PLoS Currents is expanding

Today, we’re pleased to announce the expansion of PLoS Currents with the launch of two new sections, one on Huntington Disease produced with support from CHDI Foundation, Inc., and the other entitled Evidence on Genomic Tests in collaboration with CDC (Centers for Disease Control and Prevention). Another section called the Tree of Life (focusing on new phylogenetic analyses) is coming soon.

PLoS Currents was launched in August 2009 with a section on Influenza. In his announcement, PLoS co-founder Harold Varmus heralded PLoS Currents as “a new and experimental website for the rapid communication of research results and ideas. In response to the recent worldwide H1N1 influenza outbreak, the first PLoS Currents research theme is influenza”. More than 60 articles have been published in PLoS Currents: Influenza with many articles posted at the height of concerns about the H1N1 pandemic.

The essential goals of PLoS Currents are to minimize the delay between the generation of data and the publication of new research findings, by providing a publication venue where contributions are reviewed rapidly by experts, can be cited so that authors gain the necessary recognition for their work, and are publicly archived so that interested researchers can effectively build on the work of others.  By accelerating the sharing of new findings in this way, PLoS Currents has the potential to accelerate the research cycle itself.

To achieve these goals, there are two key features that make PLoS Currents different, and much faster, than a conventional journal.  First, each section of PLoS Currents is run by a Board of Reviewers – a group of expert researchers led by the Editors of the section.  This group reviews all submissions and determines as rapidly as possible if the conception, structure, and presentation of the submission indicate that it is a legitimate work of science and does not contain any obvious methodological, ethical, or legal violations. As long as the work passes this test, it is published.  Many contributions are published without significant revision, and experts outside of the Board of Reviewers are only rarely consulted during the review process.

The second key difference from conventional journals is that the submissions to PLoS Currents are written and published using a web-based tool, called Google knol.  Authors are in complete control over the content and appearance of their submission, and once it has passed the review process, articles are published immediately under the Creative Commons Attribution License used by all PLoS Journals. Upon publication they are also archived at PubMed Central, where they are given a unique ID, so that the work can be cited.

The Editors for the new section of PLoS Currents on Huntington Disease are Gill Bates (King’s College London, UK), Mike Levine (University of California, Los Angeles, USA) and Sarah Tabrizi (University College London, UK).  The Editors for the new section focusing on Evidence on Genomic Tests are W. David Dotson and Muin J. Khoury – from the Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA.  They have written a nice introduction to the site here. Both sets of Editors are supported by outstanding teams of expert researchers who review the new submissions.

Gill Bates indicated that she has taken on a leadership role in the Huntington disease section because “there is an urgent need to facilitate the publication of a wide range of datasets that currently never see the light of day. The concept of PLoS Currents: Huntington disease has received a great deal of enthusiasm from the HD research community.”  Simon Noble (Director, Scientific Communications, CHDI Foundation) said “The rapid publication of data at PLoS Currents: Huntington Disease that otherwise might not be published in traditional journals will, we hope, accelerate the exchange of scientific data and ideas, enabling investigators to plan research programs with more relevant information at hand. CHDI Foundation is delighted to support this publishing platform, which we think will be particularly important as Huntington disease research gets ever closer to the clinic.”

The CDC also see tremendous potential in the PLoS Currents approach for evaluating genomic tests.  Muin Khoury said “we need a strong evidentiary foundation for the integration of genomics into clinical and public health practice. The new PLoS Currents will fill a much needed niche in authorative synthesis of emerging information on genomic tests”.

We welcome feedback on all aspects of this expansion to mpatterson@plos.org.

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Announcing PLoS Blogs

Today we are pleased to announce the launch of PLoS Blogs a new network for discussing science in public; covering topics in research, culture, and publishing.

PLoS Blogs is different from other blogging networks, because it includes an equal mix of science journalists and scientists. We’re excited to be welcoming our new bloggers, including Pulitzer Prize winner Deborah Blum to the network.

To start things off, we’re delighted that Steve Silberman (a long time writer for Wired, Time, the New Yorker etc) has published a new interview with Oliver Sacks in which for the first time he reveals fascinating details of his personal experience with an ocular melanoma in his right eye and talks about his new book “The Mind’s Eye” which will be published in October and is about vision.

Oliver Sacks, Columbia, 2008

The launch of this network is a natural extension of the support that PLoS has always offered to bloggers in recognition of the excellent work that they do in bridging the gap between scientific and medical articles and mainstream media headlines. For example, we give bloggers access to our Press Releases on exactly the same terms as journalists and we work closely with key figures in the community such as Bora Zivkovic from Blog Around the Clock.

The three existing PLoS blogs: PLoS.org, everyONE and Speaking of Medicine (the PLoS ONE and PLoS Medicine community blogs respectively) can also now be found on this new network. If you are wondering where we got the beautiful image for the PLoS blog header it came from the September 2009 cover of PLoS Biology and is a virtual bead breaking out of its shell – credit is due to: Mark J. Dayel, University of California Berkeley.

Here’s a run down of all the blogs and the excellent people who are working with us:

Our scientists:

Take As Directed:

David Kroll, Ph.D. is a cancer pharmacologist who investigates natural anticancer drugs and is best known under his blog pseudonym, “Abel Pharmboy”. He has appeared regularly on NPR and ABC News Now.

Neuroanthropology:

Daniel Lende, Ph.D. is a medical, psychological, and biological anthropologist.  He worked as an assistant professor in anthropology at the University of Notre Dame and is now associate professor at the University of South Florida. Daniel co-founded Neuroanthropology.net in 2007.

Greg Downey is currently a Senior Lecturer in Anthropology at Macquarie University in Sydney, Australia.  He has published extensively on capoeira (an Afro-Brazilian art form), no-holds-barred fighting, coaching, dance, music etc.

Obesity Panacea:

Peter Janiszewski has a PhD in clinical exercise physiology from Queen’s University in Canada. He’s a science writer/editor, a published obesity researcher, university lecturer, and an advocate of new media.

Travis Saunders is a PhD student in health physiology at the University of Ottawa, who investigates sedentary lifestyles and chronic disease risk in children.

Gobbledygook:

Martin Fenner, M.D. works as a medical doctor and cancer researcher in the Hannover Medical School Cancer Center in Germany.  Since 2007, he has regularly written about how the internet is changing scholarly communication.

GenomeBoy:

Misha Angrist, Ph.D. is Assistant Professor of the Practice at the Duke University Institute for Genome Sciences & Policy. In 2009 he had his full genome sequenced at Duke.

The Language of Bad Physics:

Sarah Kavassalis has a B.S. in physics and mathematics and is currently a graduate student at the University of Toronto. She discusses semi-popular papers that lack an accurate basis in math and physics.

Our science journalists:

Speakeasy Science:

Deborah Blum is a Pulitzer prize-winning science writer and is a Professor of Journalism at the University of Wisconsin-Madison.  Her latest book, The Poisoner’s Handbook, was published in February 2010.

NeuroTribes:

Steve Silberman is a long-time writer whose articles have appeared in Wired, the New Yorker, Salon, Time, and many other national publications all with a Neurological slant.

The Gleaming Retort:

John Rennie is an adjunct professor in graduate Science, Health and Environmental Reporting at New York University.  John was the editor in chief of Scientific American and has appeared on PBS, NPR, ABC etc

Body Politic:

Melinda Wenner Moyer is an award-winning science writer focusing on health and policy, and has a master’s degree in science journalism from New York University. Her work has appeared in Scientific American, Slate, The Oprah Magazine etc.

Wonderland:

Emily Anthes is a freelance science writer and has a master’s degree in science writing from MIT. Her work has appeared in Scientific American Mind, Psychology Today, Popular Mechanics, Discover and elsewhere.

All these excellent bloggers are supported by PLoS Community Manager Brian Mossop. Here’s what he had to say about the launch of this new network (you can read more from him here):

Blogging is generally a force for good because it brings science and medicine to life for a broad audience. PLoS Blogs aims to take scientific and medical communication one step further by doing two things: 1) creating a network that an equal number of science writers/journalists and scientists call home, and 2) building a collaborative environment – both within our blogger network and across the web by featuring content from other blog networks – to make science and medicine more inclusive, and fun

PLoS is built on the principle that the public deserves access to information, which is the heart of the open access movement.  PLoS Blogs will follow suit, not only making its content open access, but by opening up the discussion, and debate, on science and medicine.

We suggest that you review our community guidelines before participating in the debate and we welcome your feedback on all aspects of our new service to bmossop@plos.org.

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Viral Archaeology

A study published in PLoS Pathogens on July 29th shows that human and other vertebrate genomes contain ancient genetic sequences from two often deadly families of RNA virus – Filovirus and Bornavirus – families not previously known to leave genetic material in vertebrate DNA.

Drs. Belyi, Levine, and Skalka compared over 5,000 genes from all known non-retroviral families with single-stranded RNA genomes against the genomes of 48 vertebrate species, uncovering 80 separate viral sequence integrations into 19 different vertebrate species. From this, they were able to identify strong connections in two virus groups – Bornaviruses (found in humans, cows, and lemurs, amongst others) and filoviruses (in guinea pigs, bats, opossums, amogst others) – the latter of which includes Ebola and Marburg viruses.

While it’s still not known how genetic material from RNA viruses (which do not use DNA to replicate) could have entered host DNA, this extensive study presents a significant leap in our understanding of the relationship between the human genome and the traces of viral material which we still carry in our DNA.

The paper has received a wide range of media coverage, including:

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PLoS publication fees held for 2010-2011

We are pleased to announce that we will not be raising the publication fees for any of the PLoS Journals this year. The main reasons for this decision are as follows.

One of key goals at PLoS is to show how open access publishing can be financially sustainable, and PLoS has made substantial progress towards this goal over the past two years in particular. This year, we are on target to achieve modest operating surplus for the first time without any need to adjust publication pricing.

At the same time, we are committed to minimizing the financial burden associated with publishing for all parties involved in the process – including funders, institutions, libraries and the research community. As a not-for-profit organization, we are not in the business of maximizing profits for shareholders or investors. Our broader mission is to drive a comprehensive shift in publishing towards more open and effective research communication.

While we cannot guarantee that we will not need to raise publication fees in the future it is our hope that advances in technology and continued refinement of our cost models will enable us to identify ways to make publishing more cost-effective.

For further information about our general progress, the 2009 PLoS Progress Update covers the highlights of the 2009 fiscal year and includes some details on our current projects.

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Update of the PLoS Journal Websites to Ambra 1.1

We will update the PLoS journal websites with the Ambra 1.1 release tonight along with server upgrades. The PLoS journal websites will be down from approximately 7:30pm PDT to 9:30pm PDT. During this time, the journal websites will display a site maintenance page directing users to PubMed Central.

The features implemented in Ambra 1.1 include:

  • Support for NLM DTD 2.3 and new XSL stylesheets. The single XSL stylesheet has been split into two stylesheets: a generic XSL stylesheet to handle NLM DTD 2.3 and an XSL stylesheet specifically for Ambra.
  • Support for HTML iframes for advertising blocks.
  • Caching of CrossRef search results on the “Find this Article Online” page.
  • Fix to author and editor search facet sorting.
  • Fix to search results for author affiliation.
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PLoS to be at ICOPA, August 2010

We are pleased to announce that PLoS Neglected Tropical Diseases will be attending the XIIth International Congress of Parasitology (ICOPA) in Melbourne, Australia, August 15–20, 2010.

Please be sure to stop by Booth 14 and speak with PLoS staff members Marina Kukso and Donna Okubo, and a few of the PLoS Neglected Tropical Diseases Editors attending, who will answer your questions about publishing in the journal and update you about open-access publishing in general. A sampling of open-access information and PLoS Neglected Tropical Diseases articles, fact sheets, buttons, and our 2010 t-shirt will be available.

We look forward to meeting you!

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Bat viruses, undead viruses, and viral vacations on TWiV


PLoS Pathogens has been a regular feature on This Week in Virology recently, with Pathogens articles being discussed in TWiV episodes 88, 89, and 90.

On Episode 88, Vincent Racaniello and co-hosts discuss the Pathogens paper ‘Reconstitution of an Infectious Human Endogenous Retrovirus’, by Young Nam Lee and Paul D. Bieniasz.

On Episode 89, titled “Where do viruses vacation?”, Vincent Racaniello and Alan Dove discuss the Pathogens paper ‘Global Migration Dynamics Underlie Evolution and Persistence of Human Influenza A (H3N2)’ by Bedford et al.

Most recently, on Episode 90, “Guano Happens”, Vincent Racaniello and hosts discuss the recent Pathogens article ‘Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh’ by Epstein et al.

Download the podcasts here!

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Announcing the PLoS Progress Update

Today, we are happy to share with you our 2009 Progress Update which covers the highlights of the 2009 fiscal year (a calendar year) and some information about what we are working on now. As you may recall, last year we published our first full Progress Report to update our community on our mission, our achievements, and our hopes for the future.

In 2009, PLoS launched new ways to measure research impact; won a prestigious award for publishing innovation; and published many landmark articles that were prominently featured in the world’s leading media and blogs to name but a few achievements.

For 2010, we’ve increased the options for finding PLoS content by improving our Search functionality and members of the development community helped us to go mobile with the introduction of applications for both the iPhone and iPad. We’re currently migrating to a new manuscript submission and review system to accommodate the ever increasing number of articles that we publish.

Everything that we do is thanks to the hard work of our dedicated staff, editorial board members, supporters, authors, users and friends. Without you we could not have come this far, this quickly and we appreciate your ongoing support.

Please feel free to share this with colleagues, friends and family. A high resolution version is available if you wish to print it.

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At last, malaria-free mosquitoes

In a study published on July 15 in PLoS Pathogens, researchers demonstrate how to genetically alter mosquitoes so they no longer transmit the Plasmodium falciparum parasite, which causes malaria in humans.

Dr. Michael Riehle and colleagues at the University of Arizona, along with partners at UC Davis, have managed to alter the mosquitoes’ genome in such a way that the Plasmodium parasite is no longer able to cause infection when ingested in malaria-infected blood. The authors explain that their genetic modification “acts like a switch that is always set to ‘on,’ leading to the permanent activity of a signaling enzyme called Akt. Akt functions as a messenger molecule in several metabolic functions, including larval development, immune response and lifespan.”

Their original intent was to alter the lifespan or growth rate of mosquitoes (Anopheles stephensi, in this case), and this genetic construct has also been shown to reduce an insect’s lifespan by up to 20%. Most importantly, this altered genetic information is passed on to later generations – if the malaria-resistant mosquitoes can be provided with additional evolutionary advantages and released into the wild (a controversial topic), they could potentially out-perform and eventually replace the malaria-infected wild mosquitoes.

The study has received a wide range of media coverage, including:

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PLoS ALM Data in Google Fusion Tables

Google Fusion Tables is a new Google labs endeavor that allows people to upload data tables from spreadsheets for sharing and visualizing data online. Google provides the Fusion Tables API for programmatic access to the data content. The PLoS Article Level Metrics data from May 18, 2010 was uploaded to Google Fusion Tables and is publicly available.

The Google Fusion Table links to the PLoS Article Level Metrics data are:

You can compare this data to the PLoS ALM data that was uploaded to Many Eyes in October 2009 and put into some nice visualizations by Mike Chelen.

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