Wednesday, December 23, 2015

B - Hijacking a journal

Bohannon J. How to hijack a journal. Science 2015;350(6263):903-905
(doi: 10.1126/science.350.6263.903)

In the past few years fraudsters are snatching entire web addresses, right out from under academic publishers, erecting fake versions of their sites, and hijacking their journals, along with their web traffic. The usual method is to build a convincing version of a website at a similar address and then drive web traffic to the fake site. Unsuspecting visitors who log into the hijacked journal sites might give away passwords or money as they try to pay subscriptions or article processing fees.

B - Authorship: myths and misconceptions

Menezes RG, Kharoshah MA, Madadin M, et al. Authorship: few myths and misconceptions. Science and Engineering Ethics e-pub Dec 15 2015;1-5
(doi: 10.1007/s11948-015-9742-1)

This article addresses and dispels some of the popular myths and misconceptions surrounding authorship of a scientific publication as this is often misconstrued by beginners in academia especially those in the developing world. While ethical issues in publishing related to authorship have been increasingly discussed, not much has been written about the myths and misconceptions of who might be an author.

B - Storing and accessing biomedical big data

Bourne PE, Lorsch JR. Green ED. Sustaining the big-data ecosystem. Nature Nov 5 2015;527
(doi: 10.1038/527S16a)

Biomedical big data offer tremendous potential for making discoveries, but the cost of sustaining these digital assets and the resources needed to make them useful have received relatively little attention. Funders should encourage the development of new metrics to ascertain the usage and value of data and when we have a better understanding of data usage, we can develop business models for storing, organizing and accessing them. Tools and rewards that incentivize researchers to submit their data to data resources in ways that maximize both quality and ease of access, are also needed.

B - Why scientists decline to review papers

Breuning M, Backstrom J, Brannon J, et al. Reviewer fatigue? Why scholars decline to review their peer's work. PS: Political Science & Politics 2015;48(4):595-600
(doi: 10.1017/S1049096515000827)          

The double-blind peer review process is central to publishing in academic journals, but it also relies heavily on the voluntarily efforts of anonymous reviewers. To evaluate the degree to which scholars suffer from the resulting “reviewer fatigue,” the authors empirically evaluated the reasons scholars offered when declining to review for the American Political Science Review. Just over one-quarter of them declined requests to review. For those who decline, reviewer fatigue is only one of several reasons: scholars are willing to review but they often face many demands on their time and substantial workloads overall.

B - Double-blind review

Menéndez J. More on double-blind review. APS News 2015;24(10):4

Letter that gives reason why double-blind review should not be optional and also thinks it would be valuable in avoiding institutional or country bias.

B - Internet influence on plagiarism

Ison DC. The influence of the Internet on plagiarism among doctoral dissertations: an empirical study. Journal of Academic Ethics 2015;13(2):151-66
(doi: 10.1007/s10805-015-9233-7)

The online environment is accelerating the decline in academic ethics. This study collected empirical data to investigate the potential influence Internet had on significant higher education artifacts by comparing dissertations written prior to widespread use of the Internet with those written in a period in ubiquitous Internet use. It utilized Doctor of Philosophy (PhD) dissertations written in English and published by accredited universities in the U.S. and Canada. A sample of 384 dissertations were analyzed. Results suggest that the Internet may not be significantly impacting the prevalence of plagiarism in advanced levels of higher education.

B - Retraction policies of top journals

Resnik DB, Wager E, Kissling GE. Retraction policies of top scientific journals ranked by impact factor. Journal of the Medical Library Association 2015;103(3):136-9
(doi: 10.3163/1536-5050.103.3.006)

The purpose of this study was to provide updated information on the retraction policies of major science journals. The specific aims were to: (1) determine the percentage of the top 200 science journals ranked by impact factor that have a retraction policy; (2) analyze the content of journal retraction policies; and (3) ascertain whether having a retraction policy is associated with impact factor, scientific discipline, or status as a review journal. Results showed that the majority of journals had a retraction policy, and almost all of them would retract an article without the authors’ permission. COPE’s guidelines appear to have had a significant influence on journal retraction policies.

Tuesday, December 22, 2015

B - The end of journals

Krumholz HM. The end of journals. Circulation  e-pub Nov. 10, 2015

According to the author, there are at least 9 deficiencies in the current publication model that fuel the sense that journals as we have known them are approaching their final act. Among them: the publication process is too long; the expense of publishing is growing rapidly; the configuration of articles prohibits a comprehensive and in-depth approach to a scientific question; peer review and the journal decision-making process occur without much external scrutiny and transparency; and so on.

Tuesday, October 06, 2015

B - Negative results

Teixeira da Silva JA. Negative results: negative perceptions limit their potential for increasing reproducibility. Journal of Negative Results in Biomedicine 2015;14:12
(doi: 10.1186/s12952-015-0033-9)

Not all negative results in science get published. Part of the problem lies with a traditional mind-set and rigid publishing framework that tends to view negative results in a negative light, or that only tends to reward scientists primarily for presenting positive findings. This opinion piece indicates that in addition to a deficient mind-set, there are also severe limitations in the availability of publishing channels where negative results could get published.

B - Increasing value and reduce waste

Moher D, Glasziou P, Chalmers I, et al. Increasing value and reducing waste in biomedical research: who's listening? The Lancet Sept. 28, 2015
(doi: 10.1016/S0140-6736(15)00307-4)

Published online during the REWARD/EQUATOR Conference in Edinburgh (September 28-30), this review provides some initial observations on the possible effects of The Lancet 2014 series of five reviews showing how dividends from the investment in research might be increased from the relevance and priorities of the questions being asked, to how the research is designed, conducted, and reported. 17 recommendations were addressed to five main stakeholders—funders, regulators, journals, academic institutions, and researchers, Some examples of individual initiatives show ways to reduce waste and increase value in biomedical research.

B - Can a medical researcher have too many publications?

Jorm AF. Can a medical researcher have too many publications? The Medical Journal of Australia 2015;203(5):230-1
(doi: 10.5694/mja15.00194)

Most prolific researchers may not be adhering to authorship guidelines: the author argues that very high publication rates should be seen as indicating poor authorship practices and should be discounted in evaluating track record.

B - The COBWEB randomized controlled trial

Barnes C, Boutron I, Giraudeau B, et al. Impact of an online writing aid tool for writing a randomized trial report: the COBWEB (Consort-based WEB tool) randomized controlled trial. BMC Medicine 2015;13:221
(doi: 10.1186/s12916-015-0460-y)

The authors developed a writing aid tool based on the CONSORT guidelines and its extension for non-pharmacologic treatments to help authors when writing a report of a randomized controlled trial (RCT). They evaluated the impact of this tool on the completeness of reporting of two-arm parallel-group RCTs evaluating pharmacologic and non-pharmacologic interventions.

Thursday, September 24, 2015

B - How to improve the medical research literature

Moher D, Altman DG. Four proposals to help improve the medical research literature. PLoS Medicine 2015;12(9):e1001864
(doi: 10.1371/journal.pmed.1001864)

The authors discuss four potential contributory actions by journals and educational institutions to help increase the value of research articles: publications officers, core competency training of medical editors, training authors to write articles “fit for purpose” , and training peer reviewers. All four ideas need to be piloted and evaluated, and if proven effective, considered for implementation. For ease of presentation and discussion, these ideas are presented separately. At the end, a discussion of possible ways to fund these initiatives.

B - Gender gap in social-science funding

Boyle PJ, Smith LK, Cooper NJ, et al. Women are funded more fairly in social science. Nature 10 Sept. 2015;525:181-183

In the biomedical sciences, women get smaller grants than men in the United States and the United Kingdom. This pattern is evident at different rates across disciplinary domains. The data presented in the article show that there is little difference between female and male social scientists in application rate, success rate and grant size. The authors discuss some lessons that these results may hold for the biomedical sciences.

B - Editorial Board meetings

Cochran A. The value in attending editorial board meetings. The Scholarly Kitchen Apr 9 2015

The author has learned a lot from her own large experience about what makes editorial board meetings successful from the publisher perspective. They are like mini focus groups: you hear about what is going on at the universities, what hot topics are bubbling up in the field, and what the pain points are for authors, reviewers and editors. These meetings are also an opportunity to ask about the competition and to ask about features or services that others are offering and see which the editors think are worthwhile. New product ideas can also come from these meetings. The author gives some advice about managing them.

Monday, September 21, 2015

B - Overflow in science and trust

Siebert S, Machesky LM, Insall RH. Overflow in science and its implications for trust. eLIFE 2015;4:e10825
(doi: 10.7554/eLife.10825)

To explore the question of how the perceived decline in reproducibility and integrity in some areas of science has affected trust in the scientific enterprise, the authors interviewed a number of senior biomedical researchers. The interviews revealed a perceived decline in trust, in large part because the quantity of new data exceeds the ability to process it appropriately. Some suggestions are provided on how this overflow in science can be managed.

B - Scientometric analysis on big data

Vivek KS, Sumit KB, Khushboo S, et al. Scientometric mapping of research on "Big Data". Scientometrics e-pub 9 Sept. 2015
(doi: 10.1007/s11192-015-1729-9)

This paper presents a scientometric analysis of research work done on the emerging area of "Big Data" in the years 2010-2014. The analysis maps comprehensively the parameters of total output, growth of output, authorship and country-level collaboration patterns, major contributors (countries, institutions and individuals), top publication sources, thematic trends and emerging themes in the field.

B - Ethical ambiguity in physics

Ecklund EH, Johnson DR, Matthews KRW. Study highlights ethical ambiguity in physics. Physics Today 2015;68(6):8-10

As part of a study entitled "Ethics Among Physicists in Cross-National Context" the authors interviewed 170 physicists at US and UK universities and the results suggest that ethical issues in physics are not as black and white as many physicists may think. Some narrowly defined unethical conduct as fabrication, falsification and plagiarism while others also included such things as accepting funding for military research, misusing research funds, abusing the peer-review system, misallocating credit and authorship, practicing cronyism, overhyping research results and exploiting subordinates. They suggest that more needs to be done to teach ethics to students and reaffirm ethical practices for research scientists.

B - Open access and peer review system

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

As numbers of published articles rise, the scholarly review system must adapt to avoid unmanageable burdens and slipping standards. The migration of scholarly journals from print to digital increases the burden on reviewers. The increased pressure means that papers are assigned to reviewers who are not experts in the area. They might have the technical ability to evaluate methods and results sections  but lack the expertise to evaluate a full paper, including introduction and discussion. 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.

B - Cluster randomized trials

Meurer WJ, Lewis RJ. Cluster randomized trials evaluating treatments applied to groups. JAMA 2015;313(20):2068-2069
(doi: 10.1001/jama.2015.5199)

Sometimes a new treatment is best introduced to an entire group of patients rather than to individual patients. One approach to evaluate the efficacy of such treatments is to conduct a cluster randomized trial. According to the authors, four points are to be considered when evaluating a cluster randomized trial. Among them, was the use of clustering well justified? Was the intracluster correlation appropriately accounted for in the design, analysis, and interpretationm of the trial?

B - FASTR legislation

Conover E. Getting up to seed on FASTR legislation. APS News 2015;24(8):1-6.

A bill that would mandate public access to federally funded research, the Fair Access to Science and Technology Research Act (FASTR) was approved by the US Senate Committee on Homeland Security and Government Affairs. This would require that peer-reviewed scientific publications from federally funded research be made freely available to the public within a year of publication. The implications of this for journal publishers is discussed.

Monday, September 14, 2015

B - A modern scientific infrastructure

Brembs B. What should a modern scientific structure look like? The Winnower 2015; 2:e143497.72726
(doi: 10.15200/winn.143497.72726)  

A fully functional infrastructure could collect data from each scientist with regard to their productivity (data, code, publications, reviews), popularity (downloads, media presence, citations, recommendations), teaching (hours, topics, teaching material) or service (committees, administration, development). What is required is an integrated, federated and centralized backbone infrastructure, into which such functionalities can be incorporated as plug-ins (or ‘apps’).

B - Access and discovery

Powell A. Availability does not equal access. The Scholarly Kitchen May 21, 2015

The link between access and discovery of information is crucial. Discovery is a complex concept, a web made of tools, technologies, infrastructure and perhaps most importantly, relationships built on an understanding of the needs of users. INASP (an international development charity working with a global network of partners to improve access, production and use of research information and knowledge) is working on each of these aspects with an ultimate goal of bringing them together on a global level.

B - Responding to reviewers

Responding to reviewers. San Francisco Edit 2015

If an author's manuscript has been provisionally accepted, he/she needs to plan a strategy for revising the paper. A list of actions is here presented that will assist authors in resubmitting a revised manuscript and responses to reviewers' comments.

B - Conflict of interest policies

Steinbrook R, Kassirer JP, Angell M. Justifying conflicts of interest in medical journals: a very bad idea. BMJ 2015;350:h2942
(doi: 10.1136/bmj.h2942)

A series of articles in the New England Journal of Medicine (NEJM) has questioned whether the conflict of interest movement has gone too far in its campaign to stop the drug industry influencing the medical profession. In this article three former senior NEJM editors respond with dismay.

B - Peer review

Bornmann L, Haunschild R. The interest of the scientific community in expert opinions from journal peer review procedure. Scientometrics 2015;102(3):2187-2188

The peer review in journals is generally regarded as a closed procedure, where the report can only be seen by the editor and the authors of the paper assessed, and the peer reviewer does not receive any credits for this input. A number of journals have changed over to publishing the expert opinions on manuscripts under the name of the expert. The authors of this article have used the F1000Prime data set to investigate the reception of expert opinions in the scientific community with the help of data from the Mendeley reference manager. As results, a total of only 11 users have saved an expert opinion in their reference manager.

Monday, September 07, 2015

B - Double-blind review

Palus S. Is double-blind review better? APS News 2015;24(7):5-6.

As of March 2015 Nature started offering anonymity for authors, a double-blind peer-review process across all its journals. This article discusses the advantages and problems of double-blind reviewing and describes a number of previous trials of the system. Questions about usefulness of the practice remain.

Thursday, September 03, 2015

B - Updated Good Publication Practice guideline GPP3

Battisti WP, Wager E, Bltzer L, et al. Good Publication Practice for communicating company-sponsored medical research: GPP3. Annals of Internal Medicine e-pub 11 August 2015
The updated Good Publication Practice (GPP) guideline, known as GPP3, builds on earlier versions (originally published in 2003 and updated in 2009 as GPP2) and provides recommendations for individuals and organizations that contribute to the publication of research results sponsored or supported by pharmaceutical, medical device, diagnostics, and biotechnology companies. The recommendations are designed to help individuals and organizations maintain ethical and transparent publication practices and comply with legal and regulatory requirement. The new areas addressed in GPP3 include: guidance on the most recent ICMJE authorship criteria; common issues regarding authorship; improved clarity on author payment and reimbursement; clarification as to what constitutes ghost or guest authorship; the role and benefit of professional medical writers; and guidance for appropriate data sharing. EASE has publicly endorsed GPP3.

B - Open access-first Spanish edition

Suber P. Acceso Abierto. Translation by R. Melero. Toluca, Mexico: National Autonomous University of Mexico; 2015.

This is the first Spanish translation of the Suber's book Open Access, published in 2012. Peter Suber tells us what open access is and isn’t, how it benefits authors and readers of research, how we pay for it, how it avoids copyright problems, how it has moved from the periphery to the mainstream, and what its future may hold. Distilling a decade of Suber’s influential writing and thinking about open access, this is the indispensable book on the subject for researchers, librarians, administrators, funders, publishers, and policy makers.
The original article is available at

Wednesday, July 22, 2015

B - An open research culture

Nosek BA, Alter G, Banks GC, et al. Promoting an open research culture. Science June 2015;348(6242):1422-1425
(doi: 10.1126/science.aab2374)

The Transparency and Openness Promotion (TOP) Committee met in November 2014 and developed guidelines consisting of eight shared standards for open practices across journals. These guidelines could help promote transparency, openness, an reproducibility of scientific research outputs. As the TOP Committee recognized that not all the standards are applicable to all journals or all disciplines, it defined three levels for each standard.

B - The erosion of research integrity

Ellis LM. The erosion of research integrity: the need for cultural change. The Lancet Oncology July 2015;16:752-754
(doi: 10.1016/S1470-2045(15)00085-6)

The success of drug development depends on robust and reproducible preclinical studies. Reports suggest that a high percentage of preclinical studies cannot be reliably reproduced. Causes could be sloppy research and data falsification or even fabrication. The author suggests approaches to improve data reproducibility, and fosters a complete cultural change.

B - Reasons for abandoning clinical trials

Couzin-Frankel J. Researchers seek clear reasons when clinical trials end early. Science July 2015;349(6245):222
(doi: 10.1126/science.349.6245.222)

About 12% of clinical trials are reported to shut down prematurely. Knowing why could help minimize the number of terminated trials going forward. A team of three computational biologists began exploring why clinical trials end prematurely. They looked at all 3122 terminated trials on the registry at the time their study began, and divided the reasons for ending early into "buckets," such as funding, ethical reasons, or business decisions, so they could see the breakdown by category.  but those explanations were often hazy.

Tuesday, June 30, 2015

B - What motivates researchers to write journal articles

Jubb M. Communication or competition: what motivates researchers to write articles for journals?Learned Publishing 2014;27(4): 251-252
(doi: 10.1087/20140403)

The author presents insights on whether competition or communication motivates researchers to write and publish articles in scholarly journals. He discusses the challenges being experienced by these researchers, the importance of informal communication, the use of social media by researchers and the interest of research institutes and other organizations to promote their works.

B - An effective poster presentation

Developing an effective poster presentation. San Francisco Edit 2015

Poster presentations provide an opportunity for researchers to present their work at scientific meetings and are preparatory for publication in a peer-reviewed journal. This brief document gives some advice to help authors in developing an effective poster.

B - Pharmacovigilance medical writing

von Bruchhausen T, Prechtel K. Pharmacovigilance medical writing: an evolving profession. Medical Writing 2015;24(2):66-71
(doi: 10.1179/2047480615Z.000000000287)

The pharmacovigilance medical writer has a key position in the preparation of documents, leading the whole document creation process. This process includes drafting the document, coordinating the input of the involved functions, providing valuable expertise on the required format and contents and detailed guideline knowledge, and coordinating the review and consolidation of comments.

Friday, June 26, 2015

B - Link rot

Perkel JM. The trouble with reference rot. Nature 2015;521(7550):111-112

Computer scientists are trying to shore up broken links in the scholarly literature. Herbert Van de Sompel and Martin Klein were interviewed by the author of this article on the work of the Hiberlink project. They have investigated the extent of reference rot on scholarly domains and their results show an alarming link rot ratio. They have also explored ways to mitigate it through more systematic web archiving practices and link decoration techniques.

B - The history of typography in Print Magazine

Shaw P. The history of typography in Print magazine. Print March 26, 2015

The author charts the bold (and at times, bizarre) evolution of typography within Print magazine in timeline format throughout the last 75 years. The magazine's typography has been an uneven barometer of the typographic trends of those years.

B - Antibody problem

Baker M. Reproducibility crisis: Blame it on the antibodies. Nature 21 May 2015;521:274-276

Antibodies are among the most commonly used tools in biological experiments, but they are littering the field with false findings. A few scientists are pushing for change and are calling for the creation of standards by which antibodies should be made, used and described. Several journals (including Nature) ask authors to make clear that antibodies used in their papers have been profiled for that particular application.

B - SciDetect: a hoax-detecting software

Bohannon J. Hoax-detecting software spots fake papers. Science 3 April 2015;348(6230):18-19

Springer announced the creation of SciDetect, a freely available programme to automatically detect automatically generated papers. The tool uses a statistical technique similar to those used by email spam filters to automatically detect papers created with SCIgen and similar programmes.

B - Misidentified cell lines

Announcement: Time to tackle cells' mistaken identity. Nature 16 April 2015;520:264

This Editorial sets out new ways to tackle the problem of misidentified cell lines.  Changes apply to all Nature journals from 1st May 2015. Authors of papers involving cell lines are asked to check their cell lines against publicly available lists of known misidentified cell lines. If the authors use a known problematic cell line, they are asked to provide a scientific justification for its use, and clearly state its identity in the Methods section.
Authors must report on a cell line's source, authentication testing, and Mycoplasma testing status.  For authentication testing, authors are asked to state the test method, test result, and when testing was last performed.

B - Public availability of data sharing

Aleixandre-Benavent R, Vidal-Infer A, Alonso Arroyo A, et al. Public availability of published research data in substance abuse journals. International Journal of Drug Policy 2014;25(6):1143-1146
(doi: 10.1016/j.drugpo.2014.07.007)

The aim of this study is to analyse the open-data policies concerning the availability of papers and raw data of the scientific research journals listed in the substance abuse area of the Journal Citation Reports (JCR). It also analyzes the relationship between the journal's impact factor and the storage and reuse policies. Results show that most journals support the possibility of data storage in thematic or institutional repositories. Journals accept additional material and reuse of data, but most of them have no specific instructions for authors to follow and present uncertainty as to the possibility of publishing the data on a website.

B - Head-to-head RCTs and industry sponsor

Flacco ME, Manzoli L, Boccia S, et al. Head-to-head randomized trials are mostly industry sponsored and almost always favor the industry sponsor. Journal of Clinical Epidemiology 2015;68(7):811-820
(doi: 10.1016/j.jclinepi.2014.12.016)

To map the current status of head-to-head comparative evidence, the authors analyzed a large sample of recently published head-to-head randomized clinical trials (RCTs) covering a wide range of clinical conditions. They evaluated trials with at least 100 participants and specifically focused on the sponsoring of these trials. The literature of head-to-head RCTs is dominated by the industry. Industry-sponsored comparative assessments systematically yield favorable results for the sponsors, even more so when noninferiority designs are involved.

B - Beyond the impact factor?

Fazel S, Lamsma J. Beyond the impact factor? Evidence Based Mental Health 2015;18:33-35
(doi: 10.1136/eb-2015-102087)

To investigate the possible differences between the Journal Impact Factor (JIF) and new journal metrics, the authors ranked the top 30 journals in the clinical neurosciences (ie, psychology, psychiatry, neuroscience and general medicine) based on their JIF and compared their JIF ranking with one that was a composite score of their JIF, h5-index, Impact per Publication (IPP), Source Normalised Impact per Paper (SNIP)  and SCImago Journal Rank (SJR) rankings. They recommend researchers and funders should support those journals that aim to increase value and reduce waste and consider a range of impacts, including different journal impact factors, when deciding on journal choice.

Wednesday, June 17, 2015

B - Identifying legitimate OA journals

Hill T. Identifying legitimate open access journals: some suggestions from a publisher. Learned Publishing 2015;28(1):59-62
(doi: 10.1087/20150109)

The author provides a set of criteria by which authors and readers can distinguish legitimate open access journals from illegitimate ones. The list is short, but at the same time applicable to a wide range of journals. The criteria refer to the following issues: readers should be considered as customers and should be offered services; journals should be included in databases and indexes (indexing indicates compliance with technical and publishing standards); publishers should be aware of ethical and legal issues and of open access conventions; and integrity of the peer review process and editorial process should be guaranteed.

B - Reporting guidelines

Golub RM, Fontanarosa PB. Researchers, Readers, and reporting guidelines. Writing between the lines. JAMA 2015; 313(16):1625-26
(doi: 10.1001/jama.2015.3837)

Recognizing the potential value of reporting guidelines for the peer review and scientific publication processes, JAMA published several of the initial guidelines, including CONSORT and MOOSE. A guideline checklist assists editors in their assessment of submitted manuscripts; makes it more likely that a published article will include the information to allow a researcher to potentially reproduce a study; helps ensure that the article will include all of the key elements necessary for a reader to conduct a thorough critical appraisal; and helps improve the quality of research and advance patient care.

B - Editorial independence

Bipeta R. Editorial independence in biomedical publishing. Andhra Pradesh Journal of Psychological Medicine 2014;15(2):145-9

The author summarized the published literature related to editorial independence. Editors should ensure that they are not influenced in their decision making. The sole criterion for publication should be merit, and editors should not be biased in their choice. All stakeholders should be careful and feel responsible to ensure editorial independence. These include the editorial team, the authors, the members of associations, and the readers. The author reported the policies by WAME and ICMJE.

B - Ethical ambiguity in physics

Ecklund E,  Howard J , David R, et al. Study highlights ethical ambiguity in physics. Physics Today 2015;68(6):8-10.
As part of a study entitled "Ethics among physicists in cross-national context" the authors interviewed 170 physicists at US and UK universities and the results suggest that ethical issues in physics are not as black and white as many physicists may think. Some narrowly defined unethical conduct as fabrication, falsification and plagiarism while others also included such things as accepting funding for military research, misusing research funds, abusing the peer-review system, misallocating credit and authorship, practicing cronyism, overhyping research results and exploiting subordinates. They suggest that more needs to be done to teach ethics to students and reaffirm ethical practices for research scientists.

Tuesday, June 16, 2015

B - Reporting systematic reviews of IPD

Stewart LA, Clarke M, Rovers M, et al. Preferred reporting items for a systematic review and meta-analysis of individual participant data. The PRISMA-IPD Statement. JAMA 2015;313(16):1657-65
(doi: 10.1001/jama.2015.3656)

PRISMA-IPD (Preferred Reporting Items for Systematic Reviews and Meta-Analyses of Individual Participant Data) is an extension of the PRISMA Statement, tailored to specific requirements of individual participant data (IPD). The PRISMA-IPD checklist includes three new items that address: methods of checking the integrity of the IPD; reporting any important issues that emerge; and exploring variation.

B - "Living figures" make their debut

Singh Chawla D. "Living figures" make their debut. Nature 2015;521(7550):112.
(doi: 10.1038/nature.2015.17382)

The living figure concept fits within a central tenet of F1000’s publishing philosophy, that papers can be continually updated. The online-only open-access site publishes articles immediately with the status ‘Awaiting Peer Review’, then invites scientists to review them and post their data. Authors can then update their articles with new versions. Living figures may allow systematic reviews to be updated rather than published afresh each time. New contributors’ names do appear in the legend of updated figures, and the updated data set and paper get their own DOIs.

Wednesday, April 01, 2015

B - Plain English in medical writing

Reeves A. Time to make it shorter: plain English in our context. Medical Writing 2015;24(1):4-8
(doi: 10.1179/2047480614Z.000000000268)

This article explores the relevance of George Orwell's six rules for clear writing, that he published in 1946, to medical writing. It makes recommendations how to apply them, and adds further rules to contribute to plain English.

B - Declaration of transparency

Catalá-López F, Peiró S, Hutton B, et al. Declaration of transparency: promoting a more complete, honest and adequate publication of scientific articles. Revista Española de Salud Pública 2014;88(2):181-186
(doi: 10.4321/S1135-57272014000200001)

To prevent and detect inappropriate conduct in scientific research, the authors of this article suggest to include a "transparency declaration" from the correspondent author when submitting papers to a journal. It should report that the manuscript submitted is a complete, honest, accurate and transparent manner of the study being reported, that no important aspects have been omitted and that any discrepancies from the study as planned have been in the manuscript.

Monday, March 30, 2015

B - Bibliographical support on quality of medical care

Pastori MM, Sarti M, Pons, M, et al. Assessing the impact of bibliographical support on the quality of medical care in patients admitted to an internal medicine service: a prospective clinical, open, randomised two-arm parallel study. Evidence-Based Medicine 2014;19:163-168
(doi: 10.1136/ebmed-2014-110021)

Some research studies suggest that library services professionally provided have an impact on health outcomes for patients. This study confirmed the feasibility of bibliographical assistance in daily medical practice in an internal medicine service of a non-university hospital in Ticino Canton (Switzerland) . In particular, it was very useful and effective for patient care to have a dedicated physician that daily sends the bibliographical research results by email to the clinical team within 12 h after asking the focused question.

B - Tweeting at scientific conferences

Ekins S, Perlstein EO. Ten simple rules of live tweeting at scientific conferences. PLoS Computational Biology 2014;10(8):e1003789
(doi: 10.1371/journal.pcbi.1003789)

Increasingly, some scientists are using Twitter as a vehicle to summarize presentations and posters at conferences in real time, which is defined as “live tweeting.” The advantage is that the information tweeted is open and free to anyone around the globe. From the authors' experiences, the success of live tweeting appears dependent on the engagement of conference organizers with Twitter and its active encouragement before, during, and after the meeting. The authors propose ten simple rules to encourage live tweeting.

Thursday, March 26, 2015

B - Retractions of scientific publications

Katavić V. Retractions of scientific publications: responsibility and accountability. Biochemia Medica 2014;24(2):217-222
(doi: 10.11613/BM.2014.024)

This evidence-based opinion piece gives a short overview of the increase in retractions of publications in scientific journals and discusses various reasons for that increase. Also discussed are some of the recent prominent cases of scientific misconduct, the number of authors with multiple retractions, and problems with reproducibility of published research. Finally, some of the effects of faulty research on science and society, as well as possible solutions are discussed.

B - Asian science and technology journals

Jang H, Kim H. Research output of science, technology and bioscience publications in Asia. Science Editing 2014;1(2):62-70
(doi: 10.6087/kcse.2014.1.62)

This paper aims to examine science and technology journals in Asia and to find ways to enhance the visibility and frequency of citation of articles. The research output of twelve countries in science and engineering over the last five years is studied, using the Scopus database. Approximately 90% of science papers come from four countries: China, Japan, India, and Korea. The authors find that a predominant number of research papers produced in developing Asian countries are in technology, and that most papers appear to have lower citation rates and are often devaluated.

B - Code share

Code share. (Editorial). Nature 2014;514:536
(doi: 10.1038/514536a)
A core element of many papers is the computercode used by authors in models, simulations and data analysis. In an ideal world, this code would always be transportable and easily used by others. Nature editorial policy now mandates that when code is central to reaching a paper’s conclusions, it requires a statement describing whether that code is available and setting out any restrictions on accessibility.

B - F1000 postpublication peer review service

Waltman L, Costas R. F1000 recommendations as a potential new data source for research evaluation: a comparison with citations. Journal of the Association for Informations Science and Technology 2014;65(3):433-445
(doi: 10.1002/asi.2014.65.issue-3/issuetoc)

Faculty of 1000, abbreviated F1000, and recently renamed F1000Prime, is a commercial online postpublication peer review service for biological and medical research. Reviews are produced by more than 5,000 peer-nominated researchers and clinicians. This article presents a large-scale analysis of F1000 recommendations, focusing in particular on comparing recommendations with citations: about 2% of the publications in the biomedical literature received at least one F1000 recommendation.

B - Data sharing

Yozwiak NL, Schaffner SF, Sabeti PC. Data sharing: make outbreak research open access. Nature 2015;518:477-479
(doi: 10.1038/518477a)

In an increasingly connected world, rapid sequencing, combined with new ways to collect clinical and epidemiological data, could transform our response to outbreaks. But the power of these potentially massive data sets to combat epidemics will be realized only if the data are shared as widely and as quickly as possible. Sharing data is especially important and especially difficult during an outbreak. Currently, no good guidelines exist to ensure that this happens.

B - Features of top-rated gold OA journals

Ennas G, Di Guardo MC. Features of top-rated gold open access journals: an analysis of the scopus database. Journal of Informetrics 2015;9(1)
(doi: 10.1016/j.joi.2014.11.007)

This study aimed to identify the features of top-rated gold open access (OA) journals by testing seven main variables: languages, countries, years of activity and years in the DOAJ repository, publication fee, the field of study, whether the journal has been launched as OA or converted, and the type of publisher. Significant results have been found for all variables, except for the types of publishers, and for born or converted journals.

B - Health care's big data

White SE. A review of big data in health care: challenges and opportunities. Open Access Bioinformatics 2014;6:13-18
(doi: 10.2147/OAB.S50519) 

Health care is a high-data volume industry. A literature review was conducted to identify recent articles about the use of big data in health care. These data has the potential to revamp the process of health care delivery in the US and inform providers about the most efficient and effective treatment pathways. The biggest challenge is determining the proper balance between protecting the patient's information and maintaining the integrity and usability of data.

B - Medical writer learning

Guillemard M. What every medical writer needs to know. Medical Writing 2014;23(2):134-135
(doi: 10.1179/2047480614Z.000000000215)

A medical writer is never done with learning. Learning means getting involved in the digital environment and using tools like social media, websites, and blogs to enhance online presence and develop career. Medical writers should have a strong online presence such as: websites with a portfolio of work, a professional profile on LinkedIn, Twitter, Facebook and Google+ accounts.

Monday, March 23, 2015

B - Academic career

Austin J. What it takes. Science 2014;344(6190):1422
(doi: 10.1126/science.344.6190.1422)

Science Careers posted a widget that lets early-career scientists calculate the probability that they will someday become principal investigators. Four factors are indicated as the most important ingredients of academic career success: be male, be selfish, be elite, publish in journals with high impact factors. They are linked to rigorous, serious, and significant research, and demonstrate the wide gap between science's ideals and incentives. Discovery and solutions to society's most compelling problems should really matter and be rewarded consequently.

B - High-impact-factor syndrome

Caves C.M. High-impact-factor Syndrome. APS News 2014;23(10):8,6

The author discusses the use of the bibliometric high impact factor used as a proxy for assessing a scientist's work, the malign influence this is having. He suggests a number of ways to try to prevent this and to conform to best practices for conducting and evaluating research.

B - Authorship matrix

Clement TP. Authorship matrix: a rational approach to quantify individual contributions and responsibilities in multi-author scientific articles. Science and Engineering Ethics 2014;20:345-361
(doi: 10.1007/s11948-013-9454-3)

The author proposes a rational method for assessing the responsibilities of an author of a  scientific multi-authormanuscript. This new paradigm conceptually divides an article into four basic elements for which individual responsibilities can be assigned: ideas, work, writing, and stewardship. The outcome is an authorship Matrix, that provides all necessary information for deciding the rank of an author.

Wednesday, March 11, 2015

B - Peer review in the digital age

Nicholas D, Watkinson A, Jamali HR, et al. Peer review: still king in the digital age. Learned Publishing 2015;28(1):15-21
(doi: 10.1087/20150104)

The article presents one of the main findings of an international study of 4,000 academic researchers that examined how trustworthiness is determined in the digital environment when it comes to scholarly reading, citing, and publishing. The study shows that peer review is still the most trustworthy characteristic of all. There is, though, a common perception that open access journals are not peer reviewed or do not have proper peer-review systems. Researchers do not trust social media.

B - Identifying legitimate OA journals

Hill T. Identifying legitimate open access journals: some suggestions from a publisher. Learned Publishing 2015;28:59-62
(doi: 10.1087/20150109)

The author outlines a set of criteria by which authors and readers can identify legitimate publishers. These criteria are based on the following considerations: readers should be regarded as customers and they should be offered a variety of services; journals should be included in databases and indexes, that indicates compliance with technical and publishing standards; publishers should ensure that authors meet ethical and legal obligations to maintain the integrity of the literature; they should also demonstrate awareness of open access conventions, and provide information on the nature of the peer-review process and of the editorial process.

B - Gender differences in conference presentations

Jones TM, Fanson KV, Lanfear R, et al. Gender differences in conference presentations: a consequence of selof-selection? PeerJ 2:e627
(doi: 10.7717/peerj.627)   

Women continue to be under-represented in the sciences, with their representation declining at each progressive academic level. The authors compared gender differences in exposure and visibility at an evolutionary biology conference for attendees at two different academic levels: student and post-PhD academic. Women presenters spent on average ∼20% less time presenting their research than men of an equivalent academic level. This highlights important gender differences in conference strategy. Potential underlying reasons for this gender bias are discussed, with recommendations to avoid similar gender biases at future conferences.

B - NIH plans to enhance reproducibility

Collins FS, Tabak LA. Policy: NIH plans to enhance reproducibility. Nature 2014 Jan. 27

The authors discuss the significant initiatives that the US National Institutes of Health is exploring to restore the self-correcting nature of preclinical research. They share the concern that the complex system for ensuring the reproducibility of biomedical research is failing. This has compromised the ability of today’s researchers to reproduce others’ findings demanding immediate and substantive action. The NIH is firmly committed to making systematic changes that should reduce the frequency and severity of this problem.

B - CoBRA: Citation of BioResources in journal Articles

Bravo E, Calzolari A, De Castro P, et al. Developing a guideline to standardize the citation of bioresources in journal articles (CoBRA). BMC Medicine 2015;13:33
(doi: 10.1186/s12916-015-0266-y)

Evaluating bioresources' use and impact requires that scientific publications accurately cite such resources. This article proposes for the first time a guideline for reporting bioresource use in research articles: the CoBRA, Citation of BioResources in journal Articles. Adopting this guideline will improve the quality of bioresource reporting and will allow their traceability in scientific publications, thus increasing the recognition of bioresources' value and relevance to research.

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 Commons (for which the author 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.