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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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Amending Published Articles: Time To Rethink Retractions And Corrections?

Academic publishing is evolving and our current system of correcting research post-publication is failing, both ideologically and practically. It does not encourage researchers to engage in consistent post-publication changes. Worse yet, post-publication updates are misconstrued as punishments or admissions of guilt. We propose a different model that publishers of research can apply to the content they publish, ensuring that any post-publication amendments are seamless, transparent and propagated to all the countless places online where descriptions of research appear. At the center, the neutral term \"amendment\" describes all forms of post-publication change to an article. We lay out a straightforward and consistent process that applies to each of the three types of amendments: insubstantial, substantial, and complete. This proposed system supports the dynamic nature of the research process itself as researchers continue to refine or extend the work, removing the emotive climate particularly associated with retractions and corrections to published work. It allows researchers to cite and share the correct versions of articles with certainty, and for decision makers to have access to the most up to date information.

scientific communication and education↗

The Readability Of Scientific Texts Is DecreasingOver Time

Clarity and accuracy of reporting are fundamental to the scientific process. The understandability of written language can be estimated using readability formulae. Here, in a corpus consisting of 707 452 scientific abstracts published between 1881 and 2015 from 122 influential biomedical journals, we show that the readability of science is steadily decreasing. Further, we demonstrate that this trend is indicative of a growing usage of general scientific jargon. These results are concerning for scientists and for the wider public, as they impact both the reproducibility and accessibility of research findings.

scientific communication and education↗

EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices

SummaryScientific posters tend to be brief, unstructured, and generally unsuitable for communication beyond a poster session. This paper describes EXPLANe, a framework for annotating posters using optical text recognition and web services on mobile devices. EXPLANe is demonstrated through an interface to the MyVariant.info variant annotation web services, and provides users a list of biological information linked with genetic variants (as found via extracted RSIDs from annotated posters). This paper delineates the architecture of the application, and includes results of a five-part evaluation we conducted. Researchers and developers can use the existing codebase as a foundation from which to generate their own annotation tabs when analyzing and annotating posters.\n\nAvailabilityAlpha EXPLANe software is available as an open source application at https://github.com/ngopal/EXPLANe\n\nContactSean D. Mooney (sdmooney@uw.edu)

scientific communication and education↗

Addressing the digital divide in contemporary biology: Lessons from teaching UNIX

Researchers in the biomedical sciences increasingly rely on applications that lack a graphical interface and require inputting code that, such as UNIX. Scientists who are not trained in computer science face an enormous challenge in analyzing the high-throughput data their research groups generate. We present a training model for use of command-line tools when the learner has little to no prior knowledge of UNIX.

scientific communication and education↗

Standardising and harmonising research data policy in scholarly publishing

Practice paper Practice paper References Research data policies influence researchers willingness to share research data to varying extents (Meadows, 2014; Schmidt, Gemeinholzer, & Treloar, 2016). A growing number of research funders and institutions are introducing policies on research data sharing. These include the National Institutes of Health (NIH), Gates Foundation, the EU Horizon 2020 programme, Wellcome Trust and the seven UK research councils (Hahnel, 2015). Policy requirements vary, with some requiring researchers to prepare data management plans and others, such as the Engineering and Physical Sciences Research Council (EPSRC), requiring evidence of public data archiving to be included in published research papers. To support publication of more reproducible research scholarly journals, societies and conferences ...

scientific communication and education↗

Looking into Pandora’s Box: The Content of Sci-Hub and its Usage

Despite the growth of Open Access, illegally circumventing paywalls to access scholarly publications is becoming a more mainstream phenomenon. The web service Sci-Hub is amongst the biggest facilitators of this, offering free access to around 62 million publications. So far it is not well studied how and why its users are accessing publications through Sci-Hub. By utilizing the recently released corpus of Sci-Hub and comparing it to the data of {small tilde}28 million downloads done through the service, this study tries to address some of these questions. The comparative analysis shows that both the usage and complete corpus is largely made up of recently published articles, with users disproportionately favoring newer articles and 35% of downloaded articles being published after 2013. These results hint that embargo periods before publications become Open Access are frequently circumnavigated using Guerilla Open Access approaches like Sci-Hub. On a journal level, the downloads show a bias towards some scholarly disciplines, especially Chemistry, suggesting increased barriers to access for these. Comparing the use and corpus on a publisher level, it becomes clear that only 11% of publishers are highly requested in comparison to the baseline frequency, while 45% of all publishers are significantly less accessed than expected. Despite this, the oligopoly of publishers is even more remarkable on the level of content consumption, with 80% of all downloads being published through only 9 publishers. All of this suggests that Sci-Hub is used by different populations and for a number of different reasons, and that there is still a lack of access to the published scientific record. A further analysis of these openly available data resources will undoubtedly be valuable for the investigation of academic publishing.

scientific communication and education↗

Why Do Scientists Fabricate And Falsify Data? A Matched-Control Analysis Of Papers Containing Problematic Image Duplications

It is commonly hypothesized that scientists are more likely to engage in data falsification and fabrication when they are subject to pressures to publish, when they are not restrained by forms of social control, when they work in countries lacking policies to tackle scientific misconduct, and when they are male. Evidence to test these hypotheses, however, is inconclusive due to the difficulties of obtaining unbiased data.\n\nHere we report a pre-registered test of these four hypotheses, conducted on papers that were identified in a previous study as containing problematic image duplications through a systematic screening of the journal PLoS ONE. Image duplications were classified into three categories based on their complexity, with category 1 being most likely to reflect unintentional error and category 3 being most likely to reflect intentional fabrication. Multiple parameters connected to the hypotheses above were tested with a matched-control paradigm, by collecting two controls for each paper containing duplications.\n\nCategory 1 duplications were mostly not associated with any of the parameters tested, in accordance with the assumption that these duplications were mostly not due to misconduct. Category 2 and 3, however, exhibited numerous statistically significant associations. Results of univariable and multivariable analyses support the hypotheses that academic culture, peer control, cash-based publication incentives and national misconduct policies might affect scientific integrity. Significant correlations between the risk of image duplication and individual publication rates or gender, however, were only observed in secondary and exploratory analyses.\n\nCountry-level parameters generally exhibited effects of larger magnitude than individual-level parameters, because a subset of countries was significantly more likely to produce problematic image duplications. Promoting good research practices in all countries should be a priority for the international research integrity agenda.

scientific communication and education↗

Anticipated effects of an open access policy at a private foundation

BackgroundThe Gordon and Betty Moore Foundation (GBMF) was interested in understanding the potential effects of a policy requiring open access to peer-reviewed publications resulting from the research the foundation funds.\n\nMethodsWe collected data on more than 2000 publications in over 500 journals that were generated by GBMF grantees since 2001. We then examined the journal policies to establish how two possible open access policies might have affected grantee publishing habits.\n\nResultsWe found that 99.3% of the articles published by grantees would have complied with a policy that requires open access within 12 months of publication. We also estimated the maximum annual costs to GBMF for covering fees associated with \"gold open access\" to be between $400,000 and $2,600,000 annually.\n\nDiscussionBased in part on this study, GBMF has implemented a new open access policy that requires grantees make peer-reviewed publications fully available within 12 months.

scientific communication and education↗

A persistent lack of International representation on editorial boards in biology

The scholars comprising journal editorial boards play a critical role in defining the trajectory of knowledge in their field. Nevertheless, studies of editorial board composition remain rare, especially those focusing on journals publishing research in the increasingly globalized fields of science, technology, engineering, and math (STEM). Using metrics for quantifying the diversity of ecological communities, we quantified international representation on the 1985-2014 editorial boards of twenty-four environmental biology journals. Over the course of three decades there were 3831 unique scientists based in 70 countries that served as editors. The size of the editorial community increased over time - there were 420% more editors serving in 2014 than in 1985 - as did the number of countries in which editors were based. Nevertheless, editors based outside the Global North (the group of economically developed countries with high per capita Gross Domestic Product (GDP) that collectively concentrate most global wealth) were extremely rare. Furthermore, 67.06% of all editors were based in either the USA or UK. Consequently, Geographic Diversity - already low in 1985 - remained unchanged through 2014. We argue that this limited geographic diversity can detrimentally affect the creativity of scholarship published in journals, the progress and direction of research, the composition of the STEM workforce, and the development of science in Latin America, Africa, the Middle East, and much of Asia (i.e., the Global South).

scientific communication and education↗

A Universal Metric For Evaluating, Optimising And Benchmarking The Performance Of A Research Technology Platform (RTP)

Research Technology Platforms (RTPs) exist to facilitate the application and utilisation of specific analytical technologies to the highest possible standard thus delivering reputable data across a broad spectrum of research themes. Specifically, RTPs centralise expertise in a given technology and provide an unparalleled level of continuity and practical knowledge retention that simply cannot be achieved by more organic, ad hoc means of support. As small non profit businesses often tasked with recovering all or a percentage of their running costs, RTPs are under significant pressure to keep pace with rapidly advancing technology and new methodologies against a back drop of dwindling funding for scientific research. At present there are a number of non-trivial issues that make assessing the operational performance of a RTP difficult to determine on a standalone basis let alone attempting to benchmark against other RTPs within the same or different technology fields. Firstly, depending on the technological speciality the RTP may work to one of essentially three operational models. RTPs such as Bio-Imaging or Cytometry provide access to well-maintained analytical systems that can be utilised by trained individuals for a timed access charge. In some cases there will be a requirement for assisted operation of certain instruments by core staff (e.g. cell sorters). Genomics and Proteomics RTPs tend to function on a project basis whereby users will not access the technology themselves rather pay for a full analytical service often with a milestone-based approach for tracking progress. Other RTPs work to a hybrid approach were technical staff provide certain elements of sample preparation for specific projects prior to analysis on core supported, user accessible instrumentation. Secondly the specific operational costs that each RTP is tasked to recover varies significantly on a local, national and international level due to institutional subsidies. These operational costs can include staff salaries, instrument maintenance, associated running consumables, and in some cases instrument depreciation but there is standardised rule as to what each RTP is tasked to recover and to what percentage.\n\nHere we present a generalised mathematical approach to describe the customisable metrics of any given RTP serviceThe general strategy how to increase performance within the framework of this approach has been identified through breaking down these customisable metrics into components and maximising them according to specific requirements. These strategies could be potentially adopted for different operational or local procedures, integrating the specifics related to the institutional or national policies. The approach laid down here should be considered as a trigger for opening a discussion around how to address optimising RTP performance and allow for benchmarking across the full breadth of RTPs.

scientific communication and education↗

Research Waste In ME/CFS

ObjectiveTo compare the prevalence of selective reporting in ME/CFS research areas: psychosocial versus cellular.\n\nMethodA bias appraisal was conducted on three trials (1x psychosocial and 2x cellular) to compare risk of bias in study design, selection and measurement. The primary outcome compared evidence and justifications in resolving biases by proportions (%) and ORs (Odds Ratio); the secondary outcome determined the proportion (in %) of ME/CFS grants at risk of bias.\n\nResultsNS (cellular study) was twice as likely to present evidence in resolving biases over PACE (psychosocial trial) (OR = 2.16; 65.6% vs 46. 9%), but this difference was not significant (p = 0.13). However, NS was five times more likely to justify biases over PACE (OR = 4.76; 46.9% vs 15. 6%) and this difference was significant (p = 0.0095; p < 0.05). PACE was weak in place (operational aspects 32%) and NS for data practices (37%). The proportion of grants were more biased in PACE (72%) than NS (28%) for evidence, and also more biased in PACE (86%) than NS (14%) for justifications.\n\nConclusionPsychosocial trials on ME/CFS are more likely to engage in selective reporting indicative of research waste than cellular trials. Improvements to place may help reduce these biases, whereas cellular trials may benefit from adopting more translatable data methods. However, these findings are based on two trials. Further risk of bias appraisals are needed to determine the number of trials required to make robust these findings.

scientific communication and education↗

Eyeballs On Science: Impact Is Not Just Citations, But How Big Is Readership?

A full evaluation of the impact of scientific publications needs to count readers who dont generate citations. But this is very difficult to do. I set up a scholarly foraging experiment to try to estimate readership for my own body of work: a personal web site with reprint pdf files available for downloading and a web statistics program engaged to count these downloads. (I made the site topically rather than author-oriented to increase potential audience size.) Despite this, human users are difficult to count. There are a lot of bots, spiders, and other web programs that increasingly mimic human behavior (e.g., with IP- and chrono-camouflage), and humans own behaviors are changing (e.g., reading papers online many times). From four years of data, after culling both automated activity (a fascinating ecosystem) and humans reading repeatedly online, my papers receive [~]4000-8000 downloads per year, about an order of magnitude higher than the number of citations they receive annually. This is a conservative minimum, because these publications can be obtained from other sources as well. On average, this body of work may be being read at an approximately 10:1 download-to-citation ratio. At a more granular scale, downloads do not correlate with citations; there are some papers being downloaded at about a 100:1 ratio, and it turns out these are exactly how they were meant to be used (e.g., an instruction manual). How intensively someone reads a paper is of course highly variable, but this exercise gives us an idea of how broad our publications impacts actually are. Citations alone dont come close to measuring it.

scientific communication and education↗

A tale of two cores: a quantitative comparative analysis of the institutional and the open access models for flow research technology platforms

Quinquennium of sorting for Cambridge Quinquennium of 'sorting for... Emerging divergence: origins Shortage of capacity: perception... Current and projected capacity... Conclusions References Biomedical specialist core facilities are major part of institutional infrastructure in academia and play important role in research by creating access to well established and emerging technologies and being a source of valuable expertise. In each particular case, the extent, range and content of services they provide are determined by the technology specialism, demands of the users and institutional/overarching policies.\n\nIn 2012, two flow cytometry core facilities embarked on a new journey in development of their services to research community in Cambridge. Both facilities started from the same initial level: ...

scientific communication and education↗

Percentage-Based Author Contribution Index. A Universal Measure Of Author Contribution To Scientific Articles

Deciphering the amount of work provided by different co-authors of a scientific paper has been a recurrent problem in science. Despite the myriad of metrics available, the scientific community still largely relies on the position in the list of authors to evaluate contributions, a metric that attributes subjective and unfounded credit to co-authors. We propose an easy to apply, fair and universally comparable metric to measure and report co-authors contribution in the scientific literature. The proposed Author Contribution Index (ACI) is based on contribution percentages provided by the authors, preferably at the time of submission. Researchers can use ACI for a number of purposes, including comparing the contributions of different authors, describing the contribution profile of a researcher or analysing how contribution changes through time. We provide an example analysis based on data collected from 97 scientists from the field of ecology who voluntarily responded to an online anonymous survey.

scientific communication and education↗

Modeling Science Trustworthiness Under Publish Or Perish Pressure

The scientific endeavor pivots on the accurate reporting of experimental and theoretical findings, and consequently scientific publication is immensely important. As the number of active scientists continues to increase, there is concern that rewarding scientists chiefly on publication creates a perverse incentive where careless and fraudulent research can thrive. This is compounded by the predisposition of top-tier journals towards novel or positive findings rather than negative results or investigations that merely confirm a null hypothesis, despite their intrinsic value, potentially compounding a reproducibility crisis in several fields. This is a serious problem for both science and public trust in scientific findings. To date, there has been comparatively little mathematical modeling on the factors that influence science trustworthiness, despite the importance of quantifying the problem. In this work, we present a simple phenomenological model with cohorts of diligent, careless and unethical scientists with funding allocated based on published outputs. The results of this analysis suggest that trustworthiness of published science in a given field is strongly influenced by the false positive rate and the pressures from journals for positive results, and that decreasing available funding has negative consequences for the resulting trustworthiness. We also examine strategies to combat propagation of irreproducible science, including increasing fraud detection and awarding diligence, discussing the implications of these findings.

scientific communication and education↗

Cooperation And Liaison Between Universities And Editors (CLUE): Recommendations On Best Practice

Journals and research institutions have common interests regarding the trustworthiness of research publications but their specific roles and responsibilities differ. These draft recommendations aim to address issues surrounding cooperation and liaison between journals and institutions about possible and actual problems with reported research. The proposals will be discussed at various meetings including the World Conference on Research Integrity in May 2017. We will also consider comments and suggestions posted on this preprint.\n\nThe main recommendations are that: O_LINational registers of individuals or departments responsible for research integrity at institutions should be created.\nC_LIO_LIInstitutions should develop mechanisms for assessing the validity of research reports that are independent from processes to determine whether individual researchers have committed misconduct.\nC_LIO_LIEssential research data and peer review records should be retained for at least 10 years.\nC_LIO_LIWhile journals should normally raise concerns with authors in the first instance, they also need criteria to determine when to contact the institution before, or at the same time as, alerting the authors in cases of suspected data fabrication or falsification to prevent the destruction of evidence.\nC_LIO_LIAnonymous or pseudonymous allegations made to journals or institutions should be judged on their merit and not dismissed automatically.\nC_LIO_LIInstitutions should release relevant sections of reports of research trustworthiness or misconduct investigations to all journals that have published research that was the subject of the investigation.\nC_LI

scientific communication and education↗

Manuscript 101: A Data-Driven Writing Exercise For Beginning Scientists

Learning to write a scientific manuscript is one of the most important and rewarding scientific training experiences, yet most young scientists only embark on this experience relatively late in graduate school, after gathering sufficient data in the lab. Yet, familiarity with the process of writing a scientific manuscript and receiving peer reviews, often leads to a more focused and driven experimental approach. To jump-start this training, we developed a protocol for teaching manuscript writing and reviewing in the classroom, appropriate for new graduate or upper-level undergraduate students of developmental biology. First, students are provided one of four cartoon data sets, which are focused on genetic models of animal development. Students are instructed to use their creativity to convert evidence into argument, and then to integrate their interpretations into a manuscript, including an illustrated, mechanistic model figure. After student manuscripts are submitted, manuscripts are redacted and distributed to classmates for peer review. Here, we present our cartoon datasets, homework instructions, and grading rubrics as a new resource for the scientific community. We also describe methods for developing new datasets so that instructors can adapt this activity to other disciplines. Our data-driven manuscript writing exercise, as well as the formative and summative assessments resulting from the peer review, enables students to learn fundamental concepts in developmental genetics. In addition, students practice essential skills of scientific communication, including arguing from evidence, developing and testing models, the unique conventions of scientific writing, and the joys of scientific story telling.

scientific communication and education↗

Transparency in Authors’ Contributions and Responsibilities to Promote Integrity in Scientific Publication

In keeping with the growing movement in scientific publishing toward transparency in data and methods, we argue that the names of authors accompanying journal articles should provide insight into who is responsible for which contributions, a process should exist to confirm that the list is complete, clearly articulated standards should establish whether and when the contributions of an individual justify authorship credit, and those involved in the generation of scientific knowledge should follow these best practices.\n\nTo accomplish these goals, we recommend that journals adopt common and transparent standards for authorship, outline responsibilities for corresponding authors, adopt the CRediT (Contributor Roles Taxonomy)1 methodology for attributing contributions, include this information in article metadata, and encourage authors to use the digital persistent identifier ORCID.2 Furthermore, we suggest that research institutions have regular open conversations on authorship criteria and ethics and that funding agencies adopt ORCID and accept CRediT. Scientific societies should further authorship transparency by promoting these recommendations through their meetings and publications programs.

scientific communication and education↗