Wednesday, March 22, 2017

B - Translational medicine data

Satagopam V, Gu W, Eifes S, et al. Integration and visualization of translational medicine data for better understanding of human diseases. Big Data 2016;4(2):97-108
(doi: 10.1089/big.2015.0057)

The authors present an integrated workflow for exploring, analysis, and interpretation of translational medicine data in the context of human health. Three Web services—tranSMART, a Galaxy Server, and a MINERVA platform—are combined into one big data pipeline. Native visualization capabilities enable the biomedical experts to get a comprehensive overview and control over separate steps of the workflow. The workflow is available as a sandbox environment, where readers can work with the described setup themselves. This work shows how visualization and interfacing of big data processing services facilitate exploration, analysis, and interpretation of translational medicine data.

B - Patient perspectives and clinical research

Crowe S, Giles C. Making patient relevant clinical research a reality. BMJ 2016;355:i6627
(doi: 10.1136/bmj.i6627)

A wide gap exists between what generally receives funding and what patients, carers, and the public would like to see examined. Incorporating patient perspectives more thoroughly into clinical research would broaden its scope and help answer the research questions likely to bring about the biggest improvements in our understanding of disease. Nevertheless several problems underlie our current inability to make research relevant to patients and the wider public. The BMJ already insists that all submitted research includes a statement describing how the authors did or did not involve patients. The journal also operates a system of patient peer review. If other medical journals follow suit, the message about patient relevant research is more likely to be heard.

B - Comparison of primary outcomes in protocols

Perlmutter A, Tran VT, Dechartres A, et al. Comparison of primary outcomes in protocols, public clinical-trial registries and publications: the example of oncology trials. Annals of Oncology 2016;mdw682
(doi: 10.1093/annonc/mdw682)

In oncology trials, primary outcome descriptions in are often of low quality and may not reflect what is in the protocol, thus limiting the detection of modifications between planned and published outcomes. The authors compared primary outcomes in protocols, and publications of oncology trials and evaluated the use of as compared with protocols in detecting discrepancies between planned and published outcomes.

Thursday, December 29, 2016

B - How scientists use social media

Collins K, Shiffman D, Rock J. How are scientists using social media in the workplace? PLoS ONE 2016;11(10):e0162680
(doi: 10.1371/journal.pone.0162680)  

This study investigates how a surveyed sample of 587 scientists from a variety of academic disciplines, but predominantly the academic life sciences, use social media to communicate internally and externally. The results demonstrate that while social media usage has yet to be widely adopted, scientists in a variety of disciplines use these platforms to exchange scientific knowledge, generally via either Twitter, Facebook, LinkedIn, or blogs. Few believed that Facebook is suitable for science communication to the general public. Similarly, a high percentage of scientists read science blogs, and approximately half had written their own science blog. Many shared science-themed blogs with their professional colleagues and most believed that blogs have a role to play in increasing public understanding of science. Scientists using Twitter appears to be a new movement,

B - Teaching medical ethics

Sokol D. Teaching medical ethics: useful or useless? BMJ 2016;355:i6415
(doi: 10.1136/bmj.i6415)

Probably for the first time in history, UK trained doctors at all levels, and in all specialties, now receive formal ethics training at medical school. Has it made any difference? It is not known whether teaching ethics to medical students makes any long term difference to their clinical practice,  especially if it is delivered in the early years. According to the author, the bulk of this teaching should take place after qualification, in the clinical setting. Before then, most students care about one thing only: passing exams. Yet, the very presence of ethics in the curriculum is important. It sends a message that ethics is an intrinsic and valued part of medical practice.

B - Publication professionals

Carey LC, Stretton S, Kenreigh CA, et al. High nonpublication rate from publication professionals hinders evidence-based publication practices. PeerJ 2016 May 10;4:e2011
(doi: 10.7717/peerj.2011)

Publication professionals, who are not ghostwriters, work with leading medical researchers and funders around the world to plan and prepare thousands of publications each year. Research presented at ISMPP Annual Meetings has rarely been published in peer-reviewed journals. The high rate of nonpublication by publication professionals has now been quantified and is of concern. Publication professionals should do more to contribute to evidence-based publication practices, including, and especially, their own.

B - Effectiveness of graphical abstracts

Pferschy-Wenzig EM, Pferschy U, Wang D, et al. Does a graphical abstract bring more visibility to your paper? Molecules 2016;21(9):pii: E1247
(doi: 10.3390/molecules21091247)

A graphical abstract (GA) represents a piece of artwork intended to summarize the main findings of an article for readers at a single glance. Many publishers currently encourage authors to supplement their articles with GAs, in the hope that it will result in improved overall visibility of the publication. To test this assumption, the authors statistically compared publications with or without GA published in Molecules between March 2014 and March 2015 with regard to several output parameters reflecting visibility. Contrary to their expectations, manuscripts published without GA performed significantly better in terms of PDF downloads, abstract views, and total citations than manuscripts with GA.

B - Authorship policies

Resnik DB, Tyler AM, Black JR, et al. Authorship policies of scientific journals. Journal of Medical Ethics 2016;42(3):199-202
(doi: 10.1136/medethics-2015-103171)

The authors analysed the authorship policies of a random sample of 600 journals from the Journal Citation Reports database. 62.5% of the journals they sampled had an authorship policy. Journals from the biomedical sciences and social sciences/humanities were more likely to have an authorship policy than journals from the physical sciences, engineering or mathematical sciences. A significant finding of the study is that none of the journals with authorship policies addressed the use of equal contribution statements.

B - ResearchGate

Nicholas D, Clark D, Herman E. ResearchGate: reputation uncovered. Learned Publishing 2016;29(3):173-82

ResearchGate (RG) is a scholarly social network possessing, probably, the most comprehensive set of reputational metrics and has the potential to supplant publishers as the prime deliverer of scholarly reputation. This study aims to assess RG's reputational facilities and its conclusions are: RG provides a rich, albeit confusing, amount of reputational data; struggles with the deployment of alternative, engagement metrics, such as Q&A and follower data, which can lead to reputational anomalies; employs usage data in an especially effective manner; and leads the field in the way it engages with the scholar.

B - Where are the data?

Announcement: where are the data? Editorial. Nature 537;138
(doi: 10.1038/537138a)

Starting September 2016, all research papers accepted for publication in Nature and an initial 12 other Nature titles were required to include information on whether and how others can access the underlying data. These data-availability statements should report the availability of the ‘minimal data set’ necessary to interpret, replicate and build on the findings reported in the paper. Where applicable, they should include details about publicly archived data sets that have been analysed or generated during the study. This new policy will be implemented across the diverse range of Nature journals by early 2017.

Wednesday, December 21, 2016

B - Medical gems

De Faoite D. Medical gems. Medical Writing 2016;2

Every discipline employs its own secretive words – jargon that allows initiates to communicate with one another in a way that excludes others. The world of medicine is no exception. The idioms used by doctors and surgeons range from the humorous to terms which seem designed to deliberately obscure the real meaning of the word. Other phrases stand out simply due to the incongruous pairing of everyday words. This article contains some real-life examples of all these because, as you know, sometimes words have two meanings.

B - If I tweet will you cite?

Tonia T, Van Oyen H, Berger A, et al. If I tweet will you cite? The effect of social media exposure of articles on downloads and citations. International Journal of Public Health 2016;61(4):513-20
(doi: 10.1007/s00038-016-0831-y)

The authors investigated whether exposing scientific papers to social media (blog post, Twitter and Facebook) has an effect on article downloads and citations. Social media exposure did not have a significant effect on traditional impact metrics. However, other metrics may measure the added value that social media might offer to a scientific journal, such as wider dissemination.

B - Scientific crowdfunding projects

Schäfer MS, Metag J, Feustle J, et al. Selling science 2.0: what scientific projects receive crowfunding online? Public Understanding of Science Sep 19, 2016;pii: 0963662516668771

Crowdfunding has emerged as an additional source for financing research in recent years. This study identifies and tests explanatory factors influencing the success of scientific crowdfunding projects by drawing on news value theory, the “reputation signaling” approach, and economic theories of online payment. A standardized content analysis of 371 projects on English- and German-language platforms reveals that each theory provides factors influencing crowdfunding success. It shows that projects presented on science-only crowdfunding platforms have a higher success rate. At the same time, projects are more likely to be successful if their presentation includes visualizations and humor
Furthermore, the security of the payment process has a strong influence on crowdfunding success.

B - Updating of systematic reviews

Garner P, Hopewell S, Chandler J, et al. When and how to update systematic reviews: consensus and checklist. BMJ 2016;354:i3507
(doi: 10.1136/bmj.i3507) 

Updating of systematic reviews is generally more efficient than starting all over again when new evidence emerges, but to date there has been no clear guidance on how to do this. The panel for updating guidance for systematic reviews (PUGs) issued this guidance to help authors of systematic reviews, commissioners, and editors decide when to update a systematic review, and then how to go about updating the review.

B - ISMPP Code of Ethics

International Society for Medical Publication Professionals (ISMPP). Code of Ethics for medical research publication. Principles for publication professionals. Nov. 1, 2016

Following the release of the previous ISMPP Code of Ethics in 2011, this 2016 revision advances ethical best practices, engages a broader community, and incorporates pivotal professional guidelines that have been published since 2011 and changes in legal and regulatory requirements. It also provides fundamental resources addressing good publication practice, recommendations regarding data sharing and increased transparency, and recognized guidelines for the ethical reporting of scientific and medical research.

Tuesday, December 20, 2016

B - Using popular culture in science communication

Zehr EP. With great power comes great responsibility - A personal philosophy for communicating science in society. eNeuro 2016;3(5):ENEURO.0200-16.2016
(doi: 10.1523/ENEURO.0200-16.2016) 

Since science continues to influence more and more aspects of daily life and knowledge, there is a parallel need for communication about science in our society. The article is based mostly on the author's own experiences - as a neuroscientist - using popular culture as the link between science and the general public, e.g., using icons in popular culture to serve as vehicles for communicating science. He discusses the middle-ground hypothesis using popular culture for science communication and applying the FUNnel model, where popular culture is used as a lead-in and wrap-up when discussing science.

B - Quantity and/or quality?

Sandström U, van den Besselaar P. Quantity and/or quality? The importance of publishing many papers. PLoS One 2016;11(11):e0166149
(doi: 10.1371/journal.pone.0166149)

Do highly productive researchers have significantly higher probability to produce top cited papers? Or do high productive researchers mainly produce a sea of irrelevant papers? This study investigates the relation between productivity and production of highly cited papers. Results show that there is not a strong correlation between productivity (number of papers) and impact (number of citations), that also holds for the production of high impact papers: the more papers, the more high impact papers.

B - Use of stings, hoaxes and irony in scientific publishing

Al-Khatib A, Teixeira da Silva JA. Stings, hoaxes and irony breach the trust inherent in scientific publishing. Publishing Research Quarterly 2016;32(3):208-19

The use of stings, hoaxes and irony in academic journals contributes to the overall level of mistrust and erosion of ethical values in science publishing. The authors focused on six such cases, providing a rationale why such studies undermine trust and integrity and why such bogus publications are best left to blogs or non-academic forms of publishing science-related topics.

B - Big data and machine learning

Obermeyer Z,  Emanuel EJ. Predicting the future —  big data, machine learning, and clinical medicine. The New England Journal of Medicine 2016;375:1216-19
(doi: 10.1056/NEJMp1606181)

To be useful, data must be analyzed, interpreted, and acted on. Thus, it is algorithms — not data sets — that will prove transformative. Machine learning will become an indispensable tool for clinicians seeking to truly understand their patients. As patients’ conditions and medical technologies become more complex, the role of machine learning will grow, and clinical medicine will be challenged to grow with it. It will dramatically improve the ability of health professionals to establish a prognosis, displace much of the work of radiologists and anatomical pathologists, and improve diagnostic accuracy.

B - The role of a publications officer

Cobey KD, Galipeau J, Shamseer L, et al. Report on a pilot project to introduce a publications officer. CMAJ 2016;188(12):E279-80.
(doi: 10.1503/cmaj.151340)

The primary objective of a publications officer should be to provide institutional guidance and support to researchers and trainees on how to prepare manuscripts for journal submission as well as advice on publication topics (open access, metrics, ethics and integrity). The authors began a pilot project in which they hired a publications officer at their institution, The Ottawa Hospital Research Institute. Their experience is described.

B - Articles on overuse of medical care

Morgan DJ, Dhruva SS, Wright SM, et al. 2016 Update on medical overuse: a systematic review. JAMA Internal Medicine 2016;176(11):1687-92
(doi: 10.1001/jamainternmed.2016.5381)

Overuse of medical care is an increasingly recognized problem in clinical medicine. This review promotes reflection on the top 10 original research articles published in 2015 that are most likely to reduce overuse of medical care, organized into 3 categories: overuse of testing, overtreatment, and questionable use of services. The number of articles on medical overuse doubled from 2014 to 2015.

B - Citation analysis

Foz CW, Paine CET, Sauterey B. Citations increase with manuscript length, author number, and references cited in ecology journals. Ecology and Evolution 2016;1-10
(doi: 10.1002/ece3.2505)

The authors examined the relationship between citations received and manuscript length, number of authors, and number of references cited for papers published in 32 ecology journals between 2009 and 2012. They found that longer papers, those with more authors, and those that cite more references are cited more. This is likely because longer papers contain more data and ideas and thus have more citable elements. There is also a perception among ecologists that shorter papers are more impactful.

Saturday, October 22, 2016

N - Changes at eLife

eLife, the open-access journal supported by three major research funders (, has announced that it will start charging from 2017. Since its launch in 2012, the journal has had no charges, supported entirely by grants from the funders. The ‘publication fee’ will be $2500. The move is explained in an editorial in the journal, and follows the announcement in June 2016 of continuing investment by the founding organisations. The journal has also announced a partnership with to create an annotation ‘layer’ for eLife.

N - Nature data policy

From September 2016, all research papers accepted for publication in Nature and 12 other Nature journals will have to include a statement on access to the study’s data. e policy, announced in an editorial in Nature will require a statement reporting the availability of the "minimal data set necessary to interpret, replicate and build on the findings reported in the paper" along with details about publicly available data sets and reasons for any access restrictions.

Thursday, October 06, 2016

B - Challenges in altmetrics

Haustein, S. Grand challenges in altmetrics: heterogeneity, data quality and dependencies. Scientometrics 2016;108(1):413-423
(doi: 10.1007/s11192-016-1910-9)

This paper focuses on the current challenges for altmetrics. Heterogeneity, data quality and particular dependencies are identified as the three major issues and discussed in detail with an emphasis on past developments in bibliometrics. The heterogeneity of altmetrics reflects the diversity of the acts and online events, most of which take place on social media platforms. Data quality issues become apparent in the lack of accuracy, consistency and replicability of various altmetrics, which is largely affected by the dynamic nature of social media events. Furthermore altmetrics are shaped by technical possibilities.

B - OA publication fees in Germany

Jahn N, Tullney M. A study of institutional spending on open access publication fees in Germany. PeerJ 2016;4:e2323
(doi: 10.7717/peerj.2323)

This study examines how much German universities and research organisations spent on open access publication fees. According to self-reported cost data from the Open APC initiative, this type of support has grown over the years. Comparing these expenditure with those from Austria and the UK, German open access funding is focused primarily on fully open access journals, raising important questions about hybrid open access journals as a publication venue.

Wednesday, October 05, 2016

B - Truth in science publishing

Südhof TC. Truth in science publishing: a personal perspective. PLoS Biology 2016;14(8):e1002547
(doi: 10.1371/journal.pbio.1002547)

Emerging flaws in the integrity of the peer review system are largely responsible for the validity of published scientific results.. Distortions in peer review are driven by economic forces and enabled by a lack of accountability of journals, editors, and authors. One approach to restoring trust may be to establish basic rules that render peer review more transparent, such as publishing the reviews and monitoring not only the track records of authors but also of editors and journals.

B - A COPE perspective on publishing ethical issues

Pierson CA. Avoiding ethics pitfalls in publishing: a perspective from COPE. Oral Diseases 2016 July 12
(doi: 10.1111/odi.12539)

Throughout its history, the Committee on Publication Ethics (COPE) has provided a forum for discussion about ethical issues related to all aspects of scholarly publishing and developed resources to assist those who write, review, and edit scholarly work. This concise review provides examples of ethical issues related to authoring, reviewing, and editing scholarly manuscripts from the perspective of COPE.

B - Authorship of clinical trial documents

Billiones R. Authorship of clinical trial documents. Medical Writing 2016;25(1):33-35

Authorship of clinical trial documents such as clinical study protocols, clinical study reports, investigator’s brochures and inform ed consent forms has not yet been given much attention. This article looks at the common practices of authorship attribution and signing off on these documents and examines the ICH guidelines.

B - Researchers under cyber attacks

Dadkhah M, Borchardt G, Maliszewski T. Fraud in academic publishing: researchers under cyber attacks. The American Journal of Medicine 2016
(doi: 10.1016/j.amjmed.2016.08.030)

Day by day, researchers receive new suspicious emails in their inboxes. In this short communication the authors review current cyber threats in academic publishing and try to present general guidelines for authors.

B - Publishing elite against impact factor

Callaway E. Beat it, impact factor! Publishing elite turns against controversial metric. Nature 2016;535(7611):210-211

Senior staff at societies and leading journals want to end inappropriate use of impact factor. They say that the measure is a broad-brush indicator of a journal's output and it should not be used as a proxy for the quality of any single article or its authors.


B - Ethical medical communications

Smalley S. Staying ahead of the game in the changing arena of ethical medical communications - Viewpoint of a freelance medical writer. Medical Writing 2016;25(2):13-17

Good publication practices as well as guidelines, regulations, codes of practice, and other guidelines governing pharmaceutical-HCP interactions and promotion of medicines play an important role in professional and ethical medical communication. It is essential for those working in the medical communications sector to stay informed of evolving guidance.