Zoom-Enhance: Identifying Trends in Article-Level Metrics

In late December 2013, PLOS ONE published an article from UK-based Psychologists Rob Jenkins and Christie Kerr titled “Identifiable Images of Bystanders Extracted from Corneal Reflections”. Using high-resolution photography, Jenkins, from the University of York, and Kerr, from the University of Glasgow, demonstrate that humans can recognize faces in the reflection of photographed eyes.

ALM post image 1As high-resolution photography becomes increasingly accessible and portable, the possibilities of linking technology with the human brain become increasingly exciting. The notion of an image within an image, or a crime scene revealed in the reflection of an eye, creates endless possibilities for the scientifically minded. There are potential applications to criminal investigations with, for instance, the identity of a suspect being revealed within the eye of a photographed victim. It’s a bit creepy, but also fascinating—it’s not difficult to see why the article might capture the public’s imagination.

But perhaps even more amazing than the technology is the ability we have to recognize faces even in the absence of fine details we might have thought were crucial. An image of a well-known politician serves as an example:

ALM post image 2In an interview with the University of York, Dr Jenkins described the research:

“The pupil of the eye is like a black mirror. To enhance the image, you have to zoom in and adjust the contrast. A face image that is recovered from a reflection in the subject’s eye is about 30,000 times smaller than the subject’s face. Our findings thus highlight the remarkable robustness of human face recognition, as well as the untapped potential of high-resolution photography.”

The study conjures scenes from science fiction, most notably Ridley Scott’s Blade Runner and the often-ridiculed “zoom-enhance” technology depicted in television crime dramas. This was a study bound to capture the attention of the internet—and it did. At the time of this writing, the article has more than 170,000 views and over 1,500 Twitter mentions. It is the fourth most-tweeted article ever published in PLOS ONE.

The overall picture of views and mentions on social media is impressive, but looking at the patterns in the Article-Level Metrics (ALMs) reveals some unexpected twists.

Take, for example, the ALMs graph illustrating cumulative views of the article:

ALM post image 3

As anticipated, the article attracted a large audience from the beginning. In the first month after publication, the article had nearly 40,000 views. We contacted Rob Jenkins for some comments on his experience:

I kept an eye on these metrics right from the start. I had done a lot of press on the day of publication—mainly radio interviews around the world—and was interested to see if this press promotion would register on the ALM tracker. I remember feeling really pleased towards the end of the day when the number of page views entered double digits. My goal of hitting 100 page views by the next day seemed within reach.

By the morning, the story had completely blown up, and the page views leaped up orders of magnitude in a matter of days. I always thought the story had the potential to capture people’s imagination, but I think the timing was the key. The paper was published on December 26th 2013, when a lot of people had free time on their hands.

But when looking at the cumulative views, what is unusual is that, after the initial attention and tapering off—a typical pattern—there was a major resurgence in views in January 2015, over a year after the article was published. Rob Jenkins commented:

Every few months I returned to the article metrics to get an idea of their trajectory. The typical pattern seems to be that page views peak in the first month and then fall off sharply. That was certainly the case here. Having originally been pleased that 100 seemed within reach, I was now slightly crestfallen that they would never reach 100,000.

Then something unexpected happened. In December 2014, one year after publication, the page views showed an anomalous spike—from a few hundred per month to nearly 9000. Curious. But I assumed that the established pattern would reassert itself the following month. In fact, January 2015 was the busiest month ever, with over 72,000 page views.

Looking at the data, it is clear that somehow (unusually) the article managed to spark a second life. With a flurry of catchy hashtags, including #Woah #BladeRunner, #Spooky, and #Enhance Enhance Enhance, the study came back into the public consciousness. While the several pages of Twitter discussions reveal a few noteworthy tweets from potential “hub” Twitter users, it is not trivial to find an apparent, specific event that triggered the second wave of article views.

Dr Jenkins was similarly perplexed:

I’m afraid I don’t know what triggered the jump in views. I’m not aware of any media coverage after the first wave early 2014. I presented the study at an Interpol meeting in Autumn 2014, and I still include it in talks to general audiences, but I can’t draw a line from any of those events to the ALM profile. I’m sorry I can’t offer any more insight.

ALM post image 4

So, unfortunately, neither the ALMs nor the author can provide a satisfactory explanation for the article’s resurgence in popularity. But, after a slightly deeper investigation, we have come up with a few theories:

Holiday viewing

Perhaps, as Dr Jenkins mentioned, it was the time of year. The second peak in views came during the holiday season, when work is a little slower and there is time to reflect upon the notable events and discoveries of the last year, with a focus on the fun, new, and imaginative. Could it be that the second wave of views came as scientists kicked back with some eggnog, behind the soft glow of their computer screens, and reflected upon the articles that captured the public’s attention over the past 12 months?


Perhaps the second wave of views could be explained through Twitter, where the article had a significant presence. One of the first notable tweets in the article’s comeback came on 29 December 2014 from Rowan Hooper, News Editor for New Scientist. He mentioned the article on his Twitter feed, garnering ~300 retweets and ~175 favorites. A few days later, Ed Yong, a British science writer with over 65,000 followers on Twitter, also mentioned the article, and his tweet was retweeted ~750 times and favorited ~500 times. It seems plausible that these notable mentions are the source of the article’s new life.

ALM post image 5Buzzfeed

When published, the article received significant media attention including coverage in The Telegraph and Scientific American, but after the first few weeks, the coverage died down. However there is a notable event that coincides with the resurgence of the article’s popularity. On 29 December, the popular website BuzzFeed published an entry titled “46 Important Things Science Taught Us In 2014,” where the article was featured at number 18. With frequent links on social media, BuzzFeed has become ubiquitous in our internet lives, and coverage at the end of the year, where there is an obsession with best-of lists, could well be responsible for bringing a new audience to the article.

ALM post image 6Finally…. The Verdict:

An investigation of the ALMs and media coverage provides a number of clues to explain the viewing pattern, but we cannot draw any firm conclusions beyond an affirmation that the world—and in particular, the Internet—is a complex and highly socially networked place. While ALMs cannot provide an interpretation, they do provide us with valuable data that reflects the way science is communicated in the 21st century. The most likely explanation is, of course, a complex one, with several factors at play, some more than others, but all playing a part.

Still, in our continuing quest for an answer, we have contacted our local CSI unit to see if we can borrow some of their forensic smarts.

You can view the ALMs and media coverage of the article via the following links. All articles published by PLOS have this information.

ALMs: http://www.plosone.org/article/Metrics/info:doi/10.1371/journal.pone.0083325

Media coverage for this article: http://www.plosone.org/article/related/info%3Adoi%2F10.1371%2Fjournal.pone.0083325

Post written by Adrian Aldcroft

Citation: Jenkins R, Kerr C (2013) Identifiable Images of Bystanders Extracted from Corneal Reflections. PLoS ONE 8(12): e83325. doi:10.1371/journal.pone.0083325


 Image 1, 2, 6: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083325

Image 3, 4: http://www.plosone.org/article/Metrics/info:doi/10.1371/journal.pone.0083325

Image 5: Capture from Ed Yong’s Twitter, https://twitter.com/edyong209/status/550299961204961281

Category: Article-Level Metrics, Author Spotlight, Interviews, Media, Social Media | Tagged | 1 Comment

Biting Off What They Can Chew: Scientists Use 3D Reconstructions to Study Animal Jaw Mechanics

Wombat Chinese giant salamander

Wombat 3D skull                Salamander 3D skull

Studying the muscles that animals use to bite and chew can tell us a lot about their eating habits. In the past, researchers often undertook painstaking dissection of animal specimens by hand to visualize the muscles used for specific tasks like chewing. Physical damage from the separation of muscle layers during dissection and the effects of dehydration post-mortem can limit the accuracy of manual dissection, making this option less than ideal. In two recent PLOS ONE studies, researchers show us that modern “digital dissection” technologies can be used to avoid the problems associated with traditional dissections in two very different animals, one cute and cuddly and one slimy and giant.

In the first study, the authors used non-destructive X-ray computed tomography (CT) and magnetic resonance imaging (MRI) techniques alongside traditional dissection to generate the first detailed model of the muscles a common wombat uses to close its jaw. While we are most familiar with these types of scans from their use in medical imaging and screening for human diseases, these same methods can be used by researchers to get a peek at an animal’s inner muscular workings.

CT and MRI scans can pinpoint specific regions of an object and create a series of bisecting images, or “slices.” Scientists can view each slice separately, allowing them to identify individual muscle groups and tissues, as in the image below.

Wombat skull CT scan (Fig. 2)

Individual slices are assembled to reconstruct the object with a detailed view of the inner structures. In the study, a 3D reconstruction of the wombat head is created by combining the information obtained from CT and MRI slices. Because these techniques allow the authors to see the inner architecture of the head, they are able to reconstruct the bones and muscles from the inside out, and see first-hand the interactions of the muscles in their position in the skull. What’s more, a neat, downloadable 3D PDF (Figure S1) is included in the paper that, when opened using Adobe Reader, is fully interactive. Readers can rotate the model 360°, isolate individual parts, or make certain parts transparent.

3D Wombat Skull (Fig6)

Authors of another recent PLOS ONE paper took their analysis one step further to study the bite mechanics of a Chinese giant salamander, the world’s largest amphibian. These researchers used CT scanning to analyze sutures that naturally occur on the skulls of adult and adolescent salamanders. The sutures are essential for skull stability and help to disperse compression forces during biting. By modeling the stress points that would occur under different biting conditions and comparing them to the skull sutures, scientists can predict which bite pattern would cause the least stress on the skull.

The authors of this study used computer simulations to model a bilateral bite, with initial equal pressure on both sides of the mouth, or a unilateral bite, with initial pressure on the left side of the mouth only. In each situation, authors simulated prey capture with the initial bite occurring toward the front versus the back of the mouth. The scientists found a clear difference in the simulated pattern of generated forces when the salamander was biting down at the front tip of the mouth versus the back.

In the video above, the authors used heat mapping to show the simulated forces exerted on various points in the salamander’s skull during the bite, with red patches indicating the greatest force, and blue patches indicating the least. The video shows what the researchers predict to be the optimal biting strategy: biting down at the front of the mouth causes less stress on the skull relative to biting down further back in the jaw.

While a bilateral bite distributes forces and allows salamanders to capture elusive or large prey, the video below shows an asymmetrical bite that may be utilized during a “sit-and-wait” strategy to capture prey in the water using a sudden strike on one side of the mouth. This asymmetrical strike is unique among vertebrates and can create a suction, pulling the prey and surrounding water into the mouth.

Both of these “digital dissection” techniques allow scientists to look at jaw mechanics in exquisite detail, without destroying the specimen, and may even help us understand the bites of extinct species. And maybe the next time you bite into a sandwich, you’ll think a whole lot more about just what goes into that chomp.



Sharp AC, Trusler PW (2015) Morphology of the Jaw-Closing Musculature in the Common Wombat (Vombatus ursinus) Using Digital Dissection and Magnetic Resonance Imaging. PLoS ONE 10(2): e0117730. doi: 10.1371/journal.pone.0117730

Fortuny J, Marcé-Nogué J, Heiss E, Sanchez M, Gil L, et al. (2015) 3D Bite Modeling and Feeding Mechanics of the Largest Living Amphibian, the Chinese Giant Salamander Andrias davidianus (Amphibia:Urodela). PLoS ONE 10(4): e0121885. doi:10.1371/journal.pone.0121885


Image 1: Phil Whitehouse, Wombat via flickr
Image 2: Toby Jungen, Chinese Giant Salamander via flickr
Image 3, 5, and 6: 10.1371/journal.pone.0117730
Image 4: 10.1371/journal.pone.0121885

Videos: 10.1371/journal.pone.0121885

Category: Aggregators | 1 Comment

PLOS ONE Update on Peer Review Process

There has been a great deal of community discussion in the last few days about a referee report that was sent to an author at PLOS ONE a few weeks ago. The report contained objectionable language, and the authors were understandably upset. Since this came to my attention I directed my team to perform a prompt investigation.


PLOS ONE has strict policies for how we expect peer review to be performed and we strive to ensure that the process is fair and civil. We have taken a number of steps to remedy the situation.  We have formally removed the review from the record, and have sent the manuscript out to a new editor for re-review. We have also asked the Academic Editor who handled the manuscript to step down from the Editorial Board and we have removed the referee from our reviewer database.


I want to sincerely apologize for the distress the report caused the authors, and to make clear that we completely oppose the sentiments it expressed. We are reviewing our processes to ensure that future authors are given a fair and unprejudiced review. As part of this, we are working on new features to make the review process more open and transparent, since evidence suggests that review is more constructive and civil when the reviewers’ identities are known to the authors (Walsh et al., 2000). This work has been ongoing for some months at PLOS ONE, and we will be announcing more details on these offerings soon.

Category: Aggregators, Peer review, Submissions, Topic Focus | Tagged | 47 Comments

Fun(d) with Science

After the money's gone

After the money’s gone

Many researchers will tell you that financing their work–writing grants, securing funding, and budgeting for varying funding levels year to year–is the least rewarding part of life in academia, but there’s no escaping the simple fact that science costs money. For decades, the majority of taxpayer-funded research dollars in the United States and much of the world has been awarded through relatively large grants from foundations or government-backed agencies. Funders seek to maximize their bang-for-buck, betting on what research will pay the biggest dividends, but both scientists and policymakers are constantly looking for new funding opportunities and reconsidering best practices for grants. This blog post highlights two articles published in PLOS ONE that examine how we pay for science.

The first study concerns a relatively new potential source of funding for research: crowdfunding, or soliciting small-dollar-amount contributions from many people via the internet. In an effort to determine how different factors contribute to the success or failure of crowdfunding campaigns to finance research projects, a group of scientists from across the United States coordinated the #SciFund Challenge. In three rounds, 159 scientists were recruited to run their own crowdfunding campaigns for relatively low-cost research projects. Using the RocketHub crowdfunding platform, scientists posted their research ideas, which were mostly conservation biology and ecology, but included other disciplines such as political science and psychology. They then promoted their campaigns via email, social media, and outreach to varying degrees as they saw fit. Between July 2011 and December 2012, these proposals brought in over $250,000 worth of funding.

Based on statistical analysis of each project’s page views, tweets, contributions, and researcher surveys, the authors of the study conclude that the success of a research crowdfunding campaign is not determined solely by pre-existing levels of public interest and awareness. Rather, scientists’ efforts in outreach and public engagement do appear to matter to the success or failure of such campaigns. The authors propose an optimal recipe for a successful campaign as follows:

  1. Develop a communication network to increase interest in the research and establish lines of communication with the public.
  2. Use email, Twitter, and other social media outlets to build upon the established communication network.
  3. Once the campaign is underway, leverage the network and interest into page views and donations.
Author's proposed funding model

Author’s proposed model for a successful crowdfunding campaign

No matter how compelling the research or how savvy the researcher, though, it’s unlikely that crowdfunding will ever replace traditional funding sources. While individual donations to crowdfunding campaigns are generally small in size, awards through grants from larger funders typically come in much larger chunks. How big should those chunks be, and is work backed by more than one funding source?

This was the topic of a 2013 PLOS ONE paper, in which researchers at the University of Ottawa examined how the size of funding grants affects the impact of scientific research. The authors of the study compared the size of grants awarded by the Natural Sciences and Engineering Research Council of Canada (NSERC) to the academic impact of the resulting work. How to best quantify the impact of research is an open question, contentious, and subjective in its own right, but these authors used four metrics:

  1. The numbers of articles published as a result of the research
  2. The numbers of citations those articles received in peer-reviewed publications
  3. The most-cited article that resulted from the research
  4. The number of highly cited articles that arose from the research

The authors found that impact (as they defined it) tended to increase with funding, but only weakly. Scientists who received grants from both the NSERC and an additional funder, the Canadian Institutes for Health Research, did not appear to produce more impactful work than those funded solely by the NSERC. The authors also found that impact and funding may be subject to the law of diminishing returns, e.g., the 100,000th dollar may not increase research impact of as much as the 10,000th dollar does. As we consider the right grant size to maximize bang for buck, this study may add to the literature suggesting that granting agencies may get more impact per dollar by awarding smaller grants to more scientists, rather than only awarding a few large grants to perceived “elite” scientists.

There are some projects and objectives for which large-scale grants are indispensable, and crowd-funding may not be an appropriate or feasible means of financing all research projects. Nonetheless, both scientists and funders may do well to consider fresh alternatives to the large-grant funding opportunities that have held primacy for decades.

Related Articles


The first image is from AndreasS via flickr. The second is Fig. 8 of the first study.


Byrnes JEK, Ranganathan J, Walker BLE, Faulkes Z (2014) To Crowdfund Research, Scientists Must Build an Audience for Their Work. PLoS ONE 9(12): e110329. doi:10.1371/journal.pone.0110329

Fortin J-M, Currie DJ (2013) Big Science vs. Little Science: How Scientific Impact Scales with Funding. PLoS ONE 8(6): e65263. doi:10.1371/journal.pone.0065263

Category: Article-Level Metrics, Social Media | Tagged , , , , | 1 Comment

Earth Day 2015: Celebrating Our Awe Inspiring World

14961414078_3807a5f721_zWe share Earth with millions of amazing plants and animals. Whether we’re relaxing in a hot spring like a Japanese macaque, or catching a glimpse of a rare bird, our exposure to Nature’s diversity enriches our lives and makes us feel closer to the wild world around us.

For Earth Day 2015, we are celebrating our diversity by highlighting some of our favorite images of flora and fauna from recently published PLOS ONE papers.

Fanged frog births live tadpoles

journal.pone.0115884.g002(1)Scientists have recently discovered a new frog species, Limnonectes larvaepartus, that resides in Indonesia and is related to fanged frogs. This newly described species has both internal fertilization and gives birth to live tadpoles, instead of laying eggs like many other frogs.

1,600 year-old ‘grandmother’ tree

journal.pone.0121170.g002These plump, trunked trees are called fony baobab and are found in Tsimanampetsotsa National Park in Madagascar. Researchers found one fony baobab tree called “grandmother,” which has three different aged stems fused together. Scientists’ radiocarbon dated the tree and found that the oldest part of the tree is likely close to 1,600 years old, possibly the oldest baobab tree in Madagascar.

You’re makin’ me yawn!

journal.pone.0105963.g001The wolves pictured above aren’t barking at each other. They’re actually experiencing a phenomenon that humans also experience, called yawn contagion. Scientists aren’t quite sure why the yawning seems to spread between these wolves, but they think that closer social bonds may increase yawn contagion.

Clues to understanding isolated dolphin populations

10.1371_journal.pone.0101427.g004With over 8 million animals inhabiting Earth, it’s difficult to study them all in depth. To search for clues about two ‘near-threatened’ and rarely studied dolphin populations, scientists looked at the Australian snubfin and humpback dolphins living in the tropical coastal waters of northern Australia. They found that these populations are genetically isolated, which the authors caution may impede their ability to adapt to environmental change.

Thanks for celebrating this great blue planet with us today.

Happy Earth Day!


Citations: Iskandar DT, Evans BJ, McGuire JA (2014) A Novel Reproductive Mode in Frogs: A New Species of Fanged Frog with Internal Fertilization and Birth of Tadpoles. PLoS ONE 9(12): e115884. doi:10.1371/journal.pone.0115884

Patrut A, von Reden KF, Danthu P, Leong Pock-Tsy J-M, Patrut RT, et al. (2015) Searching for the Oldest Baobab of Madagascar: Radiocarbon Investigation of Large Adansonia rubrostipa Trees. PLoS ONE 10(3): e0121170. doi:10.1371/journal.pone.0121170

Romero T, Ito M, Saito A, Hasegawa T (2014) Social Modulation of Contagious Yawning in Wolves. PLoS ONE 9(8): e105963. doi:10.1371/journal.pone.0105963

Brown AM, Kopps AM, Allen SJ, Bejder L, Littleford-Colquhoun B, et al. (2014) Population Differentiation and Hybridisation of Australian Snubfin (Orcaella heinsohni) and Indo-Pacific Humpback (Sousa chinensis) Dolphins in North-Western Australia. PLoS ONE 9(7): e101427. doi:10.1371/journal.pone.0101427

Images 1, 2, 3, 4, 5: View of Rocky Mountain National Park by Andrew E. Russell, Figure 2, Figure 2, Figure 1, and Figure 4

Category: Ecology, Fun, Images | Tagged , , , , , , , | Leave a comment

Head Rattling Results: Fin Whales Hear with Their Skulls

Front (whale)

Many of us have heard the haunting call of a whale ‘song,’ but how do the whales themselves hear sound? Similar to the way that animals see color in different ranges of the visible light spectrum, the mechanism by which they hear sound can also vary and in some cases is still not well understood.

The authors of the recently published PLOS ONE article, “Fin Whale Sound Reception Mechanisms: Skull Vibration Enables Low-Frequency Hearing,” investigated how sound interacts with a fin whale’s skull. Specifically they looked at low-frequency sounds such as those used by whales, likely to communicate across long distances. The researchers obtained a whale skull after an unsuccessful attempt to rescue a beached newborn fin whale on Sunset Beach, Orange County, CA. They took a computed tomography (CT) scan of the skull and used it to construct a finite element model, which allowed them to simulate and make predications regarding the mechanism by which fin whales hear sound.

second (whale)

For the majority of animals that have what we normally anatomically identify as ears, the vibration of bones within the ear allows them to hear sounds. Fin whale ears work the same way, and by watching the simulated response of the bones in their model to sound, the authors were able to identify two main mechanisms by which fin whales hear. The first, and most prevalent, is known as the ‘bone conduction mechanism,’ where the vibration of the ear bones is caused by the movement of the skull in reaction to sound. The second mechanism is called the ‘pressure mechanism,’ which describes the way sound directly interacts with the whale ear bones after moving through the water and head tissue. In the figure below, the authors provide a colorful image from their model of the ear bones interacting with sound.

third (whale)

It is important to note that while the authors found that the ‘bone conduction mechanism’ seemed to be the main mechanism for hearing in their model, it may only be applied specifically to fin whales since it was the only skull type that they studied. However since fin whales are a type of baleen whale, distinguished from toothed whales by their baleen which filters food out of the water in place of teeth, it is possible that other baleen whales utilize the ‘bone conduction mechanism’ as well. The physiology of most toothed whales is much different than baleen whales, and a group of ligaments actually separates the ear bones from the rest of the skull making it more difficult for skull vibrations to reach the ear bones.

The fact that fin whales communicate using low-frequency vocalizations also pairs with the authors’ findings. Low-frequency sounds tend to scatter and therefore do not have the ability to apply much direct pressure on ear bones. Therefore the sound’s contact with the skull would account for the majority of how they hear these low-frequency sounds and the ‘pressure mechanism’ would be less impactful. Although a calf skull (see below) was used in this study, the authors note that these mechanisms should not change in the adult skull, as the components of hearing physiology develop at a young age.

fourth (whale)

How marine animals perceive sound has been a topic of growing discussion as the amount of man-made noise increases in the ocean. Tools such as sonar, often used by the military to detect objects underwater, have been suggested as a cause of some fin whale behavior that has been interpreted as confusion or even a possible cause of beaching. The authors mention that the results of their study may assist policy-making bodies, to protect our ocean’s species from things such as the inadvertent effects of sonar. Keep an ear to the ocean and if you are lucky enough to hear a whale call, you can now listen with a well-informed ear.

Citation: Cranford TW, Krysl P (2015) Fin Whale Sound Reception Mechanisms: Skull Vibration Enables Low-Frequency Hearing. PLoS ONE 10(1): e0116222. doi:10.1371/journal.pone.0116222
Images: Fin Whale by Amila Tennakoon via Flickr. Fig. 1 and Figs. S4 and S9 of the published article.

Category: Aggregators | Tagged , , , , , , , | 2 Comments

Who Let the Microbes Out: A Paw Print of Doggy Skin Bacteria

A house is not a home without a dog, and a dog isn’t a “D-O-double-G” without its microbial “crew.”


Human microbiome research is progressing rapidly, and we are always learning how the bacteria living on and inside of us contribute to our survival and well-being. Although we are making some headway to understanding the role of human flora in our bodies and in disease progression, we know far less about the microbial flora in our pooch friends.

The diverse microbial landscape on skin is essential for all animals, as it helps maintain essential oils and plays “guard” in the first line of immune defense. However, living on animal skin isn’t easy—it’s exposed to the world and all its creatures, and endures some serious physical contact with them. There are many skin diseases that may alter skin microbe colonization, such as atopic dermatitis (AD), one of the most common skin infections in dogs (and people). Dogs that do develop AD have an increased sensitivity to many allergens. Additionally, many dogs with allergic AD are subject to bacterial skin infections. With this in mind, a group of researchers at Texas A&M recently published a study in PLOS ONE where they identify the microbial makeup of dog skin. The authors “hired” a crew of healthy dogs, as well as a group of dogs with allergic AD, to characterize the differences in their bacterial communities.

To obtain samples of as many skin-inhabiting critters as possible, the researchers brushed swabs back and forth on 12 different skin sites from the “healthy” dog squad, and 4 different skin sites from the allergic AD dogs, with the sites shown in the image below.



After extracting and sequencing the DNA from the swab culture samples, the authors were able to characterize the microbial inhabitants of the dogs’ skin for each site, and compare the species distribution found on the healthy dogs’ skin to those found on the allergic dogs. In healthy dogs, the lowest abundance of species, also called species richness, were found in their mucosal areas, such as the nostrils; whereas the haired-skin areas, such as the groin and axilla, had the highest species richness. Notably, ears took the “bone” with 866 different species present!

Among all dogs tested, the authors found a total of 17 different phyla, with Proteobacteria being the most abundant phylum. Ralstonia was the most abundant genus, likely because it’s found in dirt and water, the favorited doggy playground. Although there was high variability among the individual dogs tested, the authors found that the proportion of Ralstonia was much lower in all allergic dogs.


The species richness was much lower in the allergic dogs as compared to healthy dogs, as seen in the image above. The authors suggest that this difference may be the result of the antimicrobial washes that allergic dogs are often prescribed by vets for treatment, as well as skin changes induced by the allergic inflammation response.

While there is much work to be done characterizing the full doggie microbiome, and this study had a limited sample size, the authors have made steps toward characterizing the bacterial ecology of dog skin, and discovered that dog skin may contain much richer and more diverse microbial communities than were previously suggested. Like with the human microbiome, researchers might now investigate the role of the dog microbiome in normal function, disease progression, and better treatments for our favorite co-pilots. So next time you let the dogs out, give a thought to their bacterial companions!

Citation: Rodrigues Hoffmann A, Patterson AP, Diesel A, Lawhon SD, Ly HJ, et al. (2014) The Skin Microbiome in Healthy and Allergic Dogs. PLoS ONE 9(1): e83197. doi:10.1371/journal.pone.0083197

Image 1: Hawaiian Burton by Sarah Nichols

Images 2-3: Figures 4 and 7 from the published article.

Category: Aggregators, Fun, Images, Worth A Thousand Words | Tagged , , | 1 Comment

Introducing the PLOS ONE Conference Page

We are excited to announce the publication of the PLOS ONE conference page. The page serves as a one-stop shop for announcements and information regarding upcoming conferences, including when and where to meet up with PLOS ONE journal staff.

You can easily navigate to the page by selecting the ‘Conferences’ tab from the EveryONE menu at the top of the page (also pictured below).

2015-03-16 11_16_56-Conferences - EveryONE_redWe hope you’ll check out the page and come meet us in person at one of the many conferences we plan on attending throughout the year.

We look forward to meeting you!

Category: Conferences | Tagged , | Leave a comment

Out on a Limb: Dwindling Trees in Cities



Of all the environmental resources we take for granted, large, older trees might be near the top of the list. Not only do we rely on trees for oxygen and wood products, but about 180 different animal species rely on the hollow-bearing features of these trees for shelter, roosting, and nesting. Unfortunately, rapid urbanization poses an enormous threat to the existence of these trees.

Large old trees take centuries to mature, and scientists are paying particular attention to the changes in wooded areas as urbanization spreads. The authors of a recent study published in PLOS ONE utilized a simulation model to determine the future of older trees in and around Canberra, Australia. In this urban area of Australia where the population is projected to double from 375,000 people by 2056, the authors found that dramatic changes to the terrestrial environment could occur.

The simulation model developed by the authors calculated the average number of trees in a given area using pre-defined rates of tree mortality and existing data for trees they had catalogued and measured. The data collection included the total number of trees, how fast new ones were growing, and how quickly existing ones were dying or being removed. By extrapolating from this data, they were able to assess tree population changes in the coming years.

Unfortunately, building for a growing human population means clearing out these older trees that may pose a safety threat or may simply be in the way. By projecting the current rate of decline for existing trees in the next 300 years, the researchers found that these trees die or are removed at a rate so rapid that it could lead to their eventual disappearance. To put that threat into numbers, it seems that the population of these hollow-bearing trees will decline by nearly 87% over the next 300 years. In a worst case scenario, we could lose all old, hollow-bearing trees within 115 years. That’s a terrifying thought.

According to the authors’ review of tree population changes, several policies may need to change to reverse the decline of these trees. Only with a combined management strategy, including planting more trees and forming more hollow-bearing habitats, would the population of the trees increase over 250 years after a short period of decline. A decline in older, hollow-bearing trees, including some endangered Eucalyptus varieties, means a decline in shelter for the birds, bats, squirrels, and invertebrates that inhabit them.

Luckily, urbanization brings new innovation, and innovation inspires new solutions to important problems. Environmental consciousness in the public requires a discussion about improving tree management, community engagement, conservation strategies, and biodiversity offsets. For example, we now have the technology to give hollow-bearing features to trees in urban areas by using other hollow-structures or artificial nest boxes.

If large older trees are facing almost certain decline due to urbanization, we need to put forth significant efforts to develop conservation and management strategies to change that. With the research available today, we can develop strategies to protect the large trees in existence, improve regeneration for ones we lose, and develop plans to build structures for animals who are displaced. We are not the only living beings on Earth, and we need to take into consideration how we effect change in our environments.squirrel

Citation: Le Roux DS, Ikin K, Lindenmayer DB, Manning AD, Gibbons P (2014) The Future of Large Old Trees in Urban Landscapes. PLoS ONE 9(6): e99403. doi:10.1371/journal.pone.0099403

Image 1: Redwoods by Michael Balint

Image 2: Squirrel by Dave Bolenbaugh

Category: Aggregators, Ecology, Images, Internet/Blogging, Topic Focus | 3 Comments

Positively Negative: A New PLOS ONE Collection focusing on Negative, Null and Inconclusive Results

“I never quit until I get what I’m after. Negative results are just what I’m after. They are just as valuable to me as positive results.” – Thomas A. Edison

Willi HeidelbachThe publication of negative results is vitally important for many reasons, not least that it helps prevent duplication of research effort and potentially expedites the process of finding positive results. However, the struggle to find a home to publish the work, and the effort necessary to submit and publish what can feel like negligible scientific contributions, has led to concerns that negative findings are becoming the missing pieces in the scientific literature.

Today PLOS ONE launches a new collection to highlight studies that present inconclusive, null findings or demonstrate failed replications of other published work. The collection has been titled ‘Missing Pieces’ in reference to the many null results filed away indefinitely and ultimately excluded from the scientific record.

Selected examples focus on the lack of a significant effect of postpartum psychological distress on mothers in rural Bangladesh, despite differing positive findings in India.

Frequency discrimination training (FDT) using integrated training with computer-gameplay has previously been reported to show limited improvement in treating the symptoms of tinnitus, however, recent results from a randomised controlled trial did not translate to therapeutic benefit.

The failure to replicate previously published work is prominently highlighted in the popular PLOS ONE psychology paper, Failing the Future. Three attempted replications on the existence of precognition failed to support the previously significant results supporting retroactive facilitation of recall.

The publication of negative results, such as the works featured in the collection, is essential to research progress. Many journals, however, reject studies reporting negative or inconclusive results because the work is not considered impactful enough. In contrast, PLOS ONE does publish such studies; our publication criteria state that we will consider all work that makes a contribution to the field independent of impact.

Through this collection we hope to demonstrate that negative results are valuable to the community in cases where the result is illuminating in the context of previous work.

This collection serves to highlight negative result studies and to encourage the submission of negative results to PLOS ONE. If you would like your work to be considered for the Missing Pieces Collection, please contact collections@plos.org

Please visit the collection at: www.ploscollections.org/missingpieces

Image: Willi Heidelbach, Wikimedia Commons

Related Posts Plugin for WordPress, Blogger...
Category: Aggregators | 2 Comments