Altmetrics: Tracking scholarly impact on the social Web – PLoS ONE Collection

The huge increase in scientific output is presenting scholars with a deluge of data.  There is growing concern that scholarly output may be swamping traditional mechanisms for both pre-publication filtering (e.g. peer review) and post-publication impact filtering (e.g. the Journal Impact Factor).

Increasing scholarly use of Web 2.0 tools like CiteULike, Mendeley, Twitter, and blogs presents an opportunity to create new filters.  Metrics based on a diverse set of social sources could yield broader, richer, and timelier assessments of current and potential scholarly impact.  Realizing this, many authors have begun to call for investigation of these metrics under the banner of “altmetrics.”  Specifically, altmetrics is the creation and study of new metrics based on the Social Web for analyzing and informing scholarship.

Despite the growing speculation and early exploratory investigation into the value of altmetrics, there remains little concrete, objective research into the properties of these metrics: their validity, their potential value and flaws, and their relationship to established measures. Nor has there been any large umbrella to bring these multiple approaches together.

Following on from a first successful workshop on altmetrics, this collection aims to provide a forum for the dissemination of innovative research on these metrics.

We seek high quality submissions that advance the understanding of the efficacy of altmetrics, addressing research areas including:

  • Validated new metrics based on social media.
  • Tracking science communication on the Web.
  • Relation between traditional metrics and altmetrics including validation and correlation.
  • The relationship between peer review and altmetrics.
  • Evaluated tools for gathering, analyzing, or disseminating altmetrics.

Papers will be reviewed on a rolling basis in-line with PLoS ONE standard practices.

Please note that all submissions submitted before January 28th, 2012 will be considered for the launch of the collection (expected spring 2012); submissions after this date will still be considered for the collection, but may not appear in the collection at launch.

Submission Guidelines

If you wish to submit your research to the Altmetrics: Tracking scholarly impact on the social Web Collection, please consider the following when preparing your manuscript:

– All articles must adhere to the PLoS ONE submission guidelines.

– Standard PLoS ONE policies and publication fees apply to all submissions.

– Submission to PLoS ONE as part of the Altmetrics Collection does not guarantee publication.

When you are ready to submit your manuscript to the collection, please log in to the PLoS ONE manuscript submission system and insert ‘Altmetrics’ in the relevant field to ensure the PLoS ONE staff are aware of your submission to the Collection.  Once you have registered, you can follow the steps for manuscript submission.

Please contact Lindsay King (lking@plos.org) if you would like further information about how to submit your research to the PLoS ONE Altmetrics Collection.

Organizers:

Paul Groth, VU University Amsterdam

Dario Taraborelli, Wikimedia Foundation

Jason Priem, UNC-Chapel Hill

About PLoS ONE

PLoS ONE (eISSN-1932-6203) is an international, peer-reviewed, openaccess, online publication.  PLoS ONE welcomes reports on primary research from any scientific discipline.

It provides:

  • Open-access – freely accessible online, authors retain copyright
  • Fast publication times
  • Peer review by expert, practicing researchers
  • Post-publication tools to indicate quality and impact
  • Community-based dialogue on articles
  • Worldwide media coverage
  • PLoS ONE is published by the Public Library of Science (PLoS), a nonprofit organization.

The “responsible conduct of research” is not limited to properly obtained consent

Today we published the article,Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results, by Wicherts et al. In the manuscript, the authors show that weaker evidence in a psychology paper published in a journal requiring signed agreements to share data is associated with a failure to comply with this signed agreement to share.

Rochelle Tractenberg

In the following opinion piece, Rochelle Tractenberg, the academic editor who handled the peer review of Wicherts et al., discusses the ways in which “research ethics” and the “responsible conduct of research” go beyond human subjects protection, to include data sharing, professional conduct, and the careful, correct and complete reporting of all analyses in published research.  Rochelle is a biostatistician and research methodologist at Georgetown University.

The article by Wicherts et al. describes their study of 1148 “statistically significant results” that were published in 49 different papers within two psychology journals. As it was being reviewed and revised, this paper sparked a vigorous debate among PLoS ONE editors and reviewers for two very different, ethics-oriented, reasons. These reasons were:

  1. Disciplines differ in their requirements that data analyzed and published should be made available to any scientist that requests the data. In some cases, the data cannot be properly de-identified, which violates a key feature of human subjects protections that all scientists are supposed to commit to whenever they carry out scientific work involving living persons. The Ethics Committee of the authors’ institution explicitly required them NOT to publicize the authors who refused to share data – and whose work was identified as being weak in terms of evidence and/or quality of results.
  2. The readers of published work are totally dependent on the quality and accuracy of the statistical results presented –and described – in any manuscript they wish to utilize as evidence in their own argument or scientific endeavor. The option to re-analyze data is critical to check the reliability of published designs, results, or conclusions. Time is a precious commodity; knowing what work is most likely to require replication prior to its use would limit our reliance on work likely to include mis-analyzed data, misinterpreted results, or both.

These considerations highlight diverse conceptualizations of the “responsible conduct of research”: in the first conceptualization, the protection of human subjects –the authors who did and did not share their data, whose published work was analyzed in this paper – is the sole concern. The second conceptualization involves the responsibility of the authors of the reviewed published papers to fulfill their professional ethical obligations as well as their contractual agreements. Wicherts et al. did obtain permission from their Ethics Committee to provide a list of authors who failed to share data – if specifically requested, but are NOT permitted to identify which authors were compliant and defiant within their paper, nor to place their data file, as is, into a public archive. Wicherts et al. analyzed the contents of published articles, and then requested the data these papers represented. The journals’ and APA ethics policies are public and require data sharing, so neither the requests nor the failures to comply with those requests can be considered privileged. In short, no feature of the data in this manuscript can be considered to be privileged. The responsible conduct of research is much more than protecting study subjects and obtaining informed consent, but the Ethics Committee did not act like it is.

As the editor shepherding this article through the review process, I applaud the effort by Wicherts and colleagues, and disagree with the Ethics Committee decision. I believe that every journal should document requests for data and the failures of authors to provide the requested data as part of the publication record. This compliance information should be accessible to all reviewers for journals and grants, and to scientists who look to the published literature for replicable, reliable, ethically obtained results.

A prior report by Wicherts et al. in 2006 found that, while journals published by the APA all require authors to sign an agreement to share their data, 73% of authors who were contacted for that study failed to do so. These 73% defied their written agreement, and professional obligation (see APA Ethical principle 8.05), to share their data. This is not responsible conduct of research; this is unethical behavior and every scientist is entitled to know whether or not an author is responsible in their conduct –and reporting – of their research. As critical as these features are to responsible conduct of research, the review of manuscripts and grants for “ethical considerations” cannot be limited to the inclusion of women and minorities, balance between male and female subjects, and properly obtaining informed consent.

Wicherts et al. conclude that policies for data archiving should be strengthened/more widespread, even though their 2006 findings that, in defiance of their signed agreements, the journals’ publishing policy, and the professional association policy on data sharing, nearly ¾ of APA published authors refused to share data when contacted. In their current study, the refusal rate was “only” 57%.

A survey of geneticists working at 100 universities in the US led to an estimate of 47% failure to share. The challenge is clearly widespread and has a prevalence rate in the 47-73% range. By contrast, in her survey of the prevalence of “unethical” or “questionable” scientific behavior, Fanelli arrived at far smaller estimates – possibly because of a lack of awareness among her respondents that a failure to share data or research resources constitutes irresponsible –not merely questionable – research practice.

A broader appreciation of how critical transparency and replicability are for good science could support the cultural shift necessary to promote the idea that the “responsible conduct of research” is not limited to properly obtained consent. A mechanism for documenting failures in these key features of responsible conduct of research would also support this shift. Every reviewer should have this information about the likelihood that an applicant or author will violate sharing policies and/or defy contracts they’ve signed and/or professional ethical science standards they should be held to.

The responsible conduct of research includes conscientious protection of human subjects. In the book, “Scientific Integrity”, Macrina  also notes, “(s)haring research materials published in the peer reviewed literature has been a traditional practice that follows from the expectation that scientific research must be amenable to replication” (p. 81) and that “…written communication is an essential part of scientific research.” (p. 83) (see also National Research Council, 1992; Board on Life Sciences, 2003). As such, these should be just as conscientiously executed as other aspects of the research enterprise. Refusals to share data harms science and constitutes violations of our obligations to be responsible conductors of research.

Rochelle Tractenberg has also written a companion piece to this article, which can be found in the comments section of the Wicherts et al. manuscript.  In the second piece, she interprets the association between weak evidence and failures to comply with data sharing requirements in a different way. Instead of supporting mandatory archiving of data, Dr. Tractenberg concludes that readers and reviewers of manuscripts and grant proposals should be notified of the author’s/applicant’s history of compliance with data sharing mandates and policies. She believes that such documentation will do more to change the culture towards one promoting science and data sharing than mandatory data archiving. To read this post, please click here.

References

Board on Life Sciences (2003). Sharing Publication-Related Data and
Materials: Responsibilities of Authorship in the Life Sciences.
Washington, DC: National Academy Press.

Campbell, E. G., Clarridge, B. R., Gokhale, M., Birenbaum, L.,
Hilgartner, S., Holtzman, N. A., et al. (2002). Data withholding in
academic genetics: Evidence from a national survey. Journal of the
American Medical Association, 287, 473–480.

Fanelli D (2009) How Many Scientists Fabricate and Falsify Research? A
Systematic Review and Meta-Analysis of Survey Data. PLoS ONE 4(5):
e5738. doi:10.1371/journal.pone.0005738

Macrina FL. (2005). Scientific Integrity: Text and Cases in
Responsible Conduct of Research, 3E. Washington, DC: American Society
for Microbiology Press.

National Research Council (1992). Responsible Science, Vol 1: Ensuring
the Integrity of the Research Process. Washington, DC: National
Academy Press.

Wicherts JM, Borsboom D, Kats J, Molenaar D (2006) The poor
availability of psychological research data for reanalysis. American
Psychologist 61:726-728.

Wicherts JM, Bakker M, Molenaar D (2011) Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results. PLoS ONE 6(11): e26828. doi: http://dx.plos.org/10.1371/journal.pone.0026828

How to Use PLoS’s Advanced Search Function

This post was written by Michael Morris. Michael is a Publications Assistant for PLoS Medicine with a Master of Library Science degree. His previous experience in the library field led to an interest in information literacy and instruction. The following piece was posted on Speaking of Medicine yesterday.

At PLoS, we’re dedicated to the tenet of Open Access, making academic literature widely available on the web. However, with an ever-growing pool of scientific literature, our goals have to consider not only making content available, but also accessible. With the breadth of articles we aggregate, you need a strong tool to find the specific information you want. Our authors have published on methods to get the most out of search engine queries and even how search engine data can yield its own important results. To help our users navigate the sea of information PLoS publishes daily, we introduced an Advanced Search function with a broad range of filters.

When searching for PLoS articles, the standard search bar at the top of the page will return all results where the term has been mentioned throughout the entire article (see Figure 1). While this is good for very specific searches, a search for a term like “influenza” will yield over 2,000 results across the PLoS journals. This is where the Advanced Search’s filtering system comes in handy.

Figure 1

Advanced Search

Advanced Search provides multiple filters for results by limiting what field you’re searching (Title, Abstract, Author Name, etc). Using the pull-down menu (Figure 2), you can search for your term in the Title or Abstract of the article, which makes it more likely that the article is focused on that subject. You can also search for specific authors, editors or author affiliations. This allows you to find papers published or edited by your colleagues or researchers at a specific institution.

You can make your search more targeted and powerful but using the search box to combine these different searches using the qualifiers AND, OR or NOT, limiting the search results further. For example, you can shorten the results by saying you want articles that mention “influenza” in the abstract, but NOT “vaccine.”

Figure 2

Advanced Filters

Below the search block is a series of filters that allows you to limit your results further: Journal, Subject Category and Article Type (Figure 3). This allows you to filter the search results down to specific PLoS journals, or a subject area you are studying (e.g., Genetics of Disease or Systems Biology) or down to a particular article type, like Research Articles or Editorials.

Figure 3

Sorting Results

After performing the search, you can sort the results using an additional drop-down menu, found at the top of the search results. “Relevance” is the default setting, but you can also sort by Most Viewed, which will yield the most popular article by page views meeting your search criteria, and Date—so you see the newest items that have published since the last time you performed your keyword search.

Related to the sorting types, each search result features links its Views, Citations and Bookmarks. Hovering over these links provides a breakdown of each statistic. Views will be broken down to the number of views in each format (HTML, XML and PDF) and Citations will break down by databases the citations are listed in (e.g., PubMed Central or Web of Science®) (Figure 4).

Figure 4

In addition to publishing the highest quality scientific research, PLoS is dedicated to making our content accessible to our audience. Our team is always working to find new ways to assist the readers of our journals, and we hope that our Advanced Search will get you the information that you seek.

Halloween Highlight 2011: An Author Spotlight with David Hughes and Harry Evans

Zombie ant jack o' lantern

In the spirit of Halloween, we’ve asked Dr. David Hughes of Penn State University and  Dr. Harry Evans of  Federal University of Viçosa Brazil to share with us a bit about their manuscript, Hidden Diversity Behind the Zombie-Ant FungusOphiocordyceps unilateralis: Four New Species Described from Carpenter Ants in Minas Gerais, Brazil.   Both were kind enough to oblige and share with us their perspective via email.

The description of ants as zombies is not a pitch to popularity-even at Halloween-  but an orchestrated attempt to identify fungal-infected ants as very different from other ants in the society. Just because something looks, walks and quacks like a duck doesn’t mean it is actually a duck. The sinister thing about parasites which manipulate host behavior is that they can easily go unnoticed. The zombie ant moniker forces us to recall that we are looking at two organisms and the ant is not in the driving seat.

Our study in PLoS ONE, which used micromorphology together with spore function to delimit and describe new species, came about as it was obvious that the diversity of zombie ant fungi must be  higher than previously supposed because ant species diversity is high. We know that ants differ in many important behaviors which of course is due to brain differences. So, if your evolutionary gambit is brain control, then diverse brains will act as diverse selection environments leading to different species. Perhaps the most exciting thing is that we now recognize that these initial descriptions are just the tip of a very large iceberg and that many more zombie-inducing fungi await discovery, especially in tropical forests such as the Brazilian Atlantic rainforest in which we set our study.

In March, our editor wrote an overview of this paper.  To see last year’s Halloween post, click here.

Image by Roel Fleuren and pumpkin carving by Charissa de Bekker.

New Twitter Functionality on PLoS ONE

Recently, we added a nice new functionality to the PLoS ONE site. On the homepage, you will now see a ‘twitter’ widget in the right hand column (to the right of the “In the News” block). Whenever anyone issues a tweet with the words ‘PLoS ONE’ or ‘#PLoSONE’ in the text then their tweet will appear in the list here.

In addition, we also have the same functionality operating at the article level. The widget is able to display tweets about a particular article by looking for the article DOI appearing in an ‘unpacked’ URL. If there are no tweets for a particular article, it will not appear.

The paper, Inner Speech during Silent Reading Reflects the Reader’s Regional Accent, is a nice example of this widget in use.

We should point out that this handy widget has a few limitations.  For one, the widget isn’t able to store tweets for all eternity.  It will only be able to show recent tweets. Also, it isn’t connected to our Article Level Metrics …yet (we’re working on it though).

Otherwise, we think this widget will make a nice new addition to our site and will be a helpful way to see what our community is saying.

PLoS ONE News and Blog Round-Up

In this month’s digest – the T. rex is larger than previously thought, babies can be altruistic and more.

The article, A Computational Analysis of Limb and Body Dimensions inTyrannosaurus rex with Implications for Locomotion, Ontogeny, and Growth, by John R. Hutchinson, Karl T. Bates, Julia Molnar, Vivian Allen,  and Peter Makovicky received coverage from Xinhua, The Christian Science Monitor, and Slashdot.

Fairness Expectations and Altruistic Sharing in 15-Month-Old Human Infants received media coverage from Science 2.0, Scientific American, and WFAA-TV.

News for Your Neurons, Surprising Science and The Thoughtful Animal covered, Use of “Entertainment” Chimpanzees in Commercials Distorts Public Perception Regarding Their Conservation Status.

For more in-depth coverage on news and blog articles about PLoS ONE papers, please visit our Media Tracking Project.

Worth a Thousand Words

This post is written by Nicholas Ellinwood, who has worked with PLoS ONE since last year. He is a Publications Assistant who focuses on assigning Academic Editors to appropriate manuscripts, managing email queries and handling our new species papers.


A CT and MRI of a red-eared slider are this week’s featured image. These pictures from Figure 1 of the article entitled “Inside Out: ModernImaging Techniques to Reveal Animal Anatomy” show how CT and MRI have different capacities in visualizing vasculature, soft tissue, and skeleton.

The paper by Lauridsen et al. includes many more three-dimensional visualizations of animal anatomy in living specimens including fish, amphibians, reptiles, mammals, and spiders.  The authors encourage other biologists to take advantage of modern imaging modalities like clinical scanners that exist in most current large hospitals.

The abstract reads:

“Animal anatomy has traditionally relied on detailed dissections to produce anatomical illustrations, but modern imaging modalities, such as MRI and CT, now represent an enormous resource that allows for fast non-invasive visualizations of animal anatomy in living animals. These modalities also allow for creation of three-dimensional representations that can be of considerable value in the dissemination of anatomical studies. In this methodological review, we present our experiences using MRI, CT and mCT to create advanced representation of animal anatomy, including bones, inner organs and blood vessels in a variety of animals, including fish, amphibians, reptiles, mammals, and spiders. The images have a similar quality to most traditional anatomical drawings and are presented together with interactive movies of the anatomical structures, where the object can be viewed from different angles. Given that clinical scanners found in the majority of larger hospitals are fully suitable for these purposes, we encourage biologists to take advantage of these imaging techniques in creation of three-dimensional graphical representations of internal structures.”

Worth a Thousand Words

A photographic series covering 5, 15 and 25 years of sessile structural species dwelling on Mediterranean coralligenous outcrops is  this week’s featured image.

This brilliant figure contains frames with sponge and anthozoan species used in the paper, Low Dynamics, High Longevity and Persistence of Sessile Structural Species Dwelling on Mediterranean Coralligenous Outcrops.

In the Abstract the authors write:

Background:

There is still limited understanding of the processes underlying benthic species dynamics in marine coastal habitats, which are of disproportionate importance in terms of productivity and biodiversity. The life-history traits of long-lived benthic species in these habitats are particularly poorly documented. In this study, we assessed decadal patterns of population dynamics for ten sponge and anthozoan species that play key structural roles in coralligenous outcrops (~25 m depth) in two areas of the NW Mediterranean Sea.

Methodology/Principle Findings:

This study was based on examination of a unique long-term photographic series, which allowed analysis of population dynamics over extensive spatial and time spans for the very first time. Specifically, 671 individuals were censused annually over periods of 25-, 15-, and 5-years. This long-term study quantitatively revealed a common life-history pattern among the ten studied species, despite the fact they present different growth forms. Low mortality rates (3.4% yr?1 for all species combined) and infrequent recruitment events (mean value of 3.1±0.5 SE recruits yr?1) provided only a very small fraction of the new colonies required to maintain population sizes.

Conclusions:

Overall, annual mortality and recruitment rates did not differ significantly among years; however, some species displayed important mortality events and recruitment pulses, indicating variability among species. Based on the growth rates of these 10 species, we projected their longevity and, obtained a mean estimated age of 25–200 years. Finally, the low to moderate turnover rates (mean value 0.80% yr?1) observed among the coralligenous species were in agreement with their low dynamics and persistence. These results offer solid baseline data and reveal that these habitats are among the most vulnerable to the current increases of anthropogenic disturbances.

This post was written by Raquel Iglesias, a publications assistant at PLoS ONE .  Raquel has been assisting authors, reviewers and academic editors since April of last year.  She also helps ensure our clinical trial submissions move through the review process smoothly.

Ask EveryONE: How to submit an appeal request

This post is by Nicholas Ellinwood, who has worked with PLoS ONE since last year. He is a Publications Assistant who focuses on assigning Academic Editors to appropriate manuscripts, managing email queries and handling our new species papers.

Can I formally appeal a final decision on my paper if I believe my paper satisfies all of PLoS ONE’s acceptance criteria?

Although PLoS ONE does not approve all appeal requests, if you feel that your paper was Rejected due to considerations outside of PLoS ONE’s acceptance criteria, then you can submit a formal appeal request to the PLoS ONE staff by emailing plosone@plos.org and including a point-by-point response to all of the reviewers comments and a detailed rebuttal letter explaining why you think your paper is publishable.

Our internal editors thoroughly review all rebuttal letters, and we do grant appeal requests if we think your paper would benefit from a re-review.

The peer-review process for an appeal is typically much longer than a normal submission because of the complexity of the manuscript’s history.  Also, we require two Academic Editors to evaluate all appeals and to jointly co-sign the decision letters.

PLoS ONE closely monitors the appeals that it accepts, and will mediate between a disagreement between the two Academic Editors assigned to the resubmission if necessary.

Before you submit an appeal request, remember that PLoS ONE requires all research articles to fulfill the following acceptance criteria:

1. The study presents the results of primary scientific research.

2. Results reported have not been published elsewhere.

3. Experiments, statistics, and other analyses are performed to a high technical standard and are described in sufficient detail.

4. Conclusions are presented in an appropriate fashion and are supported by the data.

5. The article is presented in an intelligible fashion and is written in standard English.

6. The research meets all applicable standards for the ethics of experimentation and research integrity.

7. The article adheres to appropriate reporting guidelines and community standards for data availability.

PLoS ONE Launches the RosettaCon 2010 Collection

Reproducing computational biology protocols is one of the difficult challenges facing computational biologists today. Often times, it is rarely feasible to replicate the computational environment of an original work because of the complexity of macromolecular modeling protocols.  Moreover,  much of this work is new research and not focused solely on the algorithms or workflows.  As a result, published results often contain method descriptions with inconsistently stated protocols and dependencies.

In the new PLoS ONE Collection: RosettaCon 2010, over 15 academic groups from Rosetta Commons have attempted to capture these protocols in a sufficiently complete and formal way. This Collection aims to make several of the latest Rosetta macromolecular modeling protocols from the 2010 Rosetta Developers Meeting accessible to all.

Three main contributions came from the meeting and are represented in the PLoS ONE Collection.

1. New Rosetta applications: Several articles describe specific applications in biology or chemistry, including de novo enzyme design, modeling classes of protein loops, design of temperature sensitive mutations, and design of peptides to inhibit large surface area protein interactions.

2. Rosetta basic science: Several of the contributions in this Collection are Rosetta basic science papers of this type.  Examples include: incorporation of non-canonical amino acids in Rosetta design, multi-state design, new Rosetta kinematics, new protein docking protocols, and anchored design. Each example has the full protocol that lead to the incorrect prediction fully described as well as the correct (“native”) structure; thus these protocols are key elements in defining and judging future improvement in Rosetta and other codes.

3. Rosetta code development: Multiple articles describe new code refactoring, extensions or improvements to the implementation of Rosetta.  Several articles discuss the creation of multi-purpose high level interfaces to the components of Rosetta.  Examples include an XML scripting interface for Rosetta, an interactive python interface to the Rosetta code, and an object oriented API for generating Rosetta fragments.

RosettaCon 2010 provides the larger community direct access to the exact protocols used in each of these papers. This construction was intended to allow other community members and Rosetta users to reproduce the work, allow competing groups to validate and improve upon the work, and finally, make it rapidly accessible to new users with similar biological applications.

It should be noted that this Collection is itself a social experiment and the collaborators wrestled with how best to capture an evolving set of processes in a way that does not overly burden authors, works across a distributed community without a central authority for methods capture, is timely, and is sufficiently self-consistent that readers will invest their time in the results.

The paper, 2010 Rosetta Developers Meeting: Macromolecular Prediction and Design Meets Reproducible Publishing, by Renfrew et al. was adapted to create this post.

Collection Citation: RosettaCon 2010 (2011) PLoS Collections: http://www.ploscollections.org/RosettaCon2010

PLoS ONE’s Media Tracking Project

Everyday we find PLoS ONE papers in the news. Whether it’s a science blogger in the United Kingdom, an online newspaper in China, or a national news channel in the United States, we see a lot of media coverage on our research articles.  In an effort to better track the coverage these papers receive, we’ve begun a Media Tracking Project.

The aim of this project is to collect all pertinent news articles from legitimate media outlets and research blogs covering PLoS ONE articles. So, how does it work? From now on, we’ll attempt to bookmark relevant news articles and blog posts about PLoS ONE articles using Diigo (a collaborative research and social content site). If you would like to see the articles we’ve collected so far, check out our library. On a weekly basis, we’ll collate these bookmarks and list the relevant media coverage in the commenting section of each research article. An example of the media coverage comment can be found on the article: Scientists Want More Children.

We recognize that – despite our best efforts to track media coverage – we will inevitably miss some (and we will not aim to exhaustively list all sources which simply re-print a standard release for any given article).  So, we would encourage you to participate as well.  If you read, write, see or hear media coverage on a PLoS ONE article, please don’t hesitate to link to it in the comments section of the paper. Our suggested format is as follows:

Publication:

Title of article:

Link:

For an excellent example of  an author documenting media coverage, take a look at the article, Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. Jonathan Eisen, one of the authors of this manuscript,  has meticulously posted links to media coverage in the comments section of his paper.  We appreciate his involvement and encourage authors to follow his lead.

In the meantime, we’ll still post PLoS ONE News and Blog Round-Ups of the most widely covered articles on a regular basis.

PLoS ONE News and Blog Round-Up

Researchers find a possible cure for the common cold and more – in this week’s media digest.

Human Pathogen Shown to Cause Disease in the Threatened Eklhorn Coral Acropora palmata was covered by The NewsHour, The New York Times, NPR, and CNN.

CNET, Hindustan Times, and Okezone covered Automatic Prediction of Facial Trait Judgments: Appearance vs. Structural Models.

The paper, Predator Cat Odors Activate Sexual Arousal Pathways in Brains of Toxoplasma gondii Infected Rats, received coverage from The New York Times, Scientific American, TIME’s Healthland, and The Loom.

Broad-Spectrum Antiviral Therapeutics received media coverage from Voice of America, LA Times, and Forbes.

Large Recovery of Fish Biomass in a No-Take Marine Reserve was covered by National Geographic (nice slideshow too), The Christian Science Monitor, Nature News, and KGTV San Diego. The image above, is taken from Figure 4 of this manuscript.

80 Beats covered the article, Artificial Skin – Culturing of Different Skin Cell Lines for Generating an Artificial Skin Substitute on Cross-Weaved Spider Silk Fibres. So did Treehugger.

The article entitled, Scientists Want More Children received media coverage from The Wall Street Journal, TIME’s Ecocentric, Science Career Blog, and Inside Higher Ed.

Elevated Non-Esterified Fatty Acid Concentrations during Bovine Oocyte Maturation Compromise Early Embryo Physiology was covered by Reuters, The Guardian, and The Press Association.

Worth a Thousand Words

Photomicrographs of Glomus versiforme (basionym Endogone versiformis) are this week’s featured image. The colorful figure contains pale spores used in the paper, Revealing Natural Relationships among Arbuscular Mycorrhizal Fungi: Culture Line BEG47 Represents Diversispora epigaea, Not Glomus versiforme.

In the abstract, the authors write:

Background

Understanding the mechanisms underlying biological phenomena, such as evolutionarily conservative trait inheritance, is predicated on knowledge of the natural relationships among organisms. However, despite their enormous ecological significance, many of the ubiquitous soil inhabiting and plant symbiotic arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are incorrectly classified.

Methodology/Principal Findings

Here, we focused on a frequently used model AMF registered as culture BEG47. This fungus is a descendent of the ex-type culture-lineage of Glomus epigaeum, which in 1983 was synonymised with Glomus versiforme. It has since then been used as ‘G. versiforme BEG47’. We show by morphological comparisons, based on type material, collected 1860–61, of G. versiforme and on type material and living ex-type cultures of G. epigaeum, that these two AMF species cannot be conspecific, and by molecular phylogenetics that BEG47 is a member of the genus Diversispora.

Conclusions

This study highlights that experimental works published during the last >25 years on an AMF named ‘G. versiforme’ or ‘BEG47’ refer to D. epigaea, a species that is actually evolutionarily separated by hundreds of millions of years from all members of the genera in the Glomerales and thus from most other commonly used AMF ‘laboratory strains’. Detailed redescriptions substantiate the renaming of G. epigaeum (BEG47) as D. epigaea, positioning it systematically in the order Diversisporales, thus enabling an evolutionary understanding of genetical, physiological, and ecological traits, relative to those of other AMF. Diversispora epigaea is widely cultured as a laboratory strain of AMF, whereas G. versiforme appears not to have been cultured nor found in the field since its original description.

All of PLoS ONE’s sporific papers are open access and free for you to read, rate and reuse.

Citation: Schüßler A, Krüger M, Walker C (2011) Revealing Natural Relationships among Arbuscular Mycorrhizal Fungi: Culture Line BEG47 Represents Diversispora epigaea, Not Glomus versiforme. PLoS ONE 6(8): e23333. doi:10.1371/journal.pone.0023333