0000-0003-1258-0746The considerations about open data and making data more accessible and reusable have increasingly come to the forefront in the agenda of funders, institutions and publishers, and they are likely to remain the subject of
At the end of 2014, we highlighted some of our favorite research videos from that year. We’re only mid-way through 2015, but we already have a number of popular research videos that we’d like to share. Here are some of … Continue reading
There has been a great deal of community discussion in the last few days about a referee report that was sent to an author at PLOS ONE a few weeks ago. The report contained objectionable language, and the authors were … Continue reading
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.
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
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.
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.
PLOS ONE is excited to participate in the American Geophysical Union’s (AGU) Fall Meeting 2013, held this week in San Francisco’s Moscone Center. Conveniently, Moscone is just down the street from our San Francisco office, so several members of PLOS staff will be in attendance and available to chat with you about the journal. We’re looking forward to meeting both current and potential Academic Editors, reviewers, and of course authors! Please stop by Booth #301 to say hello.
Last week was a very geophysics-oriented one for us, with both the publication of Hansen et al.’s work “Assessing “Dangerous Climate Change”: Required Reduction of Carbon Emissions to Protect Young People, Future Generations and Nature” and with the announcement of our call for papers in a new collection entitled “Responding to Climate Change.” What’s more exciting is that James Hansen will be in attendance at AGU and will be giving a talk today (December 10th) on this topic, in support of taking significant, active measures to reduce fossil fuel emissions.
Last year, at AGU 2012, we were a little bit of an unfamiliar face to many. This year, we hope to continue our conversation with the physical sciences community about our commitment to open access and the publication of sound scientific research in all areas of science and medicine, including geoscience, space science, chemistry, and physics.
After AGU, look out for the PLOS booth again in just a few days at the American Society for Cell Biology!
Image Credit: Detailed view of Arctic Sea Ice in 2007, from NASA Visible Earth.
From snakes that look like they have two heads to color-shifting chameleons, deception is at the heart of many animals’ survival strategies. Both visual and chemical predator deterrence are well-documented phenomena in the animal world, but new research on ant-mimicking spiders, published in PLOS ONE, may be the first documented case of a species that uses visual deception to elude one group of predators, and chemical deception to escape another.
Ant mimicry, or myrmecomorphy, is a tactic used by numerous spider species, and with good reason, since many predators steer clear of preying on ants due to their aggressive tendencies and often unpleasant taste. Ant-mimicking spiders can have body shapes that closely resemble those of ants, as well as colored patches that look like ant eyes. Combine these characteristics with behaviors such as waving their front legs in the air to resemble probing ant antennae, and these spiders can successfully convince predators to look elsewhere for their next meal. The jumping spider Peckhamia picata is one such ant mimic whose visual signals are an effective deterrent for visually focused predators, such as other species of jumping spiders. The picture below shows a jumping spider on the left and the ant it imitates on the right.
The PLOS ONE study shows that the ant-mimicking spider can also elude predators that rely heavily on chemical signals to identify their prey. In the current study, the spiders successfully eluded spider-hunting mud-dauber wasps (pictured below), and received significantly less aggression from the ants they mimic than other non-mimicking jumping spiders. The researchers presented wasps with a choice between freshly killed ant-mimicking and non-mimicking spiders. In all of the trials conducted, the wasp probed both types of spiders with their antennae, but every time the wasps chose to sting and capture a spider (seven out of eight times), it chose the non-mimicking spider.The researchers also staged encounters between Camponotus ants and live ant-mimicking and non-mimicking spiders. After probing them with their antennae, the ants were significantly less likely to bite the ant-mimicking spiders than non-mimicking ones. These results demonstrate that the jumping spider has a remarkably effective ability to deceive potential predators who focus on chemical cues when selecting prey.
The researchers point out that the spider is not a chemical mimic of the ant species it emulates. Insects rely heavily on hydrocarbons secreted from their cuticles (the hard outer covering of invertebrates) to identify and signal one another. It turns out that ant-mimicking spiders have very low levels of these molecules, only a small fraction of the amount found in non-mimicking spiders and the ants themselves. While further research is required to fully explain the jumping spider’s chemical mechanism for predator evasion, a likely explanation is that the low level of these chemicals does not register as significant to a probing ant or wasp, and the chemical evasion is accomplished in this way.
This study may be the first to describe an animal using a “double-deception” strategy: visual tricks and a deceptive chemical signature, both intended for different audiences. The authors hypothesize that this kind of chemical deception is likely widespread among other visual mimics in the animal kingdom.
Citation: Uma D, Durkee C, Herzner G, Weiss M (2013) Double Deception: Ant-Mimicking Spiders Elude Both Visually- and Chemically-Oriented Predators. PLoS ONE 8(11): e79660. doi:10.1371/journal.pone.0079660
Images: Images come from Figure 1 of the manuscript
Emphasizing the fact that clinical trials can influence treatment decisions, the recent AllTrials campaign has called for all trials past and present to be registered, and the results reported. As one of the initiating organisations behind this initiative, PLOS is committed to continuously developing and adopting policies that might help rectify publication bias in the trials literature. Following in the footsteps of PLOS Medicine, this campaign has led the editorial staff at PLOS ONE to re-evaluate how we handle unregistered trials.
Previously, in line with the International Committee of Medical Journal Editors (ICMJE) policy and like several other journals, we required all clinical trials that began after July 1, 2005 to be registered prospectively (before patient recruitment) in a publicly available registry approved by the World Health Organization (WHO). To stress the need for prospective registration, papers that did not fulfill these criteria were rejected, but this potentially prevented the results of some trials from being published. Thus while we still expect prospective registration to be standard practice, as of today, we will also consider retrospectively registered clinical trials to help ensure the medical community has access to the results of these trials.
These retrospectively registered clinical trials must however meet the following criteria:
1) The trial must be registered in a WHO-approved registry before submission to the journal
2) The authors must explain the reason for late registration within the methods section of the manuscript
3) They must include a statement confirming that all ongoing or future related trials are registered
As a reminder, when determining what constitutes a clinical trial, PLOS ONE follows the WHO’s definition: “a clinical trial is any research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes.” The ICMJE further clarifies that “health-related interventions include any intervention used to modify a biomedical or health-related outcome (for example, drugs, surgical procedures, devices, behavioral treatments, dietary interventions, and process-of-care changes). Health outcomes include any biomedical or health-related measures obtained in patients or participants, including pharmacokinetic measures and adverse events”.
The ICMJE also recommends that if scientists are unsure whether their trial meets the above definition, they should err on the side of registration.
We believe that while prospective trial registration remains the gold standard, this change in policy will be a positive step towards increased transparency and accountability and is in line with another recent initiative supported by PLOS ONE, the RIAT (Restoring Invisible and Abandoned Trials) initiative. This is also in accordance with the core values of the journal to publish all papers, including studies reporting negative results, provided they are technically sound and done to high scientific and ethical standards.
Image: by NHS Confederation on Flickr
Most readers are by now familiar with the core principle behind PLOS ONE: to publish all papers that are scientifically and technically sound, regardless of their perceived impact or importance. Another publication criterion that has received far less attention until recently is our commitment to the quality and completeness of reporting.
PLOS ONE considers reporting quality to be of importance in two main areas: first in relation to completeness of authors’ descriptions of study methods and results, and second in assuring readers of the ethical basis underlying the work. The rationale for ensuring high standards of reporting and ethical oversight is aligned with our core mission to facilitate the re-use of open-access research; if studies aren’t reported appropriately, or don’t have the necessary ethical oversight, it is much more difficult for others to replicate the work or incorporate the data as part of a larger study.
The natural follow-up question might be: how do we as a journal maintain these standards? Here, we’d like to outline briefly our standards, the reasons for them, and the process for ensuring that authors adhere to them. By doing this, we hope to shed light on some of our internal processes, both for the journal’s community, as well as for interested readers that appreciate sound, well-done science as much as we do.
PLOS ONE is a large, international, open-access scientific journal that considers all manuscripts reporting the results of primary scientific research. Day to day, the journal receives many types of studies, including experimental and observational work on animal and human populations, as well as a range of computational and theoretical work. These are submitted by researchers around the world who are not necessarily bound by common standards of reporting or ethical oversight.
As an international journal, however, PLOS ONE has a responsibility to establish and maintain consistent and high standards for publication. Therefore, we require that authors assure us on submission of appropriate ethical review and approval for experimental work involving animals and human participants; relevant permissions for field studies or observational work; and adherence to appropriate discipline-specific guidelines for the reporting of taxonomic, paleontological, or archaeological specimens. In some areas, there are also more prescriptive guidelines to ensure the full description of study methods and results—including CONSORT for reporting randomized clinical trials and PRISMA for reporting systematic reviews in relation to human participants—and we provide links to many more in our manuscript guidelines.
How do journal staff check for these standards when we receive so many submissions each day? At PLOS ONE, we’ve found that the most effective way to ensure papers meet our requirements is to perform a series of checks at submission. This ensures that by the time articles are assigned to Academic Editors for detailed review, crucial information about ethical oversight and study conduct will be available for their consideration. By screening papers before the formal peer-review process, we provide support to our Editorial Board and reviewers, who volunteer their time and offer an invaluable service to the journal and the scientific community as a whole. Equipping our Academic Editors with additional, important details when they agree to handle a manuscript allows them to focus their specialized expertise where it is most valued: on the scientific and technical quality of the paper.
That said, we consider our Academic Editors as partners in our goal of maintaining high standards for reporting, research ethics, and integrity. We ask our Editorial Board members for advice in difficult situations, and greatly appreciate the expert input that they provide. In certain situations we seek the advice of additional experts in reporting or ethics to provide oversight on specific papers, and are currently setting up dedicated advisory boards to assist us. We also consult Editorial Board members when developing new internal policies, or when robust community guidelines (such as CONSORT for randomized clinical trials or the proposed ARRIVE for experimental animal research) are not yet available for specific study types.
We appreciate the support of PLOS ONE authors, editors, and reviewers in helping us maintain the highest standards possible.
Posted on behalf of the in-house editors at PLOS ONE:
Associate Editors Gina Alvino, Sarah Bangs, Meghan Byrne, Christna Chap, Michelle Dohm, Matt Hodgkinson, Anna Schmidt, and Elizabeth Silva; Senior Editors Eric Martens and Emma Veitch; Consulting Editors Catriona MacCallum and Iratxe Puebla; and Editorial Director Damian Pattinson
Effective as of midnight, October 1st, 2013, the US government is closed for business, which means that all nonessential US federal services and agencies have stopped operating until further notice. Please note that anyone affiliated with a US federal agency may not be working. Below is our understanding of the details and implications for PLOS ONE services. (Any of you who are affiliated with a US government agency, and who may have more accurate information to offer, please do comment.)
Those who work for US federal agencies will not go to work, and we have been informed that some may not access or use email. Therefore, PLOS ONE reviewers and editors employed by or affiliated with the US government may or may not be available to handle manuscripts. The work these folks do for us is voluntary—and much appreciated—but these services may be directly associated with their US government employment.
We kindly ask all PLOS ONE authors to please be aware that they may experience delays in manuscript handling due to these closures. Editors and reviewers who have already agreed to evaluate a manuscript may not be reachable at this time. We will do our best to keep everyone abreast of the status of their manuscripts, but please feel free to email us with questions or concerns (email@example.com).
A non-exhaustive list of affected agencies is as follows: CDC, DOD, DOE (and all national labs), DOI, EPA, FDA, HHS, NASA, NCBI, NCI, NHGRI, NIH (all institutes, which may affect those at hospitals), NIMH, NIOSH, NIST, NOAA, NSF, USDA, USFS, and USGS.
We apologize for the inconvenience, and hope that all government services will resume shortly.
Laughter, fungi, pipettes and ants – last month, PLOS ONE papers made headlines with an array of research. Here are some of our May media highlights:
Not all laughter is the same and your brain knows it. In recently published research, scientists studied the effects of three types of laughter (joyous, taunting, and “tickling”) on the human brain. Participants listened to recordings of these laugh and were asked to discern the type and count how many bouts had occurred. The researchers found that the participants could discern joyous and taunting laughter at comparable rates and that it was slightly more difficult to discern laughter in response to tickling. Participants were able to count the number of taunting laughs more accurately than joyous and tickling laughs. Read more about this study in the Huffington Post UK, TIME, and Los Angeles Times.
There are fungi afoot! New research confirms that the chytrid fungus (Batrachochytrium dendrobatis), which has decimated amphibian populations around the world, can be found in frogs in California. Scientists swabbed 201 South African clawed frogs (Xenopus laevis) in the California Academy of Sciences’ collection, 23 of which were caught in California. Eight specimens tested positive for chytrid, including one frog caught in San Francisco County in 2003. This frog species was once imported to aid in pregnancy testing. To read more, visit the National Geographic, Science News, ABC and the Smithsonian blog, Smart News.
Pipettes are a staple lab equipment, but not without their drawbacks. According to a new PLOS ONE paper, certain methods of dispensing and diluting liquids can introduce errors in experimental data. The researchers of this study compared pipetting, or tip-based transfer, with an acoustic dispensing technique and found that laboratory results depended greatly on the dispensing technique. Learn more about this study by reading the Royal Society of Chemistry’s Chemistry World, Nature’s Methagora blog, and In the Pipeline.
There are plenty of odd couples in nature. For one example, just look at the unlikely partnership of the ant and the pitcher plant. A recent study finds that a particular ant species, Camponotus schmitzi, has formed a mutually beneficial relationship with the carnivorous Nepenthes bicalcarata, a pitcher plant. Scientists observed that the ants provide pitcher plants with nitrogen and preys on other insects, such as mosquitoes, that may otherwise steal nutrients from the plant. In return, the pitcher plant provides a home and a steady source of sustenance. You may find more about this study at Discovery News, The Scientist, and the New York Times.
Image: Figure 1 from “A Novel Type of Nutritional Ant–Plant Interaction: Ant Partners of Carnivorous Pitcher Plants Prevent Nutrient Export by Dipteran Pitcher Infauna”
Wildgruber D, Szameitat DP, Ethofer T, Brück C, Alter K, et al. (2013) Different Types of Laughter Modulate Connectivity within Distinct Parts of the Laughter Perception Network. PLoS ONE 8(5): e63441. doi:10.1371/journal.pone.0063441
Vredenburg VT, Felt SA, Morgan EC, McNally SVG, Wilson S, et al. (2013) Prevalence of Batrachochytrium dendrobatidis in Xenopus Collected in Africa (1871–2000) and in California (2001–2010). PLoS ONE 8(5): e63791. doi:10.1371/journal.pone.0063791
Ekins S, Olechno J, Williams AJ (2013) Dispensing Processes Impact Apparent Biological Activity as Determined by Computational and Statistical Analyses. PLoS ONE 8(5): e62325. doi:10.1371/journal.pone.0062325
Scharmann M, Thornham DG, Grafe TU, Federle W (2013) A Novel Type of Nutritional Ant–Plant Interaction: Ant Partners of Carnivorous Pitcher Plants Prevent Nutrient Export by Dipteran Pitcher Infauna. PLoS ONE 8(5): e63556. doi:10.1371/journal.pone.0063556