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Podcast with Jamie Alexandre from Learning Equality

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In this podcast, I talk with Jamie Alexandre from Learning Equality. Learning Equality focuses on technology solutions which are optimized to work in areas where Internet access is lacking or costly. Their project KA Lite is an offline version of Khan Academy, used in over 170 countries. Based on feedback from KA Lite users, the Learning Equality team is actively developing Kolibri, their next generation platform which allows for curriculum alignment of a broader set of content.

Learning Equality builds educational technology solutions that leverage open-licensed content and low-cost hardware to enable a broad range of NGOs, schools, governments, and individuals to implement programs that improve educational outcomes in their communities.

 

Creative Commons explained in 3 minutes

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There are many good resources about Creative Commons on the web. I have used a film from Creative Commons New Zealand whenever someone have asked me to explain CC Licences. The short video is a really good introduction with great drawings and examples.

To make it even more suitable to be used as part of my standard OER talk I have re-mixed it and made a version that is just over 3 minutes.

In this short version I have stripped it down and focus only on the core elements and the explanation of these.

European Commission lacks vision for copyright in the digital age

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The copyright reform proposal presented by the European Commission in september 2016 fails to meet the needs of citizens, educators, and researchers across Europe. Instead of strengthening the information economy, the proposal preserves a status quo defined in the analog age.

The Link Tax

This includes unprecedented new Link Tax powers for publishing giants, as well as requirements for websites to monitor and filter content. This will hurt your right to access and share content.

The European Commission has proposed, as part of the Copyright Directive on the Digital Single Market to allow news publishers to claim an additional copyright over the snippets of text which automatically appear alongside most links.

As a result linking to online news content would therefore require a license and explicit permission from the publisher.

It would give press publishers the right to charge fees for websites operating any form of business using snippets of text when they link to content from press publishers.

The European Commission promised to modernise copyright, but instead of creating a well-functioning legal framework addressing the concerns of creators and end-users it proposes to protect old business models by creating what it claims to be a “well-functioning marketplace”.

A disaster for educators, non-profits and individuals

The European Commission is also demanding that companies create or buy expensive new technologies to monitor and filter the content we create. This means every website or service that allows users to upload content will have to build expensive robot programs to spy for material that rightsholders want to block. What’s worse is that these bots won’t be able to make exceptions for parody, public interest, fair use, and many other legal forms of expression.

Because the draft of the Copyright Directive does not limit the implementation of this proposal to aggregators and search engines, it may also allow press publishers to charge non-profits, social media websites, or even individuals who communicate online using hyperlinks. The proposed educational exception, despite having some good elements, will overall worsen the legal environment for educators.

And it likely will introduce major costs for public educational systems around Europe.

Access to most audio-visual content will continue to be hampered by geo-blocking (which the Commission had earlier committed to end), and online platforms might be forced to collaborate with rights holders on censoring content that is shared by users on these platforms. The whole package lacks forward-looking, innovation-friendly measures that embrace digitization as an opportunity for users, creators, businesses, and public institutions in Europe.

We have to act now

Despite opposition from over 120,000 Internet users and dozens of civil society groups, the European Commission charged ahead with its wrong-headed plan. But now that it has reached the European Parliament, we have a real chance to stop it in its tracks. This will have the same impact in Norway as in any if we were full members of EU.

The European community is joining forces to send a clear message to the EU Parliament. We urge everyone that think the web is a wonderful thing to fill out this petition at OpenMedia.

Alek Tarkowsky, Director, Centrum Cyfrowe and Christer Gundersen are co-authors of this text.

Resources used in this text:

CC-BY is the ideal license for OER

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I believe that the CC-BY license is the ideal Creative Commons license for open textbooks and other open educational resources. If you are part of a project funded with money from a donor trying to get the most out of every invested dollar the more restricted licenses would create unwanted barriers. Sometimes there could be good reasons for adding restrictions but more often the not, CC-BY is the best way to go.

Why? Here are some of the most obvious reasons:

  • It increases the overall goal of sharing, translation and re-contextualization of books and OER.
  • The CC BY license is easy to understand and follow, requiring simply that attribution be provided to an open textbook author(s).
  • Content with a CC-BY license can be remixed** with all non-ND CC licenses, making it easier to remix others’ OER into an open textbook.
  • I believe an ND (no-derivatives) licensed textbook is not an open textbook because ND licenses do not allow two of the five Rs: revising and remixing.
  • The NC license also reduces remix options.
  • The SA license reduces remix options.
  • The NC license often causes confusion and limits the spread, adoption and use of OER. Creators should consider carefully whether their reasons for using an NC license justify the limitations it will impose on users.
    • NC license has been used to claim that OER cannot be printed by a commercial print shop for use in classrooms.
    • Some Colleges have assumed that because they charge tuition, they can’t use NC-licensed OER. Others worry about printing and selling (cost recovery only) NC-licensed open textbooks.

This article is a derivative of “Open Textbook Community Advocates CC BY License for Open Textbooks” by Mary Burgess, David Ernst, Hugh McGuire, David Wiley used under CC-BY 4.0 International License. This article is licensed under CC-BY 4.0 International License by Christer Gundersen.

 

 

A PLOS Response to Open in Action with Open Science

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With the theme of Open in Action, International Open Access Week 2016 served as a call for researchers, policymakers, funders and publishers around the globe to take “concrete steps to open up research and scholarship.” In direct response to this call, PLOS thought carefully about Open Science and what it means for us.

Reflections on Open Science at PLOS

PLOS has proven that making quality research openly available for anyone to read, download and reuse is a viable business model. Our collaborative efforts with like-minded organizations have inspired others – from individual researchers to the larger publishing industry – to move toward a more open ethos. In this environment, Open Access is no longer constrained to free access to research, it’s also about open data and a more open way of working together. Examples of this at PLOS include our pioneering a forward-thinking data policy at scale and contributions to the community-developed open-standard taxonomy of contributions – the CRediT Project – that provides specific and comprehensive attribution on research articles for all who participate in generating a published work.

We are proud to be Open in Action collaborators with other publishers including The Royal Society, eLife, Science journals and EMBO Press in making a public commitment to implement persistent identifiers such as ORCID iDs by year end. These iDs enable researchers to receive credit for a wide range of research outputs in addition to publications (for example blog posts at PLOS) and we are well on the way to meeting this goal. With many of these same collaborators (The Royal Society, eLife, ScienceEMBO Journal, Nature and Professor of Structural Biology Stephen Curry and Associate Professor of Information Science Vincent Larivière) we committed to publish citation distributions of our journals to demonstrate a key flaw with impact factors—they simply do not reflect article citation rates. In publishing this data, PLOS hopes to “strengthen a call for action originally voiced by Stephen Curry, one of the authors, and to encourage other journals to follow suit.” The original paper and dataset are posted on bioRxiv for all to access.

Open Policies and Open Research

Data sharing and Open Access are a matter of course for PLOS authors, providing open and rapid dissemination of their original research in all areas of science. PLOS supports authors who wish to share early versions of their research manuscripts to receive feedback before – or in parallel to – formal peer review, and encourages researchers to share via preprint servers either before or after submission to a PLOS journal. PLOS has a long-standing policy of accepting manuscripts previously posted to preprint servers, however we have eased the process for authors for this rapid dissemination vehicle that also brings transparency to the review process. Authors can now use bioRxiv’s direct transfer to journal service drop-down menu to submit directly to PLOS.

We have exemplified Open in Action as the first publisher to react to the Zika outbreak with a Call for Research and The Zika Collection. This placed PLOS on the map for rapid dissemination and discovery of results during the outbreak. As a result, work of authors who published with PLOS caught the attention of legislators: The US Capitol called PLOS to ask for additional information regarding the PLOS Currents: Outbreaks article, “Travel Volume to the United States from Countries and U.S. Territories with Local Zika Virus Transmission” as they were considering this information for use in upcoming legislation.

The practical impact of Open Access and open data may not always be immediate. The International Union for Conservation of Nature (IUCN), publishers of the IUCN Red List of Threatened Species, voted in September 2016 to adopt the Environmental Impact Classification for Alien Taxa (EICAT) for classifying invasive species, work originally published in PLOS Biology in 2014. Author Tim Blackburn stated “IUCN has approved the motion on our method for classifying alien species impacts…The adopted text requires a consultation before EICAT becomes an IUCN standard… [but] it is an extremely positive development… Getting the paper published somewhere so high profile (and open) really made a difference, so thank you!”

Actionable knowledge on an international scale extends beyond conservation efforts to inform human health and disease initiatives. The WHO Estimates of Foodborne Disease Collection reports the first estimates by the World Health Organization (WHO) Foodborne Disease Burden Epidemiology Reference Group of the incidence, mortality and disease burden caused by 31 foodborne hazards. Outcomes reported in the Collection – from PLOS, WHO and F1000Research authors – can contribute to improvements in food safety throughout the food chain when incorporated into policy development at regional, national and international levels.

If you choose to be Open in Action with PLOS, you can also have a bit of intellectual fun. The PLOS Paleo Community held a competition for the paleontology research community for the Top 10 Open Access Fossil Vertebrates of the year, to honor researchers that have thought long and worked hard to provide our community quality research that is openly available to all. Articles represent the vertebrate diversity published in Open Access journals, from PLOS ONE to PeerJ, Science Advances and Paleontologia Electronica.

Encouraging the Next Generation of Open

PLOS supports the growth of Early Career Researchers (ECRs) as they build skills in science communication, become champions of Open Science and develop into ambassadors of change for a future where all research is freely available, all work is evaluated fairly and all members of the scientific community have opportunity to participate in the dialogue of and about science. To support the efforts of ECRs, we are continuing to offer our Early Career Researcher Travel Award (ECRTA) program, launched in 2015. For its first round in 2016, applicants were asked to describe characteristics of the optimal peer review process and how they might build this in a way that makes science more transparent and research more rapidly available. Winners were profiled and we’ve now completed a second award round asking what ECRs consider to be the value of a preprint server and how its broad adoption might benefit the scientific community and society.

As a participant in OpenCon 2016, a conference focused on educating and empowering the next generation in the areas of Open Access, Open Education and Open Data, PLOS will have the opportunity to hear directly from participants regarding their desires and concerns for the future of science communication. In a video welcoming address, Publisher Louise Page acknowledges the inspiration provided by this annual gathering of Open Science thinkers and presents highlights of the past year at PLOS that reflect how the organization is Open in Action.

“PLOS was founded with the researcher foremost in our minds and we want to work with you to continue our journey from Open Access to Open Data, Open Source and ultimately to Open Science,” says Page.

The brief video is an introduction to an OpenCon Community Webcast with Peter Suber, Director of the Harvard Office for Scholarly Communication. You can also listen to the OpenCon 2015 video address by PLOS Executive Editor Véronique Kiermer on The Future of Science Communication.

Open Access Is Open in Action

In an increasingly vibrant research world where multimedia data, new types of research outputs and real-time online discussions are altering the way the community works, communicates and cooperates, Open Access is more than ever Open in Action. PLOS is proud that our founding core principles exemplify Open in Action. What makes us notable among other publishers is that we were Open in Action from the start: 24/7, 52 weeks a year.

Our View of Open Science As a leading Open Access publisher, PLOS pursues a publishing strategy that optimizes the openness and integrity of the publication process by aiming to ensure that research outcomes are discoverable, accessible and available for discussion and that science communication is constructive, transparent and verifiable. We strive to implement policies and innovations that promote reproducibility, credit and accountability, as these priorities support establishment of an Open Science culture, with open data, early sharing of work and clear contributor recognition. We see the benefit of Open Access content in relation to future advances in machine-readable formats and text and data mining.

We look forward to hearing your Open Science stories and the outcomes, large or small, that you have achieved. Leave a comment here or email to communications@plos.org.

 

Image Credit: SPARC

Podcast with Purvi Shah talking about Storyweaver

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StoryWeaver is an open source platform by Pratham Books for multilingual children’s stories. It addresses all the issues around the lack of content by using an open access framework and technology as force multipliers combined with a platform that supports translation and re-mixing av stories.

I had the great pleasure of co-organizing a workshop at the mEducation Alliance Symposium in Washington on Oct 18–20. After the workshop I sat down with Purvi Shah for a talk about Pratham Books and their latest project StoryWeaver.

Bonus track

Jennryn Wetzler is the Senior Program Designer at U.S. Department of State Bureau of Educational and Cultural Affairs’ Collaboratory. She organised a great workshop at the mEducation Alliance Symposium on OER and in this short podcast she talks about why education is important.

Free culture is winning

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To help authors choose a CC license Creative Commons have made it easy to distinguish between the different licenses. The license selector also makes it easy for those who are completely inexperienced users of Creative Commons licenses to determine the correct license. Statistics from 2015 shows that most of us choose the free culture licenses, and that is great news for all that love to re-use and re-mix. 

Illustration by Creative Commons, CC BY 4.0

I get many questions on how many limitations you should choose to associate with a picture, video or text. There is an axis between more open licenses with few limitations and the most restrictive ones that have limitation on derivatives and commercial use.

License CC-BY and CC-BY-SA (includes CC0) is often defined in a separate category licenses that support the “free culture.” My advice is that you should use these licenses as often as you can. The statistics that summarises the use of CC licenses globally also shows a clear trend that these “free culture” licenses are the most popular. This is good news because it provides even greater freedom for those who want to reuse, even for those who engaged in commercial activities.

The most popular license is CC Attribution-Share Alike (BY-SA). 37% of all work published are released under this license. By comparison, only 14% have chosen to use CC Attribution-Noncommercial-No processing (CC BY-NC-ND). One of the most restrictive licenses.

 

The Best of Both Worlds: Preprints and Journals

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For some time now PLOS has discussed new initiatives designed to accelerate research communication, from development of Aperta™, our streamlined manuscript submission system that facilitates a faster time to first decision to our Content Management System that allows for rapid creation of curated PLOS Collections. These efforts span the range of ways we are accelerating access to discovery of not just the final publication but the entire research life cycle.

Stake a Claim

An additional strategy – early posting of articles before formal peer review through the use of preprints – can also advance science faster, more openly and with broader participation. In posting preprints, authors are able to make their findings immediately available to the scientific community and to receive feedback on draft manuscripts before they are submitted to journals. The benefit extends beyond making early work openly and freely available prior to or during consideration at a journal; in posting a preprint, an author or author group stakes an intellectual claim to methods, results and ideas contained within that paper. This can be especially important for scientists looking to change the focus of their research and connect with engaged colleagues in new fields; for those on the job market needing to show the status of their current research, their collaborative nature and their ability to embrace change for a more open way of doing science; and for early career researchers who may find opportunity to interact with new contacts interested in their work.

PLOS supports authors who wish to share early versions of their research manuscripts to receive feedback before – or in parallel to – formal peer review, and encourages researchers to share via preprint servers either before or after submission to a PLOS journal. Preprints are an excellent way to:

  • Establish intellectual precedence for ideas, methods, results
  • Receive early feedback from engaged colleagues
  • Obtain and document citations to a work before publication in a peer-reviewed journal
  • Contribute to accelerating scientific discovery and increasing research efficiency

PLOS has a long-standing policy of accepting manuscripts previously posted to preprint servers, however we recently collaborated with bioRxiv to ease the process as a reflection of the importance we assign to this rapid dissemination vehicle for authors that also brings transparency to the review process. Authors can now use bioRxiv’s direct transfer to journal service drop-down menu to submit directly to PLOS. While authors posting to bioRxiv can choose the reuse options under which to make their article available (various CC BY options or no reuse), licensing terms of PLOS content has not changed. To inform authors and the public of the current and more seamless arrangement with bioRxiv we have updated our preprint policy on all journal ethical publishing practice and related manuscript sections as well as the Wikipedia page that describes the landscape of publisher’s preprint policies.

Researchers First

With preprints, authors – not publishers – are in control of when they publicly timestamp their intellectual property as well as when they want it to go for review. They decide when their research paper is ready to post and when they’re ready to submit their paper for formal peer review. In an open environment, the community can evaluate what any individual scientist’s standards are for their work and their online interaction with colleagues. By posting work and commenting on the posted work of others, authors are more in control of their own reputations. In essence, the use of preprints is analogous, in a very public and large-scale version, to the more intimate practice of sending a complete manuscript draft to a colleague to get their opinion with potential to improve the manuscript before submitting to a journal. Some have likened it to going public with a conference abstract or presentation.

How it Works

In the same way that not all Open Access is created equal, not all preprint servers work the same way. Launched in 2013 by Cold Spring Harbor Laboratory, bioRxiv is now in its third year with more than 5,000 preprints posted to the site and more than 1 million article views each month. At bioRxiv, all posted research papers receive a digital object identifier (DOI) that remains associated with the original preprint. When a manuscript is transferred to PLOS from bioRxiv, PLOS stores the preprint DOI; if that manuscript is accepted for publication it then receives a PLOS DOI and we deposit both the preprint and the final article DOI to CrossRef so the two works can be associated with each other.

Importantly, whether posting a preprint or submitting to a journal, authors can help themselves ensure full recognition for both the preprint and the final article by including their ORCID iD at all times.

At PLOS, preprints are acceptable resources for inclusion in the reference section of an article. Should anyone follow a link from an article citation to a preprint that has subsequently been peer reviewed and published, they would be directed from the preprint to the article on the PLOS journal website.

DOI: 10.1371/journal.pone.0164504

 

Value Perspective

Preprints do not diminish the need for reputable peer-reviewed journals. In fact, the combination provides scientists the best of both worlds; preprints accelerate making work public and provide an opportunity for early feedback for those willing to share their work whereas journals provide a mechanism for formal assessment, curation and dissemination. Journals reinforce standards for ethical and reporting guidelines, plagiarism checks, conflicts of interest and work with organizations such as CrossRef to ensure seamless and complete metadata transfer. Publishing in journals has the added benefits of validating the quality of work through rigorous peer review; placing work in context through perspectives, editorials and incorporation into collections; providing opportunities for online dialogue with authors through PLOS Science Wednesday AMAs and tracking article influence through Article-Level Metrics. Our current work with bioRxiv is one more example of how we are putting researchers at the center of science communication and placing authors in control of their manuscripts. In the future, expansion of Aperta to the full suite of PLOS journals and incorporating aspects of community review to our processes will place PLOS in the space necessary to accelerate dissemination of research results and conversation surrounding a scholarly work.

Those wanting an objective look at the value of preprints might find Breaking Down Pros and Cons of Preprints in Biomedicine of interest; for a detailed discussion of preprints by one active participant listen to the PLOScast with James Fraser, Associate Professor at UCSF and a founding member of ASAPbio, an initiative of the biology community to encourage use of preprints. When you’re ready, go ahead, post that paper, place your results and ideas in the mix and we’ll advance science forward faster, together.

 

Image Credit: Lisa Ann Yount

Jenny Machida Appointed to PLOS Board of Directors

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PLOS is pleased to announce that Jenny Machida has joined the PLOS Board of Directors, effective October 21, 2016. “Jenny’s deep business knowledge with a focus on strategy, growth and organization performance will greatly contribute to PLOS as we strive to build a better publishing experience for authors in 2017 and beyond,” said Board Chairman Gary Ward.  “We are delighted that she is joining our Board of Directors and look forward to benefiting from her depth and breadth of experience.”

Machida received her BA summa cum laude from Yale University and earned an MBA from the University of California at Berkeley. Machida is currently a Managing Director at IMB Development Corporation, a private equity investment and operating firm. Prior to IMB, she co-founded and led business development at a medical technology start-up company called Sevident and helped to build out an academic research and advisory center at Columbia University focused on advancing diversity in higher education. Machida was also a Principal at Booz & Co. and a Principal and Co-founder of the Healthcare and Diversity & Inclusion practice areas at Katzenbach Partners.

Open Access Week 2016 – Open in Action

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Now in its ninth year, Open Access Week celebrates progress and promotes awareness to help make Open Access – the founding principle of PLOS – the new norm in scholarship and research globally. Join PLOS in celebrating Open Access Week by being Open in Action.

 

  • Register for an ORCiD ID – distinguish yourself and create a record of your scholarly contributions.
  • Join the conversation about Open Access Tools with PLOS authors Lenny Teytelman and Hilda Bastian on 10/26 10am PT for a special OA week edition of PLOS Science Wednesday – the Ask Me Anything (AMA) series on redditscience.
  • Get a sneak peak of PLOS’ upcoming projects with PLOS Publisher Louise Page in this OpenCon 2016 Community Webcast.
  • Listen to a special episode of PLOScast – a podcast focused on science, academia and the future of scholarship – featuring UCSF’s James Fraser discussing the use of preprints in the life sciences.
  • Meet PLOS staff and editors at SVP or iGEM – stop by the booth, learn more about Open Access publishing and pick up a giveaway.
  • Browse the Open Highlights Collection, with research from across PLOS journals and the wider Open Access literature curated by staff editors to provide depth of coverage on select topics.

Have a great Open Access Week!

Influential Work from PLOS Authors Garners Lasker Awards

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The Lasker Awards recognize the contributions of scientists, physicians and public servants who have made major advances in the understanding, diagnosis, treatment and prevention of human disease. Each year since 1945, dedicated scientists benefit from the mission of the Albert and Mary Lasker Foundation to recognize research excellence, public education and advocacy.

As a champion of biomedical research, Mary Lasker worked to increase public appreciation for and government funding of medical sciences. As a result of her advocacy efforts, several NIH Institutes were newly created, including the National Heart Institute, the National Institute of Mental Health and the (originally named) National Institute of Neurological Diseases and Blindness. Lasker helped change the biomedical research landscape in the United States and the scientific community to this day benefits from her dedication.

PLOS is proud that six of this year’s seven Lasker awardees have published research or an interview with PLOS, and we are fortunate to benefit from the expertise of Charles M. Rice of The Rockefeller University in his role as an Academic Editor for PLOS Pathogens.

Here are the 2016 Lasker Award honorees with a summary of their PLOS research and interviews, spanning five journals and The PLOS Blog Network, for a collective total of 38 articles and two interviews. Oxygen sensing—an essential process for survival:

Gregg L. Semenza’s three PLOS ONE articles cover the role of NADPH oxidase in Hypoxia Inducible Factor-1α (HIF-1α) activation, the dependency on tumor suppressor p53 for macrophage migration inhibitory factor’s effect on HIF-1 activation, and the ability of HIF-1α to regulate the expression of cell adhesion molecule CD44.

Peter J. Ratcliffe published two PLOS ONE articles and one each in PLOS Biology and PLOS Medicine. Some of this work examines the relationship between the von Hippel-Lindau (VHL) tumor suppressor gene, HIF-1 and extracellular matrix in C. elegans, the role of VHL-HIF pathway in human cardiopulmonary physiology and function at standard and high altitudes, and most recently the investigation of compounds that inhibit the hypoxia sensors of the HIF system, the HIF prolyl-hydroxylases, with implications for therapeutic treatment of stroke or other diseases of cerebral ischemia.

DOI: 10.1371/journal.pbio.0020289

 

 

 

 

 

 

William G. Kaelin’s PLOS Biology article – published in the journal’s inaugural year – explores the relationship between inactivation of the VHL gene, subsequent HIF2α activity and renal carcinoma tumor formation.

Hepatitis C replicon system and drug development:

Charles M. Rice has eight articles with PLOS; three in PLOS ONE and five with PLOS Pathogens. His virology research – while primarily focused on hepatitis C virus (HCV) – also addresses arthropod-transmitted viruses in the Flaviviridae family, such as yellow fever virus, and natural inhibitors of HIV identified from simulation screening of the pan-African Natural Product Library followed by cell-based testing. A subset of Rice’s HCV work published in PLOS Pathogens covers direct deregulation of the cell cycle in HCV infection as a contributor to liver disease, host cell protein and lipid mapping to uncover temporal and global changes as a result of HCV infection and a mutational structural analysis of the p7 protein revealing positions important for particle assembly and infectivity.

DOI: 10.1371/journal.ppat.1000719 DOI: 10.1371/journal.ppat.1005297

 

 

 

 

 

 

Ralf Bartenschlager tops the PLOS list with 27 articles; 20 in PLOS Pathogens and seven in PLOS ONE. Select key early work on HCV includes the role of cyclophilin A in HCV replication and polyprotein processing, the role of HCV p7 protein as a membrane pore involved in production and release of infectious virions and the dependence of HCV envelope glycoprotein secretion on assembly of triglyceride rich lipoproteins.

Bartenschlager’s team also determined the nonstructural protein 5A (NS5A), a component of the viral RNA replication machinery, as a key factor for the formation of infectious HCV particles through an assembly determinant domain and lipid droplets. Bartenschlager’s seminal microscopy work on the intracellular membranes of HCV infected cells is visually stunning and included in the PLOS Pathogens 10th Anniversary Collection.

More recent articles describe use of a yeast two-hybrid screening strategy to generate an interactome of cellular proteins that may function with influenza virus non-structural proteins NS1 and NS2, potentially informing therapeutic interventions, and work on Dengue virus that provides a genetic map of determinants involved in viral RNA replication and extends the list of functions ascribed to the enigmatic nonstructural protein 1.

DOI: 10.1371/journal.ppat.1005277 DOI: 10.1371/journal.ppat.1003056

 

 

 

Discoveries in DNA replication and leadership in science and education:

In 2012, PLOS GeneticsJane Gitschier Interviews turned to this year’s Lasker-Koshland Special Achievement Award in Medical Science awardee Bruce Alberts for his memories of how he got into science and his thoughts on learning from failure and getting committees to reach consensus. More recently Alberts shared with PLOS his insights into issues facing scientists today, such as journal impact factors, new forms of recognition for contributions to the scientific publication process and the role of senior as well as junior researchers in changing the culture of science.

For those wanting more information on the significance of the work of this year’s winners and the award in general, The Lasker Foundation and Cell provide coverage.  Cell has also curated Collections dedicated to Hypoxia-Inducible Factors and virus infections. Much, but not all, of the content is Open Access.

PLOS has previously profiled author recipients of the 2016 Breakthrough Prize in Life Sciencesso bookmark The Official PLOS Blog and visit this site as future scientific prizes are awarded.

 

Image credit: The Lasker Foundation

PLOS appoints Dr. Joerg Heber Editor-in-Chief of PLOS ONE

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PLOS announced today that after an extensive search, Dr. Joerg Heber has been appointed Editor-in-Chief of PLOS ONE. Heber will be responsible for setting the editorial course of the journal and continue its mission of improving scholarly communication. His appointment is effective November 21, 2016.

“Joerg’s deep understanding of scholarly publishing and his passion for Open Access will be tremendous assets to me and our editorial staff, and most importantly to PLOS ONE’s 6,000 Academic Editors and our authors,” said Veronique Kiermer, Executive Editor of PLOS. “PLOS ONE has been a driver of changes in scientific communication since its launch ten years ago. It is an enormous responsibility and I am entirely confident in Joerg’s ability to lead the journal through its next phase, to further develop its mission and meet the needs of the scientific community.”

“I am delighted to be joining PLOS” said Heber. “PLOS’ commitment to Open Access and to innovation has been transformative, and PLOS ONE is ideally placed to support Open Access and open science with continued advancements in scholarly communication. I’m excited to work with the PLOS ONE team to serve science as a whole.”

Prior to joining PLOS, Heber was Executive Editor of Nature Communications. In this role Heber had responsibility for the journal’s overall editorial strategy. He was instrumental in Nature Communications transparent peer review initiative, implementing its Data Availability Statements and contributed to the journal’s move to full Open Access publishing. Heber also worked as a Senior Editor for Nature Materials and his previous experience includes a visiting professorship at the University of Tokyo and lecturer at Philipps-University Marburg, Germany.

Heber obtained his PhD in semiconductor physics at Imperial College London, UK, and did post-doctoral work at Bell Labs, New Jersey.

Riding A Wave Towards Improved Truth in Science Communication

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It is an exciting time in scientific publishing. Initiatives such as digital identifiers for authors through ORCID, more granular recognition of collaborative work with standardized language for specific roles with CRedIT, and more competition in the Open Access publishing world benefit researchers and move the scientific endeavor toward a more transparent and accountable future.

Yet, the write up and publication of results is one of the most challenging aspects of the endeavor, with peer review and reproducibility at the heart of this stage of the research lifecycle. We have previously acknowledged on The Official PLOS Blog that the public

“relies on the belief that content published in peer-reviewed journals is trustworthy, despite the fact that this is too often not the case.”

We have also acknowledged that we must do better: all stakeholders, including publishers, are accountable. Although the overall concept of peer review is an accepted form of quality control and valued by the scientific community, in practice it suffers from imperfections that prevent it from achieving that one great thing: advancing research communication.

In a thoughtful consideration of Truth in Science Publishing: A Personal Perspective, Thomas Sudhof eloquently describes peer review and reproducibility as flawed checkpoints that impair the “validity of published scientific results” and impede trust in science.

As a recipient of both the Nobel Prize and the Lasker Award for his work on synaptic transmission, Sudhof brings perspective and integrity to his thought leadership. Highlighting hidden conflicts of interest, too little accountability for journals and reviewers, and lack of competition between journals as three problems with peer review that have “corrupted the process, decreasing its value,” Sudhof endorses more transparency in the peer review process to reduce bias.

At PLOS there are a range of ways to improve the process without diminishing those aspects that the community values. Current tools and systems that address these limitations include the posting of research to preprint servers before formal publication, to enable researchers to improve their work and share it earlier. There is an opportunity to improve review forms that may be cumbersome or insufficient to provide thoughtful and constructive feedback to authors. Appropriate and rigorous reviewer and editor training can help to mitigate potential reviewer bias and mentor early career researchers. With improved technologies and processes, publishers have an opportunity to improve efficiencies, quality, trustworthiness and authenticity of the process.

As for reproducibility, Sudhof outlines increasingly complex experiments that are impossible to reproduce, “tweaked or selected” results that do not hold up with repetition, lack of validation of reagents and methods, and the “near impossibility” of publishing negative results as contributors to the problem.

Providing opportunity to showcase peer-reviewed articles that address the reproducibility issue is an important value of PLOS and PLOS ONE; the journal welcomes submission of negative, null and inconclusive results. PLOS Biology’s Meta-Research section welcomes experimental, observational, modeling and meta-analyses that address research design, methods, reporting, verification or evaluation.

PLOS Biology and PLOS Genetics authors can contribute to the reproducibility effort by identifying model organisms, antibodies or tools with a unique Research Resource Identifier (RRID). PLOS is a part of the Research Resource Identification Initiative, a cross-publisher effort to promote reproducibility in science and enable effective tracking of the use of particular research resources across the biomedical literature.

PLOS works toward a future where research is published without unnecessary delays, and continual assessment and commentary is provided by a robust and ethical system of visible, engaged pre- and post-publication peer review. We strive to engage a global editorial and reviewer contributor community, appropriately trained, recognized and incentivized. With regard to journal-facilitated peer review, rigorous input from experts in a relevant field of research is highly valued by both authors and readers, and contributes to trust of research results for working scientists, clinicians, patient advocates, policymakers and educators.

Addressing the issues and challenges that perversely incentivize unreliable research or prevent peer review from achieving its scholarly ideal will not be easy or quick. The challenges are substantial and the solutions must be as well, and satisfy a diverse researcher and stakeholder community. Broader adoption of reproducibility efforts and better recognition for the range of contributions made by researchers and reviewers will not be enough without the engagement of early career researchers, junior investigators and senior leadership with the power to influence change.

 

Image credit: one-vibe, pixabay.com

The simple magic of reuse, sharing and collaboration

GoOpen.no -

Two weeks ago I posted a blogg with a timeline of OER. After reading this, my friends in Addis Ababa, Ethiopia picked up the timeline and translated it into Amharic. This involved a different language, different plattform and context. The common thread is H5P, a tool I have blogged about many times before, that allows anyone to create, share and reuse interactive HTML5 content in their browser.

 

The important thing to notice here is that the team in Addis could reuse all the effort that I put in the timeline and at the same time just by translating it the timeline was available in a new language, something that would be impossible for me to do simply because I don´t know Amharic.

There is a growing edTech and OER community in Addis and this last weekend they organized a workshop where they also made their own timeline describing important events in Ethiopian history(see it at the end of the bloggpost). As a part of the same workshop they made an interactive test where you can test your skills on the most common Amharic words.

 

This put me up to the idea that I could make a new resource based on what they have made, and in fact make an OER in Amharic, a languages that I do not master. How? I made all the «cards» in the object below based on text from the team in Addis. Our common ground is that we all understand English.

 

When advocating for Open education resources, open source and open standards the message sometimes is lost in the complexity of all the technical issues. I myself have on more then one occasion struggled to explained the «magic of OER». In this case working with a small usecase like this just seams like a great way to demonstrate the magic of open educational resources.a

Check out this timeline on Ethiopian history:

What can the «anti OER lobby» learn from former Microsoft CEO Steve Ballmer?

GoOpen.no -

Occasionally I bump in to representatives from the «anti OER lobby» and they often start of by talking about how open educational resources ruins the marked, and if the OER is financed with public money they go on about how the government is using their position to compete in the marketplace handing out «free content».

The problem with this claim is of course that it belongs in another paradigme, a paradigme without what we now call «the internet». This is a global issue but we could use Norway as an example. The idea that the Norwegian government, municipalities and counties should not be able to let teachers(with public paycheck) share content on the web under a free license is just ridiculous.

Last week I met a guy from an organization that lobby hard against OER and while talking to him I came to think about Steve Ballmer, former CEO at Microsoft. It was sort of a deja vu moment and it took me back to 2001.

During an interview with the Chicago Sun-Times on June 1, 2001 Ballmer said that «Linux is a cancer that attaches itself in an intellectual property sense to everything it touches»

15 years later Microsoft has shifted their stands completely and invest substantially in open source and even Balmer him self is quoted saying «We now considers that the threat from Linux is over». Current chief at Microsoft Satya Nadella took it even further and went public 2 years ago saying that Microsoft loves Linux.

In the 15 years that has past Microsoft has lost its position in many markets and is now overtaken by Google and Android in the mobile market while Linux dominates everything from the server market to devices running in cars or in the kitchen.

For anyone that has been a part of both the open source movement and the OER movement its obvious that they share principles,  philosophy and methodology.

So my simple question is: What can the «anti OER lobby» learn from former Microsoft CEO Steve Ballmer?

We value “Open” as a fundamental quality in education and in our learning resources.

GoOpen.no -

“Open” produces better outcomes than “Closed”. This gives us a new responsibility. We must now prioritize our time and resources accordingly. The time has come to value “Open” as a fundamental quality in education and in our learning resources. – Head of NDLA, Øivind Høines

The Norwegian Digital Learning Arena (Nasjonal digital læringsarena) is a joint enterprise operating on behalf of the county councils in Norway. Our goal is to develop and publish high quality, internet-based open educational resources (OER) in subjects taught at upper secondary school level and make these freely available.

The term “open” is a cornerstone in all our projects and an important part of our strategy as we develop new subjects and open educational resources. From the beginning in 2007, head of NDLA Øivind Høines and his team started working on how NDLA could build the plattform, content and organization with “Open” as an important quality.

For NDLA as an organization this materializes in four focus areas:

  • Open standards
  • Open source
  • Open interfaces
  • Open methodology
  • Open standards

    A major reason for us at NDLA to use open standards is that we would like our content to be reused and remixed by anyone. By using open standards we aim to make it easier for systems from different parties using different technologies to interoperate and communicate with our content and technology.

    Another important aspect of open standards is to hinder confinement to a single vendor or proprietary technology, and to provide better conditions for free competition between all technology vendors and content creators. Open standards set out to prevent unfortunate interlocking, monopolization and competition bias.

    An important area of focus is the use of standardized protocols and specifications where it is deemed relevant. This is pertinent both in between components internally in the NDLA solution, but also in NDLA’s communication with third-party services.

    A few examples of such standards and specifications:

    • HTML5: a mark-up language intended for the formatting of webpages with links and other information that can be viewed in a browser|, and which is used to structure the information. HTML5 incorporate several new kinds of content (e.g. audio and video) than previous versions than the HTML standard.
    • CSS: Cascading Style Sheets is a mark-up language used to define the layout of files written in HTML or XML.
    • Tin Can: a standardized API for learning technology making it possible to gather data on user experiences. To a larger extent than today, NDLA will be built upon this notion of open standards and known specifications.
    Open source

    Open sources is an important part of all development at NDLA. We have based our plattform on Drupal and contributed significantly to the development of H5P as a platform for easier creation, sharing and reuse of the developed content and applications.

    H5P is not a standard, but an implementation that supports HTML5. H5P is being used for the development of different kinds of interactivity in NDLA. H5P is an open source-based framework for the development of HTML5 based content (video, interactive presentations, multiple choice assignments, timelines, etc.). We are proud to say that more than 2400 websites all over the world now run H5P.

    Why open source?

    Open source software is software that is distributed with the assumption that the source code is being made readily available for reuse. The opposite is software that keeps the source code secret/closed or protected through legislation. The main strategy of NDLA has always been geared towards open source , but in certain contexts it has proven difficult to avoid using third-party products or components that follow other regimes of licencing. In the future, NDLA will go further and demand open source software in all vital parts of a solution.

    Open Interfaces

    We are interested in sharing our content in any way we can. In addition to developing our own website and servise we develop AAPI’s (i.e. application programming interfaces) or open interfaces to make it easier to reuse our content by any third-party.

    By developing and using such open, well-documented API’s, NDLA will facilitate a modularity that deems the solution more service based and flexible to change. Additionally, both the data and the modules become easier to reuse by third-party.

    What is an API?

    API’s (i.e. application programming interfaces) are the interfaces between different software components. API’s link the components together in standardized ways. The API describes what will happen in different circumstances, e.g. finding or saving specific data in a database. An open API is an interface that is openly described, i.e. that is a known matter how it operates so anyone can develop a solution that can link to and benefit from it.

    Open methodology – crowdsourcing

    For us at NDLA, crowdsourcing is an methodology where the individual teacher and pupil can create, co-create and develop content themselves. The concept of crowdsourcing makes it possible for a larger group of people, e.g. teachers, to revise an academic plan, curriculum or the actual content in learning resources.

    Crowdsourcing is a work practice based on voluntary participation, where a large amount of contributors execute a task based on a sense of community, participation and self-organization, rather than managerial control. Numerous actors thus contribute to the improvement of quality on a specific product.

    The word “Open” has for us a pedagogical foundation. Learning as an activity thrives in an open landscape where information is truly liberated and free. We learn better when we freely can participate, when we openly share what we make, when we are allowed to remix the work of others, and our own contributions becomes part a wider and connected society. – Head of NDLA, Øivind Høines.

     

    OER Global Search – makes it easy for you to find open educational resources

    GoOpen.no -

    The last couple of weeks I have been working on a project that I have called OER Global Search. The idea behind OER Global Search is to make it easy for you to find educational resources that allows reuse, re-contextualization and translation.

    It can be very difficult for users to distinguish between what is called Open educational resources and other services that simply provide content for free. Even some websites that use the term Open in their name are not always offering content with a free license. For individuals or projects that plan to change, re-mix or translate content it is important to find OER, not free as in gratis.

    OER Global search solves this by using what is called Google Custom Search targeting 15 to 20 of the most widely used websites that are not only free, but actually offer content with free license.

    The most well known OERs are MIT OpenCourseWare, Khan Academy and CK-12.org. Here is a complete list of the service that are included in the search. http://searchoer.com/list-of- oer.html

    We are seeing a dramatic increase open educational resources covering different subjects at all levels. At the launch of our service a keyword such as “Algebra” returns 387.000 results. The technical development of the service is fairly simple so the main focus will be to develop the search further by identifying good services in different languages.

    The main language on the web is English but we also included some resources languages Hindi, Spanish, Norwegian, Portuguese and French.

    GoOpen Talk with Meredith Jacob

    GoOpen.no -

    In this GoOpen Talk I have a conversation with Meredith Jacob, Assistant Director at American University Washington College of Law. Meredith is a part of the legal team at Creative commons US and a leading expert on IP and Copy right issues. In this videoblogg she talks about the OER situation in American schools and the GoOpen campaign launched by the The U.S. Department of Education.

    GoOpen talk with Meredith Jacob from GoOpen.no on Vimeo.

    Author Credit: PLOS and CRediT Update

    Plos -

    Our January update on author credit focused on how PLOS was moving forward with the use of ORCID identifiers (iDs) for researcher identification. Starting with authors, that effort allows us to know and unambiguously credit who participated in the work being published and forms the base for plans to eventually provide credit to all participants in the research outputs ecosystem. Today’s update is about providing authors attribution for what they contributed. Specific and comprehensive attribution moves the needle for institutions’ and funders’ abilities to evaluate researchers based on the roles they play in published works, rather than on the journals in which their articles appear or their placement within the byline.

    Collaborative Development

    PLOS has for many years required that authors state what contributions they made to their work, as have many other publishers. The author contributions statements published in articles provide transparency in credit and accountability for all authors. What’s new is that there is now a community-developed open-standard taxonomy of contributions intended to replace over time the many disparate lists currently in use.

    PLOS participated along with many other publishers and stakeholders (including funders, researchers and university administrators) in the development of this taxonomy, under the auspices of CASRAI (Consortia Advancing Standards in Research Administration Information) and with the participation of NISO (National Information Standards Organization). Articles in Learned Publishing and Nature – and related documents on the CASRAI site – provide background about the work that led to this open standard.

    Author Benefit

    For a given published work, the CRediT taxonomy makes transparent who participated and the roles they played. It remains simple by design but offers more granularity than previous lists used by PLOS and other publishers. More finely-grained information will help make the ordering of authors less important and will facilitate a shift in focus for tenure and promotion committees – and other evaluators – away from how many times an individual is a first-or last-named author and toward their specific contributions to the scholarly record.

    Importantly, the CRediT taxonomy is not meant to determine who qualifies as an author. Each author on a paper may have one or more CRediT contribution roles, yet having a role described by the taxonomy does not automatically qualify someone as an author. Authorship is determined by following PLOS guidelines, which are based on the ICMJE (International Committee of Medical Journal Editors) requirements.

    As PLOS continues to implement its new submission system, Aperta™, we will make author contributions machine readable, with each individual’s contributions coded into the article’s XML. This is already in place for PLOS Biology, the first journal to launch in Aperta. For every article (identified by a Crossref DOI) and every author (all to be identified – eventually – by an ORCID iD), there will be one or more associated contributions (identified by CRediT). It is the confluence of these persistent identifier systems that will underlie future applications to increase transparency and allow discovery of individual contributions.

    Future Functionality

    Eventually, the coding of individual contributions in article metadata will allow contributions to be surfaced in CVs and researcher profiles. In the short term, it will improve the display of contributions within PLOS articles, currently presented in paragraph form within the article—whether PDF or HTML. The mock-up images here illustrate the approach PLOS is exploring for presentation in the author tab and for roll-over display in the author byline.

    Process and Policy

    The corresponding (or submitting) author will be required to provide the relevant contributions for their co-authors, just as they do now, when submitting a manuscript (see our Authorship Guidelines). We strongly encourage each group of researchers to think about, discuss and decide on their various contributions during the course of manuscript preparation. The task of assigning contributions to individuals should be collegial, and the corresponding author should ensure that contributions are agreed on amongst authors before submission, in the same way that the ordering of authors should be agreed on before submission. The CRediT taxonomy offers a framework for discussion to reach this agreement.

    It’s worth repeating—before submission, decide and get agreement on:

    • Who will be included in the author list
    • What contributions each author has made
    • In what order the authors will appear

    And if there are contributors whose input does not rise to the level of authorship, ensure that proper acknowledgements are included. Every person named – authors and those acknowledged – must be aware of and agree to their inclusion. When preparing your next manuscript, take some time to discuss author contributions using CRediT as a common language. Don’t have an ORCID iD yet? Get one here and log in to the PLOS manuscript submission system with it—when your next article is published with PLOS we’ll automatically update your ORCID record. In the future, that update will also include your contributions.

     

     

    Image Credit: Fabricio Rosa Marques

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