Tuesday, April 04, 2017

B - Institutional OA publishing

Shashok K. Can scientists and their institutions become their own open access publishers? arXiv:1701.02461  

This article offers a personal perspective on the current state of academic publishing, and posits that the scientific community is beset with journals that contribute little valuable knowledge, overload the community's capacity for high-quality peer review, and waste resources. Open access publishing can offer solutions, but commercial journal publishers have influenced open access policies and practices in ways that favor their economic interests. One way to free research from constraints on access is the diamond route of open access publishing, in which institutions and funders that produce new knowledge reclaim responsibility for publication via institutional journals or other open platforms.

Wednesday, March 29, 2017

B - Full discovery: the publisher's role

Dove JG. Full discovery: what is the publisher's role? Learned Publishing 2017;30(1):81-86
(doi: 10.1002/leap.1086)

Efforts over the years to improve content discoverability have made great progress, but an increasing amount of freely available content brings up new issues. Readers of all kinds rely on a variety of ‘discovery pathways’, such as search engines, library systems, and various electronic links, some of which are blind to the content they desire. The National Information Standards Organization (NISO)’s Discovery to Delivery (D2D) Topic Committee has developed a grid comparing various ways in which content is shared with various ways in which users discover such content.This article brings to light a few of the current obstacles and opportunities for innovation by publishers, aggregators, search engines, and library systems.

B - Evidence-based review of Open Access

Tennant JP, Waldner F, Jacques DC, et al. The academic, economic and societal impacts of Open Access: an evidence-based review. F1000Research 2016;5:632
(doi: 10.12688/f1000research.8460.3)

This review presents published evidence of the impact of Open Access on the academy, economy and society. Overall, the evidence points to a favorable impact of OA on the scholarly literature through increased dissemination and reuse. OA has the potential to be a sustainable business venture for new and established publishers, and can provide substantial benefits to research- and development-intensive businesses, including health organisations, volunteer sectors, and technology. The social case for OA is strong, in particular for advancing citizen science initiatives, and leveling the playing field for researchers in developing countries.

B - Accountability in publishing

Mani H. Foot print of a paper: accountability in academic publishing. The Lancet 2016;338(1004):562-563
(doi: 10.1016/S0140-6736(16)31217-X)

At the moment, the publishing process is unaccountable to the readers and is not transparent. In a published paper, there is no record of previous submissions to other journals and the comments it might have received in the journey to the final publication. A transparent and openly recorded submission and review process would result in accountability, improve the quality of papers and the peer review process, and reduce the chances of previously reported systematic cheating. The scientific input of a reviewer can also be included in their academic activities. A database for registering any paper before submission could issue an internationally recognised identification number that could help to track the submissions.

B - Journal self-citations

Heneberg P. From excessive journal self-cites to citation stacking: analysis of journal self-citation kinetics in search for journals, which boost their scientometric indicators. PLoS One 2016;11:e0153730

Little is known about kinetics of journal self-citations. The author hypothesized that they may show a generalizable pattern within particular research fields or across multiple fields. Currently used scientometric indicators provide only limited protection against unethical behaviors. An algorithm is needed to be developed to search for potential citation networks, allowing their efficient elimination. The algorithm could be based on differences in a number of citations received from a respective journal during the impact factor calculation window (post-publication years 1–2) and the number of citations received only later (e.g., post-publication years 4–7).

B - Publication ethics statement

Gasparyan AY, Yessirkepov M, Voronov AA, et al. Statement on publication ethics for editors and publishers. Journal of Korean Medical Science 2016;31(9):1351-1354
(doi: 10.3346/jkms.2016.31.9.1351)

Editors and publishers are frequently encountered with the fast-growing problems of authorship, conflicts of interest, peer review, research misconduct, unethical citations, and inappropriate journal impact metrics. The aim of this Statement is to increase awareness of all stakeholders of science communication of the emerging ethical issues in journal editing and publishing and initiate a campaign of upgrading and enforcing related journal instructions.

B - Systematic reviews

Barbui C, Addis A, Amato L, et al. Can systematic reviews contribute to regulatory decisions? European Journal of Clinical Pharmacology 2017;73(4):507-509
(doi: 10.1007/s00228-016-2194-y)

Discusses the potential usefulness of systematic reviews in responding to regulatory needs. By collecting, analysing and critically appraising all relevant studies on a specific topic, they may be used by different stakeholders as a basis for making clinical and policy recommendations, including regulatory recommendations. They may simultaneously produce new findings and summarize existing knowledge, with the potential of informing regulatory decisions more pragmatically and more rapidly than other research designs.

Tuesday, March 28, 2017

B - How to improve writing


Leventhal P. A checklist to improve your writing. Medical Writing 2017;26(1):

In this article, a checklist of eight items to improve author's writing are provided. Several of the checklist items are discussed in detail in other articles in this issue of Medical Writing, although this article provides explanations and  examples for each item as well as a series of exercises to help put them into practice.

B - Reproducibility

Allison DB, Brown AW, George BJ, et al. Reproducibility: a tragedy of errors. Nature 20163 Feb. 3 530(7588):27-9
(doi: 10.1038/530027a)

Mistakes in peer-reviewed papers are easy to find but hard to fix. Post-publication peer review is not consistent, smooth or rapid. Many journal editors and staff members seemed unprepared or ill-equipped to investigate, take action or even respond. The authors summarized their experience, the main barriers they encountered, and their thoughts on how to make published science more rigorous.

B - Are pseudonyms ethical in publishing?

Teixeira da Silva JA. Are pseudonyms ethical in (science) publishing? Neuroskeptic as a case study. Science and Engeneering Ethics 2016.
(doi: 10.1007/s11948-016-9825-7)

In science publishing, there are increasingly strict rules regarding the use of false identities for authors, the lack of institutional or contact details, and the lack of conflicts of interest, and such instances are generally considered to be misconduct. The author focuses on Neuroskeptic, a highly prominent science critic, primarily on the blogosphere and in social media, highlighting the dangers associated with the use of pseudonyms in academic publishing.

B - India's publication in predatory journals

Seethapathy GS, Santhosh Kumar JU, Hareesha AS.  India's scientific publication in predatory journals: need for regulating quality of Indian science and education. Current Science 2016;111(11):1759-1763
The objective of this study was to estimate which category of educational and research institutes predominantly publishes in predatory open access journals in India and to understand whether academicians in India are aware of predatory journals. Results showed that India is lacking in monitoring the research carried out in higher educational and research institutes.


B- Writing an effective article submission letter

Writing an effective journal article submission cover letter. San Francisco Edit 2017

The journal editor is going to decide whether to send the article to the reviewers by reading the letter and the abstract of your manuscript. The cover letter is an important component of the submission process. It should contain information which will generate interest and encourage the journal editor to evaluate the manuscript.

B - History of peer review

Baldwin M. In referees we trust? Physics Today 2017;70(2):44-49
(doi: 10.1063/PT.3.3463)
The imprimatur bestowed by peer review has a history that is both shorter and more complex than many scientists realize. This article reviews the history of peer review both for journals and grant-giving  bodies and reveals that it has had many changes only becoming the standard for scientific acceptability relatively recently. It discusses the present situation and the pressures it faces today.

B - Review of altmetrics

Gonzalez-Valiente CL, Pacheco-Mendoza J, Arencibia-Jorge R. A review of altmetrics as an emerging discipline for research evaluation. Learned Publishing 2016;29(4).229-238
(doi: 10.1002/leap.1043)

This article analyses the scientific production of publications on altmetrics as an emergent discipline for research evaluation with the aim to identify the investigative tendencies that characterize the subject. About 253 documents indexed by Web of Science and Scopus databases were retrieved, showing a growth in articles 2005–2015. Half of the publications come from the USA and the UK.
The highest co-occurrence of terms was social media-altmetrics, followed by Twitter-altmetrics.

B - Evolution of impact and productivity

Sinatra R, Wang D, Deville P, et al. Quantifying the evolution of individual scientific impact. Science 2016;354(6312)
doi: 10.1126/science.aaf5239

Are there quantifiable patterns behind a successful scientific career? Sinatra et al. analyzed the publications of 2,887 physicists, as well as data on scientists publishing in a variety of fields. They quantified the changes in impact and productivity throughout a career in science, finding that impact, as measured by influential publications, is distributed randomly within a scientist’s sequence of publications.

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 ClinicalTrials.gov 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, ClinicalTrials.gov and publications of oncology trials and evaluated the use of ClinicalTrials.gov 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.