posting Rights Level 2)

Comments:

Machine readability is another example of a good practice to encourage which should not be required for inclusion in DOAJ. There will be variations in the ease with which different journals can achieve machine readability. Even PLoS uses locked-down PDFs, for example. More research is needed to determine whether machine readability of journal articles is always desirable. For example, if pictures of people are included, does the researcher have rights to permit facial recognition software? With the PLoS locked-down PDFs, do we really want the PDFs unlocked to facilitate data mining – wouldn’t it be much more useful to work towards having scholars share the data as open data, preferably linked to from the journal but housed elsewhere? Sometimes machine readability does make sense and is highly desirable – for example, I’d like to see the default for electronic works in general to be works that can be instanteously translated into the format of the reader’s choice, whether PDF, html, daisy or braille. Here, what is needed is not refusal to include journals in DOAJ if they are not at this standard, but rather education and support to help journals develop this capacity.
 
Provides free readership rights to all articles immediately upon publication is very basic to the definition of open access; this makes sense. I suggest adding the word “global” to avoid confusion with regionally limited free access, to: “Provides free global readership rights to all articles immediately upon publication”

Reuse is subject to certain restrictions; no remixing. It is good to see that journals that prefer to include some restrictions can be included in the Directory of Open Access Journals, but this statement is confusing and counter-productive. For example, as stated any journal that does allow re-use should rejected, so good-bye to the likes of PLoS and BMC!

Allow authors to retain copyright in their article with no restrictions (Copyrights Level 1)  Comment: it may be useful to encourage author rather than journal copyright retention, however this is not an essential part of open access and may not always be possible or desirable. For example, in the case of works-for-hire, some authors will not be able to claim copyright ownership. Another example came up at a recent conference, where scholars working with First Nations peoples are granting copyright in research articles to the First Nations peoples. A narrow requirement of author copyright retention would tend to prevent innovations in scholarly copyright at a period in time when I would argue that encouraging experimentation (articulating the commons) is optimal. Plus if a journal retains copyright but is clearly open access, the journal should be included in DOAJ.

Author can post the final, peer-reviewed manuscript version (postprint) to any repository or website (Author Posting Rights Level 2)

Comment: suggest add “at minimum” to encourage the common practice of allowing deposit of any version including the final version. Finally, thanks very much to DOAJ, PLoS and everyone else involved in this initiative and the Open Access Spectrum. While as this post likely makes clear I strongly disagree with many of the specifics, I do greatly appreciate all the work that the people involved in these initiatives have contributed towards open access. Update June 13: PLoS participating in the selection criteria team is a conflict of interest, because PLoS is one open access publisher and what they are attempting to do here is to control the definition of open access – if this is accepted, this will give them a competitive advantage over other open access publishers. Reader comments that meet the standard for commenting on IJPE are welcome, i.e. no anonymous comments and if you work for or are affiliated with a journal, publisher, or other initiative with an interest in these questions this affiliation must be stated in the comment.

Other posts on IJPE on related topics include the Creative Commons and Open Access critique series and through the open access definition label.

MicrobiologyOpen Publishes Issue 2:3

MicrobiologyOpenYou can read Issue 2:3 of MicrobiologyOpen online now!

MicrobiologyOpen is a broad scope, peer reviewed journal delivering rapid decisions and fast publication of microbial science.  The journal gives priority to reports of quality research, pure or applied, that further our understanding of microbial interactions and microbial processes.

Editor-in-Chief, Pierre Cornelis has highlighted the papers below from the latest issue:

purple_lock_openTruncation of type IV pilin induces mucoidy in Pseudomonas aeruginosa strain PAO579
T. Ryan Withers, F. Heath Damron, Yeshi Yin and Hongwei D. Yu

Summary: Schematic diagram of summarizing the induction of alginate production and mucoid conversion by PilA in Pseudomonas aeruginosa strain PAO579. The sigma factor RpoN is required for transcription of pilA108 and algW. PilA108 is transported to the periplasm where it activates the periplasmic protease AlgW which proteolytically degrades the anti-sigma factor MucA releasing the sequestered sigma factor AlgU.

purple_lock_open

A novel l-isoleucine-4?-dioxygenase and l-isoleucine dihydroxylation cascade in Pantoea ananatis
Sergey V. Smirnov, Pavel M. Sokolov, Veronika A. Kotlyarova, Natalya N. Samsonova, Tomohiro Kodera, Masakazu Sugiyama, Takayoshi Torii, Makoto Hibi, Sakayu Shimizu, Kenzo Yokozeki and Jun Ogawa

Summary: The genes encoding HilA and HilB from Pantoea ananatis AJ13355 were cloned and expressed in Escherichia coli. The culturing of E. coli cells expressing hilA (E. coli-HilA) or both hilA and hilB (E. coli-HilAB) in the presence of l-isoleucine resulted in the conversion of l-isoleucine into two novel biogenic compounds: l-4?-isoleucine and l-4,4?-dihydroxyisoleucine, respectively. In parallel, two novel enzymatic activities were detected in the crude cell lysates of the E. coli-HilA and E. coli-HilAB strains: l-isoleucine-4?-dioxygenase (HilA) and l-4?-hydroxyisoleucine-4-dioxygenase (HilB) activities, respectively.

purple_lock_openUbiquitination dynamics in the early-branching eukaryote Giardia intestinalis
Carlos A. Niño, Jenny Chaparro, Paolo Soffientini, Simona Polo and Moises Wasserman

Summary: Ubiquitation is an active and dynamic process in Giardia. Different types of ubiquitin modifications are present in this ancestral unicellular eukaryote and vary in terms of temporal and spatial distribution from trophozoites to cyst maturation. Using a proteomics approach, we identified around 200 high-confidence ubiquitinated candidates that vary their ubiquitination status during differentiation.

Submit you paper here>   Sign up for eToC Alerts here>

Read the June Issue of Cancer Medicine Online Now!

Cancer Medicine

Issue 2:3 of Cancer Medicine is live and available to read online

The journal brings together articles on a range of oncology specialties, covering cancer biology, clinical cancer research and cancer prevention, with authors from across the globe.

Below are some top articles which Editor-in-Chief Prof. Qingyi Wei has highlighted from the issue.  We hope that you enjoy this exciting new content.

purple_lock_open

Prognostic impact and the relevance of PTEN copy number alterations in patients with advanced colorectal cancer (CRC) receiving bevacizumab
Timothy J. Price, Jennifer E. Hardingham, Chee K. Lee, Amanda R. Townsend, Joseph W. Wrin, Kate Wilson, Andrew Weickhardt, Robert J. Simes, Carmel Murone and Niall C. Tebbutt

Summary: Phosphatase and tensin homologue (PTEN) remains controversial as a predictive and prognostic marker. There also remains uncertainty as to the best method to assess PTEN status. Here, we use PTEN copy number and assess the association of outcome and PTEN loss, as defined by copy number variation.

purple_lock_open

A contemporary analysis of morbidity and outcomes in cytoreduction/hyperthermic intraperitoneal chemoperfusion
Michelle Haslinger, Valerie Francescutti, Kristopher Attwood, Judith Andrea McCart, Marwan Fakih, John M. Kane III and Joseph J. Skitzki

Summary: In the contemporary setting, cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (CS/HIPEC) are associated with a low mortality and improved survival. When present, complications are associated with a decreased overall survival. This treatment modality should be considered within the context of multidisciplinary care for select peritoneal carcinomatosis patients.

purple_lock_open

Comparison of the accuracy of Hybrid Capture II and polymerase chain reaction in detecting clinically important cervical dysplasia: a systematic review and meta-analysis
Hung N. Luu, Kristina R. Dahlstrom, Patricia Dolan Mullen, Helena M. VonVille and Michael E. Scheurer

Summary: The selection of a screening test is important to detect clinically relevant cases of Human papillomavirus (HPV) infection while avoiding the unnecessary cost, stress and compromise of the cervix to patients associated with over-treating mild cytological abnormalities. Given the clinical relevance and importance of cervical cancer worldwide, our results support the use of Hybrid Capture II (HCII) in cervical screening programs.

Cancer Medicine is a peer reviewed, interdisciplinary journal providing rapid publication of cutting-edge research from global biomedical researchers across the cancer sciences.

Submit your paper here>    Sign up for eToC Alerts here>

Open Access Empowers 16-year-old Jack Andraka to Create Breakthrough Cancer Diagnostic

Open Access Empowers 16-year-old to Create Breakthrough Cancer Diagnostic: An Interview with Jack Andraka and Dr. Francis Collins, Director of the National Institutes of Health

Jack Andraka is a perfect example of the power of Open Access, the free availability of all academic research articles online with full reuse rights. Only 16 years old, Jack discovered a breakthrough pancreatic cancer diagnostic using carbon nanotubes. Jack’s test costs $0.03 and takes 5 minutes to run with nearly 100% accuracy so far, making it 26,667 times cheaper, 168 times faster, and 400 times more sensitive than the current test commonly used for pancreatic cancer. Jack went on to win the 2012 Intel International Science and Engineering Fair. His story would not be possible without Open Access.

“I hit a lot of paywalls, like you have to pay $40 per article, and unfortunately I couldn’t shell out a lot of that,” said Andraka. “So, instead, I would have to cheat and copy the article title back into Google and look for PDF versions, and a lot of the time I actually found them on the NIH PubMed site.”

Jack has previously said he used free online academic journals “religiously” as well as the National Institute of Health’s online article database, called PubMed Central (PMC). PubMed Central is a centralized database of articles in the biomedical sciences that has become an invaluable resource to students, researchers, and practitioners in the field:

“PubMed Central gets 830,000 hits and about 1.6 million articles downloaded every day,” said Francis S. Collins, M.D., Ph.D., Director of the National Institutes of Health. “We have a policy that papers from NIH-funded researchers must be made available through PubMed Central within 12 months of publication. The goal is that all scientific papers are open access. . . it’s making such a difference.” 

The 2008 NIH policy described by Dr. Collins results in more than 90,000 articles being made freely available through PMC each year. This policy is a strong start, but it only covers a fraction of all the scientific and scholarly articles published annually. This means access barriers still frequently prevent researchers who want to build on the cutting edge from doing so. As Jack says, “There are millions of people like me. If you can just get on Google and Wikipedia and find these amazing articles, we could have this great innovation, but these paywalls are stopping us.”

On February 22nd, the Obama Administration made Open Access “a priority at the highest level,” according to Dr. Collins, by issuing an Executive Directive expanding the NIH policy to require all federal science agencies to make the articles resulting from the research they fund freely available online within 12 months of publication in a journal. This directive is an important step in the right direction.

We need more Jack Andrakas, and Open Access empowers anyone to explore their scientific curiosity freely and make breakthroughs, unexpected or otherwise. As Dr. Collins mentions, “[For] anybody who cares about science, the idea of having Open Access is going to be crucial for the future.”

This interview is presented by the Right to Research Coalition, with support from the Scholarly Publishing and Academic Resources Coalition (SPARC) and the Society for Science and the Public.

For press inquiries, contact Nick Shockey, Director of the Right to Research Coalition
Phone: 202-296-2296
Email: nick [at] arl [dot] org

Open access is global unrestricted access

This post is in response to an initiative to digitize Canadian historical materials ironically “leaked” on Bibliocracy. This leak describes a plan by Canadian and Library and Archives Canada to digitize and put online Canadian historical materials for exclusive access by CRKN members with “open access to Canadians” opened up at a rate of 10% per year. This is described as an opportunity to partner in “Canada’s largest Open Access Initiative”.

There are two major definitional problems with this proposal with respect to open access, and both are major and important problems:

 1. A plan involving exclusive access to subscribers, even for a limited time frame, is NOT open access. There are many toll access publishers that provide free access to back issues of journals in much less then ten years. It would not be acceptable to have this kind of embargoed open access permitted in response to funding agency open access policies. Library associations in Canada and elsewhere have supported strong open access policies; we should not be implementing plans that involve open access definitions that our own community would not consider acceptable.

2. National access is NOT open access. The open access movement is global in scope. There are journals and open access archives in every continent. If we each restricted access to the people in the countries where the works were produced, we would all have a very great deal less. In Canada, it is mind-boggling that anyone would consider putting forth such a proposal. The proportion of the world’s knowledge produced in Canada is small – if each country only gained access to its own cultural and scholarly output, we would not have much. One way to think of this: do we want to U.S. to follow this example? Would we like our free access to PubMed and PubMedCentral switched to U.S. national access?

Anyone who is confused about the meaning of open access should learn the basic definition before using the phrase. I recommend Peter Suber’s short, highly readable and affordable book, “open access”, and/or his free Open Access Overview, and the Budapest Open Access Initiative, for starters. I have developed and taught a course at SLAIS on open access; convened the CLA Task Force on Open Access; and drafted responses to the CIHR open access consultations for CLA and BCLA. Feel free to send questions about open access my way (no charge). There are many other librarians and academics with expertise in OA who would say the same thing.

 One way to engage people like me in this process would be to follow an open meetings approach, as does the Digital Public Library of America. This would be a great way to implement the goals of the Open Government Partnership. There is no good reason for an initiative to digitize and make available Canada’s heritage to be planned behind closed doors. Surely this is not a state secret? Opening up the process can help to avoid errors of this nature – and get Canadian engaged in and excited about the initiative.

RoMEO Updates for May

New publishers:

  • Azad University, Mahlkesi Branch, Mechanical Engineering Department [30/5/13] – Blue
  • Bundesinstitut für Bevölkerungsforschung (Federal Institue for Population Research) – Blue [16/5/13]
  • Church Monuments Society – Yellow [31/5/13]
  • Colegio Oficial de Doctores y Licenciados en Bellas Artes de Andalucía (COLBAA) – Blue [8/5/13]
  • Editorial Delirio – Green [8/5/13]
  • Faculty of 1000 – Green [10/5/13]
  • Göteborgs Universitet, Förvaltningshögskolan – Blue [30/5/13]
  • Higher Education Academy – Yellow [31/5/13]
  • OmniaScience – Blue [8/5/13]
  • PeerJ – Green [16/5/13]
  • Scuola Internazionale Superiore di Studi Avanzati (SISSA) – Blue [30/5/13]
  • Universidad Nove de Julho (UNINOVE) –Blue [8/5/13]
  • University of Kent – Green [30/5/13]
  • University of the Free State, Faculty of Theology – Green [16/5/13]
  • Univerzitet Crne Gore, Biotehnicki Institut Podgorica – Green [17/5/13]

 

Total publishers: 1257 [31/5/13] 3 provisional [24/1/13]

Total added in May: 16

Updated entries

  • American Podiatric Medical Association – Blue to White [3/5/13]
  • Botanical Society of America – added paid option [3/5/13]
  • MIT Press – pre-print and post-print information updated [23/5/13]
  • Portland Press – paid option url [3/5/13]
  • University of California Press [31/5/13] – JSTOR must now be mentioned
  • Wiley-VCH Verlag Berlin to Wiley-VCH Verlag [23/5/13] and removed link to Wiley-Blackwell at request of W-B

 

New Policy Exceptions

  • Institute of Mathematical Statistics
    • OAJ [13/5/13]
  • Ernst und Sohn
    • Online Open [20/5/13]
  • Wiley-Blackwell
    • No OnlineOpen [21/5/13]
  • Wiley-VCH
    • No OnlineOpen [21/5/13]
  • University of Kent
    • Political Almanac [30/5/13]

Open Access Priorities

Michael Eisen is basically right on the fundamentals: There would be a huge conflict of interest if compliance with the White House Open Access (OA) mandate were left to publishers instead of researchers and their institutions, and publishers would do everything possible to sabotage the policy.

Nothing much can be said in favor of David Wojick’s long series of comments except that it is true that Michael’s focus is largely on Gold OA publishing, PMC, and re-use rights (“Libre OA”) over and above free online access rights (“Gratis OA”), whereas the White House Open Access mandate is for Green OA self-archiving in researchers’ OA repositories.

Further re-use rights are also more controversial than free online access rights because they encourage publisher embargoes (to prevent immediate free-riding by rival publishers); nor are they needed nearly as urgently and universally as immediate free online access is needed by authors and users in all disciplines today. (As much Libre OA as users need and authors wish to provide will certainly follow after universal Green Gratis OA has been successfully mandated and provided globally, but it must not be made into a needless obstacle today.)

Sleep May Solve Grammar Gremlins

Beinecke Library

Do you know when to use who versus whom? Affect versus effect? If you’re stumped, first crack open your textbook, but then make sure to get a good night’s sleep – it could help! According to newly published research, sleep plays an important part in learning grammar, and perhaps other complex rules as well.

In their study the researchers used an invented grammar to develop sets of letter sequences. They also assessed each sequence for its “associative chunk strength,” or memorable letter clusters. Sequences with lots of these “chunks” could be easy to memorize, which the authors differentiate from learning, or rule acquisition. Participants were then shown these sequences and asked to recreate them from memory. They were not told that the letter sequences were constructed according to a set of grammatical rules.

The participants then waited 15 minutes, 12 hours, or 24 hours before being tested to see whether they had retained or learned the rules. Participants in the 12 hour group that started in the evening and those in the 24 hour group slept between experimental phases. When the testing began, participants were told that grammatical rules were in use and asked to judge whether letter sequences were grammatical.

Participants that slept between stages, i.e. those in the 12 hour and 24 hour groups, performed significantly better than those who did not sleep prior to the test. Specifically, those who slept between tests were better able to discern grammatical from not-grammatical letter sequences. The same was true for letter sequences with fewer chunks of memorable letter clusters. Their results also indicate that the length of the waiting period, whether it was 15 minutes or hours, did not significantly affect the participants’ performance.

Students, the next time you think you can forgo a good night’s sleep, think again! Sleep may just help you learn those tricky grammatical rules.

Citation: Nieuwenhuis ILC, Folia V, Forkstam C, Jensen O, Petersson KM (2013) Sleep Promotes the Extraction of Grammatical Rules. PLoS ONE 8(6): e65046. doi:10.1371/journal.pone.0065046

Image: Childrens talk, English & Latin by Beinecke Library.

"CHORUS": Yet Another Trojan Horse from the Publishing Industry

The OSTP should on no account be taken in by the Trojan Horse that is being offered by the research publishing industry’s “CHORUS.”

CHORUS is just the latest successor organisation for self-serving anti-Open Access (OA) lobbying by the publishing industry. Previous incarnations have been the “PRISM coalition” and the “Research Works Act.”

1. It is by now evident to everyone that OA is inevitable, because it is optimal for research, researchers, research institutions, the vast R&D industry, students, teachers, journalists and the tax-paying public that funds the research.

2. Research is funded by the public and conducted by researchers and their institutions for the sake of research progress, productivity and applications — not in order to guarantee publishers’ current revenue streams and modus operandi: Research publishing is a service industry and must adapt to the revolutionary new potential that the online era has opened up for research.

3. That is why both research funders (like NIH) and research institutions (like Harvard) — in the US as well as in the rest of the world — are increasingly mandating (requiring) OA: See ROARMAP.

4. Publishers are already trying to delay the potential benefits of OA to research progress by imposing embargoes of 6-12 months or more on research access that can and should be immediate in the online era.

5. The strategy of CHORUS is to try to take the power to provide OA out of the hands of researchers so that publishers gain control over both the timetable and the insfrastructure for providing OA.

6. And, without any sense of the irony, the publisher lobby (which already consumes so much of the scarce funds available for research) is attempting to do this under the pretext of saving “precious research funds” for research!

7. It is for researchers to provide OA, and for their funders and institutions to mandate and monitor OA provision by requiring deposit in their institutional repositories — which already exist, for multiple purposes.

8. Depositing in repositories entails no extra research expense for research, just a few extra keystrokes, from researchers.

9. Institutional and subject repositories keep both the timetable and the insfrastructure for providing OA where it belongs: in the hands of the research community, in whose interests it is to provide OA.

10. The publishing industry’s previous ploys — PRISM and the Research Works Act — were obviously self-serving Trojan Horses, promoting the publishing industry’s interests disguised as the interests of research.

Let the OSTP not be taken in this time either.

Giles, J. (2007) PR’s ‘pit bull’ takes on open access. Nature 5 January 2007.

How to Write a Clinical Case Report

stethoscopeCase reports are important. Although much maligned over the last decade or so, case reports are now more widely recognised for their significant potential benefits: brilliant vehicles for delivering concise clinical-guidance messages to promote best practice; excellent teaching aids in case-based learning; the foundation for subsequent larger research programs; and a very useful training in the art of how to publish pretty-much anything at all.

However these benefits rely on two key challenges; being able to write the report in a clear and engaging way, and then being able to persuade someone else to publish it. I’ll write a few notes below on my views on report-writing, and then in the next blog in this series I’ll touch on publishing tips and strategies.  

As the editor of a new case report journal, Clinical Case Reports, one of the bits of my editor-role I enjoy most is helping authors write and shape their case reports to really drive home their message effectively. My view is that a brilliant report has to be clear, concise and relevant to its audience – like a clinician to clinician telephone referral. The crucial issue about the report’s message, is that it must have one! I read so many case reports which are interesting descriptions, but as the reader I am left thinking… “Yeah, but so what??”. Every case report must set out to tell the readers something they really need to know. This message needs very high external validity – it needs to be practical (people can do ‘it’ if they want to), important (people will see the need to do ‘it’), and generalisable (‘it’ not relating exclusively to only 1 small child in the whole world who has now got better anyway!). And in this last point, I think and hope we are seeing an important evolution in case reports that could have a profound impact on their relevance to clinical medicine. In the past case reports typically had humorous (which was bad), or pseudo-humorous (even worse), titles typically describing a really really rare thing. The rarer the better. Think “The dangers of goat soup”, or the “Rare chance association of Osgood Schlatters disease and pre-tibial tuberculosis in an elderly lady football player.” Two problems here: however hard you try the title will never really be funny; and if the case is truly that rare, why does anyone else need to read about it?

My view is that generalisability is key. The reports which authors should be writing describe important clinical situations which are common, but still cause management problems. Because they are common their message will be relevant to many more clinicians than the once-in-a-lifetime reports, and their important message will make them valuable to read and understand. As we move into a clinical era where practice is increasingly influenced by guidelines and meta-data, if case reports can illustrate how the tricky bits of guidelines or systematic review recommendations can be done in those common situations, then that’s even better still!

3 top tips when writing a case report:

  1. Keep an eye out for challenging cases – they don’t have to be rare.
  2. Select one which has an important message, ideally relevant to lots of other clinicians.
  3. Write the report to focus on the message and present it like the best telephone referral you have ever made.

To see a recent webinar on “How to write Case Reports”, please view this recorded video at: http://bit.ly/videoCR

by Dr. Charles Young, Editor-in-Chief – Clinical Case Reports

Making the News in May

journal.pone.0063556.g001

Laughter, fungi, pipettes and ants – last month, PLOS ONE papers made headlines with an array of research. Here are some of our May media highlights:

Not all laughter is the same and your brain knows it. In recently published research, scientists studied the effects of three types of laughter (joyous, taunting, and “tickling”) on the human brain. Participants listened to recordings of these laugh and were asked to discern the type and count how many bouts had occurred. The researchers found that the participants could discern joyous and taunting laughter at comparable rates and that it was slightly more difficult to discern laughter in response to tickling. Participants were  able to count the number of taunting laughs more accurately than joyous and tickling laughs. Read more about this study in the Huffington Post UK, TIME, and Los Angeles Times.

There are fungi afoot! New research confirms that the chytrid fungus (Batrachochytrium dendrobatis), which has decimated amphibian populations around the world, can be found in frogs in California. Scientists swabbed 201 South African clawed frogs (Xenopus laevis) in the California Academy of Sciences’ collection, 23 of which were caught in California. Eight specimens tested positive for chytrid, including one frog caught in San Francisco County in 2003. This frog species was once imported to aid in pregnancy testing. To read more, visit the National Geographic, Science News, ABC and the Smithsonian blog, Smart News.

Pipettes are a staple lab equipment, but not without their drawbacks. According to a new PLOS ONE paper, certain methods of dispensing and diluting liquids can introduce errors in experimental data. The researchers of this study compared pipetting, or tip-based transfer, with an acoustic dispensing technique and found that laboratory results depended greatly on the dispensing technique. Learn more about this study by reading the Royal Society of Chemistry’s Chemistry World, Nature’s Methagora blog, and In the Pipeline.

There are plenty of odd couples in nature. For one example, just look at the unlikely partnership of the ant and the pitcher plant. A recent study finds that a particular ant species, Camponotus schmitzi, has formed a mutually beneficial relationship with the carnivorous Nepenthes bicalcarata, a pitcher plant. Scientists observed that the ants provide pitcher plants with nitrogen and preys on other insects, such as mosquitoes, that may otherwise steal nutrients from the plant. In return, the pitcher plant provides a home and a steady source of sustenance. You may find more about this study at Discovery News, The Scientist, and the New York Times.

To find out what other PLOS ONE papers were in the news in May, check out our Media Tracking Project.

Image: Figure 1 from “A Novel Type of Nutritional Ant–Plant Interaction: Ant Partners of Carnivorous Pitcher Plants Prevent Nutrient Export by Dipteran Pitcher Infauna”

Citations:

Wildgruber D, Szameitat DP, Ethofer T, Brück C, Alter K, et al. (2013) Different Types of Laughter Modulate Connectivity within Distinct Parts of the Laughter Perception Network. PLoS ONE 8(5): e63441. doi:10.1371/journal.pone.0063441

Vredenburg VT, Felt SA, Morgan EC, McNally SVG, Wilson S, et al. (2013) Prevalence of Batrachochytrium dendrobatidis in Xenopus Collected in Africa (1871–2000) and in California (2001–2010). PLoS ONE 8(5): e63791. doi:10.1371/journal.pone.0063791

Ekins S, Olechno J, Williams AJ (2013) Dispensing Processes Impact Apparent Biological Activity as Determined by Computational and Statistical Analyses. PLoS ONE 8(5): e62325. doi:10.1371/journal.pone.0062325

Scharmann M, Thornham DG, Grafe TU, Federle W (2013) A Novel Type of Nutritional Ant–Plant Interaction: Ant Partners of Carnivorous Pitcher Plants Prevent Nutrient Export by Dipteran Pitcher Infauna. PLoS ONE 8(5): e63556. doi:10.1371/journal.pone.0063556

Academic libraries could fund a fully open access journal system – and save money, too

The title expresses the gist of my article, Economics of scholarly communication in transition, published today in First Monday. Abstract Academic library budgets are the primary source of revenue for scholarly journal publishing. There is more than enough money in the budgets of academic libraries to fund a fully open access scholarly journal publishing system. Seeking efficiencies, such as a reasonable average cost per article, will be key to a successful transition. This article presents macro level economic data and analysis illustrating the key factors and potential for cost savings.

The transnational open access movement: paper to be presented at the Global Communication Association conference in November

My proposal for the Global Communication Association‘s 7th annual conference this November in Ottawa has been accepted! The Global Communication Association is the founder of the innovative suite that is the open access Global Media Journal. The title and abstract of my proposal follows

The transnational open access movement

Open access is literature that is digital, online, and free of most copyright and licensing restrictions (Suber, 2013). The focus of the global open access movement is the scholarly literature, including peer-reviewed journal articles, monographs, and emerging forms of scholarly communication such as research data. The growth in resources that are freely available is remarkable, and the growth rate dramatic (Morrison, 2004 – ). The potential of the open access movement is a global knowledge commons of knowledge, a free pool of all of the knowledge of humankind available to everyone (assuming an internet connection) for free, from which all may draw and all can contribute.

This paper will analyze the global open access movement in the context of the transnational advocacy networks described by Keck and Sikkink (1998). Transnational advocacy networks involve distinct groups working across borders to achieve a common set of goals. Transnational advocacy networks often share a set of motivations, such as the achievement of shared instrumental goals, shared causal ideology, and/or shared principles or values.

The Budapest Open Access Initiative of 2002 defined open access and coalesced this global movement with a common definition and a vision of what open access can achieve which reads: The public good…is the world-wide electronic distribution of the peer-reviewed journal literature and completely free and unrestricted access to it by all scientists, scholars, teachers, students, and other curious minds. Removing access barriers to this literature will accelerate research, enrich education, share the learning of the rich with the poor and the poor with the rich, make this literature as useful as it can be, and lay the foundation for uniting humanity in a common intellectual conversation and quest for knowledge.

After more than a decade, the open access movement has achieved considerable success: more than 8,000 fully open access, peer-reviewed scholarly journals, over 1,200 open access repositories containing millions of items, and over two hundred funding agencies and universities have open access mandate policies.

Areas of emerging division within the open access movement include sub-instrumental goals (e.g. specific definitions, open access journals versus open access archiving), fundamental ideology (e.g. neoliberal emphasis on scholarly publishing as industry versus state subsidy and scholar-led publishing) and fundamental principles and values (sharing the learning of the poor with the rich and the rich with the poor versus fueling capitalist innovation for private profit).

This paper explores the potential for the open access movement as a natural experiment in achieving an effective transnational advocacy network outside of the issues involving obvious harm to human rights identified by Keck and Sikkink as most likely to succeed. The shared basic goal of open access to scholarly works may open up the possibility of a high level global conversation on the impact of neoliberal ideology with scholarly communication as an example. The potential for various participants to overcome differences in sub-instrumental goals to achieve the greater (but less specific) common vision of open access will be explored.

References

Budapest Open Access Initiative (2002). Retrieved April 22, 2013 from http://www.opensocietyfoundations.org/openaccess/read

Keck, M. E., & Sikkink, K. (1998). Activists beyond borders: Advocacy networks in international politics. Ithaca, N.Y.; London: Cornell University Press.

Morrison, H. (2004 – ). The dramatic growth of open access. The imaginary journal of poetic economics. Retrieved April 22, 2013 from http://poeticeconomics.blogspot.ca/2006/08/dramatic-growth-of-open-access-series.html Suber, P. (2013). Open access overview. Retrieved April 22, 2013 from http://legacy.earlham.edu/~peters/fos/overview.htm