Current Publication System Research Articles

David versus Goliath: Early career researchers in an unethical publishing system.

The publish-or-perish culture in academia has catalysed the development of an unethical publishing system. This system is characterised by the proliferation of journals and publishers-unaffiliated with learned societies or universities-that maintain extremely large revenues and profit margins diverting funds away from the academic community. Early career researchers (ECRs) are particularly vulnerable to the consequences of this publishing system because of intersecting factors, including pressure to pursue high impact publications, rising publication costs and job insecurity. Moving towards a more ethical system requires that scientists advocate for structural change by making career choices that come with risks, many of which disproportionately impact ECRs. We illuminate major issues facing ECRs in Ecology and Evolution under the current publishing system, and propose a portfolio of actions to promote systemic change that can be implemented by ECRs and established researchers.

Message or messenger, that's the right question

Current publication system is based in a continuous pressure for publish in “high-rated” journals, in the consideration that this is a synonymous of research-quality, forgotten both the sense of research: the generation of knowledge, nor the publication in specific journals; and that after the emergence of internet, the current editorial system should have been fully rethought.

The international scientific visibility’s means

Aim: Péter Sasvári and Anna Urbanovics present the importance, place and role of contemporary use of science metrics in this volume. The purpose of the presentation of science metrics is clearly the dissemination of knowledge that draws attention from young scientists to professors for everyone applying this knowledge system in a consciously planned manner.Methodology: The authors used a description and analysis of science metrics studies to achieve the set goals. This analysis has been prepared up-to-date and illustratively.Findings: The authors have clearly achieved their goal by presenting current publishing systems. Not only are formal requirements introduced but they also logically build the most important aspects of modern publishing in a step by step, logical way.Values: „Creating science metrical analysis to the individual from its own research area with its 21st century IT tools no longer requires a lot of time and is not too complicated. At the same time, like all other real useful competence, this knowledge becomes the researcher’s habit of measuring the performance of their own sciences, not only knowing how to cultivate publication, but makes it possible from time to time.” (Sasvári & Urbanovics, 2021).

A practical guide to Registered Reports for economists

The current publication system in economics has encouraged the inflation of positive results in empirical papers. Registered Reports, also called Pre-Results Reviews, are a new submission format for empirical work that takes pre-registration one step further. In Registered Reports, researchers write their papers before running the study and commit to a detailed data collection process and analysis plan. After a first-stage review, a journal can give an In-Principle-Acceptance guaranteeing that the paper will be published if the authors carry out their data collection and analysis as pre-specified. We here propose a practical guide to Registered Reports for empirical economists. We illustrate the major problems that Registered Reports address (p-hacking, HARKing, forking, and publication bias), and present practical guidelines on how to write and review Registered Reports (e.g., the data-analysis plan, power analysis, and correction for multiple-hypothesis testing), with R and STATA codes. We provide specific examples for experimental economics, and show how research design can be improved to maximize statistical power. Last, we discuss some tools that authors, editors, and referees can use to evaluate Registered Reports (checklist, study-design table, and quality assessment).

Challenges faced in the peer review system in open access journals

Challenges faced in the peer review system in open access journals

Ensembles of knowledge graph embedding models improve predictions for drug discovery.

Recent advances in Knowledge Graphs (KGs) and Knowledge Graph Embedding Models (KGEMs) have led to their adoption in a broad range of fields and applications. The current publishing system in machine learning requires newly introduced KGEMs to achieve state-of-the-art performance, surpassing at least one benchmark in order to be published. Despite this, dozens of novel architectures are published every year, making it challenging for users, even within the field, to deduce the most suitable configuration for a given application. A typical biomedical application of KGEMs is drug-disease prediction in the context of drug discovery, in which a KGEM is trained to predict triples linking drugs and diseases. These predictions can be later tested in clinical trials following extensive experimental validation. However, given the infeasibility of evaluating each of these predictions and that only a minimal number of candidates can be experimentally tested, models that yield higher precision on the top prioritized triples are preferred. In this paper, we apply the concept of ensemble learning on KGEMs for drug discovery to assess whether combining the predictions of several models can lead to an overall improvement in predictive performance. First, we trained and benchmarked 10 KGEMs to predict drug-disease triples on two independent biomedical KGs designed for drug discovery. Following, we applied different ensemble methods that aggregate the predictions of these models by leveraging the distribution or the position of the predicted triple scores. We then demonstrate how the ensemble models can achieve better results than the original KGEMs by benchmarking the precision (i.e., number of true positives prioritized) of their top predictions. Lastly, we released the source code presented in this work at https://github.com/enveda/kgem-ensembles-in-drug-discovery.

177 Peer Community in Animal Science: A Free Publication Model for Transparent and Open Science

Abstract The scientific publication system should evolve into practices that enhance free dissemination and full access to research findings. At the same time, it should ensure reproducibility and transparency and safeguard scientific integrity from the detrimental effects of the current “publish or perish” culture. The objective of this contribution is to introduce the Peer Community In (PCI) Animal Science initiative (https://animsci.peercommunityin.org/), which represents an alternative to the current publication system under the umbrella of the “Peer Community In” project (https://peercommunityin.org/ ). PCI Animal Science is an international community of researchers working in animal science and related areas and it promotes open science and research transparency. Although PCI Animal Science is not a scientific journal, it operates similarly with editors (here: recommenders) and reviewers. Currently, the PCI Animal Science community has 64 recommenders from 20 countries. PCI Animal Science is a non-profit initiative, run and managed by researchers. The PCI Animal Science community performs, at no cost, rigorous open reviews of preprints that have been deposited on repositories such as bioRxiv and Zenodo from a wide range of research areas related to animal science. Based on independent reviews, a recommender decides whether a paper is recommended or not. Recommended preprints are peer-reviewed and citable stand-alone articles of high scientific value that do not need publication in traditional journals. However, if the authors wish, they can also publish their recommended preprint in the Diamond Open Access Peer Community Journal (https://peercommunityjournal.org/section/animsci/) at no cost. Authors can also submit their recommended manuscript to PCI-friendly journals (i.e., journals that consider the PCI evaluation in their own review processes) or to other journals. This contribution shows the workflow of the evaluation of manuscripts by PCI Animal Science and the advantages of adopting this new publishing model.

Why do we digitize books instead of knowledge?

Besides text and images, contemporary e-books can include multimedia, interactivity, pronunciation information and text-to-speech ready content. The current EPUB 3 standard provides all the technical solutions necessary for designing and displaying highly functional and content rich e-books, but the implementation is impaired by the e-reader industry, publishers and distributors. Local and global book digitization has been an ongoing process for years, encompassing publications ranging from classical literature to current technical textbooks. Textual expression of knowledge is a remnant of the past but it is still dominant today, even though interactivity and video content are known to significantly enhance the learning process. However, multimedia and interactive content for e-books is not produced because it requires time, technical knowledge and specific tools. Within the current publishing system, authors are expected to produce and design all the content for books on their own, but because of the extreme content diversity, it is unrealistic to expect that they really possess such knowledge and skills. Better collaboration among authors, publishers, distributors, the professional community and the related industry is necessary for knowledge digitization to function.

Preregistration in experimental linguistics: applications, challenges, and limitations

AbstractThe current publication system neither incentivizes publishing null results nor direct replication attempts, which biases the scientific record toward novel findings that appear to support presented hypotheses (referred to as “publication bias”). Moreover, flexibility in data collection, measurement, and analysis (referred to as “researcher degrees of freedom”) can lead to overconfident beliefs in the robustness of a statistical relationship. One way to systematically decrease publication bias and researcher degrees of freedom is preregistration. A preregistration is a time-stamped document that specifies how data is to be collected, measured, and analyzed prior to data collection. While preregistration is a powerful tool to reduce bias, it comes with certain challenges and limitations which have to be evaluated for each scientific discipline individually. This paper discusses the application, challenges and limitations of preregistration for experimental linguistic research.

Do Behavioral Observations Make People Catch the Goal? A Meta-Analysis on Goal Contagion

Goal contagion is a social-cognitive approach to understanding how other people’s behavior influences one’s goal pursuit: An observation of goal-directed behavior leads to an automatic inference and activation of the goal before it can be adopted and pursued thereafter by the observer. We conducted a meta-analysis focusing on experimental studies with a goal condition, depicting goal-directed behavior and a control condition. We searched four databases (PsychInfo, Web of Science, ScienceDirect, and JSTOR) and the citing literature on Google Scholar, and eventually included e = 48 effects from published studies, unpublished studies and registered reports based on 4751 participants. The meta-analytic summary effect was small − g = 0.30, 95%CI [0.21; 0.40], τ² = 0.05, 95%CI [0.03, 0.13] − implying that goal contagion might occur for some people, compared to when this goal is not perceived in behavior. However, the original effect seemed to be biased through the current publication system. As shown by several publication-bias tests, the effect could rather be half the size, for example, selection model: g = 0.15, 95%CI [–0.02; 0.32]. Further, we could not detect any potential moderator (such as the presentation of the manipulation and the contrast of the control condition). We suggest that future research on goal contagion makes use of open science practices to advance research in this domain.

Make like a glass frog: In support of increased transparency in herpetology

Across many scientific disciplines, direct replication efforts and meta-analyses have fuelled concerns on the replicability of findings. Ecology and evolution are similarly affected. Investigations into the causes of this lack of replicability have implicated a suite of research practices linked to incentives in the current publishing system. Other fields have taken great strides to counter incentives that can reward obfuscation –chiefly by championing transparency. But how prominent are protransparency (open science) policies in herpetology journals? We use the recently developed Transparency and Openness Promotion (TOP) Factor to assess the transparency promotion of 19 herpetology journals, and compare the TOP scores to broader science. We find promotion of transparent practices currently lacking in many herpetological journals; and encourage authors, students, editors, and publishers to redouble efforts to bring open science practices to herpetology by changing journal policy, peer-review, and personal practice. We promote an array of options –developed and tested in other fields– demonstrated to counter publication bias, boost research uptake, and enable more transparent science, to enrich herpetological research.

Swedish researchers’ responses to the cancellation of the big deal with Elsevier

In 2018, the Swedish library consortium, Bibsam, decided to cancel big deal subscriptions with Elsevier. Many researchers (<em>n</em> = 4,221) let their voices be heard in a survey on the consequences of the cancellation. Almost a third of them (<em>n</em> = 1,241) chose to leave free-text responses to the survey question ‘Is there anything you would like to add?’. A content analysis on these responses resulted in six themes and from these, three main conclusions are drawn. First, there is no consensus among researchers on whether the cancellation was for good or evil. The most common argument in favour of the cancellation was the principle. The most common argument against cancellation was that it harms researchers and research. A third of the free-text responses expressed ambivalence towards the cancellation, typically as a conflict between wanting to change the current publishing system and simultaneously suffering from the consequences of the cancellation. The general support for open access in principle reveals a flawed publishing system, as most feel the pressure to publish in prestigious journals behind paywalls in practice. Second, it was difficult for researchers to take a position for or against cancellation due to their limited knowledge of the ongoing work of higher education institutions and library consortia. Finally, there are indications that the cancellation made researchers reflect on open access and to some extent alter their publication pattern through their choice of copyright licence and publication channel.

Is basic science falling behind? A mixed methods study of bibliometric data and expert interviews in the field of cardiovascular research

Abstract Introduction Scientists in the field of cardiovascular research face many difficulties today and find themselves under considerable pressure to be successful with their projects and publish their results on a regular basis (the publish or perish aphorism). Purpose The objective of this mixed methods study that included quantitative and qualitative research methods was to analyse prospects of scientific success and how scientists see opportunities, risks and how they try to adapt to the current publication system. Methods An analysis of all publications that were published by our department in the years 2014–2019 (total of 104 publications) was performed. Publications were allocated to the sub-categories basic science, clinical science, register studies/database studies and others (letters, reviews, editorials). Further specific characteristics (impact factor, number of authors/institutions, utilization of an animal model and project costs) were also collected. Furthermore, a total of 14 interviews with experts in the field of cardiovascular research were conducted. Interviews were recorded and transcribed. For quantitative text analysis MaxQDA software and the method proposed by Philipp Mayring was used. Results When analysing the publication output of our department we found that achieved impact factors points were equally distributed between basic science, clinical science and register/database studies. Project costs were considerable higher for basic science studies compared to clinical studies and even more to register/database studies (p=0.0001). A correlation between costs and impact factor was found for basic science studies only (r=0.66, p=0.004). A multivariable regression analysis showed that project costs, number of authors and the use of an animal model, but not the number of institutions, was associated with a higher impact factor. Experts in the field shared the opinion that it might be “easier” to be successful with clinical science studies as they require less resources such as grant money, personnel and technical equipment. Moreover, upcoming risks such as competition for grant money, pressure to publish results, inadequacy of the impact factor system, securing ones job, rising publication costs and more pressure of time due to patient care, research and teaching duties for academic personnel were also highlighted to worsen the situation. Conclusion Based on own data and the views of experts it seems much more effort- and cost-efficient to pursue projects in clinical science. Researchers in the current academic system are pressured by multiple risks. After interpretation of the obtained quantitative and qualitative material, one could hypothesize that it might be easier to be successful with focussing on clinical studies when starting ones research career. These data give support to the concerns that the field of basic science might fall behind and less young scientists would opt for a career path in this field. Funding Acknowledgement Type of funding source: None

The Future of Academic Journals in a COVID-19 World

Many academics are critical of the current publishing system, but it is difficult to create a better alternative. This review relates to the Sciences and Social Sciences, and discusses the primary purpose of academic journals as providing a seal of approval for perceived quality, impact, significance, and importance. The key issues considered include the role of anonymous refereeing, continuous rather than discrete frequency of publications, avoidance of time wasting, and seeking adventure. Here we give recommendations about the organization of journal articles, the roles of associate editors and referees, measuring the time frame for refereeing submitted articles in days and weeks rather than months and years, encouraging open access internet publishing, emphasizing the continuity of publishing online, academic publishing as a continuous dynamic process, and how to improve research after publication. Citations and functions thereof, such as the journal impact factor and h-index, are the benchmark for evaluating the importance and impact of academic journals and published articles. Even in the very top journals, a high proportion of published articles are never cited, not even by the authors themselves. Top journal publications do not guarantee that published articles will make significant contributions, or that they will ever be highly cited. The COVID-19 world should encourage academics worldwide not only to rethink academic teaching, but also to re-evaluate key issues associated with academic journal publishing in the future.

Game of Tenure: the role of “hidden” citations on researchers’ ranking in Ecology

Field ecologists and macroecologists often compete for the same grants and academic positions, with the former producing primary data that the latter generally use for model parameterization. Primary data are usually cited only in the supplementary materials, thereby not counting formally as citations, creating a system where field ecologists are routinely under-acknowledged and possibly disadvantaged in the race for funding and positions. Here, we explored how the performance of authors producing novel ecological data would change if all the citations to their work would be accounted for by bibliometric indicators. We collected the track record of &gt;2300 authors from Google Scholar and citation data from 600 papers published in 40 ecology journals, including field-based, conservation, general ecology, and macroecology studies. Then we parameterized a simulation that mimics the current publishing system for ecologists and assessed author rankings based on number of citations, H-Index, Impact Factor, and number of publications under a scenario where supplementary citations count. We found weak evidence for field ecologists being lower ranked than macroecologists or general ecologists, with publication rate being the main predictor of author performance. Current ranking dynamics were largely unaffected by supplementary citations as they are 10 times less than the number of main text citations. This is further exacerbated by the common practice of citing datasets assembled by previous research or data papers instead of the original articles. While accounting for supplementary citations does not appear to offer a solution, researcher performance evaluations should include criteria that better capture authors’ contribution of new, publicly available data. This could encourage field ecologists to collect and store new data in a systematic manner, thereby mitigating the data patchiness and bias in macroecology studies, and further accelerating the advancement of ecology and related areas of biogeography.

Comfortably Numb? Researchers’ Satisfaction with the Publication System and a Proposal for Radical Change

In this preregistered study we evaluate current attitudes towards, and experiences with, publishing research and propose an alternative system of publishing. Our main hypothesis is that researchers tend to become institutionalized, such that they are generally discontent with the current publication system, but that this dissatisfaction fades over time as they become tenured. A survey was distributed to the first authors of papers published in four recent issues of top-15 Work and Organizational Psychology (WOP) journals. Even among this positively biased sample, we found that the time it takes to publish a manuscript is negatively associated with whether authors perceive this time to be justifiable and worthwhile relative to the amount their manuscript has changed. Review quality and tenure buffer the negative relationship with perceived justifiability, but not for perceived worth. The findings suggest that untenured (WOP) researchers are dissatisfied with the publishing times of academic journals, which adds to the pile of criticisms of the journal-based publication system. Since publishing times are inherent to the journal-based publication system, we suggest that incremental improvements may not sufficiently address the problems associated with publishing times. We therefore propose the adoption of a modular publication system to improve (WOP) publishing experiences.

A platform for reproducibility

This is an open editorial about the issues on reproducibility and the current publication system that led us to launch the Journal for Reproduciblity in Neuroscience.

The Future of Open Science

The topic of this episode is the future of Open Science, and what it is like to be an outspoken critic of the current publishing system. Our guest is Jon Tennant, paleontologist, independent researcher and the founder of Open Science MOOC. The host of this episode is Erik Lieungh.&#x0D; This episode was first published 21 December 2018.

Future Challenges and Opportunities in Academic Publishing

Digitization and the rise of Open Access publishing is an important recent development in academic communication. The current publishing system exhibits challenges with cost, where many universities are forced to cancel journal subscriptions for economic reasons, as well as access, as scholars and the public alike often lack access to research published in paywalled subscription journals. Open Access publishing solves the access problem, but not necessarily cost problems. Universities and researchers are currently in a challenging, interstitial stage of scholarly publishing. Subscription journals still dominate scholarly communication, yet a growing imperative to fund and support Open Access alternatives also exists. Stakeholders, including faculty, university administrators, publishers, scientific funding institutions and librarians and governments alike currently strategize and fight for their professional and economic interests in the broader publishing system. Four main trends are suggested that will characterize the future of scholarly publishing: 1) antagonism with scholarly associations; 2) changes and innovations to peer review; 3) Scientific/Intellectual Movements around Open Access 4) publishing and new professional niches in the publishing landscape. This article suggests potential trajectories and outcomes for these various conflicts over the costs and benefits of academic publishing.

Fight academic apartheid to advance equality and quality in the sciences! Europe’s Open Access Champions

Watch the VIDEO of the presentation.“Fight academic apartheid to advance equality and quality in the sciences!”“Stop discriminating against Open Access publications in research evaluation.”“The next generation of researchers will care less about status and more about relevance.”These are some of the voices from Europe’s rectors, vice-chancellors, professors, senior and junior researchers on what still needs to be done to achieve more Open Access.Despite seeing significant international and national Open Access policy development across Europe, both the library and academic communities are still having challenges in implementing Open Access policies on various levels. We can anticipate far more OA take-up when the research community and senior administration votes with their feet against traditional publishing practices and for new forms. In addition, these groups have the power to stabilise and strengthen the sustainability of such change by changing the way that research is currently being assessed and evaluated. It is for this reason that SPARC Europe is highlighting the importance of the people in our research communities who are helping make Open Access happen and who are speaking out for such change.SPARC Europe is doing this by bringing champions together in an online showcase, Europe’s Open Access Champions. This features a range of academics and senior administrators or champions who are making the case for Open Access amongst their peers. They are generating more momentum for more access to Europe’s research results within their research communities. They tell us why and how – in their own words – on the Europe’s Open Access Champions site.In the first instance, this presentation will share a range of complementary but also very different views from champions from various research roles, disciplines and countries. What needs to be done to change the current scholarly publishing system in their view? Where does academic integrity come in and how can more OA here potentially affect research careers / employment conditions? Above all, how can the academic community make the necessary change to the way research is currently assessed and evaluated to make OA work? The presentation will then go on to share lessons learnt by various libraries across Europe on what makes a good OA champion.To conclude, this presentation seeks to inspire the open scholarly communication community to engage more with champions from the research community who have the potential to make more rapid Open Access to Europe’s research results.