Honey for Your Boo Boo

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An apple a day might keep the doctor away, but honey may fight some infections.

Bacterial cell walls are not only responsible for sustaining the cell’s shape but are also necessary for the bacteria’s growth, survival, and reproduction. A class of antibiotics called beta-lactams, which includes the familiar antibiotics penicillin and ampicillin, attack the cell wall’s proteins, causing the cell wall to fall apart and die. While this is effective for treating many common bacterial infections in people, microbes have long been developing resistance to antibiotic drugs, referred to as antibiotic resistance. In the race to protect ourselves from these bugs, scientists are looking for promising alternatives that may combat microbes with the same effectiveness as antibiotics.

Previous studies have investigated honey’s ability to kill and halt growth of certain strains of bacteria. Taking this into account, researchers compared the efficacy of Canadian honey on killing E. coli, strains of bacteria commonly associated with feces and contaminated food, as well as a vital part of all human bodies. The authors of the study, published in PLOS ONE, investigated honey’s antibacterial activity and its potential ability to inhibit growth of antibiotic-resistant strains of E. coli.

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The authors conducted a series of experiments by applying various concentrations of honey or antibiotics to bacterial cell cultures and then visualizing changes in the cell structure to determine the necessary concentrations of each to inhibit growth and kill cells. Using scanning electron microscopy (SEM), as seen in the image above, the authors observed the transformation in cell structure over time as they increased the amount of added honey or ampicillin. Flourishing E. coli are typically rod- shaped with filaments, but within 18 hours of application of honey or ampicillin, the shape appeared to transform into “spheroblasts,” as seen in the image below. Spheroblasts are what remains after the cell wall has been broken by an antibiotic drug, as well as the debris of the dead cell. According to the authors, the results may indicate that like ampicillin, honey can interfere with E. coli’s ability to survive and reproduce.

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Many strains of E. coli are resistant to beta-lactams like ampicillin, and to test honey’s effect on these strains, the researchers repeated their experiments with honey on ampicillin-resistant strains of E. coli and again visualized cell shape changes and inhibition of bacterial growth. The honey appeared to halt the growth of the ampicillin-resistant bacteria with the same efficiency as it halted non-resistant strains.

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The image above illustrates the destruction of the cell wall and the death of the ampicillin-resistant cell after exposure to honey (panel A before treatment, and panel B after honey application). Recent studies have suggested that honey’s antibacterial mechanisms may be attributed to the concentration difference between honey and water molecules, referred to as high osmolarity, and honey’s ability to inhibit bacterial communication. Honey is a natural mixture of many compounds, and while scientists have yet to confirm the exact compounds responsible, the results of the above study support the idea that honey and ampicillin may have similar antibacterial efficacies, with possibly different mechanisms of attack.

As microbes become increasingly resistant to our standard treatments, it’s important to investigate alternative mechanisms of antibacterial defense. Although more work remains to be done here, the authors’ evidence of honey-induced cell death with apparently similar efficacy to ampicillin may pioneer future studies in the field. In other words, honey could be just what the doctor ordered.

Citation: Brudzynski K, Sjaarda C (2014) Antibacterial Compounds of Canadian Honeys Target Bacterial Cell Wall Inducing Phenotype Changes, Growth Inhibition and Cell Lysis That Resemble Action of β-Lactam Antibiotics. PLoS ONE 9(9): e106967. doi:10.1371/journal.pone.0106967

Image 1: Viscosity Manifest by Beny Shlevich

Images 2-4: Figures 3, 5, and 9 from the article

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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 and controversial findings.

All year long, the staff editors at PLOS ONE carefully scan newly submitted manuscripts before they’re sent to our Editorial Board for assessment and scientific peer review. Among the thousands of titles that each PLOS ONE staff editor has seen over the past year, there were bound to be some year-end favorites! We polled the PLOS ONE staff editors and asked them to send along their picks, presented in no particular order.

1. Media Multi-Tasking on the Brain

 

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As we increasingly rely on multimedia devices in our personal and professional lives, we may wonder what impact our habits have on our brains. Studies have indicated that media multi-tasking—that is, the concurrent use of multiple media devices—may have a negative impact on a number of cognitive functions, but the neural changes responsible for these declines remain largely unexplored.

Using MRI to explore structural associations with our use of media, the authors of “Higher Media Multi-Tasking Activity Is Associated with Smaller Gray-Matter Density in the Anterior Cingulate Cortex” show that users who frequently engage in media multi-tasking may have a lower density of gray-matter in the anterior cingulate cortex, a region in the brain crucial for a number of higher cognitive processes. While the authors cannot yet state that media multi-tasking causes decreased gray matter, it does make us wonder whether our devices are, quite literally, becoming a substitute for our brains.

 

2. Improving Zebrafish Care and Welfare in the Lab

 

zebrafishImage from article

The use of zebrafish in developmental and biomedical research has increased substantially in recent years. The popularity of this relatively new model species has sparked an interest in assessing—and potentially improving—their welfare in the lab environment. Evaluating the “humaneness” of euthanasia is a critical research aim, since nearly all zebrafish are sacrificed at the end of an experiment.

In “Conditioned Place Avoidance of Zebrafish (Danio rerio) to Three Chemicals Used for Euthanasia and Anaesthesia,” the authors report the results of a behavioral test designed to evaluate and compare the animals’ aversion to three commonly used euthanasia agents: tricaine methanesulfonate (referred to as TMS or “MS-222”), clove oil, and metomidate hydrochloride. The researchers found that zebrafish exposed to TMS spent less time in the side of the experimental tank that they had previously preferred, indicating aversion. Exposure to the other two chemicals did not elicit such a response, leading the authors to conclude that clove oil and metomidate hydrochloride are less aversive to zebrafish and could be pursued as “humane alternatives” to TMS for euthanasia. This finding may play an important role in the updating of guidelines for the care and use of zebrafish in the research setting.

 

3. Supercentenarian Genomes

 

christmas dna Image from Flickr

This paper was picked by two PLOS ONE Editors! Do our genes determine whether we could live to be 110? To answer this question, the authors of “Whole-Genome Sequencing of the World’s Oldest People” sequenced the genomes of 17 supercentenarians and compared their DNA to that of the general population. Despite trying several ways of searching, the researchers did not find any specific genetic variations associated with supercentenarians, but they did generate a unique, publicly available dataset and a useful resource that may help us someday uncover the genetic code for a long life (or else determine that one may not exist)!

 

4. Paper Microscopes, < $1 each

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 This was another paper that got more than one vote from the PLOS ONE Editors. The Stanford University authors of “Foldscope: Origami-Based Paper Microscope” bring microscopy to the masses with their invention. Fabricated from paper and assembled in 10 minutes using origami folding techniques, the Foldscope comes in at a per unit cost of less than $1 and represents an exciting opportunity to inexpensively fabricate microscopes in bulk. It uses an LED light that provides up to 50 hours of light on a single button battery, making it usable for field applications. The Foldscope may find its way into the hands of students, educators, and scientists worldwide for a wide-range of purposes, including future disease-specific designs for rapid diagnoses in the field.

 

5. Yeast with Mitochondria, Please!

 

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Anyone who has worked in or near a Drosophila lab will appreciate how much flies love yeast, but not everyone may have guessed the contribution of yeast mitochondria to the flies’ attraction to yeast. Through a genetic screen designed to identify attractive yeast strains, the authors of “Saccharomyces cerevisiae mitochondria are required for optimal attractiveness to Drosophila melanogaster” may have unveiled the importance of yeast mitochondria metabolism for fly attraction and more generally, yeast ecology.

 

6. Plant Xylem = Water Filter?

 

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This study from MIT, published way back in January, held strong as one of our favorites throughout this year. With the problem of waterborne diseases causing up to ~1.8 million deaths annually, “Water Filtration Using Plant Xylem” describes the use of plain old sapwood from coniferous trees as a way to remove bacteria and pressure-filter up to several liters of clean drinking water per person per day. Like the Foldscope mentioned above, this method may be useful for the public, readily available, inexpensive, and to top it off, completely biodegradable and disposable. If implemented, this method may be able to help address the need for clean water in developing countries and areas where resources are otherwise limited.

 

7. Glial Cells Involved in Schizophrenia

 

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Schizophrenia and biopolar disorder are highly heritable, but the genetic contributions to these disorders are not well understood. In “Pathway Analyses Implicate Glial Cells in Schizophrenia,” the authors used publicly available data from the Psychiatric Genomics Consortium and sought associations between these illnesses and biological pathways (groups of genes), rather than studying single gene associations. Results showed that a glia-oligodendrocyte pathway was associated with both disorders, supporting a model in which genetic factors contribute to white matter abnormalities observed in brains of patients with schizophrenia. This methodological advance may be instrumental in increasing our understanding of multi-genic diseases and disorders that have eluded geneticists for decades.

 

8. SAFE 2013: Exploring Sexual Harassment in Science

 

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In “Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault,” authors detail a self-selected survey of 666 field researchers, where nearly two in three surveyed reported experiencing sexual harassment, and over one in five reported suffering sexual assault. According to the study, women were more likely than men to be subject to harassment or assaults, and unlike men, the women reported receiving abuse more from superiors than from peers. Unfortunately, victims felt they had limited awareness of policies and reporting mechanisms. Published in July, this study has helped open up a conversation about sexual harassment and assault in anthropology and scientific research more broadly, including extensive discussion in media and blogs lasting much long than the usual media cycle for a publication. The study was also quoted by a member of the US Congress. It was one of our most-viewed PLOS ONE articles in 2014, and in the top ten by social shares—the most tweeted PLOS ONE article this year—and has 79 media links so far.

 

9. Disease-Fighting Drugs in Sloth Hair

 

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As legend has it, penicillin was discovered when an unwelcome fungus floated through an open window, landed in a petri dish, and blocked the growth of bacteria. If this serendipitous event could transform modern medicine, what is the potential of the over 5 million fungal species that have yet to be characterized? In “Sloth Hair as a Novel Source of Fungi with Potent Anti-Parasitic, Anti-Cancer and Anti-Bacterial Bioactivity,” the authors visited the microbe-rich tropics of Central America and offered nine wily three-fingered sloths a free haircut. The hair samples yielded dozens of novel fungal strains, many of which displayed activity against bacteria, parasites, and cancer cells. These findings may provide leads for drug development and underscore the untapped potential hiding in microbial biological diversity.

 

10. New Caledonians Continue to Amaze Us

 

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The videos for this paper are amazing, and we weren’t the only ones that thought so! The video above was by far our most popular on our Youtube channel this year. In “Using the Aesop’s Fable Paradigm to Investigate Causal Understanding of Water Displacement by New Caledonian Crows,” the authors employ the established Aesop’s Fable paradigm to show that New Caledonian crows are able to causally understand water displacement, similar to the understanding in a 5-7 year-old child. A few months later, the authors published a second study with us on the same topic.

 

11. Chickens Walking Like Dinosaurs

 

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Although birds are direct descendants of theropod dinosaurs, they cannot be used confidently to gain insights into certain aspects of dinosaur biology because their bodies have changed so much over the course of evolution.  In an effort to explore chickens as a model for dinosaur locomotion, the authors of “Walking Like Dinosaurs: Chickens with Artificial Tails Provide Clues about Non-Avian Theropod Locomotion” attached an artificial tail to two-day-old chicks to substitute for the bony tail of dinosaurs that was lost to evolution.  As adults, the chickens exhibited a displaced center of mass, and changes in limb posture and range of motion, creating a potential model for investigating dinosaur locomotion mechanics and energetics.

 

12. Working Together, Not Against: The Tale of H4K16ac and ISWI

 

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Histone proteins, assembled into a nucleosome structure, are essential for compacting DNA into tiny nuclei inside eukaryotic (membrane-bound) cells. However, access to specific regions of DNA is necessary during a cell’s lifetime, and chromatin remodelers such as ISWI, alongside chemical modifications to the histones, such as acetylation of Lysine 16 on Histone (H4K16ac), can help unravel the DNA. Somewhat paradoxically, evidence seems to suggest that H4K16ac actually works against ISWI and inhibits it. As all evidence indicating that H4K16ac inhibits ISWI was performed using peptides or arrays containing just one nucleosome, the authors of “ISWI Remodelling of Physiological Chromatin Fibres Acetylated at Lysine 16 of Histone H4” decided to approach the puzzling question using nucleosomes arrays made of 25 nucleosomes to more closely mimic the chromosome. Using this system, researchers showed that H4K16ac did not in fact stop ISWI in its remodeling capabilities as previously thought, putting the conundrum to rest.

 

13. How Available are the Results of Clinical Trials?

 

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Clinical trial reporting and transparency is an important editorial issue that we at PLOS support. In “How Frequently Do the Results from Completed US Clinical Trials Enter the Public Domain? – A Statistical Analysis of the Clinicaltrials.Gov Database,” the authors analyzed data from 400 randomly selected clinical trials registered in the ClinicalTrials.gov (CTG) database and found that almost one third had failed to achieve public disclosure of results within 4 years of completion, either by publishing the primary outcomes in a peer-reviewed journal, or posting the results to the CTG database.

Studies were less likely to publicly disclose the results if i) they were a phase 2 versus a phase 3/4 clinical trial, ii) if the sample size was small, or iii) if the study design involved randomization. These findings broadly support previous studies of clinical trial reporting, including a PLOS ONE study in 2013 by Huser et al.

There you have it! A diverse selection of papers that we hope gives you a taste of the scope and breadth of research published in PLOS ONE. Here’s to another huge round of exciting research in 2015!

Happy New Year!

The PLOS ONE Staff Editors

Damian Pattinson, Iratxe Puebla, Catriona MacCallum, Meghan Byrne, Michelle Dohm, Matt Hodgkinson, Eric Martens, Adrian Aldcroft, Gina Alvino, Sarah Bangs, Christna Chap, Eileen Clancy, Alejandra Clark, Renee Hoch, Jessica Rozek, Nicola Stead, and Edward Sucksmith

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

Orca_Andy WrightPost 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 of long, drawn-out research projects, and give scientists a chance to approach a question they’ve never considered before?

This was the idea behind the ‘Research Derby’—an intense event that gives researchers the chance to ask and answer a question relevant to conservation biology, ecology, or evolution. This event was modeled on ‘hackathons’ in the IT world—small teams lock themselves away and produce the best product they can given limited time. After the event, all participants focus on one of the teams’ research questions and develop it into a full publication over the next year.

Last winter, we ran a Derby at the University of Victoria in British Columbia, Canada. We brought together undergraduates, graduate students, and postdoctoral fellows from multiple departments. The two of us, both postdoctoral fellows at the time, landed on the same team. Over the two-day event, we brainstormed potential research topics and eventually decided on a topic that interested all of us—the effectiveness of species conservation in Canada. Specifically, we decided to examine aspects of Canada’s endangered species recoveries, combining Caroline’s expertise about Canada’s endangered species legislation with the Derby team’s collective aim to look at the overall picture of species conservation in Canada.

The process of species protection in Canada is far from straightforward. For a given species, the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) first provides an assessment, which is then forwarded to the federal government to decide whether or not to list that species under Canada’s Species at Risk Act (SARA). Once listed under SARA, a series of legal obligations for protection set in; for example, for endangered species, critical habitat must be identified where possible in the Recovery Plan.

Up to 2013 we found: of 369 species examined more than once by COSEWIC, 86% had become more endangered or failed to improve.[1] We also examined whether being protected by SARA was associated with improved COSEWIC assessment outcomes relative to unlisted species—the answer was “no,” unfortunately. Further, we found that for more than half of eligible SARA-listed species, critical habitat had not been fully identified; without identification, this habitat cannot be fully protected.

This paper proved to be highly impactful. Discussed in Canada’s parliament (twice), passed around government departments, and widely covered in the media, our findings have been broadly disseminated to decision makers, other conservation scientists, and the general public. From a 24-hr research event to publication in less than a year, this was a rapid and influential scientific effort that resulted from a unique collaboration. While the event was only 24 hours, we spent several months after the Derby checking our data, refining our methods, and developing our quick-and-dirty findings into a mature product fit for a peer-reviewed, open-access, and widely read publication. All Derby research members participated on each stage of the research, but we each used our strengths and collaboratively developed our final product. And most importantly—it was a lot of fun from start to finish.

Dr. Brett Favaro is a Liber Ero postdoctoral fellow, and a Research Scientist at the Fisheries and Marine Institute of Memorial University of Newfoundland. His mission is simple: do science that informs the way we manage our natural resources, especially biodiversity. Primarily a marine biologist, Brett’s research examines ways to make commercial fishing more sustainable. However, since many conservation problems are inherently political, he studies environmental policy as well. Brett completed both his Bachelor’s of Science and Ph.D. at Simon Fraser University in Burnaby, British Columbia, Canada.

Dr. Caroline Fox is a postdoctoral fellow with Raincoast Conservation Foundation and the Department of Geography at the University of Victoria. Her research interests revolve around marine-terrestrial interactions, marine predator ecology and efforts to measure and mitigate human impacts in coastal ecosystems. As a big-picture ecologist and conservation scientist, her research spans a diversity of coastal ecosystems and taxa, including kelp forests, seabirds and black bears. Caroline completed her B.Sc. and Ph.D. at the University of Victoria and M.Sc. at Case Western Reserve University.

[1] Favaro B, Claar DC, Fox CH, Freshwater C, Holden JJ, et al. (2014) Trends in Extinction Risk for Imperiled Species in Canada. PLOS ONE 9(11): e113118. doi:10.1371/journal.pone.0113118

Image: Orca by Andy Wright

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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

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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

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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.

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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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