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Direito autoral no tratado comercial Mercosul-UE: poucas melhoras e muitos retrocessos

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Publicado originalmente em inglês em 6 de abril de 2018. Tradução: Ana Luiza Araújo

Uma proposta recém vazada do tratado de livre comércio entre o Mercosul e a União Europeia mostra pequenas melhorias no capítulo sobre propriedade intelectual. Agora parece que a extensão desnecessária e injustificada dos prazos de direito de autor por 20 anos não está mais no tratado, e as partes introduziram alguma flexibilidade para que os usuários contornem as medidas técnicas de proteção com o objetivo de exercer seus direitos. Mas, em sua maior parte, as negociações continuam a favorecer um maior endurecimento do direito de autor às custas das proteções de direitos dos usuários e dos bens comuns. Como explicaremos abaixo, as medidas para apoio do domínio público continuam a ser diluídas, a cláusula que requer a compensação obrigatória — indiferentemente se o criador a deseja ou não — está mantida, e a seção que delimita as exceções e limitações aos direitos autorais foi reduzida ao mínimo.

No ano passado, em colaboração com diversos parceiros de nossa rede global, a Creative Commons publicou uma breve análise de políticas, cobrindo diversos problemas relacionados ao direito de autor em um esboço do capítulo sobre propriedade intelectual do tratado de livre comércio Mercosul-UE.

A União Europeia (UE) e o sub-bloco regional da América Latina, formado por Argentina, Brasil, Paraguai e Uruguai (o Mercosul) vêm negociando um tratado de livre comércio (TLC) desde o ano 2000. O TLC UE-Mercosul é amplo, abarcando o comércio de bens industriais e agrícolas, potenciais mudanças nas regras aplicáveis a pequenas e médias empresas e às compras públicas, e provisões sobre propriedade intelectual como patentes e direito de autor. Nessa análise, nós examinamos as questões que afetariam o domínio público, a criatividade e o compartilhamento, e os direitos de usuário na era digital.

As negociações do TLC Mercosul-UE acontecem em um ambiente no qual as políticas de direito de autor se estabelecem de maneira crescente por meio de acordos de comércio multilaterais. Dentre os principais pontos defendidos em nossa análise, destacamos os seguintes:

  • Os prazos de proteção do direito de autor não devem ser estendidos;
  • Os direitos dos usuários devem ser protegidos mediante a expansão das limitações e exceções;
  • A remuneração obrigatória interfere com o licenciamento em Creative Commons;
  • Medidas de proteção tecnológica não devem limitar o exercício dos direitos dos usuários.

Nós também compartilhamos do princípio de senso comum de que negociações para acordos comerciais devem ser transparentes e incluir o público, não secretas e decididas atrás de portas fechadas.

Desde a nossa análise, mais duas versões provisórias do capítulo sobre propriedade intelectual foram vazadas. Uma foi publicada pelo Greenpeace em dezembro de 2017, com base na 28ª rodada de negociações. Outra foi publicada na última semana pelo site  bilaterals.org, com base no texto consolidado ao final da 32ª rodada de negociações que teve fim em março.

Como escreveu Jorge Gemetto no blog da Communia Association, o texto do capítulo sobre propriedade intelectual revelado pelo Greenpeace mostrou um significativo desentendimento entre as partes.

É fácil perceber que, enquanto o interesse da União Europeia é o de aumentar os prazos e áreas de proteção da propriedade intelectual, assim como impor novas penas para as infrações, os países do Mercosul procuram evitar padrões mais altos de propriedade intelectual, incorporar limitações e exceções obrigatórias para o direito de autor, e favorecer a identificação e proteção do domínio público.

Como adverte Gemetto, há uma grande discrepância entre os poderes de negociação de cada parte, com a UE claramente tendo a vantagem. E com a UE já alinhada com o restritivo marco regulatório “TRIPS Plus”, há uma procura por exportar essas medidas mais duras de proteção e aplicação em outros lugares.

Por fim, chegamos ao capítulo mais recente sobre propriedade intelectual publicado pela organização bilaterals.org, no qual temos algumas mudanças notáveis desde a versão do Greenpeace.

A menção ao domínio público será diluída e enterrada

A versão vazada pelo Greenpeace (em dezembro de 2017) revelou a discussão entre as partes sobre se (e como) deveria haver uma menção de apoio ao domínio público no Artigo 4 (Princípios). A UE propôs a linguagem “As Partes reconhecem a importância de um domínio público robusto, rico, e acessível”, enquanto os países do Mercosul defenderam a redação “As Partes levarão devidamente em conta a necessidade de preservar um domínio público robusto, rico e acessível, e devem cooperar mutuamente para identificar os diferentes materiais que ingressaram no domínio público.”

A versão da UE ganhou. O texto consolidado compartilhado pela bilaterals.org agora diz “As Partes reconhecem a importância de um domínio público robusto, rico, e acessível”. Além disso, uma nota no documento muda o texto da seção de “Princípios” para a seção de “Cooperação”.

A remuneração obrigatória fica

A versão anterior publicada pelo Greenpeace mostrava que as partes estavam discutindo se haveria a remuneração obrigatória (Artigo 9.6) para os intérpretes, músicos executantes e produtores musicais. A UE queria que a redação do texto fosse “As Partes conferem um direito para garantir que uma única remuneração equitativa seja paga pelo usuário aos intérpretes, músicos executantes e produtores de fonogramas, se um fonograma for publicado para fins comerciais, ou a reprodução de tal fonograma for utilizada para a difusão por meios sem fio ou para qualquer comunicação ao público.” Os países do Mercosul queriam apenas fazer deste um direto opcional, sugerindo que o texto fosse “As Partes poderão conferir…”

A versão da UE venceu. O texto consolidado diz “conferem”. Essa mudança repete um tema comum visto entre as negociações: cláusulas que se referem à aplicação da propriedade intelectual e à proteção dos detentores de direitos incumbentes são obrigatórias (“devem”), enquanto cláusulas que iriam beneficiar os usuários e o interesse público são apenas opcionais (“podem”). Este tipo de arranjo poderia interferir na operação de algumas licenças de Creative Commons ao exigir um pagamento mesmo quanto a intenção do autor seja o compartilhamento de seu trabalho criativo com o mundo de graça.

A extensão do prazo do direito de autor foi posta em suspensão

O texto provisório revelado pelo Greenpeace mostrava que as partes continuaram a discutir sobre os prazos do direito de autor (Artigo 9.7). A UE queria direitos vitalícios + 70 anos, enquanto os países do Mercosul os mesmo vitalícios + 50 anos.

O texto consolidado agora diz “transcorrerá durante a vida do autor e por não menos do que 50 ou 70 anos quando assim prover a legislação nacional das Partes…”.

A versão do Mercosul venceu porque o texto afirma que se aplicarão os termos nacionais existentes. Essa é uma melhora significativa no sentido de que não exige que os países com prazos mais curtos aumentem-os para o prazo mais longo. Estender ainda mais os prazos do direito de autor não faz nada para promover a criação de novos trabalhos, e até exacerba os desafios relacionados com prazos maiores, como o problema de obras órfãs.

Exceções e limitações reduzidas ao mínimo

A versão do Greenpeace mostrou que as partes estavam discutindo sobre o escopo da seção sobre limitações e exceções (Artigo 9.9). O Mercosul queria incluir uma lista não-exaustiva de usos aceitáveis a serem cobertos sob as limitações e exceções, incluindo críticas, notícias, educação, e pesquisa.

No entanto, o texto consolidado publicado pela bilaterals.org não inclui a lista não-exaustiva. Ao invés disso, ele essencialmente volta a se apoiar no texto da regra dos três passos (“Cada Parte irá estabelecer exceções e limitações para os direitos exclusivos apenas em certos casos especiais que não entrem em conflito com a exploração normal da obra e não prejudiquem de maneira injusta os interesses legítimos dos titulares de direitos”).

Medidas de proteção e aplicação dos direitos de autor devem sempre ser equilibradas com considerações do interesse público; em outras palavras, os direitos dos autores devem sempre ser moderados, reconhecendo-se e defendendo-se os direitos dos usuários no ecossistema dos direitos de autor. O texto consolidado somente provê o mínimo de considerações para os direitos de usuários.

Alguma flexibilidade para o exercício de direitos sob os esquemas de medidas tecnológicas de proteção

Por último, a versão do Greenpeace revelou que a UE estava propondo uma nova linguagem sobre medidas tecnológicas de proteção (Artigo X.15). Neste esboço anterior, não havia a inclusão de um texto que permitisse qualquer circunvenção de medidas tecnológicas para que um usuário possa exercer seus direito sob uma exceção ou limitação.

No entanto, o texto consolidado agora inclui a seguinte linguagem: “As Partes (UE: quando for permitido de acordo com suas leis nacionais) deverão (UE: poderão) garantir que os detentores de direito deixem à disposição do beneficiário de uma exceção ou limitação, na medida necessária para beneficiar-se dessa exceção ou limitação”. Então, parece que haverá pelo menos alguma consideração legal para proteger a capacidade de usuários de contornar as medidas tecnológicas de proteção para exercer seus direitos sob uma exceção ou limitação.

Conclusão

Ao mesmo tempo em que é positivo que ao menos as partes estejam chegando à conclusão de renunciar à desnecessária extensão do prazo dos direitos de autor, a maioria das mudanças na versão consolidada do texto mostra um contínuo endurecimento da proteção do direito autoral, o que favorece os titulares de direitos às custas dos usuários e dos bens comuns.

Além disso, as negociações continuam essencialmente secretas e fechadas, com pouco conhecimento público, salvo por esses úteis vazamentos, e poucas oportunidades para o público expresse suas preocupações. As negociações devem ser reformadas para apoiar plenamente um processo que seja transparente, inclusivo, e responsável.

 

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Copyright in Mercosur-EU trade agreement: A little better, but mostly worse

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A recently-leaked draft of the Mercosur-EU free trade agreement shows minor improvements to the chapter on intellectual property. It appears that the unnecessary and unwarranted 20 year copyright term extension is now dropped from the agreement, and the parties have introduced some flexibility for users to get around technical protection measures in order to leverage their rights. But for the most part, the negotiations continue to favor increased tightening of copyright at the expense of protections for user rights and the commons. As we explain below, measures to support the public domain continue to be watered down, the provision which requires mandatory compensation—whether creators want it or not—is retained, and the section outlining exceptions and limitations to copyright is pulled back to a minimum.

Last year, in collaboration with several partners from our global network, Creative Commons published a brief policy analysis covering several copyright-related issues presented in a draft of the intellectual property chapter of Mercosur-EU free trade agreement.

The European Union (EU) and the Latin American sub-regional bloc consisting of Argentina, Brazil, Paraguay, and Uruguay (Mercosur) have been negotiating this free trade agreement (FTA) since 2000. It’s expansive, addressing trade in industrial and agricultural goods, potential changes to rules governing small- and medium-sized businesses as well as government procurement, and intellectual property provisions such as copyrights and patents. We examined issues that would affect the public domain, creativity and sharing, and user rights in the digital age.

The Mercosur-EU FTA negotiations take place in an environment where an increasing level of copyright policy is being constructed through multilateral trade agreements. In our policy brief, the main points we argued included the following:

  • copyright terms should not be extended
  • user rights must be protected by expanding limitations and exceptions
  • mandatory remuneration interferes with CC licensing
  • technical protection measures must not limit the exercise of user rights

We also echoed the longstanding commonsense principle that trade agreement negotiations must be transparent and involve the public, not secret and decided behind closed doors.

Since our analysis, there has been two subsequent leaked drafts of the chapter on intellectual property. One was published by Greenpeace in December 2017 based on the 28th round of negotiations. Another was published last week by the website bilaterals.org, based on the consolidated text as it stood at the completion of the 32nd round of negotiations which ended last month.

As Jorge Gemetto wrote on the Communia Association blog, the text of the IP chapter leaked by Greenpeace showed significant disagreement between the parties.

It is easy to see that, while the interest of the European Union is to increase the terms and scope of IP protection, as well as to impose new penalties on infringement, Mercosur countries seek to avoid higher IP standards, incorporate mandatory limitations and exceptions to copyright, and favor the identification and protection of the public domain.

As Gemetto warns, there’s a big discrepancy in the bargaining power leveraged by each party, with the EU clearly holding the upper hand. And with the EU already aligned with the more restrictive “TRIPS Plus” IP framework, they’re looking to export these increased protection and enforcement measures elsewhere.

Finally, we arrive to the recent leaked intellectual property chapter published by bilaterals.org. There are a few notable changes since the Greenpeace version.

Mention of public domain will be watered down, and buried

The Greenpeace leak (Dec 2017) found the parties arguing whether (and how) there should be a mention of support for the public domain in Article 4 (Principles). The EU sought the language, “The Parties recognise the importance of a robust, rich, and accessible public domain,” while the Mercosur countries (MCS) advocated for, “The Parties shall take due account of the need to preserve a robust, rich, and accessible public domain, and shall cooperate with each other in identifying subject matters that have fallen into the public domain.”

The EU version won. The consolidated text shared by bilaterals.org now reads “The Parties recognise the importance of a robust, rich, and accessible public domain”). In addition, a note on the document moves the text from the “Principles” section to the “Cooperation” section.

Mandatory remuneration stays

The earlier Greenpeace version showed that the parties were arguing whether there will be mandatory remuneration (Article 9.6) for performers and producers of music. The EU wanted the text to read “The Parties shall provide a right in order to ensure that a single equitable remuneration is paid by the user to the performers and producers of phonograms, if a phonogram published for commercial purposes, or a reproduction of such phonogram, is used for broadcasting by wireless means or for any communication to the public.” MCS wanted to only make this right optional, suggesting that the text should read “The Parties may…”

The EU version won. The consolidated text now reads “shall.” This change repeats a common theme seen within the negotiations: provisions that have to do with enforcement and protecting incumbent rights holders are mandatory (“shall”), while provisions that would benefit users and the public interest are only optional (“may”). This type of arrangement would interfere with the operation of some Creative Commons licenses by requiring a payment even when the intention of the author is to share her creative work with the world for free.

Copyright term extension put on hold

The draft leaked by Greenpeace found that the parties continued to argue about copyright term (Article 9.7). EU wanted life + 70 years, while MCS life + 50.

The consolidated text now reads “shall run for the life of the author and not less than 50 years or for 70 years where the domestic legislation of the Parties so provides…”.

The MCS version won because the text states that existing national terms will apply. This is a significant improvement in that it doesn’t require the countries with the shorter term to increase to the longer term. Further extending copyright terms does nothing to promote the creation of new works, and even exacerbates related challenges, such as the orphan works problem.

Exceptions and limitations pulled back to a minimum

The Greenpeace leak showed that the parties were arguing about the scope of the section on limitations and exceptions (Article 9.9). MCS wanted to include non-exhaustive list of acceptable uses to be covered under limitations and exceptions, including for criticism, news reporting, teaching, and research.

However, the consolidated text published by bilaterals.org does not include the non-exhaustive list. Instead, it mostly goes back to relying on the 3-step test language (“Each Party shall provide for exceptions and limitations to the exclusive rights only in certain special cases which do not conflict with a normal exploitation of the subject matter and do not unreasonably prejudice the legitimate interests of the right holders.”).

Copyright protection and enforcement measures should always be balanced with public interest considerations; in other words, the rights of authors should always be tempered by recognizing and upholding the rights of users in the copyright ecosystem. The consolidated text only provides the bare minimum consideration for users rights.

Some flexibility to exercise rights under TPM schemes

Finally, the Greenpeace version found that the EU was proposing new language around technological protection measures, or TPMs (Article X.15). In that earlier draft, there was no inclusion of text that permits any circumvention of technological measures in order for a user to exercise their rights under an exception or limitation.

However, the consolidated text now includes the following language: “The Parties (EU: where permissible in accordance to their domestic law) shall (EU: may) ensure that right holders make available to the beneficiary of an exception or limitation the means of benefitting from that exception or limitation, to the extent necessary to benefit from that exception or limitation.” So it appears that there will be at least some legal consideration to protect the ability of users to circumvent TPMs in order to exercise their rights under an exception or limitation.

Conclusion

While it’s positive that at least the parties are coming to the conclusion to forego the gratuitous copyright term extension, most of the changes in the consolidated text show a continued tightening of copyright protections that favor incumbent rights holders at the expense of users and the commons.

Furthermore, the negotiations remain mostly secretive and closed, with little public knowledge save for these helpful leaks, and few opportunities for the public to voice their concerns. The negotiations must be reformed to fully support a process that is transparent, inclusive and accountable.

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Chris Bourg on the Compelling Vision for an Open Digital Commons

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Chris Bourg, by L. Barry Hetherington, available under a CC-BY license

MIT Libraries Director Chris Bourg is one of the most salient voices in the library community for open access, diversity and inclusion, ethics in scholarly publishing, and social justice. As a keynote speaker for this year’s CC Global Summit, she’ll be discussing the nuances of the Open movement as an advocate for the digital commons and director of a major open access initiative.

Chris’s tweets and blog are must-follows – her dog, Jiffy, is an adorable and frequent guest star. In this interview, she discusses tech optimism, storytelling, diversity, and the fallacy of neutrality. Join Chris and more than 400 open advocates at the CC Global Summit in Toronto from April 13-15.

As an open movement, it’s become difficult to live our values as the web’s content Commons have become increasingly enclosed and the halcyon days of internet utopianism seem long over. As a prominent figure in the movement and a crusader for open, how can we do better? What are tangible and intangible steps we can take to move the needle? How can libraries play a role?
I think that generally speaking, I’m an optimist, but not a tech utopian. So I think we keep focusing on the ultimate goal and reasons for promoting an open digital commons. There are compelling stories to be told about the harms of information scarcity and knowledge monopolies, and there are equally compelling stories about ways in which open access to knowledge and culture helps us solve big (and small) challenges across the globe. We have to unearth and tell those stories, and bring more people and communities in to the cause. In some ways, the increasing commercialization of not just scholarship, but of our own personal, social, and behavioral data may be the wake-up call that leads to the next wave of organizing around creating a truly open, non-commercial, digital commons. I think libraries can play a role by acting as the trusted facilitators of information creation, exchange, and preservation that we have always been. A digital commons that combines the values of openness and sharing with the values of privacy and informed choice sounds an awful lot like a library to me – or at least the kind of network of libraries that many of us aspire to create and maintain.

In your position as Director of MIT Libraries, you are an outspoken advocate for open access and knowledge resources. The question of why libraries need to stand up for open access has been answered in a variety of places, but why are the MIT libraries central to this fight?
A big part of what drew me to this job at MIT is the fact that MIT, and the MIT libraries in particular, combine a strong cultural commitment to openness with an equally strong commitment to building the infrastructure needed to openly share knowledge resources. MIT has led before in making the fruits of its research and teaching open to the world; with Harvard in 2008 and 2009 on passing Faculty Open Access Policies, and before by launching Open CourseWare in 2000, with the mission of sharing all of MIT’s course content online, for free. When the MIT Faculty passed the OA policy in 2009, they turned to the libraries to implement the policy. The libraries at MIT have long been seen as a key player in facilitating the dissemination of MIT research to the world, and frankly, we’ve been pretty good at it. Nearly 50% of MIT faculty journal articles written since 2009 are openly available to the world – that’s nearly 27,000 articles, downloaded nearly 9.5 million times.

We are in a great position in the MIT libraries to be able to partner with leading scholars across the Institute, in Engineering, Sciences, Business, Humanities and Social Sciences, and Architecture and Planning, to strategize on what’s next for open access. Through the work of the recently launched Ad hoc Task force on Open Access to MIT’s Research, which I am co-chairing with Electrical Engineering and Computer Science Professor and founding director of Creative Commons, Hal Abelson, we are basically asking what’s next? How can we push the needle further, and how can MIT continue to lead? Creating a more open scholarly record will require changes at the technological, legal/regulatory, political, and social levels; so our task force has experts from all those perspectives represented. We are also reaching out to experts across the globe to inform our recommendations.

We talk a lot in libraryland about whether the open access movement and/or institutional repositories have been successful, but/and I think what MIT has been able to do in getting nearly 50% of the journal articles of our faculty in our open repository is a compelling success story. And that success story is an MIT Libraries story, so I feel some obligation to build on that success and to leverage it for the broader community of libraries and other organizations who share the goal of opening up our cultural and scholarly heritage to a global audience.

In his ALA talk this year, Junot Diaz pulled no punches when it came to the issues of diversity in libraries. “I wish that libraries would finally have a reckoning and know that [staffs that are] 88% white means 5000% percent agony for people of color, no matter how liberal and enlightened you think you are,” he said. You cited this quote in a recent talk as well. In your opinion, how can we do better as a movement for free and open knowledge? As librarians, researchers, scientists, and artists? How can we, in his words, “decolonize libraries,” or in the parlance of this conference, “decolonize open?”
I think we always have to ask who and what is missing, and continue to work to not just be more inclusive, but also to decenter white, western knowledge; and center the knowledge of marginalized communities.

But/and, instead of doing it ourselves we need to look to the people who are doing this work in and with those communities. Two examples I love are the work being done by Anasuya Sengupta and her colleagues at whoseknowledge.org, and P. Sanaith’s work creating and maintaining the People’s Archive of Rural India.

Decolonizing scholarship and decolonizing the web will require radical collaboration across many social, geographical, and political divides; and will have to be based on mutual exchanges of knowledge and skills. All of that requires trust, which is something that takes time to build and is based on relationships and authentic human connection. So if we want to decolonize open, then maybe we need to decolonize our social networks first.

One of the longest running and most frustrating conversations within libraries is whether they are “neutral.” (As you write, you are strongly on the “hell no” side.) Can you speak to the politics of neutrality within open, and particularly as it regards seemingly “neutral” actors like CC licenses and libraries? How does the conversation about “neutrality” relate to issues of diversity and inclusion within the free knowledge movement?
I don’t think of CC licenses or libraries as neutral. They are both predicated on the idea that people ought to have the ability to freely create, share, and access knowledge and cultural materials. That’s actually a pretty radical idea. Even if CC licenses and libraries can be and are used to provide access to a huge range of ideas and viewpoints, that doesn’t make them neutral. One of the arguments I make is that you can’t be neutral if one side argues that certain ideas should not be available in libraries (whether those ideas are contained in books representing LGBTQ families, or in gatherings of neo-Nazis) and another side argues that you have to include all ideas and viewpoints. You can’t satisfy both sides – you can’t keep the LGBTQ book and not keep the LGBTQ book at the same time. I may start calling this the Schrodinger’s Library argument against neutrality.

The fact that libraryland continues to have these debates about neutrality is really frustrating, and is very much related to issues of diversity and inclusion. So many of the library debates about neutrality are theoretical and academic and detached, and I think that reflects the stark lack of diversity in our profession. Too often the argument that it is a moral imperative for libraries to represent all sides of an issue, and to serve all patrons regardless of beliefs, come from a position of privilege and relative safety. For marginalized folks, it can feel like these debates about neutrality are really debates about whether we have to honor and engage with people who deny our very humanity and seek our destruction. Many of us would argue that allowing those who deny the humanity and basic dignity of others to coopt the legitimacy of our libraries and our profession to spread their hatred and intimidation is not in any way a neutral choice.

What is the need for Creative Commons today and why are you coming to keynote the Summit?
What I love about Creative Commons and the CC community is that it is driven by a compelling vision of an open digital commons, and that it provides the tools for people across the globe to choose how they want to participate in that commons. That combination of an abiding belief that openly accessible culture and knowledge are good for society, with a commitment to honoring individual choice is powerful; and it resonates with what I think is needed to advance the perpetual project of decolonizing and opening up the internet.

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PLOS Update

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When I was appointed PLOS’ CEO last year, I committed myself to transparency with the communities we serve. That’s why, while this is a difficult blog to write, it’s important for me to share that I am making the hard decision to eliminate 18 positions at PLOS. Much of this is related to a strategic decision to shift from developing a proprietary platform for submissions to creating innovation partnerships with a wider community (Most readers are already aware of this from my previous blog.) It’s also driven by the need to be fiscally responsible and remain a sustainable nonprofit organization that continues to lead transformations in scientific communications.

I’d like to reiterate what we’ve communicated internally. Our people and their passion are the most important part of what makes PLOS so special. The people whose roles have been eliminated are all excellent at what they do, and their leaving is a result of operational decisions, not performance.

Moving forward, we’ll be a leaner organization. This doesn’t mean we won’t continue to fully support our researchers and scientists. We’ve been careful in where we’ve streamlined operations and those who engage with us should not see any disruption.

This is a pivotal moment in the life of PLOS and Open Access (OA) as it was envisioned by our founders 17 years ago. While OA has seen strong adoption, much has evolved in the landscape. Changing how and when we share, access and evaluate all research outputs is more critical to science than ever. It will take many of us working together, in various forms of partnership, to accelerate and advance a culture and ecosystem of open innovation.

Over the past two decades, I’ve been part of multiple transformations in publishing. This is what’s most exciting and daunting about our industry. Disruption takes stamina and a willingness to embrace the unknown while acting responsibly in the moment. This is our goal and commitment as we explore ways to drive innovation in our industry forward.

You’ll continue to hear from me throughout the year as I share our wins and our challenges toward that vision. It’s my hope that through transparency and open dialogue, we can maintain the trust our community has placed in us.

Thank you for reading.

Alison Mudditt

Display without Delay: Search, Browse & Cite PLOS Articles with Quick Abstracts from Google Scholar

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Working off your mobile device? No problem. We just made it easier to use your phone to find and scan PLOS articles.

If you’re someone who’s out in the field more than in the lab, you may have been challenged finding research on the fly. That’s now in the past. To expedite discovery and access to PLOS research articles, we’ve worked with Google Scholar to include PLOS abstracts in their new Quick Abstracts feature. Researchers around the world can now view complete abstracts and explore citations quickly and efficiently from any mobile device. For scientists, educators, policy makers and journalists, this means more efficient and timely access to the academic literature.

How It Works

Google Scholar Quick Abstracts allows researchers to tap on any search result to browse the full abstract text of a PLOS article directly on their cell phone, then either return to the search results or swipe right and left to read additional abstracts. From a link at the bottom of the abstract text, readers are taken directly to the complete article. Quick Abstracts even serves up preprint abstracts from bioRxiv, further extending discoverability of work by authors who opt to post their preprints at time of submission to PLOS journals.

Quick Abstracts includes all the expected features of Google Scholar, including saving to “My Library” through the star button, and display of citing and related articles. Additionally, an entire discovery network is available through use of search strings on the Google Scholar homepage. For example, entering “site:journals.plos.org” in the search bar retrieves abstracts of the entire database of PLOS research articles.

Innovation for All

Research, discovery and knowledge on the go shouldn’t be restricted to technology-driven economies. While the majority of cell phone users in the United States and Europe benefit from 3G, and even 4G, technologies and fast data delivery speeds on their mobile devices, this is not the case globally. Quick Abstracts integrates mobile network optimization that enables abstract display without delay, especially important for communities in the global south browsing and reading journals such as PLOS Neglected Tropical Diseases, PLOS Pathogens, PLOS Medicine and related research in additional PLOS journals.

Open. Fast. Global.

The adoption of Quick Abstracts is a logical extension of our ongoing relationship with Google Scholar—one based on making research more open and available throughout the global scholarly research community. Our CC BY licensing, Open Access ethos and mobile-ready delivery of journal content enables innovators like Google Scholar to bring their latest technologies to PLOS, for the benefit of our authors and the wider scientific community. Like our partnership with protocols.io for laboratory methods citations and collaboration with bioRxiv for preprints with our journal submissions, this is just one more example of how we’re working with external collaborators to transform research communication.

No more waiting to get back to your desk, lab or laptop to explore a potential new project, prepare for journal club or add to your reference list—head to scholar.google.com from your cell phone for abstract display without delay.

 

PLOS Extends a Profound Thank You

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To all our Reviewers, Guest Editors and Editorial Board members, thank you! 2018 marks the fourth year that we formally and publicly acknowledge our community of reviewers and editors for sustaining public access to rigorous peer-reviewed research, enhancing our journals’ abilities to communicate the work of researchers and communities, and inspiring the work of our staff.

A Passion to Go Beyond

Our contributor community selflessly guides papers through the editorial process and provides feedback to authors. Many also actively stand up for Open Access, open data and Open Science as they attend conferences, debate with colleagues or share research via social media, email or even, yes, conversation! Our reviewers and editors devote time and energy to PLOS Collections, Special Issues, PLOS Channels, Editorials, Perspectives, blog posts, interviews, career advice, educational material and more to enrich the primary literature, provide context and engage the public. These endeavours help make PLOS a unique place to publish and for that we are greatly appreciative.

Those who volunteer their services to PLOS, and the greater scientific community, are more than just dedicated scientists: they share an entrepreneurial spirit as we advance scholarly communication with requirements for ORCID iDs for corresponding authors, implementation of CRediT for author contributions, community engagement for improved evaluation, integration of preprint Editors and experimentation with software development. Throughout all of these innovations, some successful (108,000 ORCID entries in our system uniquely identify authors to ensure complete and accurate recognition of work, regardless of changes to name or institution) and others less so, PLOS continues to be, in the words of our CEO, an organization “willing to take risks in order to best serve scientific communities.” We have tremendous appreciation for Reviewers, Guest Editors and Editorial Board Members who are confident to travel the road with us toward a world of readily discoverable, freely available, thoroughly reliable and fully reusable research outcomes.

An Impressive Community Workload

Continuing our quest for transparency in the publishing process, we include the number of newly submitted and published research articles brought to the public in 2017 in each of the seven journals’ thank you articles. We released this information for the first time last year and will continue to do so as it provides additional insight and appreciation for the workload of our reviewers and editors. That workload in 2017 supported publication of more than 23,000 research articles.

Our global network of more than 74,000 reviewers and 7,200 editors ensures that Research Articles, Perspectives, Editorials and more achieve the highest quality possible. The more than 15 million article views per month (on average) this past year hints at the enthusiasm that PLOS reviewers and editors share, for science and scientists. Enthusiasm is not enough, however. This geographically diverse contributor community also shares a commitment to responsible and fair examination of the science, ethics, reporting guidelines, data availability and journal publication criteria associated with each submission.

Efforts to Ease Process and Enrich Training

We’ve listened to our reviewer and editor communities who want more training, especially Early Career Researchers. In response we developed the PLOS Reviewer Center, to provide detailed, journal-agnostic peer review guidance from experienced researchers, staff editors, Editorial Board members, and other reviewers. The Reviewer Center is still under development, so we encourage you to take a look around and let us know what you find useful or missing via the feedback form.

Through the PLOS Reviewer Center anyone can:

  • Learn the basics of peer review and get helpful tips for handling reviewer tasks, from accepting a review invitation to completing a review
  • Access video, templates, checklists and other customized tools for reviewers
  • View recent articles and commentary about trends and studies on peer reviewers, the peer review process, and other related topics

In addition to the Reviewer Center, we’ve made more comprehensive our guidelines for Reviewers and Editors, provided editors more journal transfer options to accelerate publication of peer-reviewed manuscripts, made reviews public to increase transparency of the review process and experimented with signing reviews. A detailed overview of the Editorial and Peer Review Process is available on all journal sites.

For the Record

A published and citable journal article thank you provides reviewers and editors recognition and an academic citation for their inspired service to colleagues, institutions, funders and the public. Each reviewer’s and editor’s name is listed in the Supporting Information of each journal’s published article; links to these articles are below.

We’re in the midst of expanding the size and scope of the PLOS ONE Editorial Board to achieve stronger subject area coverage across all relevant disciplines. If you’d like to learn more, please email us at edboardmgmt@plos.org.

Once again, thank you!

PLOS Collaborates on Recommendations to Improve Transparency for Author Contributions

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In a new report, a group convened by the US National Academy of Sciences and including a dozen journal editors reflects on authorship guidelines and recommends new ways to make author contributions more transparent.

What does it mean to be author number seven on a twenty-five–author article?

Establishing transparency for each author’s role in a research study is one of the recommendations in a report published today in the Proceedings of the National Academy of Sciences (PNAS) by a group led by Marcia McNutt, President of the National Academy of Sciences. The recommendations issued by this group, which included one of us, were adapted based on community feedback and peer review from an original draft presented as a preprint. PLOS supports the recommendations for increased transparency and has already put some of them in practice.

A more systematic description of author contributions is a prerequisite to providing due credit for roles that are instrumental to the research enterprise, especially those roles that are too often ignored or devalued. For example, collecting, curating and sharing a dataset or developing a new methodological approach that can be reused by others are key contributions that may not always land a ‘first author position’ but have applications beyond a single article and deserve recognition.

Transparency also brings more accountability to a system where questionable and even detrimental practices (such as guest, ghost or conscripted authorship) have been documented. While transparency requirements cannot entirely eliminate abuse, transparent description of individual author contributions can deter inaccurate representations and can expose institutionalized authorship practices that should be questioned.

Paradoxically, a concern often heard about emphasizing contributions is that they risk diluting individual author responsibility for the overall integrity of a study. The recommendations address this concern by stipulating authorship standards that require each author to be “personally accountable for [their] own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature.” Thus, having one’s contributions precisely described does not absolve any author of responsibility for the accuracy and rigor of the entire study.

The paper also recommends mechanisms by which publishers can bring a minimum level of standardization to the description of author contributions. In particular, the group advocates for the implementation of ORCID identifiers and the CRediT taxonomy as emerging standards in the industry. While many journals already require specification of author contributions, a more fully integrated system of persistent identifiers (like ORCID iDs for authors and DOIs for articles) connected via a standardized vocabulary of relationships (like the CRediT taxonomy for contributions) will make the information both human- and machine-readable and allow it to be surfaced more easily.

PLOS journals have adopted both ORCID and CRediT since 2016; the roles and ORCID iDs provided by authors are now visible with one click on the author name in the by-line. ORCID information is passed on to CrossRef, which updates ORCID records with authors’ permissions.

In our experience, the CRediT taxonomy has worked well, but the definition of some individual terms could be improved. In particular, those related to data may benefit from some refinement to distinguish generation of data from its subsequent curation. As others examine the possibility of using the taxonomy, we encourage a collaborative approach with CASRAI’s CRediT Committee, the taxonomy steward, to match the needs of different communities.

Not all roles in the CRediT taxonomy immediately qualify a participant for authorship; that qualification is determined by journal policy. To determine who should be an author, PLOS currently follows the recommendation established by the International Committee of Medical Journal Editors (ICMJE) for medical journals which posits that authorship should be associated with a substantive intellectual contribution as well as participation in drafting or revising the manuscript. While PLOS Medicine checks that all four ICMJE criteria are met by all authors, the experience at other PLOS journals indicates that in fields outside medicine, not all authors state they have participated in the drafting or revising of the manuscript. The proposed adaptation of authorship criteria in the current PNAS report, which includes writing as a qualification for authorship but does not require it, aims not to exclude important contributors from authorship. Conversely, the inclusion of writing without other intellectual contribution to a study as a role worthy of authorship may not find acceptance in all disciplines. The intent is not to impose a monolithic approach to authorship, but to accommodate a broad range of community standards transparently. When contributors do not meet authorship criteria, CRediT can also serve to document their precise contributions as acknowledged colleagues, supported by other means of credit like citations of protocols and datasets.

On a new website, the report’s authors commit to reflect upon and improve current authorship guidelines and practices at the journals they represent, and they encourage other journals to do the same. Such introspection and subsequent discussion are timely, as research studies are increasingly large-scale and multi-disciplinary affairs. As more work goes into providing due credit for scholarly contributions like methods development, data collection and data sharing, transparency in authorship roles should advance in tandem.

Competing Interests Disclosure: Veronique Kiermer is an author of the recommendations discussed and Chair of the ORCID Board. Larry Peiperl serves on the ICMJE.

 

Image Credit: Wikipedia

Rare Disease Day Spotlight on PLOS Authors: Open Data Repositories in Practice

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Science increasingly involves collaborative research groups, program partnerships and shared learnings to encourage transparency, reproducibility and a responsible transition to a more open way of doing science. Open Science policies and best practices are currently under discussion, definition and development across the wide spectrum of activities that make up the research cycle, from open notebooks, open data and transparent peer review to the interoperability of meta-data and digital identifiers. In particular for open research practices, adoption of emergent and recent policies (i.e. PLOS Data Policy) could be strengthened if accompanied by examples of successful implementation. Examples can serve as a powerful motivator for improved understanding and behavioral change for those confronted with the uncertainties of a more open landscape for the practice and communication of science.

Perhaps it’s a question of making clear to the broad stakeholder community, at all stages and across multiple disciplines, the practical benefit of these polices moving us all toward a more Open Science. It’s not just a theoretical pursuit of Open Science for the sake of being open. The current energy behind Open Science in the European Union, as well as in the United States, stems also from a frustration over wasted resources, time and talent. Practicing Open Science well does enhance reproducibility through improved clarity of methods and reagents, and accelerated reuse of data and code by others.

A Celebration of Open Data

A major benefit of open data is that data can be reused, not only for validation work but also for pushing science forward. Teams of scientists with diverse expertise collaborated to explore preexisting data sets to advance breast cancer research, in the US National Cancer Institute’s Up For A Challenge (U4C) Contest. Finalists in the US National Institutes of Health, Howard Hughes Medical Institute and Wellcome Trust Open Science Prize competition (which included projects by PLOS authors and their related publications) “demonstrated the huge potential for data to be reused to develop new applications and uncover new knowledge,” wrote Robert Kiley, Head of Open Research, and David Carr, Programme Manager, Wellcome Trust, in Figshare’s State of Open Data Report 2017. The report provided insight into how researchers approach publishing their data. In response to surveys asking where they published their data, researchers most commonly did so as an appendix to an article (slightly over 30%) or in a data repository (slightly under 30%), with 20% having published data in a data journal (see the summary infographic).

Open Data Day (March 3, 2018) is an opportunity to showcase the benefits of open data and open data systems, and, according to the grassroots collective’s website, “to encourage the adoption of open data policies in government, business and civil society around the world.” This year, the focus is on four key areas where open data can help solve universal problems: opening research data, tracking public money flows, informing open mapping projects and providing open data for equal development. In Copenhagen, Open Data Day will include announcement of the Danish Open Data Award and in London activities are planned related to Open Science and reproducible research. Participants in The Philippines will benefit from a roundtable discussion on open research as it applies locally and globally. There are no shortage of ideas and data sources for Open Data Day.

Publisher Actions

PLOS took a leadership position in open data in 2014 with our strengthened Data Policy, and since 2015 our journals maintain a list of recommended repositories to help authors share their data. When we assess repositories for inclusion in our list we are guided by criteria that meet the FAIR principles on open data. We consider this our responsibility as a publisher. The FAIR guiding principles state that beyond making data open as an important component in the data ecosystem, data also need to be Findable, Accessible, Interoperable and Reusable. For inclusion on PLOS’ list of recommended repositories, several criteria were developed, some of which are listed below. For a more complete description of repository criteria, visit the EveryONE blog on Open Data Day!

  1. Datasets should be available at no cost. All PLOS articles are available to readers free of charge and we believe cost should not be a barrier to access either the scientific literature or accompanying datasets. Repositories are not considered for our recommended list if they charge readers access or subscription fees.
  2. Repository with stated licensing policies should offer CC 0 or CC BY licenses (or equivalents), for maximum reproducibility and reuse.
  3. To ensure that datasets will be permanently accessible at the specified location, repositories must issue a stable identifier at publication, such as a digital object identifier (DOI) or an equally robust accession number.
  4. FAIRsharing.org works with a community of journals, funders and databases in support of standards, polices and educational material to enable funders, librarians, journals, researchers and developers to thrive in the open data world. The repository chosen by PLOS authors should have an entry created in the FAIRsharing database, to allow it to be linked to the PLOS entry.

In addition to considering the PLOS Data Policy and providing a Data Availability Statement for their individual data and datasets, selecting the appropriate data repository is an important part of a researcher’s overall experimental and data plan. To assist authors in choosing the best repository, in addition to the current list of recommended repositories, the complete list of repository criteria will soon be available on PLOS journal websites.

Researcher Participation

What is the practical importance of open data? As one specific example we can look to a coincidence of timing: February 28 is Rare Disease Day. Rare diseases constitute a group of more than 6,000 different diseases and affect more than 300 million people worldwide. To put this number in perspective, 1 in 20 people live with a rare disease in their life, according to EURORDIS, an alliance of over 700 patient organizations from nearly 70 countries in Europe. In light of Rare Disease Day’s close temporal alignment with Open Data Day, we highlight a selection of articles on rare diseases published at PLOS that utilize a variety of repository options to best make their associated data available. These are examples of authors doing the right thing to advance rare disease research, collective knowledge, and future therapeutic interventions.

  • Sorenson et al. (2017) used the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository to store their genomic and transcriptomic data relating to fibrolamellar hepatocellular carcinoma (a rare variant of liver cancer).
  • Guilhem et al. (2017) used the Data Archiving and Networking Services (DANS) EASY repository to deposit data files from their research on hereditary hemorrhagic telangiectasia (a disease leading to abnormal blood vessel formation). The EASY repository is one of PLOS’ recommended repositories.
  • Andersen et al. (2017) carried out a bibliometric analysis on multiple myeloma research (a cancer of white blood cells). Few, if any, dedicated repositories exist exclusively for bibliometric work, so data underlying work like this can be deposited to a discipline-independent repository—in this case Figshare. While subject-specific repositories are preferred, in cases where they are not available authors may use a cross-disciplinary repository.
  • Hytönen et al. (2016) published genome data relating to their work on three rare bone diseases in the European Nucleotide Archive (ENA) hosted by EMBL-EBI.
  • Piersanti et al. (2015) also used the GEO repository to store their microarray data on gene expression changes in brain cells following infection with viral vectors. This work contributes to the development of gene therapy that could be used in the treatment of several rare diseases affecting the brain.

The theme for Rare Disease Day this year is a carry-over from last year—research. If scientists working in these disease areas make their data open and available for reuse and re-examination, they can extend the impact of their efforts and may open a window to unrealized diagnoses, therapies and perhaps even cures.

In the pursuit of Open Science, practical and even incremental change has the power and potential to bolster momentum and encourage a spirit of collaboration that ultimately brings about large-scale cultural shift. We have seen evidence of this most recently with the preprint movement in biomedical and life sciences. Making open data the norm, whenever possible, and following FAIR sharing principles are additional practices that, like preprints, have the capacity to transform the work and culture of science.

Join the PLOS Communications LinkedIn Group to stay up to date on author interviews, research and organisation highlights.

PLOS and Cold Spring Harbor Laboratory Enter Agreement to Enable Preprint Posting on bioRxiv

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Editor’s Note: This press release also appears on the Cold Spring Harbor Laboratory Newsstand.

Public Library of Science (PLOS) and Cold Spring Harbor Laboratory (CSHL) announce an agreement that enables the automatic posting of research articles submitted to PLOS journals on bioRxiv, CSHL’s preprint server for the life sciences. This collaboration between bioRxiv and PLOS empowers authors to share their work on a trusted platform before peer review, accelerating the pace of biomedical research.

PLOS is committed to enhancing the integrity of preprints and confidence in them as research outputs. PLOS will perform initial manuscript screening compatible with bioRxiv standards, covering scope, plagiarism, and previous publication, as well as other basic ethical and technical criteria. Articles will then post automatically to the bioRxiv server without the need for additional actions by the author. By allowing their submission to be posted on bioRxiv, authors accelerate the dissemination of their work and invite commentary by a broader community, which the PLOS editors will evaluate as part of peer review. Authors may choose to opt-out of this process when they submit papers to PLOS.

PLOS and CSHL also plan to work collaboratively towards solutions for preprint licensing that enable broad dissemination and reuse; the addition of badges to papers which signal that additional services for authors have been performed by PLOS and potentially other organizations; submission and screening standards in the biomedical sciences; and the implementation of new forms of manuscript assessment to augment or improve current methods of peer review.

“The opportunity to partner with a like-minded organization such as CSHL to realize a longstanding PLOS goal is a strategy for us moving forward,” said Alison Mudditt, Chief Executive Officer, PLOS. “A key part of our mission has always been to act as a catalyst, not only demonstrating the viability of new models through our own operations but also supporting them elsewhere. In the case of preprints, we can magnify our impact by partnering and helping shape how that future develops for all posted content on bioRxiv.”

The bioRxiv preprint server was initiated by CSHL in November 2013 and received major support in May 2017 from the Chan Zuckerberg Initiative. It currently hosts over 20,000 manuscripts from bioscientists in 104 countries and has a rapidly rising rate of submission.

“Helping researchers communicate at the speed of science has been the principal goal of bioRxiv since its launch,” said John Inglis, co-founder of bioRxiv at CSHL, “and over one hundred thousand authors have taken advantage of that opportunity. We are delighted to have reached an agreement with PLOS to offer that benefit to tens of thousands more authors who are ready to share their work and open it up to the community response and feedback that bioRxiv makes possible.”

“This collaboration highlights PLOS’ commitment to the growing preprint movement in the biological sciences and bioRxiv’s support for scientists’ desire to share their research freely and widely,” said Louise Page, Chief Innovation Officer, PLOS. “The screened submissions to bioRxiv from PLOS illustrate how publishers can drive preprints and create new outputs in response to researcher-led initiatives that increase transparency and promote early dissemination of science.”

Retrospection and Direction: A Q&A with Peter Walter

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“In our panel it is the stated and adhered to policy that we will not consider where a paper is published. Rather, in our evaluations we assess its real impact in a field. Change of this sort and defiance of the status quo is badly needed in all committees and panels that make decisions that impact the future of our next-generation scientists, even if it entails a bit more work.”-from “On Publishing and the Sneetches: A Wake-up Call?

These are words written by Dyche Mullins and Peter Walter, in 2016. Walter is one of this year’s Breakthrough Prize in Life Sciences recipients and a leader in the scientific community not only for his scientific investigations but also for his continuous dedication to mentoring and teaching younger scientists, and for taking a progressive but circumspect stand on issues that impact the quality of scientific life. As a follow-up to last month’s Breakthrough Prize overview, PLOS interviewed Walter on some of the broader issues surrounding his work and publishing in general. Walter has strong opinions related to impact factors and Open Access; he remains open minded regarding preprints. His valuable and modest insights are below, with minimal editing.

 

Image courtesy of UCSF

PLOS: Which of your PLOS articles were most impactful for your work related to the prize, and why?

Walter: The Brickner and Walter paper [“Gene Recruitment of the Activated INO1 Locus to the Nuclear Membrane”] stands out, in my view, as this story organically grew out of our ongoing work on the unfolded protein response, yet opened an entirely new field: that the physical location of a genetic locus inside the nucleus can be dynamic and affect gene regulation. This paper also served to seed Jason Brickner’s independent career: Shortly after this publication, he was recruited to Northwestern University. Since then, his lab has vastly expanded upon this topic and he is now internationally recognized as one of the very leaders of cell biological mechanisms that control transcriptional memory.

PLOS: Do you have a personal favorite among your PLOS publications? Perhaps one that was either controversial or that sparked scientific debate/conversation at time of publication?

Walter: The Pincus et al. paper [“BiP Binding to the ER-Stress Sensor Ire1 Tunes the Homeostatic Behavior of the Unfolded Protein Response”] is one of my all-time favorites: It demonstrates the power of computational modeling for generating new hypotheses and then experimentally testing them. In this case, modeling suggested experiments that we would not have thought of otherwise, and the results showed beyond reasonable doubt that BiP dissociation from the ER-resident stress sensor Ire1 is not the regulatory switch that activates the UPR. The work inspired rethinking, and it is now clear that in both, yeast and metazoans, unfolded proteins per se are agonists that bind directly to the stress sensors Ire1 (and PERK). Despite the seminal insights provided in this publication, the field remains attached to the notion that BiP dissociation is causal for Ire1 activation—providing an important insight into the surprisingly inflexible thinking of established scientists (including myself, at times…).

PLOS: In your experience speaking with the public or non-scientists in general, what concept(s) about the unfolded protein response pathway do they typically find most interesting or resonates strongly?

Walter: Trained as a chemist, I personally cherish the many unorthodox molecular mechanisms by which the unfolded protein response regulates ER [endoplasmic reticulum] homeostasis. However, beauty at a molecular scale is mostly appreciated by aficionados and only rarely resonates with the public and non-scientists. We are now in a most fortunate era where our work tangibly links to a broad spectrum of diseases, including cancer and neurodegeneration, where our knowledge has become foundational to the exploration of new treatment strategies. As such, our work provides a wonderful platform on which to demonstrate the power and value to society of curiosity-driven research in which we seek understanding of how healthy cells work in disease-agnostic approaches and then use that knowledge to learn what goes wrong in disease and how to fix it.

PLOS: Our readers span the range of career stages. What is your opinion of the value or challenge to publishing in Open Access journals?

Walter: The challenge for the next generation of researchers is to break out of the stranglehold that the for-profit publishing industry has put on our community. The misguided emphasis on abstruse metrics, e.g., impact factor, in addition to the poorly transparent review procedures by our “vanity journals” and their hand-me-down cousins distort our most fundamental values. My colleagues and I have clearly laid out our views on this topic [in addition to the ASCB Newsletter referenced in the opening quote see the commentary co-authored with Martin Raff and Alexander Johnson, entitled “Painful Publishing”].

Just as with scientific models, old patterns are hard to break. We need our young scientists to recapture control. The myth that one can only get a job/grant/promotion with [high impact factor journal] papers has been debunked internationally (e.g., Jason Brickner and Liang Ge in China). The challenge ahead is to spread the word and make sure that no young scientist who made an important discovery will ever be held back by the name of the journal where ground breaking findings were published.

“Open-access and publishing (to “make public”) are synonymous in my view, and scientist-run non-profit open-access journals that manage to deliver consistently customer-friendly, transparent, and constructive reviews and timely feedback are destined to lead the movement.”

PLOS: Finally, have you or collaborator ever posted a preprint? If not, would you consider doing so, and why/why not?

Walter: To date, we have posted two preprints—I consider them experiments with the new forum. For now, I remain agnostic to the process. Science is moving fast enough for my taste (if not too fast sometimes), and I remain unsure whether an invitation to put un-reviewed stories out there will be that beneficial overall. Many things will need to be worked out: Does a preprint establish priority for a discovery? How will “better-first-and-sloppy-than-second-and-who-cares” science be regarded by the community? How will we deal with predatory scientists who appropriate ideas and results from our students or postdocs and then race to scoop them? Also, personally, I read most papers only once, and it is the first impression that sticks. The concept of looking at evolving versions rather than a final, best-as-can-be product is rather vulnerable in my opinion. We’ll see; I remain open-minded.

 

Editor’s Note: Some of the issues Walter raises above are covered in the PLOS Computational Biology article “Ten simple rules to consider regarding preprint submission.” Major funders including Wellcome Trust and NIH, and publishers such as PLOS, PeerJ and eLIFE are actively working on external policies and internal practices to facilitate authors’ use of preprints; PLOS Biology has formalized a policy whereby complimentary studies (those submitted within six months of publication or preprint posting and already addressing the same question) will be considered for publication. Newly minted scientists are encouraged to use preprints as a way of, as Walter recommends, recapturing control. The cartoon above on use ideas for preprints from the group PREreview is available for download on figshare.

 

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Peter Walter is Professor, Department of Biochemistry and Biophysics at the University of California, San Francisco (UCSF) and Investigator, Howard Hughes Medical Institute. He served as President of the American Society of Cell Biology in 2016 and as Department Chair in Biochemistry and Biophysics at UCSF from 2001 until 2008. He is an elected member of the German Academy of Natural Scientists Leopoldina, the US National Academy of Sciences, the National Academy of Inventors, the American Association for Arts and Science, and the European Molecular Biology Organization. He is recipient of multiple awards including the Breakthrough Prize in Life Sciences (2018), Vilcek Prize in Biomedical Science (2015) and Lasker Basic Medical Research Award (2014). He is co-author of the widely-used textbooks Molecular Biology of the Cell and Essential Cell Biology and alumnus of the Djerassi Artist-in-Residence program.

 

Image Credit: Peter Walter lab; University of California, San Francisco

The Editor’s Note was updated on 1/30/3018 to indicate the policy at PLOS Biology is formalized and to provide the link to the Criteria for Publication on the journal’s information page.

Transformational Work Over a Career: Breakthrough Prize in Life Sciences for PLOS Authors

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How do you measure lifetime achievement? It’s not by assessing individual works but by consideration and evaluation of consistent contributions to a discipline over time. Contributions may be independently substantial, but in science, a researcher’s impact is more often made through gradual insights that accrue meaning as a discipline advances. Over the course of a career, creative thinkers and leaders in science can significantly influence a field, and humanity more broadly.

A recently established award provides one measure of lifetime achievement for life sciences—the Breakthrough Prize. Established in 2013, the Breakthrough Prize in Life Sciences honors “transformative advances toward understanding living systems and extending human life.” The prize encourages celebration and recognition of “outstanding minds.” Those scientists who “think big, take risks and have made a significant impact on our lives” each receive $3 million for their work that provides fundamental and far-reaching understanding of biological mechanisms.

The Breakthrough Prize in Life Sciences is designed to bring public attention, financial reward and a bit of glamor to outstanding scientists who over the course of their careers have changed the way scientists think about basic principles. Through a central component of the award, the impact of honored scientists’ work is extended to a broader general audience. Recipients are invited to present public talks – with recorded lectures made available to the public – “allowing everyone to keep abreast of the latest developments in life sciences, guided by contemporary masters of the field,” according to the Breakthrough Prize website. Breakthrough Prizes are also awarded in fundamental physics and mathematics.

This year, five scientists received life sciences prizes; collectively these creative thinkers have published 30 papers in PLOS journals (13 in PLOS Biology, 16 in PLOS ONE and one in PLOS Genetics), providing their work to the global community free of access and reuse restrictions. The 2018 Breakthrough Prizes in Life Sciences were awarded to:

    • Joanne Chory, for pioneering work elucidating mechanisms by which plants “optimize their growth, development, and cellular structure to transform sunlight into chemical energy.” Chory has published work with PLOS on how the circadian clock coordinates plant growth through synchronized gene expression, on growth patterning in the model plant system Arabidopsis and a novel approach to identify required gene regulatory elements, and on diurnal and clock-regulated transcription factors and their target cis-regulatory elements in additional plant models. The Chory team first published with PLOS in 2004.
DOI: 10.1371/journal.pbio.0060225
    • Kim Nasmyth, for elucidating the “sophisticated mechanism that mediates the perilous separation of duplicated chromosomes during cell division and thereby prevents genetic diseases such as cancer.” Nasmyth’s work in PLOS Biology covers the influence of excess heterochromatin (highly packed DNA) segments and cohesin protein accumulation on sister chromatid separation, and that the protein shugoshin protects centromeres until chromosomes are ready to separate. He and colleagues from the Research Institute of Molecular Pathology, in Vienna, Austria, first published with PLOS in 2005.
DOI: 10.1371/journal.pbio.0030086
    • Don Cleveland, for characterizing molecular mechanisms involved in the pathogenesis of inherited Amyotrophic Lateral Sclerosis (ALS), “including the role of glia in neurodegeneration, and for establishing antisense oligonucleotide therapy in animal models of ALS and Huntington disease.” Cleveland’s work using post-mortem human tissue samples and transgenic mice showed that mRNA oxidation is an early event associated with motor neuron deterioration in ALS, and possibly other neurological diseases. His work on the enzyme superoxide dismutase, responsible for breaking down toxic, charged oxygen molecules known as superoxide radicals, included assessing the therapeutic effect of human fetal spinal neural stem cells grafted into the lumbar spine of transgenic rats presymptomatic for ALS. Cleveland and his many colleagues first published with PLOS (twice) in 2008.
DOI: 10.1371/journal.pone.0042614

Two scientists, Kazutoshi Mori of Kyoto University, Japan, and Peter Walter of the University of California, San Francisco, received Breakthrough Prizes for their independent work on “elucidating the unfolded protein response, a cellular quality-control system that detects disease-causing unfolded proteins and directs cells to take corrective measures.” The unfolded protein response (UPR) is a phylogenetically conserved endoplasmic reticulum-to-nucleus signaling pathway that senses unfolded proteins early on in the biosynthetic process, and then transmits that information to the cell nucleus. This information stimulates a genetic transcription program designed to re-establish cellular homeostasis by increasing the intracellular machinery and processes that help proteins fold.

    • Various cellular insults, writes Mori in his team’s PLOS Biology article, “including exposure to pharmacological agents that perturb protein folding, genetic mutation of ER chaperones or chaperone substrates, viral infection, metabolic demands, and even normal differentiation and function of professional secretory cells” impact the UPR in similar and unique ways. His earlier work published with PLOS examined the differential influence of low-level, severe and chronic stress on UPR activation. More recently, Mori has extended his investigations to the development of a high-throughput screening assay that incorporates a molecular biosensor to identify small molecule activators of the endoplasmic reticulum stress response in malignant glioma cells.
DOI: 10.1371/journal.pbio.0040374
    • Since 2004, Walter has published 12 papers with PLOS covering the role of endoplasmic reticulum expansion in the UPR in yeast; a teasing out of the relationship between cell proliferation, cell death and protein folding in human embryonic kidney cell lines; and the importance of targeting a key transcription factor to the cell membrane, to provide the appropriate cellular response to protein folding status in bacteria. Walter’s first two papers published in PLOS Biology, presented as a series together with a Synopsis, described amplitude adjustment signals for the UPR in yeast. Prior to this work, the UPR was thought to largely be a binary, on or off, function.
DOI: 10.1371/journal.pone.0003528

Perhaps more than other prize recipients, Joanne Chory was surprised by her inclusion as an awardee, explaining to the San Diego Union-Tribune, “this prize has been more associated with biomedical things.” The award may be a nod to the relevance of Chory’s current work to climate change. Those interested in the connection between mechanisms of sunlight and clock-regulated plant development to global warming may find of interest the Ecological Impacts of Climate Change Collection and newly launched Responding to Climate Change Channel.

International lifetime achievement awards are given in many fields, including economics, music and physical sciences, among others. With support of founding sponsors Mark Zuckerberg, Priscilla Chan, Sergey Brin, Anne Wojcicki and Yuri Milner, life sciences has another prize of its own, with a musical perk. This year’s awardees were honored at a gala hosted by Morgan Freeman with a performance of “See You Again” by Wiz Khalifa and Nana Ou-Yang.

 

Hero image credit: breakthroughprize.org

Samtale mellem kulturminister Mette Bock og Creative Commons’ Martin von Haller

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Photo by Finn Årup Nielsen – Own work, CC BY-SA 4.0 (source)

På torsdag har du mulighed for at være med, når kulturminister Mette Bock og Creative Commons Danmarks Martin von Haller skal tale om fællesskab og kulturdannelse. Arrangementet foregår i Klub i København torsdag den 11. januar 2018 kl. 14.30 til 15.15, og der er gratis entré (tilmelding nødvendig).

Kultur er fællesskaber. Fællesskaber skabes gennem fælles historier, billeder, sange, viden og kunst. Styrken af fællesskaber er direkte proportionalt med, hvor meget vi deler vores kultur. Fælles kultur forudsætter fri adgang til deling. Noget kultur skabes af private aktører, som kan kontrollere adgangen og kræve betaling for deling. Det er deres valg. Anden kultur skabes af samfundet f.eks. gennem statslig støtte. Resultat bliver vores alles fælles kultur. Hvor kan vi ikke frit dele og bruge det kulturindhold, som vi alle har medfinansieret? Hvor kræver vi ikke, at alt indhold, der skabes via kunststøtte, licensbetaling til DR og så videre stilles kvit og frit til rådighed for samfundet?

Sammen skal kulturminister Mette Bock og Martin von Haller snakke om fællesskabet og kulturdannelse i Klub og betydningen af fællesskabet for vores samfund – hvorfor fællesskabet er med til at få vores samfund til at fungere. Kom og giv din mening til kende, argumenter for dine holdninger om fællesskabet eller lyt blot til andre medlemmer og deres syn på fællesskabet. 

Adressen på Klub er Linnésgade 25, 1361 København K. Du kan tilmelde dig på booking@klub.io og skrive ‘Klubsamtale’ i emnefeltet.

Unique Opportunity for Communication of Cell Motility Research: ASCB Celldance Videos

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Cell biology research relies heavily on all types of microscopy to capture – for visualization and analysis –  cell structures, cell movements and cell-cell interactions. For the eighth consecutive year, the American Society for Cell Biology (ASCB) has supported interested cell biology labs in the creation of video projects describing their work for interpretive and educational value.

Posters advertising past Celldance videos, courtesy of ASCB

The Celldance video program provides participating labs financial support to develop video stories of their cell motility research, in addition to post-production assistance for sound and editing services. PLOS supports this ASCB Public Information Committee program that helps showcase the value of basic research, aids in communicating complex scientific concepts to the public and provides scientists a unique opportunity to fine-tune their communication skills.

This year, two labs working in collaboration and a third lab developed Celldance videos for presentation at the joint ASCB|EMBO 2017 Annual Meeting. Dyche Mullins’ lab at the University of California, San Francisco, in collaboration with the Lillian Fritz-Laylin lab at the University of Massachusetts, Amherst, created a video honoring foundational research on actomyosin and muscle movement by Albert Szent-Gyorgyi and describing how the molecules that constitute the cell’s skeleton, or cytoskeleton, influence the way a cell moves through both wide open and narrow matrices. The Guillaume Duménil lab at the Institut Pasteur created a video that emphasizes the value of cohesive basic and clinical research programs and describes the group’s studies on infection caused by the Gram-negative bacterium Neisseria meningitidis, responsible for meningitis and sepsis.

One of the reasons the Mullins lab submitted work to the ASCB Celldance contest was to be able to convey the fundamental importance of molecular and cellular motion to a general audience. Mullins appreciates that fundamental problems in cell biology are often challenging to explain to non-specialists. Article types such as PLOS Research Matters, for both PLOS Pathogens and PLOS Biology, can help in this regard, by enhancing public understanding of science and the benefits of basic research to public health, society, life, and the environment. In addition, “A short film can explain concepts that are extremely difficult to convey in a brief elevator conversation or even a long lecture,” says Mullins.

Paring down several initial ideas the group wanted to convey was key to creating a coherent narrative. The team decided to begin with the importance of molecular and cellular motion, then to introduce the idea that “this is a universal feature of life, even microscopic life living in ponds,” says Mullins. Once the images were in place, the team experimented with audio voice-overs but eventually settled on captions to guide the viewer through the story. “It’s like an old-fashioned silent movie,” he says.

We Know Life by Motion; Mullins/Fritz-Laylin

Sometimes even scientists need help understanding what they see under the microscope. Fascinating 3D lattice light sheet movies of crawling cells from the Fritz-Laylin lab were also motivation for wanting to participate in Celldance. “There is so much information in these movies that we had a hard time understanding what we were seeing,” says Mullins. By enlisting the help of visualization experts, the research teams could “suddenly see a wealth of new details. We were no longer seeing cells as ghostly apparitions, barely discernible at the business end of a microscope, but as real, three-dimensional beasts. We wanted to share this experience with a wider audience.”

 

Neisseria Meningitidis: At Home in Human Capillaries; Duménil

 

 

 

 

 

Says Duménil of his Celldance experience, “From a scientific point of view, I find it useful to see an infection as a story that starts with the encounter of the pathogen and its host, the story develops with the different stages of the infection, cellular barriers are crossed, cells invaded, organs infected and the outcome can be happy or sad.” For Duménil, the opportunity was not only about explaining science to the public in an accessible format. It was also, he says, “an opportunity to show the people who do the actual research and our lab environment at the Institut Pasteur.” For more on the work of the Duménil lab and video, see the upcoming partner Celldance blog on Speaking of Medicine.

Neisseria Meningitidis: At Home in Human Capillaries; Duménil

An Open Letter to the Community from PLOS CEO, Alison Mudditt

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As the new PLOS CEO, I’ve spent my first months assessing the organization and planning for a thriving future. We are in the midst of shaping our next innovative steps in pursuit of maximal openness and transparency in research communication, and assessing what changes we need to make as an organization. Some of these changes will likely go unnoticed outside of PLOS. Others may cause speculation. For clarity and transparency’s sake, I’ve chosen to write an open letter to the communities PLOS serves, so we can encourage open dialogue and so that you can share in our continuing evolution.

Since the very beginning PLOS has been a publisher, advocacy organization and innovator. Our roots in innovation run deep; from mobilizing scientists’ desire for free and Open Access to the literature and building PLOS ONE to the journal it is today, to pioneering Article-Level Metrics as an alternative to journal impact factors and launching our forward-thinking data policy to positively influence credit, recognition and reproducibility.

One of our top priorities this coming year is to improve the author experience since our authors are at the center of everything we do. Among their top concerns are ‘time to first decision’ and ‘time to publication’. We share their concerns and are committed to reducing this time as much as possible across all our journals. We are embarking on an ambitious plan to reinvigorate PLOS ONE’s editorial board, increase the efficiency of reviewer assignment, and develop and deploy new analytical capabilities to ensure no manuscript is unnecessarily stalled.

Part of this initiative will involve changes around the workflow system – Aperta™ – we set out to develop several years ago with the goal to streamline manuscript submission and handling. At the time we began, there was very little available that would create the end-to-end workflow we envisioned as the key to opening research on multiple fronts. But the development process has proved more challenging than expected and as a result, we’ve made the difficult decision to halt development of Aperta. This will enable us to more sharply focus on internal processes that can have more immediate benefit for the communities we serve and the authors who choose to publish with us. The progress made with Aperta will not be wasted effort: we are currently exploring how to best leverage its unique strengths and capabilities to support core PLOS priorities like preprints and innovation in peer review. This will be part of our planning for 2018.

Innovation is not unlike science itself; there are hurdles to success, determination is integral to advance in one’s work, and knowing when to set aside any particular project to move forward is key. What I, and hopefully others, appreciate is that PLOS continues to be an organization willing to take risks in order to best serve scientific communities across the full spectrum of topics and interests.

Moreover, it’s our goal to optimize the openness and integrity of the publication process by ensuring that research outcomes are discoverable, freely available and reusable and that science communication is constructive, transparent and verifiable. You will be hearing more from me on our core initiatives in early 2018.

PLOS is steadfast in our commitment to our mission and communities and I look forward to sharing our milestones with the scientific and publishing community in 2018 and beyond.

Sincerely,

Advancing Evaluation: Moving Forward with DORA

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“The declaration itself remains unchanged, but our aim is to spread the word much more effectively—about DORA and, especially, about the good practices it has already helped to establish in many institutions.” – Stephen Curry, Imperial College, London

Five years ago at the American Society of Cell Biology Annual Meeting in San Francisco, leading cell biologists, editors and publishers dissatisfied with the near exclusive reliance on journal impact factor as the primary means of measuring success in academia began creation of what would several months later become known as the San Francisco Declaration of Research Assessment, or DORA. The declaration calls attention to the inappropriate and flawed use of journal impact factors and the community need for assessment tools to measure research outcomes other than peer-reviewed publications.

The Current State

DORA states there is a “pressing need to improve the ways in which the output of scientific research is evaluated by funding agencies, academic institutions, and other parties.” The erroneous and inflated value of publishing in high-impact journals is seriously affecting the way that scientists judge each other, as well as adversely impacting the reproducibility of research. To make more fair and broaden the way scientists are evaluated, within DORA specific recommendations for publishers, funders, institutions, metrics organizations and, perhaps most importantly, researchers themselves, were built around the following tenets:

  • eliminate the use of journal-based metrics, such as Journal Impact Factors, in funding, appointment, and promotion considerations
  • assess research on its own merits rather than on the basis of the journal in which the research is published
  • capitalize on the opportunities provided by online publication (relaxing page, figure and reference limits, and exploring new indicators of significance and impact)

Anniversaries are often a time for retrospection, and as this year’s ASCB/EMBO meeting marks the fifth anniversary of the ASCB conference where DORA was born, those involved are taking the opportunity not only to look back at what has been achieved, but also to look forward at what more can be done. “DORA has been very useful in stimulating discussion and action on what truly robust processes of research and researcher evaluation should look like. It is focused on addressing the deleterious effects that the journal impact factor have had, particularly on research careers, but also on the pace and integrity of the scientific record,” says Stephen Curry of Imperial College London, one of the original signatories. Now, he says, is time for the initiative to “gain new ground, not just in Europe and North America, but all around the world.”

Grassroots Transitions

Those working now on revitalizing DORA see this upcoming anniversary year as an opportune window for an energetic transition from consensus-building to action. Says Bernd Pulverer, also an original signatory, “We’re seeing three stages, if you will, of DORA. The original declaration of the critical need to move away from journal impact factors was followed by a phase of community-building and signature gathering through the website. The stage has been set; all stakeholders, from scientists and policymakers to funders and publishers, need us to take action.”

Curry hopes that those stakeholders (especially researchers, funders, universities) who have been thinking about how to improve their research evaluation processes will be motivated to actually implement alternative or additional evaluation tools once they hear what is already taking place, often under the radar. “At my own institution, Imperial College, which is now a signatory, DORA was a valuable element in helping us to think through how to improve our hiring and promotion procedures.” The problem however, is that a critical mass of grassroots initiative and effort are needed to help propel the scientific community forward in this area. “To be sure,” says Pulverer, “change is not trivial to implement at either individual or institutional level, and one important function of the revitalized DORA project is to point to concrete examples of positive change and best practice.”

The barriers to shifting conversation to action are real: some countries offer direct financial incentives to authors for publishing in certain impact factor journals, in other places tenure and funding are often linked to those same publications. Early career researchers often feel compelled to restrict themselves to those journals (or have no input as to where their work is submitted), delaying publication. Sharing stories of change, both small and large, will help remove institutional and individual bias, integral considerations for DORA to be successful moving forward.

The Future State

To enable the revitalization, coming in 2018 are a new DORA website, extended outreach, and real-world examples of practices at institutions already thinking about and implementing innovative assessment mechanisms. There is no one size fits all solution to the research assessment quagmire, but those actively engaged with DORA believe that the scientific community is empowered to change the system in a grassroots manner. “Every one of us can act to change the system for the better—even without formal policy changes,” says Pulverer. “Research assessment invariably involves the research community, either directly as referees, as hiring principal investigators or in an institutional leadership function.”

The fact that misuse of journal impact factors transcends geography and subject area is illustrated by the wide variety of disciplines and countries represented both in the list of institutional and individual signatories of DORA. Plans for 2018 are shaping up. An influx of new funding has facilitated the hiring of a community manager to help promote DORA online and at conferences and meetings. Says Curry, “There are lots of exciting plans for 2018!” With discussions of appropriate recognition and credit for openly sharing data, datasets, microscopy images and analytical tools, the next five years hold promise for bringing the rhetorical concepts of DORA into practical implementation for the benefit of science and scientists of all career stages and in all geographies.

 

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For this post PLOS interviewed Stephen Curry, Assistant Provost (Equality, Diversity & Inclusion) and Professor of Structural Biology, Department of Life Sciences at Imperial College in London and Bernd Pulverer, Chief Editor, The EMBO Journal, and Head of Scientific Publications at EMBO in Heidelberg.

Unrestricted Text and Data Mining with allofPLOS

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Content mining, machine learning, text and data mining (TDM) and data analytics all refer to the process of obtaining information through machine-read material. Faster than a human possibly could, machine-learning approaches can analyze data, metadata and text content; find structural similarities between research problems in unrelated fields; and synthesize content from thousands of articles to suggest directions for further research explorations. In consideration of the continually expanding volume of peer-reviewed literature, the value of TDM should not be underappreciated. Text and data mining is a useful tool for developing new scientific insights and new ways to understand the story told by the published literature.

Application and Challenges

Researchers have leveraged text mining of abstracts and NCBI databases to advance precision medicine through discovery of disease-gene-variant relationships, employed text mining of journal articles for sleep disorder terminologies to determine publication trends, and used text mining to cluster and relationship-map BioMed Central journal content. A study posted on bioRxiv found that text mining full articles gave significantly better information that mining abstracts only, as expected. However, the authors of this study described challenges in the way content was presented and in the need to obtain copyright permissions. In addition to content availability and license status, support for early adopters and training for future practitioners are also cited as barriers to broad use of TDM for research purposes. The foundational value of CC BY licensing for TDM is that no additional permissions or documentation are required. Open Access facilitates TDM:

  • not on case-by-case basis, but for all people, in all places, and at all times
  • without lengthy legal agreements or restrictions
  • by providing unrestricted reuse, remix and mining rights
No Restrictions, No Conditions: allofPLOS

With more than 200,000 fully Open Access research articles available for content mining, PLOS can help advance the discussion and application of content mining through real-world experiences. Through our API we provide article text and meta-data in a single XML file format according to the Journal Article Tag Suite (JATS), the National Information Standards Organization (NISO) standard tag suite for archiving and exchanging journal article content.

The new allofPLOS project is a step forward in providing researchers easier opportunities for new discovery and illumination of non-obvious connections between data, research articles and fields of study. With allofPLOS, in addition to the content of every PLOS article (excluding Figures or Supplemental Data) provided in JATS XML format, the XML parsing tools are provided. By including tags, content and parsing tools together, we hope to simplify and streamline the process for those wanting to experiment with content mining and TDM tools.

With content mining, scientists, educators, policymakers and others can identify and map patterns and trends across millions of articles, extract the information they want, and gain new insights to advance research. TDM results can be shared as a new research article or as a database for others to use.

Setting the Stage for a Text and Data Mining Future

To support policies and public awareness that TDM for research purposes is compatible with current and future publishing industry practices, in 2015 PLOS participated in construction of The Hague Declaration on Knowledge Discovery in the Digital Age, a set of five core principles and a roadmap for action to enable researchers to carry out TDM of digital content on the web without legal repercussions. Unrestricted access to the scientific literature together with standards that promote machine readability of the facts, data and ideas contained within ensures that journal content is available for maximum discovery and reusability.

“We are producing so much information, not just as published literature but as even data from sensors, from monitoring activities, monitoring the planet, and monitoring species, and living things and nonliving things it is simply not humanely possible to attract full value from this, let alone value that we don’t even know that exists inside it,” says Puneet Kishor, former Science and Data Policy Manager, Creative Commons, in a video on The Hague Declaration website. “Using computers and machines is the only way programmatically to figure out what’s hidden inside,” he says.

Next Steps

Visit the PLOS Text and Data Mining page to download the PLOS research article corpus and XML parsing tools, and stay tuned to this space for upcoming stories of how researchers are using these tools. Download one of the HowOpenIsIt?®  Open Access Spectrum guides to see where various permissions for machine readability fall on the Open Access continuum.

Anytime You’re in Listening Mode: PLOScast Two-year Anniversary

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In today’s fast-paced world with its onslaught of environmental, societal and political challenges, science-related podcasts can provide an interesting, educational and even entertaining escape. Podcasts bring an interactive, personal approach and sense of intimacy to topics that might be dry when presented in written form. Plus, you can listen during your commute to the lab, library or office, while you’re exercising, cooking, or anytime you’re in headphone mode.

The growth in science podcasts provides evidence of their potential to deliver important stories to a broad audience. Podcasts are not just about stories, though. Ciencia Puerto Rico (CienciaPR) has increased the amount of culturally relevant scientific news content in Puerto Rico through essays, articles and articles distributed as podcasts, and the University of California considered podcasts as a mechanism to enhance and accelerate research. Podcasts were integral to an early proposal for an online bioinformatics curriculum and are an appropriate component to transform science communication through incorporation of rich media.

At PLOS, we’re celebrating the two-year anniversary of our own podcast, PLOScast. According to PLOScast founding host and PLOS staff researcher Elizabeth Seiver, PLOScast was established to give the organization a modern forum for thought leadership in the publishing space, but it quickly moved beyond this boundary. PLOScast engages listeners through interviews with innovators and thought leaders on the changing experiences of scientists in a digital world, the future of academia and its ongoing challenges, and scholarly publishing developments in an increasingly diverse landscape. These are serious issues, and PLOScast approaches them with integrity, diligence and humor. The show explores all things Open (access, peer review and science), including research tools; ideas for improving science communication; and exemplary, practical habits of successful scientists in all disciplines.

“PLOScast enables us to discuss issues that are important to scientists, with some of the thought leaders in their fields. It also increases the visibility of the work that the greater scientific community contributes, every day.”—Elizabeth Seiver

When PLOScast launched at the end of 2015, development involved getting the logistics and day-to-day operations straightened out. None of the team members had experience with podcasting, so they needed to learn the basics, including what kind of equipment was needed, how to edit a sound file, and how to best promote each episode. Over time, the script itself has evolved to better engage the audience and optimize the listener experience. “I try to keep the listener in mind more now,” says Seiver. “I think at the beginning I was more focused on having the conversation itself, but now I try to have a running voice in the back of my mind thinking about the listener, asking ‘will other people understand this reference? Is this what other people want to know about this topic?’”

Scientists and those interested in academics are certainly listening—PLOScast has over 16,000 plays in the past two years. With its reputation growing, plans are to diversify beyond the traditional one-on-one interview format and to expand its voice to provide early career researchers (ECRs) an opportunity to participate. The manager of PLOS’ ECR Community, Sara Kassabian, recently joined the PLOScast hosting team (yes, two people make a team), contributing an interview with preprint maven Jessica Polka for her inaugural episode. In “How ECRs like Jessica Polka are reinventing science publishing,” Polka goes beyond the topic of preprints to discuss opportunities for ECRs in #scicomm and the role of twitter in creating positive change in #science.

The top 10 most popular episodes by number of plays cover issues ranging from altmetrics and their history (episode 14) to big data in the social sciences (episode 23) and how to work with public information officers to increase the visibility of your science (episode 8). The top 10 (including number of plays as of October 31, 2017) in order are:

  1. Episode 8: How to Communicate Science: An interview featuring Matt Shipman (969 plays)
  2. Episode 2: The Postdoc Crisis featuring Liz Silva (856)
  3. Episode 9: The History of Scientific Publishing: An interview featuring Aileen Fyfe (769)
  4. Episode 3: Managing Scientific Data featuring Tracy Teal (738)
  5. Episode 1 Part 1: Open Peer Review and Scientific Communities (706)
  6. Episode 17 Part 1: The Science of Science featuring Eamon Duede (694)
  7. Episode 23: Big Data in the Social Sciences: An interview featuring Ian Mulvany (668)
  8. Episode 14: Understanding Altmetrics with Stacy Konkiel (636)
  9. Episode 22: Building Taxonomies: An interview featuring Bob Kasenchak (598)
  10. Episode 20: Science Communication and Critique: An interview featuring Hilda Bastian (598)

Interestingly, PLOScast launched with a broad ranging discussion on collaboration and publications with Cameron Neylon, formerly PLOS’ Advocacy Director. Part of this conversation covered bioRxiv, prior to that preprint server’s current phase of rapid growth. The second year began with an interview with James Fraser from UCSF on preprints and their ability to help authors stake a claim on ideas, methods or results. The interview with Polka marks the beginning of year three for PLOScast; as with the rest of the scientific community, preprints are an increasingly central part of PLOS’ conversation on how to move science communication forward.

To mark this achievement milestone for PLOScast, we have a new icon that’s fun and quirky yet at its core remains PLOS. We leave listeners around the globe with the top five favorites of the PLOScast crew:

New PLOScasts are posted monthly; you can find PLOScast on iTunes, SoundCloud, Google Play or sign up for an RSS feed on the PLOScast main page so you don’t miss an episode.

CC-licenser bliver strategisk værktøj hos Dansk Design Center

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Dansk Design Center, den delvist offentligt finanserede organisation til fremme af brugen af design i det danske erhvervsliv, er seneste store danske aktør, som introducerer brugen af Creative Commons-licenser som nyt strategisk værktøj i deres daglige arbejde.

Men hvor flere andre danske aktører primært bruger CC-licenserne på udvalgte værker, tager man helt anderledes fat i Dansk Design Center: Her vil alle organisationens producerede materialer fremover udgives under den mest åbne licens, CC BY, og dermed være til fri anvendelse og videre bearbejdning til ethvert formål. Dermed opfordrer de alle til at remixe, sample, videreudvikle og sprede den viden, de skaber.

“Som offentlig organisation er det en selvfølge, at alt hvad vi laver bør være frit tilgængeligt for alle, der ønsker at følge vores arbejde og anvende den viden, de indsigter og de resultater, vi producerer. Denne transparens har til formål at skabe så meget værdi for pengene som muligt i de økosystemer og netværk, vi bevæger os i. Vi kalder det “Open by Default” – at vi som organisation altid vil være så åben, nysgerrig og lærende som muligt,” udtaler organisationens direktør, Christian Bason.

I pressemeddelelsen uddyber han endvidere:

“Deling af viden er nøglen til øget velstand i dagens informationsdrevne samfund – ikke kun i Danmark, men også internationalt. Værdi skabes i stigende grad på tværs af sektorer, brancher og ikke mindst landegrænser, og ved at lære af hinanden accelererer vi innovationen og står på hinandens skuldre. Begreber som samskabelse, co-creation og remixing er blevet store vækstmotorer, og det ønsker vi at tilskynde og dermed sikre, at viden om dansk design når ud til så mange som muligt.”

Organisationens nysgerrighed overfor potentialerne i åbenhed og deling begrænser sig dog ikke til udelukkende til brugen af CC-licenser på producerede materialer. I programmet REMODEL udforsker Dansk Design Center og en række af danske virksomheder eksempelvis nye open source-baserede forretningsmodeller for produktionsvirksomheder, og åbne data er et af omdrejningspunkterne i deres udviklingsarbejde omkring digitalisering og fremtidens byer.

Læs mere om organisationens brug af Creative Commons-licenser i annonceringen “Brug og del: We are now open“.

PLOS Channels Provide Opportunity for Discovery, Exploration and Contextual Insights

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Last month, the new PLOS Cholera Channel joined existing Veterans Disability & Rehabilitation Research, Tuberculosis and Open Source Toolkit Channels in providing distinct and cohesive scholarly homes for research communities. These innovative forums increase the visibility of curated, quality research and reliable news and commentary, bridging a gap in relevance that contributes to public misunderstanding of research.

The Channels Program launched with Veterans Disability & Rehabilitation Research (VDRR), and as Veterans Day in the US approaches it’s an opportunity to take a moment to relay the channels origin story, highlight the latest content and re-introduce the editors behind this program.

“It is imperative that scientists and consumers explore novel and innovative strategies to share research findings. Towards this end, as an editor of the PLOS Channel for Veterans Disability and Rehabilitation Research, I look forward to highlighting research aimed at helping Veterans with disability and/or chronic illness increase function and participation in daily life.”—Lisa Brenner, VDRR Channel Editor

For those intimately involved with the generation, use or reuse of research, channels provide a central information source for the latest developments, whether published in PLOS journals or elsewhere.

Beyond Traditional Journal and Editorial Boundaries

As global forums for research, news and discussion, all PLOS Channels deliver a similar contemporary layout for easy navigation and reading, developed with feedback from multiple audiences in mind: basic and clinical scientists, policymakers, science journalists, educators, students and patients. The Featured Research section pulls from PLOS and other Open Access article sources. A Related Content section contains news, occasional events and journal commentary that speak directly and with integrity to the channel topic. Although not peer reviewed, web articles and commentary in the Related Content section are selected by channel editors for the reliability of the source, relevance to the topic and when possible, to provide broad perspective on global issues from local journalists. PLOS hopes the mix of quality peer-reviewed research and exploratory journalistic content will help bridge current knowledge and communication gaps between scientists and the lay public.

Channel editors, selected either from existing PLOS Editorial Board members or recruited together with the channel focus, are an integral component of any given channel. Their expertise and ability to bring in supplementary material through commentary, blogs, news and more helps research communities and the public stay up to date with the latest advances, research trends and societal impact of work in the field of focus. To highlight their foundational work and dedication to this innovative effort in science communication, these editors are profiled at the bottom of the respective channel.

Stories of Channel Origins

Channels originate either from community demand or engaged editors or partners. VDRR provides a new home for the community formerly served by the Journal of Rehabilitation Research & Development (JRRD), no longer published by the US Department of Veterans Affairs. VDRR offers international researchers and practitioners a dedicated online space to share and read state-of-the-art research, information and resources to assist Veterans with chronic illness and disabilities worldwide. Meet the four editors on the Channels and Collections blog.

Editors of the Tuberculosis Channel exemplify the academic strength, community knowledge and dedication to science and medicine this position provides for each channel. The channel was proposed by Dr. Soumya Swaminathan during her tenure as Secretary, Department of Health Research, Ministry of Health & Family Welfare, Government of India, and Director General of the Indian Council of Medical Research. In October, Swaminathan was appointed Deputy Director-General of the World Health Organization in Geneva, the second-highest position at the health agency. Meet both TB Channel editors.

Born as the PLOS Open Source Toolkit: Hardware Collection, the Open Source Toolkit Channel builds on the success of the Collection and now includes peer-reviewed and web articles addressing software and its application. The dedication of this community to all aspects of open source in advancing science and medicine was a determining factor in transitioning this PLOS Collection to a PLOS Channel. Meet the two editors.

The recently launched Cholera Channel was proposed by Dr. Andrew Azman, Deputy Editor of PLOS Neglected Tropical Diseases; he is joined as a channel editor by international experts in global health and infectious disease. Those engaged in the fight against cholera include academics, healthcare workers, policymakers, patients and civil society—all sharing a vision that collective action can stop cholera transmission and end cholera deaths through strengthened international collaboration and improved coordination. Meet the four editors on the Speaking of Medicine blog.

Supporting this community, until now with no specialist journal or centralized publication venue for their work, is key to PLOS Channels’ mission to serve as resources for research communities. Current Editor’s Picks

Each Channel showcases an Editor’s Pick, updated regularly, to bring the latest research front and center to readers. On the VDRR Channel, the latest Editor’s Pick covers a study for early screening of Parkinson’s disease using voicing tasks and text-dependent speech options, published in PLOS ONE.

Editors of the Tuberculosis Channel focus on research that demonstrates an in vitro diagnostic test commonly used to accurately detect Mycobacterium tuberculosis complex and rifampin resistance in high-incidence TB settings performs comparably in low TB-incidence settings. Editors of the Open Source Toolkit Channel chose to feature a PLOS Biology Community Page describing a tool for ethomics, the high-throughput approach to behavioral studies. “Ethoscopes: An open platform for high-throughput ethomics” originated as a preprint on bioRxiv and describes open source software and hardware solutions for monitoring animal behavior.

Currently the Cholera Channel highlights “Identification of burden hotspots and risk factors for cholera in India: An observational study” describing disease hotspots and risk factors for transmission. Using district-level data from the Integrated Disease Surveillance Program, the authors offer their open research results to policymakers for development of a cholera prevention and control roadmap.

From epidemiological studies using existing census data to translational research and innovations for behavioral studies of experimental model organisms, these diverse choices highlight channel editors’ broad perspective in curating content of interest for their scholarly communities.

A Focus on Cholera: PLOS’ Newest Channel

While universal access to safe water and appropriate sanitation is the key to cholera prevention, global progress towards these goals has been slow. The disease remains a global public health threat, with ongoing risk factors that include poor sanitation, lack of enough clean drinking water and poverty. The Cholera Channel features articles on applied and basic research related to the global fight against this disease and spans a range of topics with application to cholera prevention and control, including computational studies exploring the dynamics and spread of cholera; epidemiologic studies and translational science. Also covered is applied field research on the efficacy, effectiveness and impact of cholera control programs such as water and sanitation interventions and oral cholera vaccines.

PLOS aspires to put researchers back at the center of science communication, working in the best interests of all stakeholders—for the benefit of science and the public. Innovations such as the Channels Program, with collaboration from like-minded organizations, push the boundaries of scientific publishing beyond traditional journal, publisher and editorial constraints. Additional channels are currently in planning; bookmark https://channels.plos.org/ or your Channel of interest and check back every two weeks for the latest research, news and developments.

Open Access Week 2017 – Open in Order to…

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As a proud co-founder of Open Access Week, we hope you will join us in celebrating progress and promoting awareness to help make Open Access – the founding principle of PLOS – the new norm in scholarship and research globally. This year’s theme is “Open in Order to…” and invites the community to focus on what openness enables.

Since PLOS’ beginning, we’ve been open in order to accelerate progress in science and medicine through publishing, advocacy and innovation to benefit the research community and beyond. PLOS is open in order to ensure that: research outcomes are discoverable, accessible and available for discussion; science communication is constructive, transparent and verifiable; and publishing advances reproducibility, transparency and accountability.

Join PLOS in an Open Access Week Event (and find other events near you):
  • Wed 10/25 5:30–8:00 pm PDT Open House & Poetry Slam at PLOS – Please join us at the PLOS office for refreshments, office tours to see how we work and an Open Mic Poetry Slam with guests invited to share poems, songs, or free verse on the OA Week theme: “Open in order to….” We’ll have fun prizes for all who choose to share!
  • Wed 10/25–Fri 10/27 FORCE 2017 | Changing the CultureAlison Mudditt, PLOS Chief Executive Officer and Emma Ganley, PLOS Biology Chief Editor will be in Berlin at this conference that brings together a diverse group of people interested in changing the way in which scholarly and scientific information is communicated and shared
Explore PLOS Journals – which have now published more than 200,000 research articles: Follow PLOS Channels: Be Open in Order to: Get involved:
  • Learn about FASTR – As Open Access takes center stage with the Fair Access to Science and Technology Research Act in Congress, PLOS reaffirms its commitment to and support of Open Access
  • Join the conversation with PLOS Science Wednesdays 1:00 pm EDT – the Ask Me Anything (AMA) series with PLOS authors on redditscience
Publish with PLOS and share your work with the world Stay in touch with PLOS

Have a great Open Access Week!
 

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