How covid-19 bolstered an already perverse publishing system | The BMJ

“This was the first global pandemic that the scientific publishing industry had ever faced—while journals existed, no organised industry did when the 1918 flu pandemic occurred—and the first in a new digital age of internet communication and publishing. An estimated 1.5 million articles were added to the global literature in 2020—the largest single year increase in history, says Vincent Larivière, who studies bibliometrics at the University of Montreal, Canada. This peaked in April 2020, when many countries were deep into lockdown or applying heavy restrictions.

Some saw it as an opportunity. There were promises of more open science and publishing: a number of journals and research institutions agreed to a data sharing pledge issued by the funder the Wellcome Trust on 31 January 2020 that intended to “ensure that research findings and data relevant to this outbreak are shared rapidly and openly to inform the public health response and help save lives.”2 But it also stoked an already, some say, twisted industry—one that thrives on competitiveness—to publish the first data or to have the greatest visibility and impact. This changed the ways that papers were produced and vetted, for good and bad….

Medical journals halved their turnaround times in the first half of 2020.5 Despite the unknown nature of the virus and its science, editors took far less rather than more time over decisions, a February 2023 analysis of 339?000 papers has found.6

Naomi Lee, senior executive editor for research at the Lancet during the pandemic, recalls how the usually rare practice of “fast tracking” select papers was expanded so that “practically everyone and everything was accelerated with the goal of disseminating critical knowledge.” The PubMed database shows that the five most cited articles in the Lancet since 2020—most reporting early coronavirus data—were accepted within 14 days and published within 22 days of receipt.

Alarms were raised early on about the mix of sheer volume and unprecedented speed….

Proponents of open science had breathlessly heralded a revolution.10 medRxiv, a BMJ affiliated preprint server, saw a 10-fold rise in submissions within two months of the first reported covid case. But this enthusiasm receded, and submissions at medRxiv and others stabilised by mid-2020.

Analysis shows that just 5% of all peer reviewed journal articles about covid-19 published in 2020 started out as preprints.11 And, while some pivotal trials such as Recovery and Solidarity were first reported as open access preprints, none of the phase 3 covid vaccine trials supported by Oxford-AstraZeneca, Moderna, or Pfizer was, and only the Oxford-AstraZeneca phase 3 trial report was published with a gold open access licence. A 2022 evaluation by Wellcome of the data sharing commitment it initiated found that fewer than half of signatories’ covid papers contained information about where and how to access available data,12 raising concern about a lack of transparency, particularly in clinical trials.

Progress towards more open research has also disappointed. While the leading publishers agreed to make their covid content open and reusable,2 Wellcome’s assessment found that just 46% of signatories’ covid papers were genuinely open access, where re-use is permitted and authors retain copyright.12

Instead, most journals retained commercial rights and simply took down a paywall (“bronze” open access15), says Larivière. He adds that, while major publishers including Elsevier, Springer Nature, and Wiley continue to make covid content freely available, only about half of papers on the climate crisis are similarly available….”

Should AJE allow submissions of manuscripts that have been previously posted on preprint servers and received media attention? | American Journal of Epidemiology | Oxford Academic

Abstract:  In weighing the question of whether AJE should accept preprints that have received press coverage, we need to keep in mind three sets of interests: the public interest, the publisher’s interest, and the author’s interest. During public health emergencies, such as a pandemic, the author’s interests (rapid communication of scientific findings to the public) are aligned with the public interest (learning about life-saving information as early as possible). However, the interests of different parties are not always aligned. In most cases, preprinted articles do not concern matters of life or death. Widespread dissemination of studies via preprint services conflicts with the journal editor’s interest in delivering fresh, original content. Dissemination of study results prior to peer review can occasionally backfire and cause unintended harm if the findings turn out to be false.

 

Open Buildings

“Building footprints are useful for a range of important applications, from population estimation, urban planning and humanitarian response, to environmental and climate science. This large-scale open dataset contains the outlines of buildings derived from high-resolution satellite imagery in order to support these types of uses. The project is based in Ghana, with an initial focus on the continent of Africa and new updates on South Asia and South-East Asia….”

Volunteers Rally to Archive Ukrainian Web Sites – Internet Archive Blogs

“As the war intensifies in Ukraine, volunteers from around the world are working to archive digital content at risk of destruction or manipulation. The Internet Archive is supporting several preservation efforts including the Saving Ukrainian Cultural Heritage Online (SUCHO) initiative launched in early March….

More than 1,200 volunteers with SUCHO have saved 10 terabytes of data including 14,000 uploaded items (images and PDFs) and captured parts of 2,300 websites so far. This includes material from Ukrainian museums, library websites, digital exhibits, open access publications and elsewhere. 

 

The initiative is using a combination of technologies to crawl and archive sites and content. Some of the information is stored at the Internet Archive, where it can be discovered and accessed using open-source software….

The Internet Archive is providing technical support, tools and training to assist volunteers, including those with SUCHO, who are giving of their time.

Through Archive-It, a customizable self-service web archiving platform that captures, stores, and provides access to web-based content, free online accounts have been offered to volunteer archivists. Mirage Berry, business development manager for Archive-It, has coordinated support with other preservation partners including the Harvard Ukrainian Research Institute, the Center for Urban History of East Central Europe, and East European & Central Asian Studies Collections librarian Liladhar Pendse at University of California, Berkeley….”

Data Sharing Across Sectors Creates Better Early Warning Systems – data.org

“The existing public sector’s early warning systems for infectious disease and climate events are commonly disconnected; there are limited mechanisms in place that relate the two. In other words, there is a lack of data that helps understand and predict the impacts of extreme weather events and environmental changes on disease risk.

Attempting to find and connect climate and health data proves next to impossible with the current infrastructure in developing countries. For instance, when faced with an outbreak of dengue fever in Peru, the health minister has data on only health and demographics. If you wanted to combine that with climate data you would need to ask the minister of the environment. Want to relate economic data? Ask the minister of the economy and finance….

 

The Harmonize Project seeks to build a digital infrastructure of harmonized databases to feed early warning systems for epidemics exacerbated by climate change in the LAC region.

 

In collaboration with the Barcelona Supercomputing Center (BSC)—and a network in Brazil, Colombia, and the Dominican Republic—and supported by Wellcome, the project will bring together ministries, universities, private companies, social impact organizations, and more to create a complex data infrastructure and collect real longitudinal data on the ground. These new data sets will provide valuable information on seasonal variation in land use and human behavior has given climate hazards, which are generally assumed to be unchanging in health impact models.

The outcome of such an infrastructure? Actionable knowledge to inform local risk mapping and create strong early warning systems to drive resilience in low-resource communities….”

Publishers Want to End How Libraries Lend Books Online – EveryLibrary Action

“A court decision could limit how you access e-books from the library.

When the pandemic began and schools and libraries around the country were forced to close their doors, teachers and librarians were at a loss over how to get digital books into the hands of young readers and their families.

The problem was so drastic that the Internet Archive (IA), a nonprofit digital library, declared a National Emergency Library (NEL) lending program. With more than a million digital books in its Open Library collection, the IA temporarily suspended its usual limit on lending digital copies one at a time during this unprecedented period.

While the move was heralded by many readers, schools, and libraries, others weren’t so happy. Several well-known authors blasted the program as “piracy.” Then, two months after it began, Hachette Book Group, HarperCollins, Penguin Random House, and John Wiley & Sons sued the IA, alleging “willful mass copyright infringement.”

Now over two-and-a-half years later, arguments have been fully briefed in the district court, but what began as a dispute over the NEL has grown into a much more complex fight over copyright law, the lending of digital books, and the future of libraries….”

HathiTrust Receives $1 Million Mellon Grant to Enhance Core Oper… | HathiTrust Digital Library

“HathiTrust, a member-based organization hosted by the University of Michigan, has received a 5-year, $1 million grant from the Mellon Foundation to fund a multi-year effort to strengthen its preservation and access mission. 

The funding will initially finance three new positions to develop an integrated program of assessment, analytics, and portfolio management for the HathiTrust organization.  “With these new capabilities in place, we can better match our resources to high impact work,” says Mike Furlough, Executive Director. “We will be able to grow our team and modernize our tools and processes, and create a more nimble and disciplined organization to meet our community’s strategic needs.”

In March 2020, HathiTrust developed the Emergency Temporary Access Service (ETAS), permitting access to digitized materials for hundreds of academic and research libraries and their communities during the height of the Covid-19 pandemic lockdowns. “Emergency services increased demand for access, and confirmed the importance of large scale digitization and long-term digital preservation. From that experience, we learned that over the next several years we need to diversify the ways that libraries and users engage with HathiTrust. I’m grateful for the Mellon Foundation’s support, which will allow us to better respond to those needs,”  Furlough says….”

 

Researcher and Academic Library Roles and User Beliefs in the Pandemic: Designing the Open-Access and Library Usage Scale (OALU) | DeZouche | Journal of Intellectual Freedom & Privacy

Abstract:  We investigated whether individuals believe they have a right to information during a crisis, and whether attitudes about crisis-related information sharing differ by age and one’s role in providing or consuming information. We measured attitudes about aspects of data sharing related to COVID-19: researchers’ obligation to share data, publishers’ obligation to share information, and libraries’ responsibility to provide them. We predicted younger individuals, especially students as consumers of information, would report stronger preference for open access to pandemic-related information. A principal components analysis was performed, and two predicted factors emerged: information-sharing obligations and libraries’ responsibility to provide resources. Age was not significantly correlated with attitudes about libraries or information-sharing. Planned analyses comparing students, faculty, and community members unaffiliated with the university revealed no differences in their attitudes regarding library resources or information-sharing. A lack of age and university affiliation-related differences can be explained by universally strong attitudes in favor of both information-sharing and library resources, with a greater desire for information-sharing. Knowing that individuals demonstrate a strong preference for open access to information and that these attitudes do not differ between those who are providing (faculty), and consuming information (students/community) can contribute to funding for these resources. This research is innovative and timely, as attitudes about access when information is urgently and globally needed, as during a pandemic, is likely to differ from those observed under different circumstances.

 

Data for Good Can’t be a Casualty of Tech Restructuring  • CrisisReady

“Technology companies like Meta, Twitter and Amazon are laying off thousands of employees as part of corporate restructuring in an uncertain global economy. In addition to jobs, many internal programs deemed unnecessary or financially infeasible may be lost. Programs that fall under the rubric of “corporate social responsibility” (CSR) are generally the first casualties of restructuring. CSR efforts include “data for good” programs designed to translate anonymized corporate data into social good and may be seen in the current climate as a way that companies cater to employee values or enable friendlier regulatory environments; in other words, nice-to-haves rather than need-to-haves for the bottom line.  

We believe the platforms built to safely and ethically share corporate data to support public policy are not a luxury that companies should jettison or monetize. The data we produce in our daily lives has become integral to how public decisions are made while planning for public health or disaster response. Our 21st century public data ecosystem is increasingly reliant on novel private data streams that corporations own and currently share only conditionally and increasingly, for profit….

We contend that the rapid sharing of aggregated and anonymized location data with disaster response and public health agencies should be automatic and free — though conditional on strict privacy protocols and time-limited — during acute emergencies….

While the challenges to realizing the full value of private data for public good are many, there is precedent for a path forward. Two decades ago, the International Space Charter was negotiated to facilitate access to satellite data from companies and governments for the sake of responding to major disasters. A similar approach guaranteeing access rights to privately held data for good during emergencies is more important now….”

The gaping problem at the heart of scientific research – The Week

“The benefits of open access have been proved beyond doubt….

National science agencies from nations including the UK, Australia, Italy, the United States and Brazil called for publishers to make coronavirus research immediately and freely accessible, which in the most part they did.

But the very need for these groups to call for research to be made available in the middle of a global emergency demonstrates the failure of the current publishing system. Making research immediately free to read, which, when combined with the use of an open publishing licence, is known as open access’ is a hot topic in science.

Global health bodies know how important open research is, especially in times of emergency, which is why they have repeatedly called for research to be made open….

The consequences of lack of access to research can be dire.

In 2015 a group of African researchers claimed that an earlier Ebola outbreak could have been prevented if research on it had been published openly….

As 2023 unfolds, it seems that the benefits of open access have been proved beyond doubt.

The next emergency in front of us, climate change, is much more complex, and there too are calls for open access.

Serious investment in a variety of approaches is essential to ensure a diverse, equitable, open access future.”

Open Science: Emergency Response or the New Normal? | Acta Médica Portuguesa

From Google’s English:  “To align with open science, the assessment of research and researchers has to be broader, valuing all contributions and results (and not just publications), and adopting an essentially qualitative perspective, based on the review by peers, with limited and responsible use of quantitative indicators. There has also been slow progress in this domain, but it is hoped that the recently presented Agreement on Reforming Research Assessment and the Coali-tion for Advancing Research Assessment10 will speed up and give greater breadth to the transformation of the assessment process. If the three conditions mentioned above are met in the coming years, open science will no longer be just the science of emergencies. And open and collaborative research practices, with rapid dissemination of results, could become dominant, being considered the correct way of doing science, without the need to designate them as open science.”

Pandemic and infodemic: the role of academic journals and preprints | SpringerLink

“In contrast, before the outbreak of COVID-19 pandemic, clinical researchers were generally reluctant to adopt widespread sharing of preprints, probably because of concern that the potential harm that could result to patients, if medical treatment is based on findings that have not been vetted by peer reviewers. For example, the BMJ group opened a preprint server (ClinMedNetPrints.org) in 1999, but was closed in 2008, because only around 80 submissions were posted during this period [7]. The BMJ group, together with Cold Spring Harbor Laboratory and Yale University launched a new server, bioR?iv in 2013, and medR?iv in 2019 [7], but they were not actively used.

Outbreak of COVID-19 pandemic triggered clinical researchers to use actively preprint servers, and during the initial few years of the COVID-19 pandemic, more than 35,000 preprints, mainly related to COVID-19, have been posted to medR?iv. This marked increase in the posting of preprints indicates that clinical researchers have found benefits of preprints in the era of COVID-19 pandemic: research outcomes can be disseminated quickly, potentially speeding up research that may lead to the development of vaccines and treatments; quality of the draft can be improved by receiving feedback from a wider group of readers; the authors can claim priority of their discovery; and unlike articles published in subscription-based journals, all the preprints are freely available to anyone….”

 

MIT Press Takes Agile Approach to Launching COVID-19 Overlay Journal: Interview with Nick Lindsay

“When COVID-19 first hit, MIT Press was quick to respond, making relevant book and journal content freely available to help scholars and the general public better understand the pandemic. But, the press’ publishing team wanted to do something more. Like so many in academia, they were becoming concerned with rising instances of false scientific claims entering the mainstream media and eager to stop the spread. Recognizing misinformation in preprints as well as misinterpretation of preprint findings as two primary causes, they began considering ways to flag questionable preprint information while boosting the signal of promising new research.

“Our Press Director Amy Brand and I were talking one day about what we could do, and that’s when the notion of launching an overlay journal of preprint reviews popped up,” said Nick Lindsay, MIT Press’ Director of Journals and Open Access. Lindsay and Brand brought the idea back to their team and began planning what would become Rapid Reviews: COVID-19 (RR:C19), the first multi-disciplinary OA overlay journal for peer reviews of coronavirus-related preprints. MIT Press launched RR:C19 in August 2020….”

Intelligent open science: viral genomic data sharing during the COVID-19 pandemic – GOV.UK

“A case study on how data was shared across borders during the coronavirus pandemic, and best practice for responding to future global emergencies….

While genomic sequencing data was shared more quickly and widely than ever before during the COVID-19 pandemic, in many cases it was shared too late, or in too partial a form, to support the emergency response.

There is broad consensus that existing norms for data sharing are not well-adapted to an emergency context in which near real-time sharing is the desired goal.

Following the open science commitments made during the UK’s G7 Presidency, BEIS commissioned this study to add depth and precision to existing recommendations on:

data sharing across borders
related research practice
related cultural issues

The findings are intended to inform understanding of open science best practice in responding to future global emergencies….”