Public Library of Science - Publishing

Announcing a new PLoS Collection, Tagging of Pacific Predators (TOPP)

Liz Allen — Thu, 14 Jan 2010 14:00:14 -0800

Today, PLoS is delighted to publish a Collection of articles highlighting biologging research from the Tagging of Pacific Predators group (TOPP), a Census of Marine Life (COML) project.

Advances in electronic marine tracking technology, also known as biologging, allow researchers to take measurements from free-swimming marine animals as they move undisturbed through their environment. Recent technology improvements, including electronic tag miniaturization and enhanced animal movement models, have revolutionized understanding of the ecology of marine top predators. This has permitted observations well beyond the reach of standard measurement techniques, and provided extensive data on the animals' behavior at the scale of and within the context of their environment. Such studies are essential for the effective management of marine ecosystems and conservation of top predator populations.

The first six articles (five from PLoS ONE and one from PLoS Biology) to be published in this Collection have examined how our understanding of animal movement and migration has been improved by electronic tagging and tracking across a diverse range of marine species including sharks, tunas, sea birds, sea turtles and marine mammals. More work will be added to this "living" collection as soon as each TOPP article is published.

In the coming months, PLoS will be publishing more Biodiversity research from other groups that make up the Census of Marine Life, a 10 year project to explore and understand the diversity and distribution of life in the oceans, past, present and future. In this so called "transparent ocean" scientists will have the tools to say where marine organisms are, how many of them there are and where they are going - knowledge which will help mankind best conserve and support these precious resources.

Here's what Dr Randy Kochevar, TOPP Marine Biologist and Science Communicator, said about his experience of working with PLoS on this collection: "TOPP is a broad, interdisciplinary program - and it's fantastic to have a range of articles represented in this PLoS collection, freely accessible online to the world thanks to open-access publishing. We are excited about the media coverage this exposure has brought us and we look forward to adding to the collection in the future – we would encourage other groups within the COML community to publish their work in PLoS ONE. They really are a pleasure to work with.”

Other member groups of COML who also want to work with PLoS to create a collection are encouraged to contact Pete Binfield (pbinfield@plos.org), the Publisher of PLoS ONE and the Community Journals for more information.

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PLoS Author Surveys 2009 – Summary Presentation

Mark Patterson — Wed, 23 Dec 2009 02:45:25 -0800

Earlier this year, PLoS sent out a series of surveys to authors whose work was considered by our journals in 2008. We wanted to find out what authors think about all aspects of our services – from submission and peer review, through to publication and the functionality of the PLoS journal web sites.

We have learned a lot from the surveys, primarily that levels of satisfaction amongst authors are generally very good. We also identified areas where services can be improved, and we’ve adjusted our services in a number ways during 2009.

We have now summarized the results of the surveys along with how we have responded to some of the suggestions during 2009 in a short presentation, which is publicly available. We feel it’s important to share these results in particular with the authors who were kind enough to complete the questionnaires, and we would like to express our thanks to the hundreds of authors who took part. We are planning to repeat the surveys next year, so that we can monitor how views have changed and can respond to suggestions for further improvements.

Meanwhile, we welcome feedback from anyone who is using our services, as an author, reviewer, editor or reader.

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New addition to Article-Level Metrics - blog posts from ResearchBlogging.org

Liz Allen — Thu, 17 Dec 2009 11:19:50 -0800

Throughout the course of 2009, PLoS has been adding a range of Metrics to each and every article that it has published. In addition to the many metrics already displayed (article pageviews and downloads, citations, social bookmarks, notes, comments and ratings), we are pleased to now add data relating to the blog coverage of any article, as measured by ResearchBlogging.org. You can find out more about the Article Level Metrics program here.

Every interested author and user can now see how many times an article has been downloaded (split into HTML Pageviews, PDF and XML downloads and displayed in a month-by-month format); how often an article has been cited (as measured by PubMed Central, Scopus and CrossRef); how many times it has been ‘socially bookmarked’ (at CiteULike and Connotea); how many times users have Commented, or left Notes, or provided Ratings; and how many blog articles have been written about it (as measured by the blog aggragators Postgenomic, Blog Lines, Nature Blogs and, from today, ResearchBlogging.org).

We've created a 2.4 minute screen shot video (with audio commentary) that you can watch to familiarize yourself with the blog aggregation functionality from ResearchBlogging.org so you can see for yourself the benefits of this part of the Article-Level Metrics program.

On launching this new functionality, Pete Binfield, Publisher of PLoS ONE and the Community Journals said:

"We're delighted to add data from ResearchBlogging.org to the Article Level Metrics program because the blogs that they index are mainly written by practicing scientists, who are well versed at providing readable summaries of the research that we publish".

Bloggers who regularly write about scientific research are able to register with ResearchBlogging.org and (provided they qualify) they are then entitled to indicate that their blog entries refer to peer reviewed scientific research by adding an icon to their posts. As a result, the ResarchBlogging.org service represents a high quality source of highly relevant articles, typically written by practicing scientists, on the topic of peer reviewed research. Since all PLoS content is peer reviewed and free to read, PLoS articles tend to be regularly covered by their bloggers. You can find the current list of qualified ResearchBlogging.org bloggers here.

Dave Munger, the co-founder of ResearchBlogging.org, said:

"We’re pleased to be working with PLoS to assess the impact of its articles. PLoS journals do a great job publishing and making research accessible to everyone, and we think coverage in thoughtful blog posts is an important component of the impact of a peer-reviewed journal article". You can read more in this blog post.

PLoS ONE and ResearchBlogging.org also collaborate on a monthly "Blog Pick of the Month" competition that we feature on everyONE, the PLoS ONE community blog. Every month, Bora Zivkovic, the Online Discussion Expert for PLoS, chooses the best blog about a PLoS ONE article that has appeared in ResearchBlogging.org and we feature it on our blog. The winning blogger and all the authors of the original PLoS ONE research article all win t-shirts. To enter, you simply need to be a ResearchBlogging.org blogger and start writing about PLoS ONE articles.

We welcome feedback and questions on any aspect of this program to alm@plos.org.

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Send PLoS a postcard from PSB

Cecy Marden — Thu, 10 Dec 2009 05:05:33 -0800

If you are attending the Pacific Symposium on Biocomputing (PSB) PLoS Computational Biology invites you to send us a postcard! PLoS Conference Postcards represent a novel way to report important innovations and current research efforts presented at a scientific conference as told by upcoming members of the scientific community. Your “postcard” will focus on one of the highlights of PSB – a keynote, paper presentation, poster session, software demonstration, or tutorial. All Postcards will be considered by the Editors and those selected will be published in PLoS Computational Biology as part of an article summarizing the conference.

If you would like to submit a Conference Postcard, here is what you need to know:

Any postdoctoral fellow or graduate student is eligible to be a reporter. Reporters may submit more than one report for consideration, but each report may only have one author.
Your Conference Postcard should be between 800-1000 words; you may submit a maximum of one image. If the image is under copyright it is your responsibility to gain explicit permission to republish under the CCAL from the copyright holder.
You should include:

A synopsis of what was presented.
Reasons why you think your chosen highlight is outstanding.
How it related to the theme of the meeting.
The impact it had on attendees.
Additional references considered useful.

Any presentation at the conference deemed to be of exceptional significance to the broader community by the reporter is eligible to be reported. No permission from speakers is required beyond those obtained by PSB as regards live and postconference coverage of presentations. Please do not submit reports on presentations given by a close colleague.
Preference will be given to reports that demonstrate evidence of additional research into the topic to support or counter the work presented, e.g., views of the work by other attendees gathered through personal interactions or blogs or information based on further discussions with the presenters.
Reports accepted by the Editors for publication will be presented as a single article with author ordering determined by the PLoS Editors. PLoS Editors may request that the reporters make (generally minor) changes to the selected reports.
As with all PLoS content, the Conference Postcards will be published under the Creative Commons Attribution License (CCAL) Agreement; made freely and fully available immediately upon publication; and deposited in PubMed Central and indexed in PubMed.
Your submission should be sent to contribute [at] plos.org with the report in the body of the email or attached as a Word document. Please list “PSB Postcards” as the subject of your email. Please list your name, institution, and the title of the session being reported.
The closing date for submissions is: January 14th 2009

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This Week in Virology features another PLoS Pathogens article

Patrick Reilly — Mon, 7 Dec 2009 10:14:28 -0800

On the Dec. 6th TWiV podcast, Vincent Racaniello and Dickson Despommier discuss the symbiotic bacterium Wolbachia, the origin of the 2009 influenza H1N1 virus, and 'the lure of original antigenic sin.'

In the course of this podcast they discuss not only the recent PLoS Pathogens article "Variation in Antiviral Protection Mediated by Different Wolbachia Strains in Drosophila simulans", but articles from PLoS Biology and PLoS Neglected Tropical Diseases as well:

PLoS Biology - "The Bacterial Symbiont Wolbachia Induces Resistance to RNA Viral Infections in Drosophila melanogaster"

PLoS Neglected Tropical Diseases - "Wolbachia Infection Reduces Blood-Feeding Success in the Dengue Fever Mosquito, Aedes aegypti"

Download the podcast here!

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PLoS Genetics Publishes Maize Genome Collection

Catherine Nancarrow — Fri, 20 Nov 2009 14:50:42 -0800

2009 PLoS Genetics Maize Genome Collection PLoS Genetics is pleased to announce the launch of the 2009 Maize Genome Collection.

Maize is an important crop in many countries of the world. It is used widely for human consumption, animal feed, and industrial materials. It is also considered an exemplar plant species for studying domestication, molecular evolution, and genome architecture. The authors of the research presented in this special collection used the first description of the B73 maize genome to probe some of the most intriguing questions in genetics and plant biology. The ten papers consider maize centromeres, new insights into transposon types and distribution, the abundance of very short FLcDNAs encoding predicted peptides, and many other “genetic jewels”.

Each peer-reviewed article, as well as Virginia Walbot’s editorial introducing the collection, is available online now at the PLoS Genetics website.

Editorial:

10 Reasons to be Tantalized by the B73 Maize Genome Walbot V

Research Articles:

The Physical and Genetic Framework of the Maize B73 Genome Wei F, Zhang J, Zhou S, He F, Schaeffer M, et al.

A Genome-Wide Characterization of MicroRNA Genes in Maize Zhang L, Chia J-M, Kumari S, Stein JC, Liu Z, et al.

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome Wei F, Stein J, Liang C, Zhang J, Fulton RS, et al.

A Single Molecule Scaffold for the Maize Genome Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, et al.

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, et al.

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, et al.

Loss of RNA-dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, et al.

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-localize with Epigenetic Marks for Open Chromatin across the Maize Genome Liu S, Yeh C-T, Ji T, Ying K, Wu H, et al.

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome Baucom RS, Estill JC, Chapparro C, Upshaw N, Jogi A, et al.

Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo DH, et al.

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Schedule of PLoS Pathogens and PLoS NTDs-Related Activities at ASTMH

Mary Kohut — Tue, 17 Nov 2009 12:34:44 -0800

Staff and editors of PLoS Pathogens and PLoS Neglected Tropical Diseases are heading to the ASTMH Meeting this week (Nov. 18-22). Please consider attending the following PLoS journal-related activities and be sure to visit us at Booth 501 to pick up giveaways and meet the team.

THURSDAY 11/19

3:15-3:45pm – Meet the Editor (Booth 501) - Xinzhuan Su, Associate Editor, PLoS Pathogens

FRIDAY 11/20

9:45-10:15am – Meet the Editor (Booth 501) - Kasturi Haldar, Editor-in-Chief, PLoS Pathogens
12:15pm – Preparation and Review of Scientific Manuscripts for the American Journal of Tropical Medicine & Hygiene (Delaware B) - James Kazura, Section Editor, PLoS Pathogens
1:30-3:15pm – Special Session: The Global Burden of Anemia: Bridging Pathogenesis and Pathology (Delaware B)

Session Organizer: Kasturi Haldar, PhD, Editor-in-Chief: PLoS Pathogens

Co-Chair: Peter J. Hotez, MD, PhD, Editor-in-Chief: PLoS Neglected Tropical Diseases

Speakers: Jennifer Friedman, MD, MPH, PhD and M. Boele van Hensbroek, MD, PhD

Anemia is a major disease pathology associated with a variety of infections, malnutrition, and poverty. Assessing the global burden of anemia is critical to revealing the major causes and evaluating mechanisms of intervention. Parasitic infections are significant contributors to anemia, and linking parasite genomics and biology to pathologies of anemia is urgently needed for effective vaccine development in many parasitic diseases. This requires understanding the complexities of pathogenic mechanisms, acute and chronic anemia, and treatment strategies. This symposium will bring together strategies in measuring anemia due to distinct infectious agents, underlying mechanisms of anemia with implications for vaccine development as well as the utilization of model systems to understand human disease.

1:30pm – Targets and Mechanisms of Acquired Immunity to Malaria (Salon 1)- James Kazura, Section Editor, PLoS Pathogens
7:15pm – Malaria Genomics and Postgenomics Update (Salon 3) - Xinzhuan Su, Associate Editor, PLoS Pathogens
SATURDAY 11/21
- 8:00am – Central Role of Macrophages in Parasite Immunity (Salon 1)- Tom Wynn, Section Editor, PLoS Pathogens
- 9:45-10:15am – Meet the Editors (Booth 501)-Maria Mota, Associate Editor, PLoS Pathogens; Tom Wynn, Section Editor, PLoS Pathogens
- 12:15-1:15pm – Workshop on Manuscript Preparation: How to get your work published (Delaware A)
- 3:45pm – Vivax Malaria Research (Washington 5) - Maria Mota, Associate Editor, PLoS Pathogens
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Feed your PLoS t-shirt obsession - announcing the new PLoS store

Liz Allen — Mon, 16 Nov 2009 15:14:47 -0800

Today, we're delighted to announce that the official PLoS Store is open for business - in time for the holidays. With a large range of t-shirts (including some designed specifically for the season of good-will) and other merchandise, you can let us solve your shopping nightmares. We would encourage all of you to shop the store, spread the word and support our cause.

The PLoS t-shirt phenomenon was started by co-founders Pat and Mike who know that in the lab, comfort is everything. They started producing cool and funky t-shirts to get the word out about PLoS and soon folks started to ask them when new designs would be available.

Realizing this was a popular and unstoppable trend, PLoS started using t-shirts to say thanks to the community for their involvement on our editorial boards. We also gave them away at conferences because it made people flock to our booth and we wanted to talk to them about open access and publishing with us. PLoS will continue to offer free t-shirts to the community - using store revenue to offset some of these costs.

The only problem was that the more popular our t-shirts became, the more labor-intensive life was getting at PLoS's San Francisco office. Often times, Allison, our Marketing Project Manager, had to organize top notch editors and publishers to stuff t-shirts by hand into envelopes (their only compensation was free pizza). On the busiest days, it felt like we had turned into a t-shirt supply company. Something had to give.

Enter Stacy, our new Marketing Intern, with a background in Information Science, a love of PLoS and Open Access, and a burn to learn. Within days of joining, she had selected Zazzle.com, the well respected on-demand merchandise company, as the right partner for PLoS - she even visited their head offices in Redwood City and grilled them for a few hours to make sure they were up to the task. Their 100% satisfaction guarantee, good product reviews, excellent client support, and localized websites that enable lower delivery costs (available in the UK, Germany, New Zealand, Australia, Canada) also convinced us that this was the right decision.

Having customized the PLoS store herself, in partnership our creative team, Stacy then embarked on a series of product sample tests which involved other members of PLoS taking t-shirts home, wearing and washing them and then reporting back on how well they held up (very nicely).

The final result is a PLoS store that has been as rigorously tested as possible with a pretty extensive product range (including hoodies, kids wear, organic, and fitted women's shirts). Every product is created digitally just for you.

We sent a link to the prototype store to a group of trusted community testers, including Kevin Zelnio, a researcher at the Marine Conservation Molecular Facility at Duke University’s Marine Lab who also blogs on Deep Sea News, the Online Laboratory, and The Other 95%, here's what he said when he saw the store:

"The store looks great, really professional and clean. The designs are strong too. My first reaction was that I was ready to buy the Open Access t-shirt. I like the logo and it makes a statement on a subject dear to my heart. Although I really want a PLoS ONE shirt too. It operates and transitions well, had no hiccups. Being able to choose from a few different colors, and to zoom in on designs is fabulous".

It's worth knowing that there is only one official PLoS store and it contains images and logos that have been approved by the organization. However, if you search on Zazzle for PLoS you will find products bearing our name that have been created by other individuals because Zazzle allows anyone to start their own store and feature their own designs. You are welcome to shop where you wish but only the official PLoS store contains our approved merchandize.

The plan is to introduce new designs as and when they become available, increase the product range (my son is waiting for the PLoS skateboard), load up cover images, introduce more user customization and make improvements based on your e-mail feedback which we welcome to store@plos.org.

Happy shopping!

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Dr. Vincent Racaniello – New Community Editor

Mary Kohut — Mon, 16 Nov 2009 10:31:13 -0800

PLoS Pathogens is pleased to announce a new partnership with Dr. Vincent Racaniello, co-creator of the weekly podcast “This Week in Virology” (www.twiv.tv). Dr. Racaniello, a virologist and Professor in the Department of Microbiology & Immunology at Columbia University, is the newest member of the journal’s Community Editor Section.

Listen to the November 15 podcast “Nipah virus in ferrets”, which discusses the recent PLoS Pathogens article “A Neutralizing Human Monoclonal Antibody Protects against Lethal Disease in a New Ferret Model of Acute Nipah Virus Infection.” Previous TWiV episodes covering PLoS Pathogens articles include: “XMRV”, “No Hysteria”, and “Much achoo about nothing”.

Watch for future blog posts, announcing new TWiV episodes that feature published articles and community members relative to PLoS Pathogens.

About the Community Editors

PLoS Pathogens Community Editors foster scholarly dialogue within the community of host-pathogen researchers. These editors aim to engage readers, authors, editors, and colleagues in discussions around published works in the journal, Open Access, hot topics in the media, experts in the field, and more.

About TWiV

Begun in September 2008, This Week in Virology (TWiV) is a podcast about viruses, hosted by Columbia University Medical Center professors Vincent Racaniello and Dick Despommier. The weekly podcast covers recently-published works from various journals, media hype, researcher profiles, and more – all in an informal yet informative conversation aimed at being accessible to everyone, regardless of science background.

About Dr. Racaniello

Vincent Racaniello, Ph.D. is Professor of Microbiology at Columbia University Medical Center. He has been studying viruses for over 30 years, starting in 1975, when he entered the Ph.D. program in Biomedical Sciences at Mt. Sinai School of Medicine of the City University of New York. His thesis research, in the laboratory of Dr. Peter Palese, was focused on influenza viruses. Over the years, his own laboratory has studied a variety of viruses including poliovirus, echovirus, enterovirus 70, rhinovirus, and hepatitis C virus. As principal investigator of his laboratory, he oversees the research that is carried out by Ph.D. students and postdoctoral fellows. He also teaches virology to graduate and undergraduate students, as well as medical, dental, and nursing students. For more information on both Dr. Racaniello and TWiV, please see here.

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PLoS at ASTMH 2009 - Booth 501

Shabnam Sigman — Fri, 30 Oct 2009 14:20:32 -0700

PLoS is getting ready for this year's ASTMH meeting (Washington, D. C., November 18–22), where you’ll find us at Booth 501 in the exhibition hall.

Meet editorial team members from PLoS Neglected Tropical Diseases and PLoS Pathogens who will be on hand to answer questions about publishing your work with PLoS, open access, and article-level metrics.

Editors-in-Chief Peter Hotez and Serap Aksoy (PLoS Neglected Tropical Diseases) and Kasturi Haldar (PLoS Pathogens) will be at the booth at selected times along with other journal editors and PLoS staff members Shabnam Sigman (Publications Manager, PLoS Neglected Tropical Diseases) and Mary Kohut (Publications Manager, PLoS Pathogens). Visit Booth 501 for the schedule.

Pick up some great giveaways:

T-Shirts—for delegates who sign up to receive free e-mail content alerts. This year’s shirt, with its unique design, is available only at this event, so be sure to stop by, sign up, and claim yours while supplies last.
Buttons/Badges—designed for our authors, Editorial Board members, readers, and supporters.
Fact Sheets—that showcase the Editorial Boards and top papers.
Postcards— to remind yourself and your colleagues why you should publish with PLoS.

We look forward to welcoming ASTMH 2009 delegates to our booth!

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