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The Post-Embargo Open Access Citation Advantage: It Exists (Probably), It’s Modest (Usually), and the Rich Get Richer (of Course)

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Many studies show that open access (OA) articles—articles from scholarly journals made freely available to readers without requiring subscription fees—are downloaded, and presumably read, more often than closed access/subscription-only articles. Assertions that OA articles are also cited more often generate more controversy. Confounding factors (authors may self-select only the best articles to make OA; absence of an appropriate control group of non-OA articles with which to compare citation figures; conflation of pre-publication vs. published/publisher versions of articles, etc.) make demonstrating a real citation difference difficult. This study addresses those factors and shows that an open access citation advantage as high as 19% exists, even when articles are embargoed during some or all of their prime citation years. Not surprisingly, better (defined as above median) articles gain more when made OA.

Material Type: Reading

Author: Jim Ottaviani

Comparison of registered and published outcomes in randomized controlled trials: a systematic review

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Clinical trial registries can improve the validity of trial results by facilitating comparisons between prospectively planned and reported outcomes. Previous reports on the frequency of planned and reported outcome inconsistencies have reported widely discrepant results. It is unknown whether these discrepancies are due to differences between the included trials, or to methodological differences between studies. We aimed to systematically review the prevalence and nature of discrepancies between registered and published outcomes among clinical trials. Methods We searched MEDLINE via PubMed, EMBASE, and CINAHL, and checked references of included publications to identify studies that compared trial outcomes as documented in a publicly accessible clinical trials registry with published trial outcomes. Two authors independently selected eligible studies and performed data extraction. We present summary data rather than pooled analyses owing to methodological heterogeneity among the included studies. Results Twenty-seven studies were eligible for inclusion. The overall risk of bias among included studies was moderate to high. These studies assessed outcome agreement for a median of 65 individual trials (interquartile range [IQR] 25–110). The median proportion of trials with an identified discrepancy between the registered and published primary outcome was 31 %; substantial variability in the prevalence of these primary outcome discrepancies was observed among the included studies (range 0 % (0/66) to 100 % (1/1), IQR 17–45 %). We found less variability within the subset of studies that assessed the agreement between prospectively registered outcomes and published outcomes, among which the median observed discrepancy rate was 41 % (range 30 % (13/43) to 100 % (1/1), IQR 33–48 %). The nature of observed primary outcome discrepancies also varied substantially between included studies. Among the studies providing detailed descriptions of these outcome discrepancies, a median of 13 % of trials introduced a new, unregistered outcome in the published manuscript (IQR 5–16 %). Conclusions Discrepancies between registered and published outcomes of clinical trials are common regardless of funding mechanism or the journals in which they are published. Consistent reporting of prospectively defined outcomes and consistent utilization of registry data during the peer review process may improve the validity of clinical trial publications.

Material Type: Reading

Authors: Christopher W. Jones, Lukas G. Keil, Melissa C. Caughey, Timothy F. Platts-Mills, Wesley C. Holland

Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals

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Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data and code policy adoption as a function of impact factor and publisher and find higher impact journals more likely to have open data and code policies and scientific societies more likely to have open data and code policies than commercial publishers. We also find open data policies tend to lead open code policies, and we find no relationship between open data and code policies and either supplemental material policies or open access journal status. Of the journals in this study, 38% had a data policy, 22% had a code policy, and 66% had a supplemental materials policy as of June 2012. This reflects a striking one year increase of 16% in the number of data policies, a 30% increase in code policies, and a 7% increase in the number of supplemental materials policies. We introduce a new dataset to the community that categorizes data and code sharing, supplemental materials, and open access policies in 2011 and 2012 for these 170 journals.

Material Type: Reading

Authors: Peixuan Guo, Victoria Stodden, Zhaokun Ma

P values in display items are ubiquitous and almost invariably significant: A survey of top science journals

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P values represent a widely used, but pervasively misunderstood and fiercely contested method of scientific inference. Display items, such as figures and tables, often containing the main results, are an important source of P values. We conducted a survey comparing the overall use of P values and the occurrence of significant P values in display items of a sample of articles in the three top multidisciplinary journals (Nature, Science, PNAS) in 2017 and, respectively, in 1997. We also examined the reporting of multiplicity corrections and its potential influence on the proportion of statistically significant P values. Our findings demonstrated substantial and growing reliance on P values in display items, with increases of 2.5 to 14.5 times in 2017 compared to 1997. The overwhelming majority of P values (94%, 95% confidence interval [CI] 92% to 96%) were statistically significant. Methods to adjust for multiplicity were almost non-existent in 1997, but reported in many articles relying on P values in 2017 (Nature 68%, Science 48%, PNAS 38%). In their absence, almost all reported P values were statistically significant (98%, 95% CI 96% to 99%). Conversely, when any multiplicity corrections were described, 88% (95% CI 82% to 93%) of reported P values were statistically significant. Use of Bayesian methods was scant (2.5%) and rarely (0.7%) articles relied exclusively on Bayesian statistics. Overall, wider appreciation of the need for multiplicity corrections is a welcome evolution, but the rapid growth of reliance on P values and implausibly high rates of reported statistical significance are worrisome.

Material Type: Reading

Authors: Ioana Alina Cristea, John P. A. Ioannidis

A reputation economy: how individual reward considerations trump systemic arguments for open access to data

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Open access to research data has been described as a driver of innovation and a potential cure for the reproducibility crisis in many academic fields. Against this backdrop, policy makers are increasingly advocating for making research data and supporting material openly available online. Despite its potential to further scientific progress, widespread data sharing in small science is still an ideal practised in moderation. In this article, we explore the question of what drives open access to research data using a survey among 1564 mainly German researchers across all disciplines. We show that, regardless of their disciplinary background, researchers recognize the benefits of open access to research data for both their own research and scientific progress as a whole. Nonetheless, most researchers share their data only selectively. We show that individual reward considerations conflict with widespread data sharing. Based on our results, we present policy implications that are in line with both individual reward considerations and scientific progress.

Material Type: Reading

Authors: Benedikt Fecher, Marcel Hebing, Sascha Friesike, Stephanie Linek

The effect of publishing peer review reports on referee behavior in five scholarly journals

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To increase transparency in science, some scholarly journals are publishing peer review reports. But it is unclear how this practice affects the peer review process. Here, we examine the effect of publishing peer review reports on referee behavior in five scholarly journals involved in a pilot study at Elsevier. By considering 9,220 submissions and 18,525 reviews from 2010 to 2017, we measured changes both before and during the pilot and found that publishing reports did not significantly compromise referees’ willingness to review, recommendations, or turn-around times. Younger and non-academic scholars were more willing to accept to review and provided more positive and objective recommendations. Male referees tended to write more constructive reports during the pilot. Only 8.1% of referees agreed to reveal their identity in the published report. These findings suggest that open peer review does not compromise the process, at least when referees are able to protect their anonymity.

Material Type: Reading

Authors: Bahar Mehmani, Emilia López-Iñesta, Flaminio Squazzoni, Francisco Grimaldo, Giangiacomo Bravo

Data sharing in PLOS ONE: An analysis of Data Availability Statements

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A number of publishers and funders, including PLOS, have recently adopted policies requiring researchers to share the data underlying their results and publications. Such policies help increase the reproducibility of the published literature, as well as make a larger body of data available for reuse and re-analysis. In this study, we evaluate the extent to which authors have complied with this policy by analyzing Data Availability Statements from 47,593 papers published in PLOS ONE between March 2014 (when the policy went into effect) and May 2016. Our analysis shows that compliance with the policy has increased, with a significant decline over time in papers that did not include a Data Availability Statement. However, only about 20% of statements indicate that data are deposited in a repository, which the PLOS policy states is the preferred method. More commonly, authors state that their data are in the paper itself or in the supplemental information, though it is unclear whether these data meet the level of sharing required in the PLOS policy. These findings suggest that additional review of Data Availability Statements or more stringent policies may be needed to increase data sharing.

Material Type: Reading

Authors: Alicia Livinski, Christopher W. Belter, Douglas J. Joubert, Holly Thompson, Lisa M. Federer, Lissa N. Snyders, Ya-Ling Lu

Badges to Acknowledge Open Practices: A Simple, Low-Cost, Effective Method for Increasing Transparency

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Beginning January 2014, Psychological Science gave authors the opportunity to signal open data and materials if they qualified for badges that accompanied published articles. Before badges, less than 3% of Psychological Science articles reported open data. After badges, 23% reported open data, with an accelerating trend; 39% reported open data in the first half of 2015, an increase of more than an order of magnitude from baseline. There was no change over time in the low rates of data sharing among comparison journals. Moreover, reporting openness does not guarantee openness. When badges were earned, reportedly available data were more likely to be actually available, correct, usable, and complete than when badges were not earned. Open materials also increased to a weaker degree, and there was more variability among comparison journals. Badges are simple, effective signals to promote open practices and improve preservation of data and materials by using independent repositories.

Material Type: Reading

Authors: Agnieszka Slowik, Brian A. Nosek, Carina Sonnleitner, Chelsey Hess-Holden, Curtis Kennett, Erica Baranski, Lina-Sophia Falkenberg, Ljiljana B. Lazarević, Mallory C. Kidwell, Sarah Piechowski, Susann Fiedler, Timothy M. Errington, Tom E. Hardwicke

A proposal for the future of scientific publishing in the life sciences

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Science advances through rich, scholarly discussion. More than ever before, digital tools allow us to take that dialogue online. To chart a new future for open publishing, we must consider alternatives to the core features of the legacy print publishing system, such as an access paywall and editorial selection before publication. Although journals have their strengths, the traditional approach of selecting articles before publication (“curate first, publish second”) forces a focus on “getting into the right journals,” which can delay dissemination of scientific work, create opportunity costs for pushing science forward, and promote undesirable behaviors among scientists and the institutions that evaluate them. We believe that a “publish first, curate second” approach with the following features would be a strong alternative: authors decide when and what to publish; peer review reports are published, either anonymously or with attribution; and curation occurs after publication, incorporating community feedback and expert judgment to select articles for target audiences and to evaluate whether scientific work has stood the test of time. These proposed changes could optimize publishing practices for the digital age, emphasizing transparency, peer-mediated improvement, and post-publication appraisal of scientific articles.

Material Type: Reading

Authors: Bodo M. Stern, Erin K. O’Shea

Sharing Detailed Research Data Is Associated with Increased Citation Rate

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Background Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available. Principal Findings We examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. The 48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with a 69% increase in citations, independently of journal impact factor, date of publication, and author country of origin using linear regression. Significance This correlation between publicly available data and increased literature impact may further motivate investigators to share their detailed research data.

Material Type: Reading

Authors: Douglas B. Fridsma, Heather A. Piwowar, Roger S. Day

A checklist is associated with increased quality of reporting preclinical biomedical research: A systematic review

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Irreproducibility of preclinical biomedical research has gained recent attention. It is suggested that requiring authors to complete a checklist at the time of manuscript submission would improve the quality and transparency of scientific reporting, and ultimately enhance reproducibility. Whether a checklist enhances quality and transparency in reporting preclinical animal studies, however, has not been empirically studied. Here we searched two highly cited life science journals, one that requires a checklist at submission (Nature) and one that does not (Cell), to identify in vivo animal studies. After screening 943 articles, a total of 80 articles were identified in 2013 (pre-checklist) and 2015 (post-checklist), and included for the detailed evaluation of reporting methodological and analytical information. We compared the quality of reporting preclinical animal studies between the two journals, accounting for differences between journals and changes over time in reporting. We find that reporting of randomization, blinding, and sample-size estimation significantly improved when comparing Nature to Cell from 2013 to 2015, likely due to implementation of a checklist. Specifically, improvement in reporting of the three methodological information was at least three times greater when a mandatory checklist was implemented than when it was not. Reporting the sex of animals and the number of independent experiments performed also improved from 2013 to 2015, likely from factors not related to a checklist. Our study demonstrates that completing a checklist at manuscript submission is associated with improved reporting of key methodological information in preclinical animal studies.

Material Type: Reading

Authors: Doris M. Rubio, Janet S. Lee, Jill Zupetic, John P. Pribis, Joo Heung Yoon, Kwonho Jeong, Kyle M. Holleran, Nader Shaikh, SeungHye Han, Tolani F. Olonisakin

Poor statistical reporting, inadequate data presentation and spin persist despite editorial advice

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The Journal of Physiology and British Journal of Pharmacology jointly published an editorial series in 2011 to improve standards in statistical reporting and data analysis. It is not known whether reporting practices changed in response to the editorial advice. We conducted a cross-sectional analysis of reporting practices in a random sample of research papers published in these journals before (n = 202) and after (n = 199) publication of the editorial advice. Descriptive data are presented. There was no evidence that reporting practices improved following publication of the editorial advice. Overall, 76-84% of papers with written measures that summarized data variability used standard errors of the mean, and 90-96% of papers did not report exact p-values for primary analyses and post-hoc tests. 76-84% of papers that plotted measures to summarize data variability used standard errors of the mean, and only 2-4% of papers plotted raw data used to calculate variability. Of papers that reported p-values between 0.05 and 0.1, 56-63% interpreted these as trends or statistically significant. Implied or gross spin was noted incidentally in papers before (n = 10) and after (n = 9) the editorial advice was published. Overall, poor statistical reporting, inadequate data presentation and spin were present before and after the editorial advice was published. While the scientific community continues to implement strategies for improving reporting practices, our results indicate stronger incentives or enforcements are needed.

Material Type: Reading

Authors: Annie A. Butler, Joanna Diong, Martin E. Héroux, Simon C. Gandevia

Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

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Currently, there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature. According to a previous evaluation of 441 biomedical journals articles published in 2000–2014, the biomedical literature largely lacked transparency in important dimensions. Here, we surveyed a random sample of 149 biomedical articles published between 2015 and 2017 and determined the proportion reporting sources of public and/or private funding and conflicts of interests, sharing protocols and raw data, and undergoing rigorous independent replication and reproducibility checks. We also investigated what can be learned about reproducibility and transparency indicators from open access data provided on PubMed. The majority of the 149 studies disclosed some information regarding funding (103, 69.1% [95% confidence interval, 61.0% to 76.3%]) or conflicts of interest (97, 65.1% [56.8% to 72.6%]). Among the 104 articles with empirical data in which protocols or data sharing would be pertinent, 19 (18.3% [11.6% to 27.3%]) discussed publicly available data; only one (1.0% [0.1% to 6.0%]) included a link to a full study protocol. Among the 97 articles in which replication in studies with different data would be pertinent, there were five replication efforts (5.2% [1.9% to 12.2%]). Although clinical trial identification numbers and funding details were often provided on PubMed, only two of the articles without a full text article in PubMed Central that discussed publicly available data at the full text level also contained information related to data sharing on PubMed; none had a conflicts of interest statement on PubMed. Our evaluation suggests that although there have been improvements over the last few years in certain key indicators of reproducibility and transparency, opportunities exist to improve reproducible research practices across the biomedical literature and to make features related to reproducibility more readily visible in PubMed.

Material Type: Reading

Authors: John P. A. Ioannidis, Joshua D. Wallach, Kevin W. Boyack

A study of the impact of data sharing on article citations using journal policies as a natural experiment

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This study estimates the effect of data sharing on the citations of academic articles, using journal policies as a natural experiment. We begin by examining 17 high-impact journals that have adopted the requirement that data from published articles be publicly posted. We match these 17 journals to 13 journals without policy changes and find that empirical articles published just before their change in editorial policy have citation rates with no statistically significant difference from those published shortly after the shift. We then ask whether this null result stems from poor compliance with data sharing policies, and use the data sharing policy changes as instrumental variables to examine more closely two leading journals in economics and political science with relatively strong enforcement of new data policies. We find that articles that make their data available receive 97 additional citations (estimate standard error of 34). We conclude that: a) authors who share data may be rewarded eventually with additional scholarly citations, and b) data-posting policies alone do not increase the impact of articles published in a journal unless those policies are enforced.

Material Type: Reading

Authors: Allan Dafoe, Andrew K. Rose, Don A. Moore, Edward Miguel, Garret Christensen

Attitudes towards animal study registries and their characteristics: An online survey of three cohorts of animal researchers

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Objectives Prospective registration of animal studies has been suggested as a new measure to increase value and reduce waste in biomedical research. We sought to further explore and quantify animal researchers’ attitudes and preferences regarding animal study registries (ASRs). Design Cross-sectional online survey. Setting and participants We conducted a survey with three different samples representing animal researchers: i) corresponding authors from journals with high Eigenfactor, ii) a random Pubmed sample and iii) members of the CAMARADES network. Main outcome measures Perceived level of importance of different aspects of publication bias, the effect of ASRs on different aspects of research as well as the importance of different research types for being registered. Results The survey yielded responses from 413 animal researchers (response rate 7%). The respondents indicated, that some aspects of ASRs can increase administrative burden but could be outweighed by other aspects decreasing this burden. Animal researchers found it more important to register studies that involved animal species with higher levels of cognitive capabilities. The time frame for making registry entries publicly available revealed a strong heterogeneity among respondents, with the largest proportion voting for “access only after consent by the principal investigator” and the second largest proportion voting for “access immediately after registration”. Conclusions The fact that the more senior and experienced animal researchers participating in this survey clearly indicated the practical importance of publication bias and the importance of ASRs underscores the problem awareness across animal researchers and the willingness to actively engage in study registration if effective safeguards for the potential weaknesses of ASRs are put into place. To overcome the first-mover dilemma international consensus statements on how to deal with prospective registration of animal studies might be necessary for all relevant stakeholder groups including animal researchers, academic institutions, private companies, funders, regulatory agencies, and journals.

Material Type: Reading

Authors: André Bleich, Daniel Strech, Emily S. Sena, Hans Laser, René Tolba, Susanne Wieschowski

Dissemination and publication of research findings: an updated review of related biases

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Objectives To identify and appraise empirical studies on publication and related biases published since 1998; to assess methods to deal with publication and related biases; and to examine, in a random sample of published systematic reviews, measures taken to prevent, reduce and detect dissemination bias. Data sources The main literature search, in August 2008, covered the Cochrane Methodology Register Database, MEDLINE, EMBASE, AMED and CINAHL. In May 2009, PubMed, PsycINFO and OpenSIGLE were also searched. Reference lists of retrieved studies were also examined. Review methods In Part I, studies were classified as evidence or method studies and data were extracted according to types of dissemination bias or methods for dealing with it. Evidence from empirical studies was summarised narratively. In Part II, 300 systematic reviews were randomly selected from MEDLINE and the methods used to deal with publication and related biases were assessed. Results Studies with significant or positive results were more likely to be published than those with non-significant or negative results, thereby confirming findings from a previous HTA report. There was convincing evidence that outcome reporting bias exists and has an impact on the pooled summary in systematic reviews. Studies with significant results tended to be published earlier than studies with non-significant results, and empirical evidence suggests that published studies tended to report a greater treatment effect than those from the grey literature. Exclusion of non-English-language studies appeared to result in a high risk of bias in some areas of research such as complementary and alternative medicine. In a few cases, publication and related biases had a potentially detrimental impact on patients or resource use. Publication bias can be prevented before a literature review (e.g. by prospective registration of trials), or detected during a literature review (e.g. by locating unpublished studies, funnel plot and related tests, sensitivity analysis modelling), or its impact can be minimised after a literature review (e.g. by confirmatory large-scale trials, updating the systematic review). The interpretation of funnel plot and related statistical tests, often used to assess publication bias, was often too simplistic and likely misleading. More sophisticated modelling methods have not been widely used. Compared with systematic reviews published in 1996, recent reviews of health-care interventions were more likely to locate and include non-English-language studies and grey literature or unpublished studies, and to test for publication bias. Conclusions Dissemination of research findings is likely to be a biased process, although the actual impact of such bias depends on specific circumstances. The prospective registration of clinical trials and the endorsement of reporting guidelines may reduce research dissemination bias in clinical research. In systematic reviews, measures can be taken to minimise the impact of dissemination bias by systematically searching for and including relevant studies that are difficult to access. Statistical methods can be useful for sensitivity analyses. Further research is needed to develop methods for qualitatively assessing the risk of publication bias in systematic reviews, and to evaluate the effect of prospective registration of studies, open access policy and improved publication guidelines.

Material Type: Reading

Authors: Aj Sutton, C Hing, C Pang, Cs Kwok, F Song, I Harvey, J Ryder, L Hooper, S Parekh, Yk Loke

Peer Review: Decisions, decisions

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Journals are exploring new approaches to peer review in order to reduce bias, increase transparency and respond to author preferences. Funders are also getting involved. If you start reading about the subject of peer review, it won't be long before you encounter articles with titles like Can we trust peer review?, Is peer review just a crapshoot? and It's time to overhaul the secretive peer review process. Read some more and you will learn that despite its many shortcomings – it is slow, it is biased, and it lets flawed papers get published while rejecting work that goes on to win Nobel Prizes – the practice of having your work reviewed by your peers before it is published is still regarded as the 'gold standard' of scientific research. Carry on reading and you will discover that peer review as currently practiced is a relatively new phenomenon and that, ironically, there have been remarkably few peer-reviewed studies of peer review.

Material Type: Reading

Author: Peter Rodgers

Preregistration Overview page

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What is Preregistration? When you preregister your research, you're simply specifying your research plan in advance of your study and submitting it to a registry. Preregistration separates hypothesis-generating (exploratory) from hypothesis-testing (confirmatory) research. Both are important. But the same data cannot be used to generate and test a hypothesis, which can happen unintentionally and reduce the credibility of your results. Addressing this problem through planning improves the quality and transparency of your research. This helps you clearly report your study and helps others who may wish to build on it.

Material Type: Reading

Author: Center for Open Science

TOP Guidelines

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The Transparency and Openness Promotion guidelines include eight modular standards, each with three levels of increasing stringency. Journals select which of the eight transparency standards they wish to implement and select a level of implementation for each. These features provide flexibility for adoption depending on disciplinary variation, but simultaneously establish community standards.

Material Type: Lesson

Author: Open Science Collaboration