Monday, June 18, 2018

Publication disclosure

Sing Chawla D. Most researchers disclose their results before publication. Physics World 2018 May 17

Over two thirds of researchers have released the results of at least one study they authored before the findings were formally published. A survey of more than 7,000 researchers across nine disciplines found that social scientists, mathematicians, biological scientists and those working in agriculture have the highest disclosure rates, around 75%. Most academics do so to get feedback from peers.

Implicit biases

Berg J. Measuring and managing bias. Science 2017;357(6354):849
(doi: 10.1126/science.aap7679)

Implicit biases - those that we are not consciously aware of - are intrinsic human characteristics that should be acknowledged and managed, rather than denied or ignored. Implicit association tests can be a useful tool for understanding and measuring implicit biases. Even those involved in research should consider randomizing and blinding experiments, including animal and other studies, when feasible.

The phrase "necessary and sufficient"

YoshiharaM, Yoshihara M. "Necessary and sufficient" in biology is not necessarily necessary - confusions and erroneous conclusions resulting from misapplied logic in the field of biology, especially neuroscience. Journal of Neurogenetics 2018;32(2):53-64
(doi: 10.1080/01677063.2018.1468443) 

In this article, the authors describe an incorrect use of logic in current biology (especially neuroscience) which involves the careless application of the "necessary and sufficient" (N&S) condition originally used in formal logic. The words N&S are not only misleading, but the way of thinking of researchers when they use them is often incorrect. In most cases, they propose to use "indispensable and inducing".

Friday, June 15, 2018

Preclinical research reporting

Lightfoot H. Reporting of preclinical research: what do we get told - when and how? Medical Writing 2017 (4):20-23
At present, there are no specific requirements for the reporting of preclinical research, and many studies, particularly those with negative results, never get published. However, routine and reliable reporting of all research – preclinical, clinical, laboratory, animal or human based, and with positive or negative outcomes – is essential to the future of collaborative and successful clinical research. There are several new ideas to promote this.

B - Publishing gendered system

Lundine J, Bourgeault IL, Clark J, et al. The gendered system of academic publishing. The Lancet 2018;391(10132):1754-56
(doi: 10.1016/S0140-6736(18)30950-4)

Despite growing numbers of women in the research workforce, most authors, peer reviewers, and editors at academic journals are men. This leads to a women's underrepresentation and disadvantage in other areas of the scientific enterprise. Women receive less research funding, and thus they publish fewer research articles, being less visible and less likely invited as peer reviewers and editors. Editors and publishers should address those gender gaps.

B - A new taxonomy of retractions and corrections

Fanelli D, Ioannidis JPA, Goodman S. Improving the integrity of published science: An expanded taxonomy of retractions and corrections. European Journal of Clinical Investigation 2018;48(4):e12898
(doi: 10.1111/eci.12898)

Journal practices for amending publications offer too little incentives for authors and editors to correct or retract articles when errors have been made. The authors present a a unique and expanded set of amendment formats and procedures, each of which addresses a distinct issue. This new taxonomy integrates and unifies the diversity of formats currently deployed and suggests five new ones.

B - Preproducibility

Stark PB. Before reproducibility must come preproducibility. Nature 2018 May 24
(doi: 10.1038/d41586-018-05256-0)

Most papers fail to report many aspects of an experiment or an analysis that are crucial to understanding the result and its limitations, and to repeating the work. The author proposes a new neologism, "preproducibility", meaning that an experiment or analysis is preproducible if it has been described in adequate detail for others to undertake it. It requires information about materials, instruments and procedures; experimental design; raw data; computational tools used in analyses; and other information.

Friday, June 08, 2018

B - Journal identity theft

Cochran A. Paper accepted... unless the letter was forged. The Scholarly Kitchen 2018 Apr 18

The American Society of Civil Engineers (ASCE) has become aware of seven fake acceptance letters for its journals over the last five years. Someone promised acceptance in a journal and misrepresented a relationship with ASCE. Also a certain number of conferences advertized that the top 10 papers submitted would be sent to one of ASCE journals. The author, ASCE Associate Publisher and Journals Director, suggests adding detailed and complete information to instructions for authors about what an author should expect to happen when submitting a paper.

B - Experimental philosophy

Colombo M, Duev G, Nuijten MB, et al. Statistical reporting inconsistencies in experimental philosophy. PLOS One 2018 Apr 22
(doi: 10.1371/journal.pone.0194360)

Experimental philosophy (x-phi) is a young field of research in the intersection of philosophy and psychology. This article investigated the prevalence of statistical reporting errors in x-phi. Results showed that the rates of inconsistencies in x-phi are lower than in the psychological and behavioural sciences.

B - Anonimity in scientific publishing

Roediger HL. Anonimity in scientific publishing. Observer 2018;31(4)

Is there room for anonymous manuscript submissions and reviews in the era of transparency in science? In this article, the Past President of the Association for Psychological Science (APS) provides some insights in publication practices. Anonymous submission helps researchers who are starting out giving them a shot at a fairer process, but there are counterarguments. And signing reviews represents a danger to young scholars who might be advising rejection of a paper of a someone senior who might later be editor or be asked to write a reference letter for the reviewer.

B - Journal selection criteria

Wijewickrema M, Petras V. Journal selection criteria in an open access environment: A comparison between the medicine and social sciences. Learned Publishing 2017;30(4)
(doi: 10.1002/leap.1113)

This study compares 16 factors that influence journal choices between medicine and social sciences using the answers given to a global survey of 235 open access journal authors. The results reveal that authors of both areas consider "peer reviewed" status as the most important factor. Those in medicine area give more consideration to: impact factor, inclusion in abstracting and indexing services, publisher's prestige, and online submission with tracking facility.

Tuesday, June 05, 2018

B - Do physicians read medical journals?

Packer M. Does anyone read medical journals anymore? Medpage Today 2018 March 28

In the past physicians kept up with the medical literature. But today dutifully physicians just click on the table of contents, and spend less than 30 seconds perusing the titles and rarely click on actual paper. Much of the literature is replete with data and analyses that are satisfying to the authors, but fall unnoticed to possible readers.

B - Analysis on peer review research

Grimaldo F, Marušić A, Squazzoni F. Fragments of peer review: A quantitative analysis of the literature (1969-2015). PLOS ONE 2018 Feb 21
(doi: 10.1371/journal.pone.0193148)

This paper examines research on peer review between 1969 and 2015 by looking at records indexed from the Scopus database. The most prolific and influential scholars, the most cited publications and the most important journals in the field were identified. The number of publications doubled from 2005, with more tradition in the US but with important research groups also in Europe. There is a lack of large-scale, cross-disciplinary collaboration.

B - Open access to bibliographic references

Shotton D. Funders should mandate open citations. Nature 2018 Jan 9

Analyses of citations can reveal how scientific knowledge develops over time and illuminate patterns of authorship. Such information is essential for assessing scholars' influence and making wise decisions about research investment. Bibliographic databases and citation indices are also crucial to individual reasearchers to find relevant papers throughout the literature. According to the author, all publishers must make bibliographic references free to access, analyse and reuse.

B - How to be a great journal editor

How to be a great journal editor: advice from eight top academic editors. Times Higher Education Features 2017, Dec. 14

Editing an academic journal is a vital and rewarding task, but also time-consuming and often frustrating. All eight top academic editors provide a contribution on their experiences  on various issues: peer review, editing a small journal, promoting good science, and other tasks.

Monday, June 04, 2018

B - Detection of duplicated images

Acuna DE, Brookes PS, Kording KP. Bioscience-scale automated detection of figure element reuse. bioRxiv 2018 Feb. 22
(doi: 10.1101/269415)

The authors describe a copy-move detection algorithm that finds reused images in the biological sciences literature even if they have been rotated, resized or had their contrast or colours changed. An analysis of figure element reuse is presented on a large dataset comprising 760,000 open access articles and 2 million figures.

B - Author credit

McNutt MK, Bradford M, Drazen JM, et al. Transparency in authors' contributions and responsibilities to promote integrity in scientific publication. PNAS 2018;201715374
(doi: 10.1073/pnas.1715374115)

The authors, a group of editors and publishers, propose changes to journal authorship policies and procedures to provide insight into which author is responsible for which contributions, assurance that the list is complete, and clearly articulated standards to justify authorship credit. They recommend that journals adopt common and transparent standards for authorship.

B - Population diversity in clinical trials

Knepper TC, McLeod HL. When will clinical trials finally reflect diversity? Nature 2018;557:157-159

Many studies show that the likelihood, nature and severity of side effects from a medication can differ between populations. For this reason, funders and researchers have repeatedly said that clinical trials should include more participants from ethnic minorities. An analysis of drug studies shows that most participants are white, even though trials are being done in more countries.

Tuesday, March 06, 2018

B - Payments from industry

Liu JJ, Bell CM, Matelski JJ, et al. Payments by US pharmaceutical and medical device manufacturers to US medical journal editors: retrospective observational study. BMJ 2017;359:j4619
(doi: 10.1136/bmj.j4619)

The authors found that US industry payments to journal editors are common and often large, particularly for certain subspecialties. Furthermore, many journals lack clear and transparent editorial conflicts of interest (COI) policies and disclosures. Journal editors should reconsider their COI policies and the impact that editor relations with industry may have on public trust in the research enterprise.

B - The choice of titles

Hartley, J. What works for you? The choice of titles for academic articles in higher education. SRHE News Blog May 2017

The range of possible forms of titles available for authors of academic articles in higher education is considerable, but few styles are actually used. This analysis of over 250 titles from the Society for Research into Higher Education (SRHE) abstracts shows that authors in higher education employ colons most, short sentences next and questions least of all.

B - Authorship and citation manipulation

Fong EA, Wilhite AW. Authorship and citation manipulation in academic research. PLoS One 2017;12(12):e0187394
(doi: 10.1371/journal.pone.0187394)

This study builds a framework around how intense competition for journal space and research funding can encourage authorship and citation manipulation. It then uses that framework to develop hypotheses about who manipulates and why they do so.

B - Editors' core competencies

Moher D, Galipeau J, Alam S, et al. Core competencies for scientific editors of biomedical journals: consensus statement. BMC Medicine 2017;15:167
(doi: 10.1186/s12916-017-0927-0)

This article describes the minimum14 key core competencies for scientific editors of biomedical journals. They are divided into three major areas, and each competency has a list of associated elements or descriptions of more specific knowledge, skills, and characteristics that contribute to its fulfillment. These core competencies should be a baseline of the knowledge, skills, and characteristics needed to perform competently the duties of a scientific editor at a biomedical journal.

B - Women's visibility in academic seminars

Carter A, Croft A, Lukas D, et al. Women's visibility in academic seminars: women ask fewer questions than men. arXiv:1711.10985

The authors aimed to determine whether women and men differ in their visibility at academic seminars and which factors might underlie any biases. They examined the women's visibility through the question-asking behaviour at local departmental academic seminars (i.e., talks, presentations, colloquia, etc.). Women audience members asked absolutely and proportionally fewer questions than male. Furthermore, when a man was the first to ask a question, women asked fewer questions. Recommendations for increasing women's visibility are proposed.

B - Resistance to replication

Gertler P, Galiani S, Romero M. How to make replication the norm. Nature 2018;554:417-419

Efforts to replicate research studies are distorted by inherent conflicts between the authors of the original work and those trying to reproduce the results. The authors surveyed 11 top-tier economics journals to find out how to fix it. A first step to getting more replications is making them easier by requiring authors to publicly post the data and code used to produce the results in their studies.

Thursday, February 22, 2018

B - Preprint badges

Davis P. Badges? We don't need no stinking preprint badges! The Scholarly Kitchen 2018 Feb. 14

Authors submitting papers to PLOS journals can now opt to transfer their manuscript automatically to the bioRxiv preprint server. In this arrangement, PLOS will perform the initial screening, which includes checking for plagiarism, previous publication, scope, ethical, and technical criteria before manuscripts are transferred to bioRxiv. It also refers to badges, that is nevertheless used to describe something still undefined, but presumably to serve as a marker to the reader that a preprint has received some as yet unknown level of reviewer/editorial scrutiny/approval.

B - Journal editors core competencies

Matarese V, Shashok K. Improving the biomedical research literature: insights from authors' editors can help journal editors define and refine their core competencies. F1000Research 2018;7:109
(doi: 10.12688/f1000research.13760.2)

Based on their experience as authors' editors, they suggest how to strengthen core competencies for journal editors so that they better respond to the needs of readers and authors. First, journal editors should ensure that authors are given useful feedback on the language and writing beyond a blanket judgement of whether the English is "acceptable" or not. Second, journal editors should be able to deal effectively with inappropriate text re-use and plagiarism.

B - Triangulation

Munafò MR, Smith GD. Robust research needs many lines of evidence. Nature 2018;553(7689):399-401
(doi: 10.1038/d41586-018-01023-3)

Several studies across many fields estimate that only around 40% of published findings can be replicated reliably. But replication is not enough. The authors recommend triangulation, that is the strategic use of multiple approaches to address one question. Each approach has its own unrelated assumptions, strenghts and weaknesses. Results that agree across different methodologies are less likely to be artefacts.

B - Prestigious journals and reliability

Brembs B. Prestigious science journals struggle to reach even average reliability. Frontiers in Human Neuroscience 2018;12:37
(doi: 10.3389/fnhum.2018.00037)

Data from several lines of evidence suggest that the methodological quality of scientific experiments does not increase with increasing rank of the journal. On the contrary, some of the data suggest the inverse: methodological quality and, consequently, reliability of published research works in several fields may be decreasing with increasing journal rank.

B - Communication regulatory science

Noar SM, Cappella JN, Price S. Communication regulatory science: mapping a new field. Health Communication 2017 Dec. 13
(doi: 10.1080/10410236.2017.1407231)

Communication regulatory science is an emerging field that uses validated techniques, tools, and models to inform regulatory actions that promote optimal communication outcomes and benefit the public. This is an opening article to a special issue on communication and tobacco regulatory science, that provides an example of 10 studies that exemplify tobacco regulatory science and demonstrate how the health communication field can affect regulation and benefit public health.

B - Ethical issues on predatory journals

Ferris LE, Winker MA. Ethical issues in publishing in predatory journals. Biochemia Medica 2017; 27(3):031201
(doi: 10.11613/BM.2017.030)

This paper discusses ethical issues around predatory journals and publishing in them. These issues include: misrepresentation; lack of editorial and publishing standards and practices; academic deception; research and funding wasted; lack of archived content; and undermining confidence in research literature.

B - Gender differences in HIV publications

Overbaugh J. Defining the barriers to women publishing in high-impact journals. Journal of Virology 2018 Jan. 24
(doi: 10.1128/JVI.02127-17)

This commentary describes gender differences in publication of HIV-related articles that raise questions about best practices in this important aspect of science.

B - Scientific presentations and writing

Kressmann C, lang S. Six communication rules for scientific presentations and writing. Medical Writing 2017;26(4):46-47

The authors defined six communication rules for scientific writing and presenting. Both presentations and research articles should not be overloaded with details or aspects that contribute nothing to the topic.

B - Database search

Delaney A, Tamás PA. Searching for evidence or approval? A commentary on database search in systematic reviews and alternative information retrieval methodologies. Research Synthesis Methods 2017 Nov. 4
(doi: 10.1002/jrsm.1282)

A commentary on the factors that call into question the appropriateness of default reliance on database searches particularly as systematic review is adapted for use in new and lower consensus fields. It discusses alternative methods for information retrieval.

B - Publications accessibility

Kasdorf B. Why accessibility is hard and how to make it easier: Lessons from publishers. Learned Publishing 2018;31(1):11-18
(doi: 10.1002/leap.1146)

The requirements for providing publications in an accessible form proves difficult to accomplish for most publishers. This article examines the issues that are challenging to publishers and their suppliers, discusses the factors that make them difficult, and suggests strategies as that of building accessibility into the production worflows upfront.

B - Animal research reporting

Osborne NJ, Ritskes-Hoitinga M, Ahluwahlia A, et al. Letter to editor - round table unites to tackle culture change in an effort to improve animal resarch reporting. BMC Veterinary Research 2017;13:314
(doi: 10.1186/s12917-017-1235-9)

A round table meeting was held s on the 25th of September 2017 in Edinburgh to discuss how to enhance the rate at which the quality of reporting animal research can be improved. A signed statement acknowledges the efforts that participant organizations have made towards improving the reporting of animal studies and confirms an ongoing commitment to drive further improvements, calling upon both academics and laboratory animal veterinarians to help make this cultural change.