Friday, February 06, 2015

N - DOAJ - Fully Functional Now for Application and Reapplication

The Directory of Open Access Journals (DOAJ) is fully functional since 2015-01-23. On this day, publishers were informed via e-mail to reapply now with all their journals which are already in the directory.

DOAJ is already using its new Journal Application Form since 2014-03-19 which grew from 6 to now 58 questions. So far this form was only opened to be used by journals that had not been in the directory before and applied now for the first time. "The simple fact that we now request more information from a publisher upfront means that our editorial team is able to assess a journal’s honesty, transparency and value more effectively than before." (DOAJ 2014a

DOAJ's aim is to become the White Lister for Open Access journals and to end the present dominance of the legally questionable practice of blacklisting Open Access journals. (DOAJ 2014b)
Lot's of work lies before DOAJ's team. Presently, there are a little under 10000 unchecked journals in the directory. 560 new journals were checked based on the new application form since March 2014 (56 journals per month) and included into the directory with the "tick" (Figure 1). For the 10000 journals "there will be a grace period of 12-15 months, depending on how all this will work out." (Bjørnshauge 2014) Journals not having reapplied after the grace period will be kicked out. Until the end of the foreseen grace period the team will have to check 740 journals per month to get it done in time, but it is "depending on how all this will work out".

Figure 1:   Journals checked based on the new application form get this "tick" in the directory

DOAJ is especially keen on six Open Access characteristics (Journal Application Form):
  1. Archiving (Portico, ...)
  2. Article identifier (DOI, ...)
  3. Delivery of metadata to DOAJ
  4. Machine-readable CC licensing information
  5. Either CC BY, CC BY-SA, or CC BY-NC
  6. To have the deposit policy registered (Sherpa/Romeo, ...)
If all six characteristics are given, the journal obtains the DOAJ Seal (which is not yet designed). Up to 2015-01-23, 82 journals of the 560 journals checked got the seal (14.6%). So, the application or reapplication check can have three outcomes:
  1. failed
  2. included without seal
  3. included with seal

Wednesday, January 21, 2015

B - Big data and public health

Khoury MJ, Ioannidis JPA. Big data meets public health. Science 346(6213):1054
(doi: 10.1126/science.aaa2709)

The term “Big Data” refers to volumes of large, complex, linkable information. Beyond genomics and other “omic” fields, Big Data includes medical, environmental, financial, geographic, and social media information. This swell of data will continue to grow. Big Data can improve health by providing insights into the causes and outcomes of disease, better drug targets for precision medicine, and enhanced disease prediction and prevention. But "Big Error" can plague Big Data. The combination of a strong epidemiologic foundation, robust knowledge integration, principles of evidence-based medicine, and an expanded translation research agenda can put Big Data on the right course.

B - A social media trial

Fox CS, Bonaca MA, Ryan JJ, et al. A randomized trial of social media from Circulation. Circulation e-pub November 18, 2014
(doi: 10.1161/CIRCULATIONAHA.114.013509/-/DC1)

In order to determine whether social media exposure to original articles improves article impact metrics, the authors conducted a randomized trial of social media with a focus on short-term impact. Articles from Circulation were randomly assigned to be promoted through the official journal's social media accounts (Facebook and Twitter feeds). The results showed that this social media strategy did not increase the number of times an article was viewed.

B - Post-publication culture

Bastian H. A stronger post-publication culture is needed for better science. PLoS Medicine 2014;11(12):e1001772
(doi: 10.1371/

The author states that both improving research quality and reducing waste in science require a stronger post-publication culture. Today post-publication evaluation is highly fragmented. Dedicated websites have been developed for discussing and sharing research among authors, and PubMed Commnos (for which the autor is editor) enables post-publication commenting and linkages by the PubMed authorship community. Skill developments should be considered in critiquing research, and capturing post-publication intellectual effort more rigorously is essential for better science.

Monday, January 05, 2015

B - Writing publications for advisory boards

Whereat A. Writing publications for advisory boards. Medical Writing 2014;23(4):277-279
(doi: 10.1179/2047480614Z.00000000252)

Medical communication publications are designed to raise awareness of medicines, cosmetics, and technology. These publications ensure that doctors are informed about the role of new and existing medicines and the literature concerning appropriate prescription for specific patient groups. Advisory boards, consisting of clinicians, are well placed to provide this advice. The pharmaceutical industry often supports independent advisory boards to consider current issues in patient care and communicate their opinions on how to best deal with these problems.

Monday, December 22, 2014

B - Medical deontology and ethics

Grammaticos PC. Medical deontology, meetings, journals, candidacy for higher posts and how to better enjoy life. Hellenic Journal of Nuclear Medicine 2014;17(2):85-86

Today few physicians care about medical deontology and medical ethics, that is how to behave and respect others when exercising the medical profession. This paper illustrates with few examples what the situation is at present, including issues as medical meetings and publishing.

B - Public access to clinical study results

Kaiser J. U.S. to expand public access to clinical study results. Science 2014;346(6213):1043

Two U.S. government proposals could expand the amount of data from clinical trials. A draft regulation from the U.S. Department of Health and Human Services would require companies sponsoring clinical trials to report summary results for drugs and devices that are never approved, not just for those that reach the market. And a proposed policy from the National Institutes of Health (NIH) would expand the requirement—which now applies only to trials regulated by the Food and Drug Administration—to all trials funded by the health agency.

B - Peer review quality

Arns M. Open access is tiring out peer reviewers. Nature 2014;515:467

According to the author, as numbers of published articles rise, the scholarly review system must adapt to avoid unmanageable burdens and slipping standards. The result of the increased pressure on peer reviewers is that papers are assigned to reviewers who are not experts in the area. The author suggests a two-tier system, in which some papers are not reviewed before publication at all and are instead subject to a post-publication peer review. This would free up peer reviewers to focus on papers with more direct societal impact, where the question of whether to publish at all is more relevant.

B - What researchers perceive as unpublishable research

Tsou A, Schickore J, Sugimoto CR. Unpublishable research: examining and organizing the "file drawer". Learned Publishing 2014;27(4):253
(doi: 10.1087/20140404)

This articles aimed to explore through a survey what researchers perceive to be 'unpublishable' research. The results suggested  that there is a perceived gap in scholarly communication. In particular, there are several types of research besides negative results that are perceived to be unpublishable yet worthy of publication, and a great diversity within and across disciplines as to what constitutes 'unpublishable' research.

B - Research data and publishing

Murphy F. Data and scholarly publishing: the transforming landscape. Learned Publishing 2014;27:S3-S7
(doi: 10.1087/20140502)

Research data has become an increasingly critical issue for publishers. Introducing a Learned Publishing special issue on research data and publishing, the author outlines some recent initiatives that are responding to policy directives, particularly the Project ODE (Opportunities for Data Exchange), funded by the European Union. She also considers how publishers are working with data and integrating their practices with other collaborative efforts.


B - Writing style: abstract thoughts

Anstey A. Writing style: abstract thoughts. British Journal of Dermatology 2014;171:205-206
(di: 10.1111/bjd.13181)

A well-written abstract is essential to direct potential readers towards your research. Most readers use electronic searches or content lists from favoured journals to identify potentially interesting papers. Data dissemination and retrieval systems operate almost exclusively at the level of titles and abstracts. This article describes main elements for an informative and concise abstract. Some tips from the AMA Manual Style are also included. The author also published Writing style: what's in a title? BJD 2014;170:1003-1004

Friday, December 19, 2014

B - Evidence-based medicine in crisis?

Greenhalgh T, Howick J, Maskrey N. Evidence based medicine: a movement in crisis? BMJ 2014;348:g3725
(doi: 10.1136/bmj.g3725)

The authors argue that, although evidence based medicine has had many benefits, it has also had some negative unintended consequences. They offer a preliminary agenda for the movement’s renaissance, refocusing on providing useable evidence that can be combined with context and professional expertise so that individual patients get optimal treatment.

B - Academia gets social

Owens B. Academia gets social. The Lancet 2014;384:1834-1835

The author examines the rise of academic social networking websites, such as and ResearchGate, and asks researchers how these sites are shaping their careers.  These academic-focused social networks operate much like Facebook or LinkedIn. Researchers upload their latest research publications, and discuss the technical aspects of their work. The number of papers and datasets uploaded is mounting at an exponential rate. The rapid feedback metrics on the number of views and downloads of the papers can help researchers decide where to focus their efforts.

B - The peer review scam

Ferguson C, Marcus A, Oransky I. Publishing: the peer-review scam. Nature 2014;515:480-482

When a handful of authors were caught reviewing their own papers, it exposed weaknesses in modern publishing systems. As the systems are made more technical and automated, there are more ways to game it. Some observers argue for changes to the way that editors assign papers to reviewers, particularly to end the use of reviewers suggested by a manuscript's authors. Journal editors are trying to plug the holes.

Tuesday, December 16, 2014

B - Publishing and evidence-based medicine in Asia

Yamshchikov GV, Schmid GP. Publication practices and attitudes towards evidence-based medicine in central Asia. The Lancet Global Health 2013;1(2):e73-e74
(doi: 10.1016/S2214-109X(13)70022-6)

To assess the current contribution of central Asian scientists to medical science, the authors analyzed the quantity and scope of medical literature from central Asia published between January 2009 and July 2011. To ascertain perceptions of the use of evidence-based medicine (EBM) in central Asia, they also did  interviews with 85 medical scientists, medical educators, and health-care professionals from central Asia. Most respondents thought that EBM is important but not used in health-care decision-making. The results of the study indicate that countries of central Asia still have barriers to integration into world scientific processes.

B - The top 100 papers

Van Noorden R, Maher B, Nuzzo R. The top 100 papers. Nature 2014;514:550-553

Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time. Surprisingly, many of the world’s most famous papers do not make the cut. Most of the 100 papers describe experimental methods or software that have become essential in their fields.
The most cited work in history, for example, is a 1951 paper describing an assay to determine the amount of protein in a solution. It has now gathered more than 305,000 citations. The list of top journals reveals how powerfully research has been affected by computation and the analysis of large data sets. But the position of any particular methods paper or database at the top of the citation charts is also down to luck and circumstance.

B - Compliance of retraction notices with COPE guidelines

Singh Balhara YP, Mishra A. Compliance of retraction notices for retracted articles on mental disorders with COPE guidelines on retraction. Current Science 2014;107(5):757-760

This study aimed at assessing the compliance of retraction notices for articles on mental disorders with COPE guidelines,  and the impact of open access on post-retraction citation of retracted articles. There seemed to be little impact of COPE guidelines on retractions. Free accessibility of the retraction notice was found to have a significant impact on the post-retraction citation of retracted article.

B - Health news and academic press releases

Sumner P, Vivian-Griffiths S, Boivin J, et al. The association between exaggeration in health related science news and academic press releases: retrospective observational study. BMJ 2014;349:g7015
(doi: 10.1136/bmj.g7015)

This article aims to identify the source (press releases or news) of distortions, exaggerations, or changes to the main conclusions drawn from research that could potentially influence a reader’s health related behaviour. Findings show that exaggeration in news is strongly associated with exaggeration in press releases. Improving the accuracy of academic press releases could represent a key opportunity for reducing misleading health related news.

B - Five-step authorship framework

Marušić A, Hren D, Mansi B, et al. Five-step authorship framework to improve transparency in disclosing contributors to industry-sponsored clinical trial publications. BMC Medicine 2014;12(197)

This article describes a research project led by the Medical Publishing Insights and Practices (MPIP) Initiative to identify current challenges when determining authorship for industry-sponsored clinical trials. As a result, the Five-step Authorship Framework was developed to provide a clear and flexible process to facilitate more transparent and consistent  authorship decisions for clinical trial publications, and help readers better assess the credibility of results and perspectives of the authors for medical research more broadly.

Wednesday, October 29, 2014

B - The rise of predatory publishers

Bartholomew RE. Science for sale: the rise of predatory journals. Journal of the Royal Society of Medicine 2014;107(10):384-385
(doi: 10.1177/0141076814548526)

Some unscrupolous publishers are exploiting the open-access (OA) model by corrupting the peer-review process, which is often absent or minimal, and by charging large fees to authors. Such publishers and their journals are referred to as 'predatory'.  Their motivation is the procurement of evaluation and publication fees, While many predatory publications would be easily recognised as such, some are highly sophisticated and operate websites that mirror prominent mainstream journals. Even experienced scientists have been duped into joining the editorial boards of bogus journals, or submitting articles. The peer review remains the benchmark of scientific assessment.

B - Visibility of Argentinean publications

Chinchilla-Rodríguez Z, Miguel S, de Moya-Anegón F. What factors affect the visibility of Argentinean publications in humanities and social sciences in Scopus? Some evidence beyond the geographic realm of research. Scientometrics e-pub 29 August2014
(doi: 10.1007/s11192-014-1414-4)
 Argentina´s patterns of publication in the humanities and social sciences were studied for the period 2003–2012, using the Scopus database and distinguishing the geographic realm of the research. The results indicate that “topics of national scope” have grown and gained international visibility. Citation is apparently not determined only by the geographic realm of research, but also by language of publication, co-authorship, and the profiles of the journals where published.

B - Rubriq: a peer review service

Stemmle L, Collier K. RUBRIQ: tools, services, and software to improve peer review. Learned Publishing 2013;26(4):265-268
(doi: 10.1087/20130406)

The authors describe the Rubriq peer review service. It is an author-pays model that facilitates a fast, independent, and standardized double-blinded peer review from three expert academic reviewers, who are paid for their efforts. This service should improve journal selection, supplement editorial reviews, and make peer review more portable between journals. The reviews are returned to the author in 1-2 weeks. Manuscripts are classified and screened for plagiarism using iThenticate and, after review, they are matched to the most appropriate journals. The authors also tested the usefulness of the Rubriq review with editors, working with six publishers.

B - Research credibility

Ioannidis JPA. How to make more published research true. PLoS Medicine 2014;11(10):e1001747
(doi: 10.1371/journal.pmed.1001747)

Currently, many published research findings are false or exaggerated, and an estimated 85% of research resources are wasted. To improve the credibility and efficiency of scientific research, some practices may help increase the proportion of true research findings. They are: adoption of large-scale collaborative research; replication culture; registration; sharing; reproducibility practices; better statistical methods; standardization of definitions and analyses; more appropriate statistical thresholds; and improvement in study design standards, peer review, reporting and dissemination of research, and training of the scientific workforce.