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. http://www.biomedcentral.com/1741-7015/13/221

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 https://mitpress.mit.edu/books/open-access

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 ClinicalTrials.gov 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.