Warming in Our Winter Wonderland: The Role of Ice in Penguin, Polar Bear, and Ivory Gull Survival

As winter grips the Northern Hemisphere tightly, many of us are happy to retreat to the comfort of our warm homes. But for some animals, this season plays a vital role in the formation of something necessary for their survival, … Continue reading »

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Meet PLOS at the Biophysical Society 59th Annual Meeting

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PLOS ONE and PLOS Biology are excited to return to the Biophysical Society’s Annual Meeting. The event will be held at the Baltimore Convention Center located in downtown Baltimore, Maryland. All are encouraged to stop by booth #636 to speak … Continue reading »

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Fossilized Footprints Lead Scientists Down a Prehistoric Path

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Whether tromping alone or running in a pack, all prehistoric creatures got around somehow. Paleontologists can use fossilized bones to learn more about what dinosaurs ate, what they looked like, and even how they might have moved, but bones are … Continue reading »

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At Year’s End: Staff Editors’ Favorite PLOS ONE Articles of 2014

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2014 has been an exciting year for PLOS ONE. We saw the journal reach a milestone, publishing its 100,000th article. PLOS ONE also published thousands of new research articles this year, including some ground-breaking discoveries, as well as some unexpected … Continue reading »

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Canada’s Species at Risk Rarely Recover: The Story Behind the PLOS ONE Article

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Post By Caroline Fox & Brett Favaro Most scientists are passionate about their work, but enthusiasm can sometimes be hard to maintain over a long project. What if we could inject the fun back into science—take away the emotional baggage … Continue reading »

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Let Me Count the Ways: Top 20 PLOS ONE Articles Based on Article-Level Metrics for 2014

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At PLOS ONE, we’ve been compiling year-end lists to reflect on the most popular articles and research videos published in our journal. But this year, we also wanted to compile an alternative list, based on article-level metrics (ALMs*), a collection … Continue reading »

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Meet PLOS at the Society of Vertebrate Paleontology 2014

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We are excited to announce that PLOS will be exhibiting at the Society of Vertebrate Paleontology 2014 Annual Meeting from 5-8th November in Berlin. This is only the second time that the meeting takes place outside North America, and the … Continue reading »

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“Low T” and Prescription Testosterone: Public Viewing of the Science Does Matter

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PLOS ONE Publishes its 100,000th Article

PLOS ONE publishes its 100,000th article – a pretty major milestone for a journal that has seen its fair share of momentous events, and a perfect opportunity to reflect on this journey.

 PLOS ONE began seven and a half years ago. On the day of its launch – as has become the legend in the PLOS offices – there was an earthquake in the Bay Area, heralding the tremors that would be felt through the science world as a result of the disruptive innovation underway. PLOS ONE was an aspirational idea for PLOS from the very beginning: our founders always intended to launch a multi-disciplinary, broad-acceptance journal that would shake off the vestiges of the print tradition – no limits to the scope of research, number of pages, or potential growth.

And grow it did. After two years PLOS ONE had published over 4,000 articles, by four years it was the largest journal in the world, and now seven years after launch has published 100,000 articles. The revolutionary model of PLOS ONE has been emulated the world over: virtually every publisher now has its own equivalent “megajournal.”

PLOS ONE is now a major force in the scientific literature. The top 2% PLOS ONE papers (by number of views) have been collectively viewed nearly 39 million times, cited on Scopus over 80,000 times, bookmarked by Mendeley readers over 150,000 times, tweeted over 59,000 times, cited 2,800 times on Wikipedia, and recommended over 300 times on F1000 Prime.

The enduring value of PLOS ONE to the scientific process lies in the solid union between the three following factors: speed to publication, high standards of science, and unrestricted scope of research.

Speed to publication:

Faster time to publication was the founding principle of PLOS ONE. It doesn’t just entail going from submission to publication more quickly (although that is also important). It means dramatically reducing the time from an author’s decision to publish their findings to the time those results appear in public. That time is often years in the old system of review, where subjective opinions of significance and scope lead to unnecessary rejections and resubmission to different journals. With PLOS ONE, where scientific rigor alone is assessed, this time window shortens to a few months.

High standards:

PLOS ONE instituted rigorous standards from the start. As the volume exponentially increased and the quality of the submissions became more variable, these checks became more important and more rigorous. For every paper the journal staff (over 100 strong, including 14 editors) now check each of the following before a manuscript is sent for review:

  • Competing interests
  • Financial disclosures
  • Quality of English language
  • Ethical approval for animal experiments
  • IRB approval for human experiments
  • Protocols and CONSORT for clinical trials
  • PRISMA for systematic reviews and meta-analyses
  • Cell line provenance
  • Field sample provenance
  • Humane endpoints in animal studies
  • Data availability
  • Plagiarism

The care that we take in reporting and oversight is rooted in PLOS’ commitment to this editorial responsibility.

Because of these checks, every PLOS ONE citation on a researcher’s CV shows that their work has reached high standards of reporting and oversight – something that matters a great deal to funders and institutions as the need for reproducibility becomes increasingly a part of their overall mission. This is an area where we feel journals can take a lead: high standards of reporting are the best way for the scientific community to regain the trust of the public and politicians in the wake of the recent spate of failures in replicating high-profile discoveries.

Unrestricted scope:

So many of the delays in sharing results are a result of journals putting unnecessary restrictions on the scope of the research they are willing to publish. Journals often withhold the release of negative findings because they are likely to be cited less, and will therefore lower their impact factor. Or they exclude papers purely due to the application of disciplinary boundaries. In this digital age, with no space restrictions on what can be published, such artificial limits only impede the flow of information. At PLOS ONE, we have thrown out these notions and will consider vital research across all subject areas (even seemingly strange and multi-disciplinary).

A heartfelt 100k thank you

The impact of PLOS ONE on scientific publishing has been tremendous and revolutionary. The world of scientific communication is a different place because of it, and that is something PLOS and its entire community of collaborators should be proud of.

The extraordinary PLOS ONE Editorial Board, reviewers and authors – who believed in the PLOS mission to accelerate research communication and gave their own time to review, edit and revise manuscripts – were critical to this transformation and share in this milestone. To each and every one of them PLOS ONE is eternally grateful.

So here’s to the 100,000th PLOS ONE article. Though thrilled to have reached this milestone, we are even more excited to see where the next 100,000 will lead.

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Meta-Analyses of Genetic Association Studies – PLOS ONE’s Approach

Meta-analysis can be a powerful way to reveal otherwise hidden or unclear associations, when done with care. In line with recent trends in biomedical literature (1), PLOS ONE has seen a consistent increase in submissions reporting meta-analyses of genetic association studies over the last few years. These submissions report analyses of potential associations between candidate gene variants (usually single nucleotide polymorphisms, or SNPs) and specific disease risks and outcomes in human populations, based on a search of the literature to identify published reports studying the association and statistical analyses that synthesize the results of the identified studies.

However, researchers in the community, among them members of our editorial board, have raised concerns about some of these meta-analyses, including the risk of false positives due to publication bias, incomplete searches of the literature, redundancy, and an insufficient assessment of the power and quality of the included studies. As noted a decade ago, “Meta-analysis is not a replacement for adequately powered genetic association studies” (2).  Many of these studies focus on a single gene variant, and many do not include data from relevant genome-wide association  studies (GWAS), some of which have failed to replicate previously reported associations between candidate genes and diseases.

While many meta-analyses of genetic association studies are still clinically relevant, especially those studying rare conditions where GWAS data are not available, and well-conducted meta-analyses can provide useful and valid clinical evidence, we strongly feel that meta-analyses of genetic association studies considered by PLOS ONE must have the rationale clearly explained and that authors must report their studies according to high standards.

In order to address these concerns and after consultation with PLOS ONE editorial board members, we are introducing a new process to handle meta-analyses of genetic association studies. Authors will now be asked to provide the following information:

  1. The rationale for conducting the meta-analysis;
  2. The contribution that the meta-analysis makes to knowledge in light of previously published related reports, including other meta-analyses and systematic reviews;
  3. Whether GWASs relevant to the meta-analysis have been published and whether these were included in the analysis;
  4. Full methodological details for the meta-analysis, including completion of a checklist that has been developed with reference to several published guidelines (3, 4, 5) and in consultation with members of the PLOS ONE editorial board.

The information supplied by the authors will be evaluated by the in-house editorial team as part of the checks undertaken on new submissions. Meta-analyses replicating studies in the literature without adequate justification will be rejected. For those manuscripts that proceed to review, PLOS ONE Academic Editors will be consulted on the adequacy of the methodological aspects of the study and the quality of the reporting in the manuscript.

This process underscores our commitment to maintaining high standards of quality and reporting in publications at PLOS ONE. We are grateful for the input we have received from our editorial board that led to this new process, and wish to thank the PLOS ONE Academic Editors who provided advice and guidance.

If you have any questions or feedback, or if you are an author who would like additional information about our requirements for meta-analyses of genetic association studies, please contact us at plosone@plos.org.

Posted on behalf of the in-house editors at PLOS ONE:

Associate Editors Gina Alvino, Meghan Byrne, Christna Chap, Michelle Dohm, Matt Hodgkinson, Alejandra Clark and Nicola Stead and; Senior Editors Eric Martens and Iratxe Puebla; and Editorial Director Damian Pattinson

  1. Ioannidis JPA, Chang CQ, Lam TK, Schully SD, Khoury MJ (2013) The Geometric Increase in Meta-Analyses from China in the Genomic Era. PLOS ONE 8(6): e65602. doi:10.1371/journal.pone.0065602
  2. Marcus R. Munafò and Jonathan Flint (2004) Meta-analysis of genetic association studies. Trends Genet. 20(9):439-44 doi:10.1016/j.tig.2004.06.014
  3. Sagoo GS, Little J, Higgins JPT (2009) Systematic Reviews of Genetic Association Studies. PLOS Med 6(3): e1000028. doi:10.1371/journal.pmed.1000028
  4. Minelli C, Thompson JR, Abrams KR, Thakkinstian A, Attia J: The quality of meta-analyses of genetic association studies: a review with recommendations. Am J Epidemiol. 2009 Dec 1;170(11):1333-43. doi: 10.1093/aje/kwp350
  5. Little J, Higgins JP, Ioannidis JP, Moher D, Gagnon F, et al. (2009) STrengthening the REporting of Genetic Association Studies (STREGA)- An Extension of the STROBE Statement. PLOS Med 6(2): e1000022. doi:10.1371/journal.pmed.1000022

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3000 Years Ago, We Were What We Ate

Efate, VanuatuFor many of us, moving to a new house means recruiting a couple good friends to help pack and haul boxes. After a day or two of work, everyone shares a pizza while resting tired muscles at the new home. But 3000 years ago, enjoying a post-move meal may have required a little more planning. Early settlers of remote tropical islands in the Pacific had to bring along all resources needed for survival, including food, from their original homes overseas.

The Lapita people were early settlers of islands in the Pacific, called Remote Oceania (pictured below). When these people, whose culture and biology links to Southeast Asian islands, first decided to sail to the island Vanuatu, they brought domestic plants and animals—or what you might call a ‘transported landscape’—that allowed them to settle this previously uninhabited, less biodiverse (and less resource-available) area. However, the extent to which these settlers and their domestic animals relied on the transported Remote Oceanialandscape at Vanuatu during the initial settlement period, as opposed to relying on the native flora and fauna, remains uncertain.

To better understand the diet and lives of the Lapita people on Vanuatu, archaeologist authors of a study in PLOS ONE analyzed the stable carbon, nitrogen, and sulfur isotopes from the bones of ~ 50 adults excavated from the Lapita cemetery on Efate Island, Vanuatu.

Why look at isotopes in human remains? Depending on what we eat, we consume varying amounts of different elements, and these are ultimately deposited in our bones in ratios that can provide a sort of “dietary signature”; in this way, the authors can investigate the types of plants, animals, and fish that these early people ate.

For instance, plants incorporate nitrogen into their tissue as part of their life cycle, and as animals eat plants and other animals, nitrogen isotopes accumulate. The presence of these different ratios of elements may indicate whether a human or animal ate plants, animals, or both. Carbon ratios for instance differ between land and water organisms, and sulfur ratios also vary depending on whether they derive from water or land, where water organisms generally have higher sulfur values in comparison to land organisms.

Scientists used the information gained about the isotopes and compared it to a comprehensive analysis of stable isotopes from the settlers’ potential food sources, including modern and ancient plants and animals. They found that early Lapita inhabitants of Vanuatu may have foraged for food rather than relying on horticulture during the early stages of colonization. They likely grew and consumed food from the ‘transported landscape’ in the new soil, but appear to have relied more heavily on a mixture of reef fish, marine turtles, fruit bats, and domestic land animals.

The authors indicate that the dietary analysis may also provide insight into the culture of these settlers. For one, males displayed significantly higher nitrogen levels compared to females, which indicates greater access to meat. This difference in food distribution may support the premise that Lapita societies were ranked in some way, or may suggest dietary differences associated with labor specialization.  Additionally, the scientists analyzed the isotopes in ancient pig and chicken bones and found that carbon levels in the settlers’ domestic animals imply a diet of primarily plants; however, their nitrogen levels indicate that they may have roamed outside of kept pastures, eating foods such as insects or human fecal matter. This may have allowed the Lapita to allocate limited food resources to humans, rather than domestic animals.

Thousands of years later, the adage, “you are what you eat” or rather, “you were what you ate” still applies. As the Lapita people have shown us, whether we forage for food, grow all our vegetables, or order takeout more than we would like to admit, our bones may reveal clues about our individual lives and collective societies long after we are gone.

Citation: Kinaston R, Buckley H, Valentin F, Bedford S, Spriggs M, et al. (2014) Lapita Diet in Remote Oceania: New Stable Isotope Evidence from the 3000-Year-Old Teouma Site, Efate Island, Vanuatu. PLoS ONE 9(3): e90376. doi:10.1371/journal.pone.0090376

Image 1: Efate, Vanuatu by Phillip Capper

Image 2: Figure 1

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Ask EveryONE: Corrections

My paper was recently published in PLOS ONE, but I’ve noticed an error. Can it be corrected?

PLOS ONE corrects major errors found in published articles via the addition of a Formal Correction to the paper. Formal Corrections are reserved for errors that significantly affect the understanding or utility of the paper.  In addition to being published on the PLOS ONE website, corrections are also indexed in PubMed Central and PubMed.

When a paper has been corrected, a correction notice will appear in a gray box at the top of the article page.  A CrossMark logo now appears on every PLOS article page and in the downloadable PDF; clicking the logo on a corrected article’s page will bring up a status box showing that the paper has been corrected.

To see the full correction, click the “View correction” link in the gray box.  This will direct you to a page with the full correction details, including any updated figures, tables, or supporting information, along with a PDF version of the correction notice available for download.  An example of a correction notice on the original article is shown below.

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Example of a Formal Correction notice (click to enlarge)

If you notice an error in your published paper, you should contact our corrections team at corrections@plos.org.  Please include the title and DOI of your paper; a description of the problem; and any corrected figures, tables, or supporting information files. PLOS staff will decide whether a Formal Correction is appropriate and will work with you to publish a correction as quickly as possible.

If there is an error in one of your figures, tables, or supporting information files, the corrected items will be included in the Formal Correction. An example of a Formal Correction is shown below.

corrections image2Example of a Formal Correction (click to enlarge)

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