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

plos_20At 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 of indicators that help us assess the impact a published article has made on the community and the public, which can be monitored over time. This list captures the top 20 articles of 2014 based on a review of ALMs data over the past 12 months and complements an earlier list we featured at the end of the summer.

Without further ado, this year’s top papers are below:

1. Text me about it: A pain in the neck

journal.pone.0084312.g001A study from January, “Texting and Walking: Strategies for Postural Control and Implications for Safety,” suggests texting while walking impacts posture and balance. Over 27,000 views and 8600 PDF downloads–the most on our list–places this study at the top of our list. Maybe it’s time to look up from our phones—­if not for other pedestrians’ sakes, at least for our own neck’s.

Published 1/22/2014, Image from the article

2. Concerns over testosterone therapy

Testosterone therapy may raise the risk of heart attack according to “Increased Risk of Non-Fatal Myocardial Infarction Following Testosterone Therapy Prescription in Men.” An EveryONE blog post from earlier this year highlighted the unusual trajectory of this paper in the media and the public, demonstrating an impact that reaches far beyond just ALMs.

Published 1/29/2014

3. Lizard tales: What lizard tails may tell us about regenerating human tissue

journal.pone.0105004.g001Scientists studied lizard tail regeneration to look for clues for how we might regenerate human tissue, according to “Transcriptomic Analysis of Tail Regeneration in the Lizard Anolis carolinensis Reveals Activation of Conserved Vertebrate Developmental and Repair Mechanisms.”

Published 8/20/2014, Image from the article

4. Baby, it’s cold in liquid nitrogen

journal.pone.0086807.g001In a study published in January, “A Leech Capable of Surviving Exposure to Extremely Low Temperatures,” scientists observed leeches surviving in liquid nitrogen for 24 hours and in -130 degrees F for up to 9 months.

Published 1/22/2014, Image from the article

5. Origami-inspired microscopes for under $1

crop.journal.pone.0098781.g001Foldscope: Origami-Based Paper Microscope,” published in June, described a low-cost, paper-based microscope called a Foldscope. Light weight and durable, the authors suggest this microscope could be useful in the field and for science education.

Published 6/18/2014, Image from the article

6. Developing tests for early cancer diagnosis

In a paper from October, “Sentinel” Circulating Tumor Cells Allow Early Diagnosis of Lung Cancer in Patients with Chronic Obstructive Pulmonary Disease,” authors analyzed the results of a blood test that could detect cells associated with chronic obstructive pulmonary disease (COPD), which may help with early diagnosis of lung cancer.

Published 10/31/2014

7. I’m a (Black Death) survivor

journal.pone.0096513.g002Mortality Risk and Survival in the Aftermath of the Medieval Black Death,” published in May, suggests people who survived the Black Death, as well as their descendants, lived significantly longer and were healthier than people who lived before the epidemic.

Published 5/7/2014, Image from the article

8. Lucky to be 110

Scientists sequenced the world’s oldest people’s genomes, but unfortunately, they didn’t find a genetic pattern to their longevity in the study, “Whole-Genome Sequencing of the World’s Oldest People.” No secret to a long life just yet.

Published 11/12/2014

9. That smarts!

Scientists analyzed Neanderthal history and genetics and suggest that maybe they weren’t less intelligent than modern humans, as previously thought, but rather interbred and assimilated with modern humans in a study “Neandertal Demise: An Archaeological Analysis of the Modern Human Superiority Complex,” published in April.

Published 4/30/2014

10. Study “yields” data for the GMO debate

A large meta-analysis suggests genetically modified crops (“GMOs”) may have widespread benefits for farmers, according to a study “A Meta-Analysis of the Impacts of Genetically Modified Crops,” published in November. This article has the most page views on our list, with over 56,000 and has nearly 5000 PDF downloads. The article contributes data to ongoing debates around the world about the role genetically modified crops should play in agriculture and society.

Published 11/3/2014

11. Let’s talk jazz

crop.journal.pone.0088665.g001Scientists found that a jazz improvisation technique called ‘trading fours,’ where soloists from an ensemble take turns playing four bars at a time, may engage language areas of the brain specialized for processing communication, according to the study “Neural Substrates of Interactive Musical Improvisation: An fMRI Study of “Trading Fours” in Jazz.”

Published 2/19/2014, Image from the article

12. Say what?

Linguists applied evolutionary analysis to the relationship between North American and Central Siberian languages and found that the relationship between them may show that people moved out from the Bering Land Bridge, with some migrating back to central Asia and others into North America, according to a study published in March, “Linguistic Phylogenies Support Back-Migration from Beringia to Asia.”

Published 3/12/2014

13. Daughter dearest

journal.pone.0086169.g001With over 19,000 views and over 1700 PDF downloads, a study, “Holsteins Favor Heifers, Not Bulls: Biased Milk Production Programmed during Pregnancy as a Function of Fetal Sex,” showing that daughters may get more milk from their mothers than sons, if you’re a cow that is, published in February.

Published 2/3/2014, Image from the article

14. Holy flying reptiles!

Scientists found a new flying reptile with a sail-shaped crest in a Brazilian boneyard, according to a study published in August, “Discovery of a Rare Pterosaur Bone Bed in a Cretaceous Desert with Insights on Ontogeny and Behavior of Flying Reptiles.”

Published 8/13/2014

15. Long labor

journal.pone.0088640.g002

Possibly showing the earliest live birth from a Mesozoic marine reptile, a fossil displaying the birth has been discovered, according to the article, “Terrestrial Origin of Viviparity in Mesozoic Marine Reptiles Indicated by Early Triassic Embryonic Fossils.”

Published 2/12/2014, Image from the article

16. 3,000-year-old cancer

journal.pone.0090924.g011

What may be the world’s oldest example of human cancer was found in 3,000 year-old bones from Sudan, according to a study from March, “On the Antiquity of Cancer: Evidence for Metastatic Carcinoma in a Young Man from Ancient Nubia (c. 1200BC).”

Published 3/17/2014, Image from the article

17. That stinks!

A failing sense of smell may be a predictor of mortality in older adults, according to a study published in October, “Olfactory Dysfunction Predicts 5-Year Mortality in Older Adults.”

Published 10/1/2014

18. Neanderthals might’ve loved their veggies

Analysis of the oldest human feces ever found may indicate that Neanderthals ate their vegetables, according to the study, “The Neanderthal Meal: A New Perspective Using Faecal Biomarkers.”

Published 6/25/2014

19. No need to re-invent the wheel…er, violin

journal.pone.0109229.g007They say imitation is the highest form of flattery. If that’s true, then according to “Imitation, Genetic Lineages, and Time Influenced the Morphological Evolution of the Violin,” Stradivarius must be blushing. An analysis of violin shape and history suggests that Stradivarius and three other families likely influenced violin shape over the last four centuries, with many imitating their designs.

Published 10/8/2014, Image from the article

20. Glowing gobies and friends

journal.pone.0083259.g001Scientists have conducting a glowing review of fish and discovered over 180 biofluorescent fish in the ocean, according to “The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon,” published in January.

Published 1/8/2014, Image from the article

It’s been another great year at PLOS ONE, and we hope you enjoyed reading this year’s top ALMs papers of 2014. If you’d like to make your own list, please check out our ALMs report.

* This list is selected from a report of papers generated based on the following ALMs ratio: PDF downloads/HTML ratios.

First Image: 20 – Cyrus Tabar

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PLOS ONE’s Top 5 Videos of 2014

Crow_still

Throughout the year we highlight research images that are worth a thousand words. For this year-end list, we’d like to extend the category to our research videos. Here, we’ve highlighted some of this year’s most popular videos, published in the Supporting Information of research articles.

To read the full research article associated with each video, click the links in the descriptions below them.

 

Nighttime Chimp Raids

What monkey business are these chimps up to at night? Wild chimpanzees living in disturbed habitats may raid nearby agricultural fields for maize at night to avoid detection by their human neighbors.

 

Tracking Dino Tracks

Perhaps a dinosaur chase is up to your speed? This model of a dinosaur chase was digitally reconstructed from theropod and sauropod footprints excavated 70 years ago.

 

Otter Talk

These giant otters communicate with one another using different calls in a surprisingly diverse vocal repertoire. Young giant otters beg for food from the adults using a contact call in this video.

 

Say Hello to the Hemihelix

Scientists define and describe a new shape using rubber bands—and they have the video evidence to show how it forms. This shape, a hemihelix, is rarely seen in Nature and could provide clues for fabricating 3D shapes from flat parts.

 

New Caledonians Rule

This video soars above all others as the most popular video from 2014, with 377,000 views at the time of this post. A New Caledonian crow drops objects of different sizes and densities into tubes of water, demonstrating that it may understand water displacement at the same level as a 5-7 year-old child.

If you enjoyed watching these top videos from 2014, feel free to check out more of our videos on the PLOS Media YouTube channel here, and don’t forget to subscribe to our channel!

Citations

Video 1: Krief S, Cibot M, Bortolamiol S, Seguya A, Krief J-M, et al. (2014) Wild Chimpanzees on the Edge: Nocturnal Activities in Croplands. PLoS ONE 9(10): e109925. doi:10.1371/journal.pone.0109925

Video 2: Falkingham PL, Bates KT, Farlow JO (2014) Historical Photogrammetry: Bird’s Paluxy River Dinosaur Chase Sequence Digitally Reconstructed as It Was prior to Excavation 70 Years Ago. PLoS ONE 9(4): e93247. doi:10.1371/journal.pone.0093247

Video 3: Mumm CAS, Knornschild M (2014) The Vocal Repertoire of Adult and Neonate Giant Otters (Pteronura brasiliensis). PLoS ONE 9(11): e112562. doi:10.1371/journal.pone.0112562

Video 4: Liu J, Huang J, Su T, Bertoldi K, Clarke DR (2014) Structural Transition from Helices to Hemihelices. PLoS ONE 9(4): e93183. doi:10.1371/journal.pone.0093183

Image and Video 5: Jelbert SA, Taylor AH, Cheke LG, Clayton NS, Gray RD (2014) Using the Aesop’s Fable Paradigm to Investigate Causal Understanding of Water Displacement by New Caledonian Crows. PLoS ONE 9(3): e92895. doi:10.1371/journal.pone.0092895

All videos are published under a Creative Commons Attribution license, and may be freely reused or remixed.

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Announcing the Latest Update to the Responding the Climate Change Collection

Responding to climate changeNew research added to the PLOS Responding to Climate Change Collection

In December 2013 PLOS ONE published a unique article, Assessing “Dangerous Climate Change: Required Reduction of Carbon Emissions to Protect Young People, Future Generations and Nature”, by James Hansen and colleagues. The article calls for action on climate change to reduce fossil fuel emissions back to pre-industrial era levels. In coordination with the publication of this review, a PLOS ONE call for papers on the topic Responding to Climate Change was made, which in turn led to the launch of the PLOS Responding to Climate Change Collection in July, highlighting research that focuses on efforts to on mitigating and adapting to the effects of the changing climate.

In the year since, the call for papers has launched PLOS into the multidisciplinary territories of earth science. The impact has been great, not only from the Assessing “Dangerous Climate Change” article (nearly 100,000 views, 18 citations and counting), but also from the breadth of research published in this newly emerging field of climate research.

By choosing to publish their research in an Open Access journal, authors’ works are much more accessible to fellow scientists, policymakers, and the public. Allowing their work to be reused under the CC-BY license means that progress in this critical field is faster and unrestricted by copyright.

PLOS is attending the AGU 2014 Fall Meeting this week and, to coincide with the anniversary of James Hansen announcing the call for papers at AGU 2013, we are excited to announce an update to the collection. This selection of research recently published in PLOS ONE covers a wide variety of disciplines from the impact of collective human behaviour to alternative energy resources, such as wind power and its potential use in Australia.

——————————–

Jenni Horsley is Editorial Project Coordinator of PLOS Collections. Find her on Twitter at @jennihy

www.ploscollections.org/respondingtoclimatechange

Image Credits (clockwise from upper left): Matt Rudge, Flickr.com; Vik Walker, Flickr.com; Vera Kratochvil, PublicDomainPictures.net; NASA Goddard Space Flight Center

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Meet PLOS at AGU 2014

AGU_CarouselPLOS ONE is excited to return to the American Geophysical Union’s Fall Meeting (AGU 2014) for a third consecutive year.  The event will be held once again at the Moscone Center in downtown San Francisco, just a few blocks south of PLOS Headquarters.  All are encouraged to stop by booth #2605 to speak with PLOS staff and learn more about our journals.  We look forward to meeting current and prospective authors, Academic Editors, reviewers and anyone else who is interested in PLOS!

At AGU 2013 we announced a call for papers for a new PLOS Collection entitled “Responding to Climate Change” which included Hansen et al.’s article, ‘Assessing “Dangerous Climate Change”: Required Reduction of Carbon Emissions to Protect Young People, Future Generations and Nature.’  To coincide with AGU 2014, we will shortly be updating this collection to feature new research articles.  These papers focus on mitigating and adapting to the effects of the changing climate and feature a range of geophysical approaches, from managing coral reefs based on thermal patterns to the potential of wind power in Australia.  Be sure to look out for the blog highlighting the updated collection in mid-December to see all of the latest additions.  The call for papers remains open; if you are interested in submitting your research to the Responding to Climate Change Collection please contact us at collections@plos.org.

In addition to our PLOS Collections articles, we publish many other great works in the geophysical sciences.  This includes one of PLOS ONE’s most popular articles this year, which solved a long-standing national park mystery by combining glaciology, petrology, and atmospheric science.  To date, Norris et al.’s “Sliding Rocks on Racetrack Playa, Death Valley National Park: First Observation of Rocks in Motion” has received nearly 202,000 page views and 5,000 PDF downloads, impressive press coverage, and massive social media buzz.  This article is just one of the many compelling and important works published in the past year.

The PLOS booth, #2605, will be active all week during AGU 2014, so please stop by any time to see more highlights and meet our staff!  You can also time your visit to coincide with one of our Meet-the-Editor sessions, where you can bring your questions directly to PLOS ONE staff Editors.  These will be held Tuesday December 16th from 2:00-3:00, Wednesday the 17th from 12:30-1:30 and Thursday the 18th from 12:30-1:30.  We look forward to seeing you!

Post written by Jessica Rozek

Images: NASA Goddard Photo and Video. Flickr.com. 2010; Petraglia MD, Alsharekh A, Breeze P, Clarckson C, Crassard R, et al. PLOS ONE. 2012. DOI: 10.1371/journal.pone.0049840; Nie Y, Liu Q, Lui S. PLOS ONE, 2013. DOI: 10.1371/journal.pone.0083973; van Breugel M, Hall JS, Craven D, Bailon M, Hernandez A, et al. PLOS ONE. 2013. DOI: 10.1371/journal.pone.0082433

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Getting Credit for Data

As the largest journal in the world, PLOS ONE publishes an incredible amount of data alongside its research articles, yet the article itself remains the gold standard for attributing credit. While data is the fundamental unit of research, it isn’t recognized as an important component of a researcher’s scholarly output. How can we change this?

At present, sharing data can be onerous work, but Data-Level Metrics (DLMs) can equip researchers with concrete evidence of the value of their efforts. PLOS, in partnership with UC3 and DataONE, has undertaken a project called Make Data Count to develop DLMs. This 12-month NSF-funded project is aimed at piloting a suite of metrics that track and measure data use so that it can be shared to funders, tenure & promotion committees, etc.

But first, we need to better understand the needs of researchers across disciplines and communities—how might you get credit for the data you produce? what do you want to know about how your data is used? Please take this 5-10 minute survey and help us craft data-level metrics: surveymonkey.com/s/makedatacount. Feel free to share widely!

We are excited to engage the PLOS ONE community in designing a new system of crediting scholarly work on data. Please contact Jennifer Lin (jlin@plos.org) for more information or to share your feedback directly.

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Our 200,000-Year-Old Ancestors: Neanderthal Bones in Northern France

Neanderthal bones

We often make new discoveries about our ancient ancestors and how they may have behaved, and we sometimes find the evidence right in their bones. For instance, researchers recently described how the jaw and teeth of a Neanderthal might suggest that they created their own toothpicks out of sticks or used small blades of grass to remove food from their teeth and relieve the pain from gum disease.

At a rescue excavation of an open-air prehistoric site, Tourville-la-Rivière in the Seine Valley of Normandy in northern France, the authors of a study recently published in PLOS ONE were in for a surprise – the discovery of three long human arm bones. The authors detail the unearthing, description, and analysis of these three partially crushed bones: a left humerus, radius, and ulna from the same upper left limb (image above).

The authors used a spectroscopic technique (electron spin resonance, or ESR) and a radiometric dating technique (Uranium-thorium dating, or U-series dating) to determine an approximate age for the Tourville human remains. The authors then scanned the bones in an X-ray and processed them on the computer (X-ray Computerized tomography, or CT) to generate a 3D cross-sectional image of the bones, allowing the authors to examine their shapes and characterize them within the Neanderthal lineage.

As a result of the analyses, the authors estimate the bones most likely belonged to a single Neanderthal adult or older adolescent from 200,000 years ago. This discovery may be the first example of the Neanderthal lineage in northwestern Europe, and the authors suggest that it may provide insight into the relationship of the Tourville remains to other human fossils from ~781,000-126,000 years ago, a period known as the Middle Pleistocene era.

The authors also describe how the shape and other features of these bones are more similar to Neanderthals than to humans. The longest part of the humerus that connects to the deltoid muscle is closer to the length of a Neanderthal bone than a modern human bone. In addition, the attachment site where the radius and ulna meet is similar in structure to Neanderthal bones. The image below displays these similarities, showing the Tourville human remains to the left of well-preserved female Neanderthal bones.

Tourville and Neanderthal arm bones

The researchers also noted that the connective tissue between the tendon and the humerus featured a rather unusual long ridge or crest—this formation is often found in older modern humans, and is located at a section of the bone connected to the deltoid, or back shoulder muscle. Since this muscle allows for the rotation and lifting of the arm, this crest may be the result of a repetitive throwing motion. The researchers suggest that this throwing motion could be connected to activities like spear throwing.

The Tourville fossils may be the oldest found in France during a rescue excavation, and may provide new material for a limited sample of fossils from northwestern Europe. Previously discovered fossil samples from the Middle Pleistocene era mainly consist of skulls and teeth, so the discovery of three arm bones may reveal an unusual shape in the connective tissue that may provide new evidence for how Neanderthals may have behaved. While the authors concede that the precise cause of this abnormality in the connective tissue is unclear, it poses an interesting question for further research on how Neanderthals behaved and whether this change may have impacted their survival as a species.

Citations:

Antoine P, Lautridou JP, Sommé J, Auguste P, Auffret JP, et al. (1998) Les formations quaternaires de la France du Nord-Ouest: Limites et corrélations. Quaternaire 9: 227–241. doi: 10.3406/quate.1998.1605

Lozano M, Subirà ME, Aparicio J, Lorenzo C, Gómez-Merino G (2013) Toothpicking and Periodontal Disease in a Neanderthal Specimen from Cova Foradà Site (Valencia, Spain). PLoS ONE 8(10): e76852. doi:10.1371/journal.pone.0076852

Faivre J-P, Maureille B, Bayle P, Crevecoeur I, Duval M, et al. (2014) Middle Pleistocene Human Remains from Tourville-la-Rivière (Normandy, France) and Their Archaeological Context. PLoS ONE 9(10): e104111. doi:10.1371/journal.pone.0104111

Images: All images are from the article.

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The Rights Stuff: Copyright, Scientific Debate, and Reuse

We’ve all monkeyed around trying to sort out the ownership of published content. In the scientific community, copyright and its (mis)application in publishing has authors, publishers, and readers grappling with questions of what is legally possible, what is desirable, and what is “allowable” by any particular party.

The most recent example of these challenges can be found in a PLOS ONE article published yesterday by Stirling et al., which focuses on a re-analysis of images used by other research groups as evidence for the creation of “striped nanoparticles”. The scientific controversy is fascinating and has been covered on blogs and in social media, but the copyright issues that cropped up during the paper’s publication process are also noteworthy.

In the study, the authors re-analyzed key results from previous work written up in the literature by other researchers and wanted to share their findings by publishing them, formally adding to the scientific literature on nanoparticles. To provide context and more effectively discuss the data, the authors of the re-analysis included figures (images) from previous studies in their own paper. However, the original figures were published in journals that owned the copyright of all the written content. And here is where we ran into a problem, and one that was far from simple.

Clearing rights for republication

These journals generally hold a copyright status of “all rights reserved”. With this restriction, there are three possible ways that these figures could be incorporated into a newly published article.

1) The authors could declare that the reproduction is “fair use” or “fair dealing”:

Traditionally, this hasn’t been done for reproduction of single images from papers. The problem from a publisher’s (and author’s) perspective with this approach is that it isn’t totally clear whether it applies in this case. Publishers are pretty risk averse about this kind of claim (as fair use is a defense against infringement rather than a license itself), so we usually prefer to ask permission.

2) The copyright holder could authorize a specific use under a limited license:

This is the traditional approach—the author would be responsible for negotiating a single use license from the rights holder. This will be a familiar experience to many authors who have written reviews that incorporate figures from other papers. It’s common enough that there are online tools to speed up this kind of transaction.

3) The rights holder could authorize the image to be republished under an open license that allows extensive reuse, with the authors as the copyright holder:

PLOS uses a Creative Commons Attribution License (CC BY 4.0) specifically to cover this issue. With the Stirling, et al. paper, we worked with the authors and the publishers on taking this approach, and we want to say thank you to The Royal Society of Chemistry, Nature Publishing Group (NPG), Wiley Blackwell, and the American Chemical Society for working with us to enable the republication of the material. NPG has a standing policy that they will authorize re-publication of images under the same license as the rest of the article, something they’ve done for us in the past. The other publishers worked hard to make it possible on this occasion, giving approval a few weeks ago. We are very grateful for their efforts.

Why the fuss?

So why did PLOS push for option three when the second was more traditional? As Kevin Smith at Duke has pointed out, it’s not a legal question or a problem with the Creative Commons licenses. It is perfectly possible to mark part of an article as being made available under a different copyright license. But as a question of policy, we make every effort to avoid mixing different licenses within articles.

We do this because, at the heart of PLOS’s work on Open Access, is enabling re-use. Every day people grab newly published articles for various kinds of processing. Some are mining text for information, some are collecting images for use in other projects, and some are working on new forms of display and article presentation. Each of these depends on the downstream user having the rights to copy, store, and transmit the articles. All the articles. And all the pieces of the articles.

On any given day, PLOS might publish a few hundred articles. It is certainly possible in principle to add a copyright statement to a single image. But downstream users would need to check every figure legend of every paper by hand to identify single images they aren’t allowed to use. By insisting on a uniform CC BY license throughout, we give the downstream users clarity and confidence in their rights.

In a perfect world, there would be a clear and consistent machine-readable way of designating sections of an article and differing copyrights within them. But such a standard doesn’t yet exist, and even if it did, there is still a clear advantage to the downstream user to have a uniform policy that grants largely unrestricted reuse.

This case has been both interesting and challenging for us and the authors (who we thank for their patience while we have addressed the licensing issues!). It has highlighted the need for publishers to be willing to authorize onward publication rights with reasonable flexibility as to the licensing arrangements. As the industry moves away from copyright assignment to “license to publish” arrangements, it is important that we get the details of those licenses right. There could be immense value in shared model “license to publish” agreements that would help consistency and support smaller publishers. Most importantly, we have learned the need for clear presentation of our legal and policy obligations when it comes to copyright and reuse.

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Next Steps in Reproducibility

In last week’s Nature and Science, the outcome of a meeting convened by NIH, Nature, and Science to discuss the issue of lack of reproducibility in the basic science research literature was published. This meeting, which brought together representatives from publishers (including PLOS), and many representatives from the NIH and other funders, produced a series of principles, Proposed Principles and Guidelines for Reporting Preclinical Research, which were endorsed by a large and diverse group of publishers, associations, and societies including ourselves. The main principles are as follows:

  • Rigorous statistical analysis
  • Transparency in reporting
  • Data and material sharing
  • Consideration of refutations
  • Consider establishing best practice guidelines for image based data and descriptions of biological data.

Everyone who works in research, as scientist, editor or funder knows that trust is a critical component of having confidence in scientific advances. It would be fair to say that until quite recently it was accepted that the somewhat unstructured narrative style of journal articles with no or little associated data along with few other accepted standard practices was considered sufficient reporting. However, both an increasing number of high profile articles which were found to be unreliable, together with a more general unease, for example around a lack of availability of data, has led journals to conclude that it is now imperative to be much more specific about what an article needs to contain in order for it to be reproducible.

These issues have long been discussed in the medical publishing world and are the rationale behind two long standing initiatives – the ICMJE’s Recommendations for the Conduct, Reporting, Editing and Publication of Scholarly Work in Medical Journals and the many reporting guidelines collected together by the EQUATOR initiative,

Hence, these new principles build on the momentum within the medical literature and are to welcomed as a baseline that all biomedical journals should now be able to adhere to in the basic science literature; they will be a concrete move towards increasing the reproducibility of papers.

However, as with all principles that are put together by committees made up of different groups with their own agenda, they do not go as far as any one party might like. As a publisher that straddles science and medicine, PLOS’s own editorial policies already go some way beyond what is currently being suggested. In two specific areas – data availability and publication of refutations – we hope that other journals move rapidly toward more robust requirements.

Availability of the data underlying a published study is probably the most significant way in which journals can, now, ensure reproducibility of the published literature. A more robust position on data availability, as PLOS has recently pushed for with its data policy, which requires deposition of data in a publicly available repository at the point of publication, would seem possible now.

On refutations, PLOS ONE has been leading the charge to get these papers published for many years. The ICMJE requirements have long noted in the need for medical journals to publish refutations, but in practice getting refutations, failed replications or negative findings published is hard. Although the reasons for this are complex, there is no doubt that in a subscription-based world there were very specific disincentives for journals doing so. In Open Access publishing by contrast, these financial disincentives disappear and journals potentially are much freer to consider such papers. It will be interesting to see whether journals do in practice follow this recommendation.

What’s next? It will be critical that journals move now to operationalize the recommendations made in this document into their workflows. This is no small feat. It will require creating tools for reviewers and editors to assess papers in a systematic, consistent fashion – for example structured review would be a good step in the right direction, although we know that reviewers are not keen on having to tick boxes and justify decisions in any kind of structured way – so journals need to figure out how to bring reviewers with them on this. Furthermore, implementing at scale is even more difficult for large publishers/journals.

We applaud the work that has been done in the recent meeting.  These principles and attributes of sound science reporting will serve as critical cornerstones for long term change for the entire industry and will require deep adoption across the industry.

 

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Fecal Matters: A Stepping Stool to Understanding Indigenous Cultures

Humans differ by opinions, traits, and baseball team preferences. But one constant factor unifies all humans–we excrete feces, and scientists have recognized that number 2 is number 1 in terms of material for ancient population studies. Humans expel hundreds of grams of feces each day, and prehistory versions of this abundant matter may provide insight into the lives of ancient humans.

Human feces contain DNA from bacteria, fungi, parasites, and even from the human herself. Suspecting that this excrement is rich in biological clues, a group of researchers conducted experiments to investigate fecal microbiomes and published a study in PLOS ONE detailing insights into the diets and lifestyles of two ancient indigenous cultures of Puerto Rico: the Saladoid and Huecoid.

The Huecoid and the Saladoid populations originated from the East Andes and present-day Venezeula, respectively. However, it is believed that they coexisted on the Puerto Rican Island of Vieques for a thousand years, beginning in 5 AD. Although previous studies and artifacts have shown religious and cultural differences between the two populations, notable biological differences had yet to be discovered until now.

journal.pone.0106833.g001

The authors of this study gathered ancient fossilized poop samples, called coprolites, from Vieques and Guayanilla, Puerto Rico, as shown in the image above. Using the excavated samples, the researchers performed DNA sequencing and parasite egg and larva extractions to evaluate the differences in the microbial communities between the two ancient cultures. Contrary to prior belief that a coprolite could not preserve ancient DNA, scientists successfully sequenced the fossil microbes contained in the coprolite core. They found that the bacterial distribution varied significantly between the two cores (as seen in the image above) but most notably, sequencing indicated that the Saladoid population had a 10% higher relative abundance of the bacteria, Bacteroidetes, overall, which may mean that the Saladoid people had a higher protein diet.

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Using the remaining coprolite core, the researchers identified parasites based on the shape and presence of dehydrated eggs or larva. According to the authors, the rates of parasite abundance may be double in Saladoid feces as compared to Huecoid. Additionally, the Saladoid core consistently contained hookworms, fish parasites, and dog parasites, providing evidence that the Saladoid people may have eaten raw fish regularly, and may have had dogs as pets. Perhaps sushi and puppies have long been staples in human life?

Researchers also found quite a different diet in the fecal remains of the Huecoid people. The presence of freshwater parasites and evidence of maize may suggest that the Huecoid ate aquatic plants or freshwater invertebrates, and that they may have helped introduce a grain diet to the island.

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As the first image shows, the Saladoid and Huecoid populations lived quite close to each other, making these biological differences in the feces appear even more noteworthy. The authors attribute the distinct microbiotas and parasitism composition to diet and cultural differences such as living arrangements, the way food was handled, and human contact with pets.

Although this is a relatively new field of research, analyzing ancient fossilized fecal matter may be useful for scientists trying to characterize indigenous diets and lifestyles. What was previously disregarded as waste may now be considered a trove of historical and scientific data; the clue is in the poo.

Related Content: 

http://www.iflscience.com/plants-and-animals/fossilized-feces-differ-among-ancient-cultures

Citation: Cano RJ, Rivera-Perez J, Toranzos GA, Santiago-Rodriguez TM, Narganes-Storde YM, et al. (2014) Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures. PLoS ONE 9(9): e106833. doi:10.1371/journal.pone.0106833

Images: Images are from Figure 1, Figure 4, and Table 5 of the published paper.

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PLOS ONE’s Spookiest Images of 2014

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As we take a look back at research articles published so far in PLOS ONE in 2014, we realize we have no shortage of images to terrify our readers, or at least sufficiently creep them out long enough to last through Halloween and possibly the whole weekend. Without further ado, we present our staff picks for figures in PLOS ONE articles that we felt were eerie, ghostly, spine-chilling, corpselike, gross, nightmarish, or just plain weird!

If you enjoy these, we encourage you to comment down below with any of your other favorite, spooky PLOS ONE images from this year.

Click on any one image to see a larger version.

Bugs

Where else would we begin? Those with phobias, look away!

 

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We started off easy and only slightly creepy. The above is actually just a neat 3D model of a bug, specifically a granary weevil.

 

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Okay, this one is definitely creepier than the last image. This is a female (top) and male (bottom) leafcutter bee at the pupal stage…just waiting to come out and say hello.

 

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Eek. This is a fossil millipede embedded in amber, with a close dorsal view of the first segments and mid-body rings. For an overload of creepiness, check out the other figures in the paper.

 

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What’s this?! If spiders can catch fish—they can, as this paper describes, on all continents except Antarctica—what can’t they do? Also, if spiders don’t need webs, are they all set to take over the world?

 

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Here we have more insects in amber. In this image, an ant and a termite hang out together in the same piece of Mexican amber.

 

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This image might look slightly unbelievable, but it shows a new species of spider wasp that may sometimes use dead ants to protect its nest. Obviously…dead ants always add a certain something to the décor, in addition to being excellent home protection!

 

Other species that give us the creeps

 

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Okay, not so bad, a creepy mushroom-lookalike. What’s slightly freaky about it is that it may be a multicellular organism that does not fit into our current phylogenetic tree, which means that it may be part of a new branch of life.

 

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Yuck. Unlike other baby animals, baby coral? Not as adorable.

 

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Slimey goodness in the form of a vocalizing Indian purple frog.

 

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What on Earth is happening in panel D? Lucky for him, the bioluminescent viper dogfish shark has protruding jaws it uses to capture his prey.

 

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This is an Eurasian brown bear breaking the bones of a deer in different ways—such talent! If she could just focus all her efforts on deer and not other species (cough, cough) that would be fantastic.

 

Carcasses under the sea

 

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Above is a set of carcasses, including a whale shark in the panel on the top left, is being devoured by fish in the deep sea.

 

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What we see here, for as long as we can bear to look, are dead pigs in the deep sea, showing carcass decomposition assisted by shrimp and crab that eat them and drag them around. Yum.

 

Let’s put the past behind us

 

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The first eerie image above compares the footprint of an early limbed vertebrate, a temnospondyl (right), with that of a salamander (left). Researchers showed that his walk, shown as a hypothetical in the second image, was probably a lot different from that of a salamander, with a forelimb-driven gait as opposed to the hindlimb-driven one of the latter species.

 

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Yikes. The “ripper” behavioral model is illustrated above for a non-avian theropod dinosaur, known for having a “killing claw” used for slashing and eating prey that are still alive!

 

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Behold a rare “bone bed” containing remnants from a newly discovered species of pterosaur. This mess of bones may indicate that the species was fairly social, outgoing, and lived in groups.

 

Mummies and the like

 

Saving the best for last, no scary image list is complete without some totally stomach-wrenching mummy pics. Enjoy!

 

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This South American mummy was likely suffering from a disease, hit in the head, and murdered.

 

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While not a mummy, this young individual may have suffered traumatic brain injury and was buried with two red deer antlers on its chest, a possibly unique funerary practice.

 

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A clothes-wrapped body was found inside this coffin, which is a possible case of cherubism in a 17th-century Korean mummy.

 

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And lastly, the above depicts three plastered skulls dating to a pre-pottery period, with the plastering process a possible representation of the shift from hunter-gathering to food-producing strategies. Scary stuff!

Happy Halloween from PLOS ONE!

 

Citations

Image 1: Slon V, Sarig R, Hershkovitz I, Khalaily H, Milevski I (2014) The Plastered Skulls from the Pre-Pottery Neolithic B Site of Yiftahel (Israel) – A Computed Tomography-Based Analysis. PLoS ONE 9(2): e89242. doi:10.1371/journal.pone.0089242

Image 2: Nguyen CV, Lovell DR, Adcock M, La Salle J (2014) Capturing Natural-Colour 3D Models of Insects for Species Discovery and Diagnostics. PLoS ONE 9(4): e94346. doi:10.1371/journal.pone.0094346

Image 3: Holden AR, Koch JB, Griswold T, Erwin DM, Hall J (2014) Leafcutter Bee Nests and Pupae from the Rancho La Brea Tar Pits of Southern California: Implications for Understanding the Paleoenvironment of the Late Pleistocene. PLoS ONE 9(4): e94724. doi:10.1371/journal.pone.0094724

Image 4: Riquelme F, Hernández-Patricio M, Martínez-Dávalos A, Rodríguez-Villafuerte M, Montejo-Cruz M, et al. (2014) Two Flat-Backed Polydesmidan Millipedes from the Miocene Chiapas-Amber Lagerstätte, Mexico. PLoS ONE 9(8): e105877. doi:10.1371/journal.pone.0105877

Image 5: Nyffeler M, Pusey BJ (2014) Fish Predation by Semi-Aquatic Spiders: A Global Pattern. PLoS ONE 9(6): e99459. doi:10.1371/journal.pone.0099459

Image 6: Coty D, Aria C, Garrouste R, Wils P, Legendre F, et al. (2014) The First Ant-Termite Syninclusion in Amber with CT-Scan Analysis of Taphonomy. PLoS ONE 9(8): e104410. doi:10.1371/journal.pone.0104410

Image 7:  Staab M, Ohl M, Zhu C-D, Klein A-M (2014) A Unique Nest-Protection Strategy in a New Species of Spider Wasp. PLoS ONE 9(7): e101592. doi:10.1371/journal.pone.0101592

Image 8:  Just J, Kristensen RM, Olesen J (2014) Dendrogramma, New Genus, with Two New Non-Bilaterian Species from the Marine Bathyal of Southeastern Australia (Animalia, Metazoa incertae sedis) – with Similarities to Some Medusoids from the Precambrian Ediacara. PLoS ONE 9(9): e102976. doi:10.1371/journal.pone.0102976

Image 9: Toh TC, Ng CSL, Peh JWK, Toh KB, Chou LM (2014) Augmenting the Post-Transplantation Growth and Survivorship of Juvenile Scleractinian Corals via Nutritional Enhancement. PLoS ONE 9(6): e98529. doi:10.1371/journal.pone.0098529

Image 10: Thomas A, Suyesh R, Biju SD, Bee MA (2014) Vocal Behavior of the Elusive Purple Frog of India (Nasikabatrachus sahyadrensis), a Fossorial Species Endemic to the Western Ghats. PLoS ONE 9(2): e84809. doi:10.1371/journal.pone.0084809

Image 11: Claes JM, Partridge JC, Hart NS, Garza-Gisholt E, Ho H-C, et al. (2014) Photon Hunting in the Twilight Zone: Visual Features of Mesopelagic Bioluminescent Sharks. PLoS ONE 9(8): e104213. doi:10.1371/journal.pone.0104213

Image 12: Arilla M, Rosell J, Blasco R, Domínguez-Rodrigo M, Pickering TR (2014) The “Bear” Essentials: Actualistic Research on Ursus arctos arctos in the Spanish Pyrenees and Its Implications for Paleontology and Archaeology. PLoS ONE 9(7): e102457. doi:10.1371/journal.pone.0102457

Image 13: Higgs ND, Gates AR, Jones DOB (2014) Fish Food in the Deep Sea: Revisiting the Role of Large Food-Falls. PLoS ONE 9(5): e96016. doi:10.1371/journal.pone.0096016

Image 14: Anderson GS, Bell LS (2014) Deep Coastal Marine Taphonomy: Investigation into Carcass Decomposition in the Saanich Inlet, British Columbia Using a Baited Camera. PLoS ONE 9(10): e110710. doi:10.1371/journal.pone.0110710

Image 15: Marsicano CA, Wilson JA, Smith RMH (2014) A Temnospondyl Trackway from the Early Mesozoic of Western Gondwana and Its Implications for Basal Tetrapod Locomotion. PLoS ONE 9(8): e103255. doi:10.1371/journal.pone.0103255

Image 16: Fowler DW, Freedman EA, Scannella JB, Kambic RE (2011) The Predatory Ecology of Deinonychus and the Origin of Flapping in Birds. PLoS ONE 6(12): e28964. doi:10.1371/journal.pone.0028964

Image 17: Manzig PC, Kellner AWA, Weinschütz LC, Fragoso CE, Vega CS, et al. (2014) Discovery of a Rare Pterosaur Bone Bed in a Cretaceous Desert with Insights on Ontogeny and Behavior of Flying Reptiles. PLoS ONE 9(8): e100005. doi:10.1371/journal.pone.0100005

Image 18: Panzer S, Peschel O, Haas-Gebhard B, Bachmeier BE, Pusch CM, et al. (2014) Reconstructing the Life of an Unknown (ca. 500 Years-Old South American Inca) Mummy – Multidisciplinary Study of a Peruvian Inca Mummy Suggests Severe Chagas Disease and Ritual Homicide. PLoS ONE 9(2): e89528. doi:10.1371/journal.pone.0089528

Image 19: Coqueugniot H, Dutour O, Arensburg B, Duday H, Vandermeersch B, et al. (2014) Earliest Cranio-Encephalic Trauma from the Levantine Middle Palaeolithic: 3D Reappraisal of the Qafzeh 11 Skull, Consequences of Pediatric Brain Damage on Individual Life Condition and Social Care. PLoS ONE 9(7): e102822. doi:10.1371/journal.pone.0102822

Image 20: Hershkovitz I, Spigelman M, Sarig R, Lim D-S, Lee IS, et al. (2014) A Possible Case of Cherubism in a 17th-Century Korean Mummy. PLoS ONE 9(8): e102441. doi:10.1371/journal.pone.0102441

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