Science journals to offer select authors open-access publishing for free

By SalM on February 5, 2021 in News

AAAS, which publishes the Science family of journals, announced today it will offer its authors a free way to comply with a mandate issued by some funders that publications resulting from research they fund be immediately free to read. Under the new open-access policy, authors may deposit near-final, peer-reviewed versions of papers accepted by paywalled Science titles in publicly accessible online repositories.

For now, Science’s approach, known as green open access, will only apply to authors of papers funded by Coalition S, a group of mostly European funders and foundations behind an open-access mandate that takes effect this month. The funders say immediate access will accelerate scientific discovery by disseminating new findings faster. Up to 31% of research papers in the flagship journal Science and four other Science titles have cited funding from Coalition S, said Bill Moran, the journals’ publisher. Until now, these papers had been available immediately only to journal subscribers, although the paywalled Science journals do make all papers free 12 months after publication.

Articles made public under the new policy will carry an open-access license, and authors will retain copyright, another of Coalition S’s conditions.

AAAS said it will pilot the new policy for 1 year, allowing it to judge whether the policy causes revenues to suffer. University librarians and others might drop subscriptions if they can access research articles for free, Moran acknowledged. But he said some librarians have told him they value Science enough that they will continue to subscribe to help keep it going. Depending on how AAAS’s revenues fare, it might even consider expanding the policy to allow other kinds of authors to publish open access in the same way, he said.

In choosing the green route, the nonprofit AAAS (which also publishes ScienceInsider) deliberately chose not to expand its use of the so-called gold open-access business model, under which authors pay a fee to make a paper’s final, published version immediately free to read. A sixth AAAS journal, Science Advances, charges a fee of $4500 per paper for publishing articles under the gold model.

Had AAAS chosen to convert its flagship Science to the gold model, the likely publication fee would have been prohibitively expensive for many authors, especially those in poorer nations or working in disciplines with meager funding, Moran said. The fee would have been “along the same lines as, if not higher” than the top charge of €9900 per article that the Nature family of journals offered starting this month for gold open-access publication, as part of its response to the Coalition S mandate. Moran said Science would need to set a high fee in order to cover the staff costs involved. What’s more, he noted, like NatureScience does not collect publishing fees for articles not containing original research, such as news stories, commentaries, and reviews. (Science’s news department is editorially independent.)

AAAS’s new policy is not a radical departure from its previous one, which allowed authors to immediately archive the near-final version, called the author-accepted manuscript, on personal websites and in institutional repositories when the final version was published. The new policy extends this to allow authors to post in nonprofit, subject-based repositories, such as the U.S. National Institutes of Health’s PubMed Central.

AAAS is not the first nonprofit scientific society that publishes journals to have adopted such a policy. The Massachusetts Medical Society announced a similar approach in October 2020 for The New England Journal of Medicinecovering authors funded by Coalition S members. Other publishers with similar policies include the American Geophysical Union, American Society for Cell Biology, the Microbiology Society, and the Royal Society.

The Royal Society started a version of the policy several years ago, and “We see high levels of subscription renewals annually (typically > 95%),” wrote Stuart Taylor, its publishing director, in an email. But in a recent blog post, he and other officials at some other nonprofit societies, which otherwise support open access, voiced worries that details of Coalition S’s policy could actually slow the increase of open-access articles and have other negative consequences. The policy includes a provision that could allow authors to immediately archive a paper’s final version, not only the near-final one. That could undermine subscription revenues and give journals little incentive to help authors make more articles open access, they wrote.

What is more, the near-final version, although usually very similar to the final one, typically lacks some useful parts that are contained in the final version, such as supplementary materials. And posting the near-final versions can make it more difficult to ensure the integrity of the scientific record, the society officials wrote: Publishers typically add any corrections or retraction notices for a paper to its final version of record maintained on their websites. But some authors may not replace articles they archive with such updated versions.

“Green has never been an ideal route to open access [OA],” the blog writers said. “It is wholly reliant upon precisely the model that the OA movement was trying to overturn—namely subscriptions. … Green has been the workaround, not the desired endpoint.”


Scientists call for fully open sharing of coronavirus genome data

By SalM on February 4, 2021 in COVID-19

Hundreds of scientists are urging that SARS-CoV-2 genome data should be shared more openly to help analyse how viral variants are spreading around the world.

Researchers have posted huge numbers of SARS-CoV-2 genome sequences online since January 2020. The most popular data-sharing platform, called GISAID, now hosts more than 450,000 viral genomes; Soumya Swaminathan, the chief scientist at the World Health Organization (WHO), has called it a ‘game changer’ in the pandemic. But it doesn’t allow sequences to be reshared publicly, which is hampering efforts to understand the coronavirus and the rapid rise of new variants, argues Rolf Apweiler, co-director of the European Bioinformatics Institute (EBI) near Cambridge, UK, which hosts its own large genome database that includes SARS-CoV-2 sequences.

“The openness of SARS-CoV-2 sequence data is crucial for the rapid response against the biggest health threat to humankind in a very, very long time,” says Apweiler.

In a letter released on 29 January, Apweiler and others call for researchers to post their genome data in one of a triad of databases that don’t place any restrictions on data redistribution: the US GenBank, the EBI’s European Nucleotide Archive (ENA) and the DNA Data Bank of Japan, which are collectively known as the International Nucleotide Sequence Database Collaboration (INSDC).

Anyone can anonymously access the INSDC’s data and use them as they want, but GISAID requires that users confirm their identity and agree not to republish the site’s genomes without permission from the data provider. This means that studies building on GISAID data — such as those that create evolutionary trees analysing how SARS-CoV-2 variants are related — can’t publish full data so that others can easily check their analyses or further build on their data set. They must direct readers back to the GISAID site.

The letter says the scientific community should “remove barriers that restrain effective data sharing”, but doesn’t mention GISAID specifically. It is signed by more than 500 scientists, including the 2020 chemistry Nobel laureate Emmanuelle Charpentier, and the head of the COVID-19 Genomics UK Consortium, Sharon Peacock. Where scientists have already established submissions to other databases, the letter states, “these submissions should continue in parallel”.

Feature not flaw

Many researchers who work with GISAID say that its terms of access are a benefit, because they encourage hesitant researchers to share data online speedily, without fear that others will use the results without credit. “The reason so many labs have provided SARS-CoV-2 genomes to GISAID is precisely because of the data-access agreement that restricts public resharing,” says Sebastian Maurer-Stroh, a bioinformatician at Singapore’s Agency for Science, Technology and Research. GISAID has worked with many labs to assist them to share data, he says.

GISAID stands for the Global Initiative on Sharing Avian Influenza Data; an international consortium of researchers helped to set it up as a nonprofit foundation in 2008, to address researchers’ reluctance to share data on influenza strains. Some nations, including Indonesia, a hotspot for avian flu, feared that pharmaceutical firms would create drugs and vaccines using the sequence data without crediting the original data providers or sharing the benefits of the work with them. But they were persuaded to share sequences rapidly in GISAID; in March 2013, for instance, China published sequences of H7N9 avian flu in the database on the same day it informed the WHO of three infections in people. “GISAID encourages and incentivizes real-time data sharing by parties who would otherwise be reluctant to share, by ensuring that they retain their rights in their data,” says a spokesperson for the initiative.

“This issue is not only about science, but also about sovereignty and equity,” says Marie-Paule Kieny, a vaccine researcher at INSERM, the French national health-research institute in Paris. “GISAID empowers the rapid flow of SARS-CoV-2 sequence data with maximal impact,” she says, because scientists depositing sequences can trust that their rights will be respected by data users.

Senjuti Saha, a microbiologist who works on SARS-CoV-2 genomes at the Child Health Research Foundation in Dhaka, says that she appreciates the call for open data beyond what GISAID offers, but worries that it may further dissuade researchers in low- and middle-income countries (LMICs) from uploading data until they have analysed them. During the pandemic, she says, some LMICS have started doing more viral sequencing, although labs often lack computational infrastructure. She says that she’s seen LMIC coronavirus data taken out of context by academics in wealthier countries who don’t consult or credit the data-providers. “We really want to share our data, but it is heart-breaking and demotivating when we know we worked so hard to generate data, but we don’t get the credit for it,” she says.

The letter, says Kieny, “seems to me like an initiative from European and high-income countries not fully informed on the critical need to ensure that low-resource countries accept to share sequences freely, so that the public-health impact of sequencing of pathogens such as SARS-CoV-2 is maximized”.

ENA head Guy Cochrane says the EBI is aware of the global issues around data and benefit sharing, and is actively involved in finding benefit-sharing mechanisms that empower countries in the global south and keep data open. But even well-resourced European countries could do more to share their data openly, he says.

Data challenges

Some researchers told Nature that besides arguments about equity and openness, there is an issue with GISAID’s differential control over how registered users can download its data. Some users must download files in small batches, for instance, but others can get an entire data set in bulk with GISAID approval. The GISAID spokesperson said that’s because the initiative needs to know who is using its data and for what reason, so that nothing is erroneously redistributed.

Cochrane adds that another challenge with GISAID’s platform is that researchers post ‘assemblies’ — or reconstructions — of viral genomes from the chunks of data read off sequencing machines, rather than the raw data. Assembly always involves some interpretation of inevitable errors in the sequencing process, Cochrane says, and this can lead to what look like mutations in a genome that are in fact artefacts of sequencing. Access to the raw data of many genomes helps scientists dig into these issues, and Cochrane says researchers should share their raw and assembled sequencing data, which they can do at the INSDC even if they also post on GISAID. Maurer-Stroh, however, says that GISAID is aware of such issues and already provides quality-control checks to flag potential mistakes in submitted genomes. Cochrane says such processes can only reduce, not eliminate, artefact errors.

An EBI-hosted data portal that brings together fully open COVID-19 data sets submitted to the INSDC currently hosts more than 270,000 raw SARS-CoV-2 sequences and 55,000 assembled genomes — fewer than GISAID. “We have a fog of incomplete knowledge,” says Apweiler. He says that some scientists might think, incorrectly, that submitting data to GISAID means that the results will automatically be shared openly at the INSDC — and he hopes that the call to share data without restriction will boost the INSDC’s data trove.

But telling scientists to resubmit their SARS-CoV-2 data to the INSDC is complex, says David Haussler, who directs a genomics institute working with INSDC and GISAID data at the University of California, Santa Cruz. Bioinformaticians are in crisis mode, rushing to get genome data and analyse it in detail, and want to share as much as they are permitted to publish about key new mutations in sequences, he says. He did not sign the open letter — although he supports restriction-free data sharing — because he hopes instead that GISAID can temporarily drop some of its access terms during the pandemic, perhaps to coordinate with the INSDC.

Kieny, however, says that could lead to some scientists losing trust in GISAID and not filing their sequences with the database so quickly. “There is no obstacle, for those who want to do it, to deposit their sequences into the INSDC,” she says.

Source: nature. com

Why women don’t speak up on Zoom calls – and why that’s a problem

By SalM on February 3, 2021 in News, Women in Research

  • Women are systematically seen as less authoritative, study shows.
  • Gender biases still shape the rules of social engagement.
  • Changing the environment in the room – rather than changing women’s behaviour – should be the goal.

Diversity efforts may have given women a seat at the table – or, in the context of the pandemic, a place on the Zoom call – but that doesn’t necessarily mean they have a voice.

With working from home now the norm for many, a growing body of research is showing that it’s not become a leveller for meetings.

Almost half (45%) of US women business leaders surveyed in September said it was difficult for women to speak up in virtual meetings on platforms like Zoom, while one-in-five women felt they’d actually been ignored on such calls.

Researchers at Brigham Young University in the US found last year that the gender dynamics shutting down women remained prevalent, even in the most well-intentioned settings.

“Women are systematically seen as less authoritative,” Jessica Preece, associate professor in political science at BYU, told BYU Magazine.

“And their influence is systematically lower. And they’re speaking less. And when they’re speaking up, they’re not being listened to as much, and they are being interrupted more.”

So what’s going on?


Women ‘less influential’

Preece and her colleagues examined the female experience in a male-dominated collegiate accounting programme, in which women were typically enrolled with better grade point averages and more leadership experience than their male counterparts.

Students pass through the programme on teams, and administrators wanted to know how to best build these groups.

In teams where women were outnumbered, the researchers discovered they were routinely seen as the least competent and influential in the group.

The problem is not necessarily intentional bias or misogyny. It is instead a systemic problem with society that often sees cultural norms and gendered messages shaping the rules of engagement, explained Preece.

We have been “slowly socialized over years to discount” female expertise and perspectives, she said.

“It’s not women who are broken; it’s society that’s broken,” she added. “I’d like to see us focus on training people to be – and creating systems that are – supportive of women who speak up.”

This means the goal needs to be changing the environment in the room, actual or virtual, rather than women themselves – so that they are empowered and listened to.

“We have lots of learning and unlearning to do.”


Towards gender parity

Gender parity can affect whether or not economies and societies thrive, according to the World Economic Forum’s Global Gender Gap Report 2020 – particularly important as countries seek to build back better after the coronavirus pandemic.

McKinsey Global Institute’s 2015 Power of Parity report estimated that advancing women’s equality could add $13 trillion to global growth by 2025.

The Forum’s report saw improvement in educational attainment, and health and survival, with the gender gap closing by 96.1% and 95.7% respectively.

Women have been disproportionately impacted during COVID-19, according to McKinsey Global Institute, with greater job losses, often as a result of increasing unpaid care.

Helping women be heard

BYU researchers say that even small changes to make sure women in a meeting, or on a call, can fully contribute or express their views can make all the difference.

Positive interjections, such as “that’s an interesting point”, can elevate and help validate women’s voices in spaces where they may otherwise be lost, they added.

The goal is to create an environment in which women can be as influential as their authentic selves, says Preece.

“If we build a world in which women’s voices are valued and listened to, they will speak up without having to be told to.”

Source : World Economic Forum

The boom of non-profit associations for medical research in 2020

By SalM on February 2, 2021 in News

The pandemic has produced a profound health, economic, and social crisis, but it is also offering the opportunity to transform the way research is conducted and shared, accelerating those processes through which it will be increasingly possible to make science more open, efficient, and collaborative. In this exceptional situation, the activity of nonprofit medical research institutions stands out within the Third Sector, and they are playing a fundamental part in providing the resources necessary to achieve treatment goals.

In this post, we will explain the reasons for the boom that has resulted in investments in non-profit medical research associations during this year, highlighting the main trends that the diffusion of COVID-19 has triggered, strengthened, and radicalized in the field of science in general and the biomedical sector, specifically.

Non-profit medical research institutes at the center of a cultural change

This crisis is providing a lesson that we hope will not be forgotten in the years to come: rather than from a no-holds-barred competition, the most effective answers to the emergency are coming from global collaboration among the protagonists of research. It seems clear that efficiency can be gained only through a radical change of attitudes, means, and people: for this reason, collaboration must be able to proceed well beyond the laboratory, and all stakeholders must be involved: public and private, industry, institutions, and operators from civil society.

In the scientific field, we are experiencing a real cultural change that is destined to transform the way that different research projects are developed. At the center of this change, non-profit medical research institutes are increasingly asserting themselves. What trends have led to this position?

Four trends for creating a unique and interdependent ecosystem

The relationship between scientific research, territory, and community is mediated by national and international policies and is extremely articulated: it is based on scientific results (and on the publications that disseminate them), but to have concrete consequences, it needs to be implemented at different levels. To give rise to a unique ecosystem in which health and research are mutually dependent, it is necessary to implement a series of initiatives that serve to achieve:

  • Faster and more comprehensive data sharing
  • A set of metrics capable of translating the complexity of reality
  • A more comprehensive and representative definition of scientific excellence, and a new, more effective way to validate and distribute research results

  1. A free exchange of data. The Sars-CoV-2 virus does not respect borders: the urgency and ubiquity of the crisis have imposed practices of wider and greater sharing on the global community of researchers, encouraging them to operate with a multidisciplinary approach that connects different domains and different sectors. In such a context, which has become more fluid and inclusive, non-profit medical research associations and institutes have been able to assert one of their important constitutive qualities: the ability to function as an interface and point of contact between all parties (patients, volunteers, local and national economic, and political entities, international bodies). The free exchange of data, sharing knowledge otherwise destined to be guarded, is now more than ever a compulsory choice.
  2. New metrics that are more representative of a multi-stakeholder context. Conventional metrics that measure the impact of the research and innovation process on health and that traditionally express mainly scientific, economic, and financial dimensions are proving dramatically insufficient in representing the needs and requirements of the various actors involved. The development of a new theoretical and operational framework that can support integrated research must also take into account the value system, based on collective sustainability, of the Third Sector and, in particular, of the specificity of those organizations that have found themselves on the front lines of the crisis, namely the non-profit medical research institutes. Appropriate new metrics for assessing the impact of health research will therefore have to incorporate the interests of all stakeholders.
  3. A more inclusive definition of scientific excellence. For many years, the concept of “Responsible Research and Innovation” (RRI) has been at the center of the international debate on science and technology. According to one of the most well-known definitions, that of the philosopher René von Schomberg, Responsible Research and Innovation refers to a transparent and interactive process through which various societal actors and innovators interact to ensure that scientific and technological design can result in processes and products that are safe for humans and the environment, ethically acceptable, and responsive to the needs and wants of individuals and society. (Source: Responsible research is research that produces a positive impact on individuals and society as a whole. A participatory multi-stakeholder approach is certainly better equipped to answer a complex question because it does not evaluate results solely in terms of scientific excellence, but includes economic and social considerations, patient and community expectations, and the responses of those key nonprofit actors operating in the biomedical and health fields.
  4. More efficient ways of validating and communicating science. The common reflection of many editorials that have appeared in scientific journals in recent months is that the pandemic has contributed to a profound change in the way research is conducted and shared nationally and internationally (here we limit ourselves to pointing out articles that have appeared on and the Scientific American blog) The way research is validated and shared has remained virtually the same over decades. However, the spread of the COVID-19 virus seems destined to profoundly change the two main systems of judging and communicating results, i.e., in-person conferences, which for security reasons have been replaced with remote online meetings, and the peer review system. In the latter case, the evaluation and recognition mechanisms, which tended to be very slow (it can take from six to nine months before a scientist’s manuscript is peer reviewed and appears in a journal) have been greatly speeded up and simplified, so much so that in the first 5 months of COVID-19 emergency, scientific journals have published about 9,500 peer reviewed articles, with Italy in third place for number of publications (906) (source:

New ways of relating and communicating between funders, researchers, institutions, and states are shaping a type of science that will have to develop the tools, including technological ones, to guide the development of smarter systems and more resilient societies.

The future of science is therefore certainly international, interdisciplinary, and open. But such a future is only possible by continuing to involve all actors, among which there are certainly non-profit medical research institutions:

  • In the participatory practices of production and transmission of scientific knowledge
  • In the communication of information of general interest to civil society
  • In the management of fundraising for the various initiatives

Non-profit biennium 2018-2020: the growth of the Third Sector

The nonprofit medical research associations we discuss in this post are part of the Third Sector, which we generically refer to when we talk about the “nonprofit” world. The entities that fall under the umbrella term “Third Sector” (different from the First and Second Sectors, i.e., the market and the State) are private organizations with a statute that act on a non-profit basis with the purpose of social utility and can take different legal forms: voluntary organizations, foundations, cooperatives, etc. They are all private legal entities and expressions of civil society, which are created to provide essential services, especially at the local level. Often, in meeting the needs of civil society, they constitute an alternative to public and private bodies. (Source: Il Terzo Settore in Italia, Silvano Venditti, degree thesis).

Structure and profiles of the nonprofit sector

According to the latest Istat report that surveys the number of nonprofit institutions active in Italy and their main structural characteristics, the nonprofit sector is confirmed to be growing: as of December 31, 2018, there were 359,574 active nonprofit institutions in Italy and they employed 853,476 people overall. The number of nonprofit institutions is increasing with average annual growth rates that are substantially constant over time (around 2%).

In the March 2019 issue of the online magazine Vita Luca Carra and Sergio Cima, editors of, confirmed this trend, stating that, each year, about €300 million is invested in biomedical research by nonprofit entities. This is pure oxygen for the 35,000 researchers engaged in Italy to study and fight diseases. While this is not the most consistent contribution to medical research, the resources of nonprofits have two characteristics that are difficult to find in other types of funding: the rigorous and independent evaluation of projects and the competitive nature of calls for proposals, which reward the most deserving after an evaluation and selection conducted by groups of international experts, often foreign, so as to avoid academic groups and preferences that are independent of the quality of the research proposed.

The world of non-profit medical research institutes, together with patients’ associations, is therefore a fast-growing world that often offers decisive support to scientific studies, thanks to fundraising, public awareness initiatives, and indications provided to researchers.

2020: Italian nonprofits during the pandemic

Italians have responded with generosity to the COVID-19 emergency, multiplying donations to non-profit organizations in the health and hospital sectors. However, the situation also presents some notable criticalities: for many third sector organizations, fundraising has increased, while for others, their very survival is at risk. While, on the one hand, there has been a historical peak in online donations and aid amounting to over €650 million has been mapped, on the other hand, 78% of the over 600 organizations interviewed by declare that they have more than halved their activities.

The results of the monitoring #ILDONONSIFERMA presented by the Italian Institute of Donation (IID) on the trend of fundraising by nonprofit organizations in Italy confirm a generally mixed picture: in the first quarter of 2020, 24% of the population would have made a donation in the field of health and hospitals, equal to about 10-12 million Italians, with an increase of about 30% compared to donations for scientific research, health and equivalents of the previous year. The health sector and the theme of health therefore definitely catalyze the attention of donors.

The data also shows a great ability of Italian nonprofits to adapt to a rapidly changing context: 24% of the entities contacted for the survey managed to avoid suspending services through the adoption of digital and remote channels and tools, transforming “action in the field into a remote relationship,” compared to 7% who had to suspend their activities completely (source: L’impatto dell’emergenza sulle donazioni).

Finally, reported evidence that emerged from a survey carried out between April and June 2020 by Italia Non Profit and Assifero, interviewing almost 1,400 subjects (Non Profit Philanthropy Social Good Covid-19 Report): in addition to 975 initiatives mapped by 722 donors, €785 million in funds were raised between April and July 2020.

The article mentioned that lockdowns halted some fundraising activities and campaigns,  and that 41% of nonprofits expect revenue to be reduced by more than 50% by 2020 (and for another 38%t, it will be reduced significantly). By 2021, they believe that a real transformation will be needed, one that diversifies revenue funds and investment in capacity building.

Future perspectives of nonprofit medical research institutions during the COVID emergency

In an article published in late June 2020, Paola Zaratin writes that Third Sector nonprofit organizations have demonstrated strategic competencies in addressing the COVID-19 pandemic, performing a subsidiary task to the state, and integrating these competencies not only into health and social care but also into research.” These competencies include:

  • Democratization of access to knowledge (Open access knowledge)
  • Science education
  • Strengthening of collaborations with multiple actors (multi-stakeholder)
  • Improvement in the capacity for transferring the results of scientific research
  • Involvement of patients
  • Activation of public policies based on “scientific evidence”
  • Collecting funding to invest in the development of innovative models of sustainability

For this reason, Third Sector organizations, including non-profit medical research institutions, “that support responsible research and innovation and thus operate in the collective interest” have earned “a more relevant recognition and role” but will immediately begin to gear up to exceed to transform their fundraising strategies, embrace digital and diversify their approach so as to use a wider range of channels. The effort will need to be directed on multiple fronts.

According to Il Sole24ore (source), the initiatives that nonprofit organizations plan to implement once the emergency is over will focus on:

  • Fundraising (19.9%)
  • The creation of financial reserves for future crises (16%)
  • Investing in brand awareness (15.2%) and training (13.4%)
  • Investing in building capacity (12.7%)

In light of the problems that will affect nonprofits in the immediate future, the challenge then is to strengthen the entire sector, in economic terms by raising sufficient funds, and in terms of awareness.

Source: doxee