Why most academic journals are following outdated publishing practices

“In his Medium article “Scholarly publishing is stuck in 1999,”

Springer Nature product manager Stephen Cornelius reproaches the outdated publishing practices many academic journals are using to produce online content. He notes that, despite decades of technological advancement, “research publishing seems stuck with those that were employed when it first went online.” Cornelius points to many areas of digital journal publishing that have been designed to mirror print publishing, such as journals formatting online articles as print-based PDFs, despite there being better ways to produce and present content online….

PDFs are rife with limitations as compared to HTML because, unlike HTML, PDFs:

Cannot support embedded multi-media research files such as videos
Have a poor layout for online reading, generally using columns that require readers to scroll up and down to read content on the same page
Are nearly impossible to read on mobile devices because PDFs are a static page (whereas HTML can be made to have a responsive design)
Do not easily allow for clickable references within the text
Are overwhelmingly not search-optimized for online browsers…

A recent article in The Atlantic titled “The Scientific Paper Is Obsolete“ explores the limitations of PDFs and the need for journals, particularly in STEM fields, to adopt internet-based publishing formats in order to support more dynamic presentations of research as well as to make it easier for readers to find articles online….”

 

Equitable data sharing in epidemics and pandemics | BMC Medical Ethics | Full Text

Abstract:  Background

Rapid data sharing can maximize the utility of data. In epidemics and pandemics like Zika, Ebola, and COVID-19, the case for such practices seems especially urgent and warranted. Yet rapidly sharing data widely has previously generated significant concerns related to equity. The continued lack of understanding and guidance on equitable data sharing raises the following questions: Should data sharing in epidemics and pandemics primarily advance utility, or should it advance equity as well? If so, what norms comprise equitable data sharing in epidemics and pandemics? Do these norms address the equity-related concerns raised by researchers, data providers, and other stakeholders? What tensions must be balanced between equity and other values?

Methods

To explore these questions, we undertook a systematic scoping review of the literature on data sharing in epidemics and pandemics and thematically analyzed identified literature for its discussion of ethical values, norms, concerns, and tensions, with a particular (but not exclusive) emphasis on equity. We wanted to both understand how equity in data sharing is being conceptualized and draw out other important values and norms for data sharing in epidemics and pandemics.

Results

We found that values of utility, equity, solidarity, and reciprocity were described, and we report their associated norms, including researcher recognition; rapid, real-time sharing; capacity development; and fair benefits to data generators, data providers, and source countries. The value of utility and its associated norms were discussed substantially more than others. Tensions between utility norms (e.g., rapid, real-time sharing) and equity norms (e.g., researcher recognition, equitable access) were raised.

Conclusions

This study found support for equity being advanced by data sharing in epidemics and pandemics. However, norms for equitable data sharing in epidemics and pandemics require further development, particularly in relation to power sharing and participatory approaches prioritizing inclusion. Addressing structural inequities in the wider global health landscape is also needed to achieve equitable data sharing in epidemics and pandemics.

Free for all, or free-for-all? A content analysis of Australian university open access policies | bioRxiv

Abstract:  Recent research demonstrates that Australia lags in providing open access to research outputs. In Australia, while the two major research funding bodies require open access of outputs from projects they fund, these bodies only fund a small proportion of research conducted. The major source of research and experimental development funding in Australian higher education is general university, or institutional, funding, and such funds are not subject to national funder open access policies. Thus, institutional policies and other institutional supports for open access are important in understanding Australia’s OA position. The purpose of this paper is, therefore, to understand the characteristics of Australian institutional open access policies and to explore the extent they represent a coherent and unified approach to delivering and promoting open access in Australia. Open access policies were located using a systematic web search approach and then their contents were analysed. Only half of Australian universities were found to have an open access policy. There was a wide variation in language used, expressed intent of the policy and expectations of researchers. Few policies mention monitoring or compliance and only three mention consequences for non-compliance. While it is understandable that institutions develop their own policies, when language is used which does not reflect national and international understandings, when requirements are not clear and with consequences, policies are unlikely to contribute to understanding of open access, to uptake of the policy, or to ease of transferring understanding and practices between institutions. A more unified approach to open access is recommended.

 

Lessons from the pandemic: Embrace ‘open science,’ confront exclusion of investigators

“Will this trend to freely disseminate research papers prior to peer review and their acceptance by journals be sustained after the pandemic, when the sense of urgency recedes? I certainly hope so. This would be a lasting, beneficial consequence of the pandemic. By reducing the power of the journals to hold research hostage through long and often unnecessarily contentious peer review, preprints not only speed up the process but also democratize science for some in other parts the world who do not have access to expensive journal subscriptions.”

Four years of chemistry preprints | Feature | Chemistry World

“Then, in August 2017, two things happened. First, the SSRN preprint server (originally for social sciences and currently run by publishing giant Elsevier) launched an offshoot called the Chemistry Research Network (ChemRN). Then, a week or so later, ChemRxiv was launched by the American Chemical Society (ACS) – it is now run as a collaboration between the ACS, the Royal Society of Chemistry and the chemical societies of China, Japan and Germany….

Neither was initially welcomed with wholly open arms into the chemistry community. An insistence – especially from some journal editors – that depositing work caused it to lose the required novelty to warrant publication in their journals was the biggest issue, explains Donna Blackmond, a professor of chemistry at the Scripps Research Institute in California, US, and a member of the ChemRxiv scientific advisory board.

 

At the start, some chemistry journals accepted submissions that had been preprinted, some did not and many others left authors guessing by not having a preprint policy at all. It took about year for all the chemistry journals to accept preprints, says Blackmond. The ACS flagship journal, the Journal of the American Chemical Society, held out the longest….

Four years after their launch, the preprint servers are now finding their feet in the chemistry community. In 2020, 5137 preprints were posted on ChemRxiv and 3538 on ChemRN. The same year, ChemRxiv preprints were accessed a total of 16,120,921 times and ChemRN pre-prints downloaded 499,553 times….”

 

The Journal of Craniofacial Surgery Advances to Preprint Ser… : Journal of Craniofacial Surgery

“It is indeed a pleasure now that I have the chance to communicate with you all, readers, authors, fans and customers, to tell you what is going to happen in the future in the brave new digital world as regards preprints and post-prints, changes that will be arriving soon and not in the distant future – preprint servers will soon be mobile and accessible to all. This will indeed require some sacrifice and attention, making you feel part of the family with a matrix base and principled pillars that cannot be shaken, stirred, or disturbed by any negativity. We are bringing this to you knowing that there will be some growing pains such as those that we have experienced previously in all the advances that we have made. We do not expect less this time as regards those who are used to burning bridges of collaboration and who are already armed with their matches ready to use at any time; our advice to them is to start their fires with their tails….

The solution for quicker presentation and dissemination of knowledge comes with preprint servers, which we are working on for our journal but which are not yet not perfected. We have seen some ugly instances of misuse of the process during the pandemic; we cannot blame particular groups of people, it is purely a matter of human nature….

What is a preprint? The paper will be submitted as a preprint contribution, there will be a ledger fee for its submission and the paper will directly progress to the submission process and to the server, which is totally separate, and within 24 hours it will have a DOI and will be available globally for viewing, downloading and dissemination of knowledge, and it will have “preprint” stamped on each page. This means it is not peer-reviewed and not cross-checked; it is there on the basis of the integrity of the author and its authenticity; this is not a process that will guarantee publication at all. A second copy will go through the process noted above and this may take 6–9 months, based on and including the revisions required, and will depend on the multifactorial processes involved in regular publication. At the end of the road the preprint will meet at high noon with the standard print; if accepted the preprint will move to PAP or if rejected it will be stamped “rejected” and removed from the preprint server; that is the ugly black eye that may result. Of course the good ones are happily in print format and are now in the cloud and access around the global medical arena will be infinite….”

Preprint advocates must also fight for research integrity

“The case for releasing preprints is clear: results from scientific studies are made more quickly and more broadly available. Overall, greater sharing and transparency boosts trustworthiness and collaboration. But efforts to promote preprints without simultaneously implementing firm measures to ensure that the research is of high quality put the cart before the horse….”

Higher Author Fees in Gastroenterology Journals Are Not Associated with Faster Processing Times or Higher Impact | SpringerLink

Abstract:  Background

Publications are an important component of academic careers.

Aims

We investigated the financial costs to authors for submitting and publishing manuscripts in gastroenterology (GI) journals in the United States (US), United Kingdom (UK), and elsewhere.

Methods

This was a cross-sectional study carried out from 11/1/2020 to 12/31/2020. We used the SCImago Journal and Country Rankings site to compile a list of gastroenterology and hepatology journals to analyze. We gathered information on the journals’ Hirsch indices (h indices), SCImago Journal Rank (SJR), Impact Factor (IF), and base countries as of 2019, processing and publication fees, open access fees, time to first decision, and time from acceptance to publication. We used t-testing and linear regression modeling to evaluate the effect of geography and journal quality metrics on processing fees and times.

Results

We analyzed 97 GI journals, of which 51/97 (52.6%) were based in the US/UK while the other 46/97 (47.4%) were based elsewhere. The mean IF (5.67 vs 3.53, p?=?0.08), h index (90.5 vs 41.8, p?<?0.001), and SJR (1.82 vs 0.83, p?<?0.001) for the US/UK journals were higher than those for non-US/UK journals. We also found that 11/51 (21.6%) of US/UK journals and 15/46 (32.6%) of non-US/UK journals had mandatory processing and publication fees. These tended to be significantly larger in the US/UK group than in the non-US/UK group (USD 2380 vs USD 1470, p?=?0.04).

Conclusions

Publication-related fees may preclude authors from smaller or socioeconomically disadvantaged institutions and countries from publishing and disseminating their work.

Guest Post – Publishers Integrate Preprints Into Their Workflows – The Scholarly Kitchen

“The number of preprint servers has increased substantially in the last five years and now stands at no less than sixty. More than thirty new servers have appeared in the past five years.  These servers are diverse, focusing on subdisciplines, or specific geographies, or specific languages, and have varying degrees of penetration and technical sophistication. Existing publishing services and workflows are now being reimagined to accommodate preprints. This essay examines how a publisher-centric approach simplifies workflows and speeds the process of peer review through preprint pre-assessment and the checks and balances being implemented by publishers and third-parties to build trust and confidence in preprints….”

Covid- 19 Influence on the Publishing Industry

“However, despite these and other issues, and although it’s been difficult for many communities and countries with large outbreaks, international collaborations flourished. Researchers began to share their data more openly, while almost all articles related to Covid-19 are free to read. Research culture also shifted. Instead of prioritizing productivity, broader issues such as work-life balance were discussed, possibly becoming a continuing trend even after the pandemic….

Similarly, UNESCO realizes the importance and value of Open Solutions; therefore, Open Access to scientific information and Open Data facilitate faster and better research. UNESCO builds upon its existing mandate of ensuring universal access to information to support various professional organizations with several data collection tools and encourages various initiatives to tap into the power of Open Solutions to combat Covid-19. To read about more initiatives and Open Access to Covid-19 data, read our data sharing and Covid-19 article….

Covid-19 has made open publishing relevant, as you can see. Pre-prints allow researchers to post studies that have not undergone scientific peer-review for more timely, open, and inclusive access to new science. This is great, in theory. Unfortunately, pre-prints of Covid-19 research can instead lead the general public and the media to believe that the work has been professionally vetted before publication, ultimately leading to misinformation. Therefore, there is an urgent need for rapid, transparent peer-review and a discussion on the harmful effects of unreviewed publishing. However, the field of academic publishing will require significant financial support to finalize these changes….”

81% of Horizon 2020 papers were published in open access journals | Science|Business

“European Commission boasts of high level of open access publishing in Horizon 2020. But researchers complain getting processing fees approved is long winded and could result in them losing out on intellectual property rights….

A large majority of Horizon 2020 researchers complied with the requirement to deposit open access publications in repositories. However, only 39% of Horizon 2020 deposited datasets are findable, with the remainder not including reliable metadata needed to track them down. Only 32% of deposited datasets can be quickly accessed via a link in the metadata….

Since then, the EU has also mandated that all papers coming from projects funded through Horizon Europe, its €95.5 billion research programme, should be published in open access journals.

 

The study estimates the average cost in Horizon 2020 of publishing an open access article was around €2,200. Processing charges for articles in subscription journals in which some of the articles are open access and some behind a paywall, had a higher average cost of €2,600. Trouble is looming, with charges for such hybrid journals no longer being eligible for funding under Horizon Europe….”

Research data communication strategy at the time of pandemics: a retrospective analysis of the Italian experience | Monaldi Archives for Chest Disease

Abstract:  Coronavirus pandemic has radically changed the scientific world. During these difficult times, standard peer-review processes could be too long for the continuously evolving knowledge about this disease. We wanted to assess whether the use of other types of network could be a faster way to disseminate the knowledge about Coronavirus disease. We retrospectively analyzed the data flow among three distinct groups of networks during the first three months of the pandemic: PubMed, preprint repositories (biorXiv and arXiv) and social media in Italy (Facebook and Twitter). The results show a significant difference in the number of original research articles published by PubMed and preprint repositories. On social media, we observed an incredible number of physicians participating to the discussion, both on three distinct Italian-speaking Facebook groups and on Twitter. The standard scientific process of publishing articles (i.e., the peer-review process) remains the best way to get access to high-quality research. Nonetheless, this process may be too long during an emergency like a pandemic. The thoughtful use of other types of network, such as preprint repositories and social media, could be taken into consideration in order to improve the clinical management of COVID-19 patients.

 

Opening doors to discovery: Partnerships are key to advancing open science

Abstract. The evolution of scholarly communications has accelerated in recent years, and 2020 for obvious reasons put even more pressure on the sector to evolve and adapt. By opening up access to research publications, by simplifying or customising the digital experience, or by improving the speed of publishing – the focus is firmly placed on the need for publishers to work more in partnership with each other, with institutions, funders, and new players in the market to develop solutions that meet the evolving needs of researchers and the wider community. Partnerships between different actors in the research process address challenges in practice and help advance open science, publishing, and the research system as a whole.

Open Grant Proposals · Business of Knowing, summer 2021

“One of those informal frontiers is crowdfunding for scientific research. For the past year, I’ve worked on Experiment, helping hundreds of scientists design and launch crowdfunding campaigns for their research questions. Experiment has been doing this for almost a decade, with more than 1,000 successfully funded projects on the platform. The process is very different than the grant funding mechanisms set up by agencies and foundations. It’s not big money yet, as the average fundraise is still ~$5,000. But in many ways, the process is better: faster, transparent, and more encouraging to early-career scientists. Of all the lessons learned, one stands out for broader consideration: grant proposals and processes should be open by default.

Grant proposals that meet basic requirements for scientific merit and rigor should be posted online, ideally in a standardized format, in a centralized (or several) database or clearinghouse. They should include more detail than just the abstract and dollar amount totals that are currently shown now on federal databases, especially in terms of budgets and costs. The proposals should include a DOI number so that future work can point back to the original question, thinking, and scope. A link to these open grant proposals should be broadly accepted as sufficient for submission to requests from agencies or foundations….

Open proposals would make research funding project-centric, rather than funder-centric….

Open proposals would promote more accurate budgets….

Open proposals would increase the surface area of collaboration….

Open proposals would improve citation metrics….

Open proposals would create an opportunity to reward the best question-askers in addition to the best question-answerers….

Open proposals would give us a view into the whole of science, including the unfunded proposals and the experiments with null results….”