Introducing the New PLOS Video Shorts

In 2011, PLOS ONE launched a series of short instructional videos to help our authors, reviewers, and Academic Editors navigate Editorial Manager, our online submission system. We recently updated and expanded these video shorts to provide a resource for PLOS authors, reviewers and Editorial Board members. The new PLOS ONE video shorts playlist is below.


If you have a question about how to use our Editorial Manager system, whether it is how to select a reviewer or submit a revised manuscript, we highly recommend that you check out our instructional videos for a step-by-step guide. You can view the video shorts on the EveryONE blog and on the PLOS Media YouTube channel.

Category: Aggregators, Ask EveryONE, Manuscript submission and peer review system, PLoS Editorial Manager | Leave a comment

We Want the Funk: The Ups and Downs of Wild Microbes in Beer

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Funky, floral, complex. No, this is not a description of a piece of vintage wallpaper. These are some of the words that are used to describe the enormous variety that exists within the world of beer. Whether you are enjoying the outdoors on a sunny day or sitting by the fire on a cold, winter night, there is a beer to match every occasion. In honor of this tasty drink, we have put together a compilation of PLOS ONE articles dedicated to the study of beer and the yeast and bacteria that mold its complexity.

 

“Spontaneity is a meticulously prepared art” – Oscar Wilde

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Figure 4 of the published article shows the different isolates found over time in the DYPAI and UBAGI agars of batch 1. 

 

The brewing process for most beers includes heating hops and grain in nearly boiling water, before cooling the liquid down and adding a carefully selected yeast strain. Lambic sours, on the other hand, undergo a process known as spontaneous fermentation. Contrary to its name, spontaneous fermentation is a lengthy and controlled process that lasts, on average, a couple of years. The process itself depends on the strains of ‘wild’ bacteria and yeast that are already present in the environment to produce a tart flavor; normally, the presence of wild microbes causes a type of contamination referred to as ‘infection.’ ‘Infected’ beers are most easily identified by their undesirable taste, color, and smell. Therefore, as you can imagine, the microbiome of beer and how it may change during the fermentation process are of much interest to researchers and beer enthusiasts alike.

By looking at the types of microbes that colonized beer samples collected from the Belgian brewery Cantillon, prized by beer-lovers around the world, the authors of one PLOS ONE study were able to see a successive pattern in the beer’s microbiome during the fermentation process. Samples were taken from two batches that were started a month apart and cooled at different temperatures, to see how the microbial biomes varied.

The image above shows the microbial composition over time from isolates in some of the agars of batch 1. Despite some initial variety in the types of identified microbes, and a considerably high degree of species diversity overall, both batches had similar progressions in microbial content as well as a similar microbial composition at the end of fermentation; they consisted of mainly Pediococcus damnosus – a species of gram-positive bacteria that frequently grows in wine and beer. In this case, it may be that spontaneity and different starting points could all lead to a similar microbial ‘colony.’

 

Brews Gone Wild

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Figure 2 of the published article shows some of the species found in the different batches of ACA over a three year period. Panel A shows the yeast, Panel B is the bacteria, and Panel C shows the lactic acid bacteria.

 

The American coolship ale is a type of beer that also utilizes the power of wild yeast and spontaneous fermentation, and is modeled after the above-mentioned Lambic style. In a 2010 PLOS ONE study, researchers investigated the microbial profiles of multiple batches of American coolship ale from a single brewer in the Northeastern United States, to see if they could establish a “microbial baseline” for this type of beer. The authors collected samples from 8 different batches throughout the 3.5- year fermentation process, and found that while the yeast and bacterial content of the beer started off with a diverse number of species, it ultimately shifted to being composed primarily of B. bruxellensis. B. bruxellensis, more commonly known as Brettanomyces bruxellensis, is the type of yeast responsible for giving beer a distinctly ‘funky,’ lightly tart flavor—it’s so distinct, in fact, that its characteristics are commonly described as ‘Bretty.’

The authors describe this particular microbial succession as likely being caused by the constantly changing environment of the beer. The strains of bacteria and yeast that initially colonized the beer produced carboxylic acid, which can limit the growth of other microbes. Once these early microbial inhabitants died off, Saccharomyces, a type of yeast commonly used in food production, and Lactobacillales were then afforded limited competition and could jump in for the main fermentation process. In the image above, the authors show how the yeast and bacterial profiles changed over time for each of the batches. They explain that since the microbial profiles and their progression are similar across all of the batches, this could be evidence that there are resident brewhouse microbiota that take over during fermentation.

It’s worth noting that studies conducted prior to this one have shown that the microbial profiles of Lambics also ultimately end up being primarily composed of B. bruxellensis, though the smaller communities of microbes differ from those found in American coolship ales.

 

Don’t Spoil It

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Figure 4 of the published article shows how the bacterial content changed in different concentrations of various acids and maltose over time. 

 

While some beers, such as the previously described sours, thrive with exposure to naturally occurring microbes, others can be ruined by it. During a ‘normal’ brewing process, it is important to ensure that all equipment coming in contact with the beer has been sterilized so that contamination or infection can be avoided. The lactic acid bacteria that helps sours achieve qualities such as their distinctive aroma, may cause other beers to spoil. Luckily, drinking a spoiled beer does not put you at a huge risk for getting sick; they are generally just unpleasant tasting and not very drinkable. Many types of bacteria are unable to grow amid hops, ethanol, and a highly acidic environment; however, a few species have grown to overcome these obstacles.

To better understand the mechanisms employed by these bacteria, researchers of this PLOS ONE study conducted a type of next-generation sequencing called transcriptome sequencing on one of the culprits of beer spoilage: a strain of Gram-positive bacteria called Pediococcus claussenii. The above image shows how the bacterial levels changed over time in relation to the concentrations of various acids present in the beer. Using transcriptome sequencing allowed these authors to determine which genes are used by bacteria when they grow in acidic, low-nutrient environments. While many of these mechanisms are still not well understood, the authors identified genes that may play a key role in the bacteria’s adapted ability to live in these conditions, such as a modification of the cell membrane to resist the acidic environment. Developing a better understanding of how these bacteria are able to live in beer may help avoid contamination in the future.

 

While beer is enjoyed by many, most don’t give much thought to the science behind the craft. As indicated here, even spontaneous fermentation is a carefully conducted and complicated process that has evolved greatly over the last 7,000 years.

There is a special place where scientist and beer lover unite, as shown by the research articles presented above, and more open access research could mean the potential for better beer, so cheers to all the beer geeks out there!

 

Citations:

Spitaels F, Wieme AD, Janssens M, Aerts M, Daniel H-M, Van Landschoot A, et al. (2014) The Microbial Diversity of Traditional Spontaneously Fermented Lambic Beer. PLoS ONE 9(4): e95384. doi:10.1371/journal.pone.0095384

 Bokulich NA, Bamforth CW, Mills DA (2012) Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale. PLoS ONE 7(4): e35507. doi:10.1371/journal.pone.0035507

Pittet V, Phister TG, Ziola B (2013) Transcriptome Sequence and Plasmid Copy Number Analysis of the Brewery Isolate Pediococcus claussenii ATCC BAA-344Tduring Growth in Beer. PLoS ONE 8(9): e73627. doi:10.1371/journal.pone.0073627

Images: Beer Sampler by Quinn Dombrowski via Flicker, Figure 4, Figure 2, Figure 4

Commercial Funding:

Transcriptome Sequence and Plasmid Copy Number Analysis of the Brewery Isolate Pediococcus claussenii ATCC BAA-344T during Growth in Beer: This research was partly financially supported by the MillerCoors, Anheuser-Busch InBev, and Brian Williams Graduate Scholarships from the American Society of Brewing Chemists Foundation, and MillerCoors Brewing Company. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale: NB has received multiple scholarships donated by commercial funding sources (Briess Malt, Cargill Malt, Wine spectator; see below). All scholarships were reviewed and awarded by third-party sources (American Society of Brewing Chemists, UC Davis Department of Viticulture and Enology) and none of these companies had any contact with the authors. This does not alter the authors’ adherence to all the PLoS ONE policies on sharing data and materials.

Category: Aggregators | 2 Comments

PLOS ONE’s Top 5 Videos of 2015 (So Far)

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At the end of 2014, we highlighted some of our favorite research videos from that year. We’re only mid-way through 2015, but we already have a number of popular research videos that we’d like to share. Here are some of this year’s most popular videos of the first half of the year, all published in the Supporting Information of each research article.

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

Java sparrow percussionists

Birds use vocalizations and movements to communicate with each other. In this video, the male java sparrow sings, and both birds produce bill-clicking sounds. Interestingly, the male java sparrow appears to coordinate his bill-click sounds with the notes of his song, which is similar to a human percussionist. The authors of the PLOS ONE study published in May suggest that bill-clicking sounds may be integrated with vocal courtship signals, as we see in this video, although further research is needed to understand the role bird vocalizations and movements play in courtship.

 

Oyster-cracking macaques

These Burmese long-tailed macaques use stones as tools to crack open oysters. The authors of this PLOS ONE study published in May found that 80% of a population of Burmese long-tailed macaques on an island in southern Thailand use stone and shell tools to crack open seafood. The video shows that there’s more than one way to crack an oyster – in fact, there are 17 different ways!

 

Not-so-silent cicadas

This insect species Karenia caelatata is called the “mute” cicada since it lacks the usual organs required to produce sounds. However, the authors of this PLOS ONE study published in February describe a new sound-production mechanism for these cicadas: banging the forewing costa, or front wings, against the operculum, or body cavity, to create impact sounds, which you can hear in this video.

 

Escaping the jaws of death

Trap-jaw ants have large mandibles, or insect mouth parts, that they use to consume prey. The authors of this PLOS ONE study published in May found that these mouth parts can also be used to escape from an antlion predator. This video depicts an ant using its mandible to jump away and escape from the antlion buried in the sand. The trap-jaw ant snaps its mandible against the wall of the pit, and the strength of the force propels it out of the pit and out of danger.

 

Joint-cracking MRI

Our most popular video from 2015 is a real-time MRI (magnetic resonance imaging) of joint cracking in a human, with over 500,000 views! For more than a half century, cracking sounds from human synovial joints, or the most common and movable type of joint, were attributed to bubbles collapsing within the joint. The authors of this PLOS ONE study published in April found evidence from MRI that joint cracking is related to the formation of cavities, rather than the sudden collapse of a cavitation bubble as was previously thought. Further research is needed on how joint cracking may impact health outcomes.

We hope you enjoyed watching some of this year’s most popular research videos, and we encourage you to check out more of our videos on the PLOS Media YouTube channel here! Feel free to subscribe to stay up-to-date on all of our latest Open Access research videos.

Citations

Image and Video 1: Soma M, Mori C (2015) The Songbird as a Percussionist: Syntactic Rules for Non-Vocal Sound and Song Production in Java Sparrows. PLoS ONE 10(5): e0124876. doi:10.1371/journal.pone.0124876

Video 2: Tan A, Tan SH, Vyas D, Malaivijitnond S, Gumert MD (2015) There Is More than One Way to Crack an Oyster: Identifying Variation in Burmese Long-Tailed Macaque (Macaca fascicularis aurea) Stone-Tool Use. PLoS ONE 10(5): e0124733. doi:10.1371/journal.pone.0124733

Video 3: Luo C, Wei C, Nansen C (2015) How Do “Mute” Cicadas Produce Their Calling Songs?. PLoS ONE 10(2): e0118554. doi:10.1371/journal.pone.0118554

Video 4: Larabee FJ, Suarez AV (2015) Mandible-Powered Escape Jumps in Trap-Jaw Ants Increase Survival Rates during Predator-Prey Encounters. PLoS ONE 10(5): e0124871. doi:10.1371/journal.pone.0124871

Video 5: Kawchuk GN, Fryer J, Jaremko JL, Zeng H, Rowe L, Thompson R (2015) Real-Time Visualization of Joint Cavitation. PLoS ONE 10(4): e0119470. doi:10.1371/journal.pone.0119470

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

Category: Aggregators, Fun, Images, Internet/Blogging, Media, Open Access, Submissions, Worth A Thousand Words | Tagged , , , , , , , | Leave a comment

PLOS Recommended Data Repositories

In line with our updated Data Policy, we are pleased to announce a PLOS Data Repository Recommendation Guide.

To support the selection of data repositories for authors, PLOS has identified a set of established repositories, which are recognized and trusted within their respective communities. To develop the list, we consulted with editors, organizations running data repositories, and other publishers in order to cover the breadth of disciplines and subject areas published by PLOS.

Additionally, the Registry of Research Data Repositories (Re3Data) is a full scale resource of registered repositories across subject areas. Researchers can browse by subject, content type, and country.  Re3Data provides detailed information on an array of criteria to help researchers identify the most suitable repository for their needs (licensing, certificates & standards, policy, etc.).

Authors are encouraged to select the repository most appropriate for their research. PLOS does not dictate repository selection for compliance with our open data policy, we just require the underlying data to be publicly available in a repository with licensing policies not more restrictive than the Creative Commons Attribution (CC BY) license that each paper is published under.

We appreciate your support of the policy and we welcome questions and feedback at data[at]plos[dot]org.

Category: Manuscript submission and peer review system, Open Access, Peer review | Tagged , | 1 Comment

I Know What You Think: Collective Intelligence in Online Communication

Have you ever wondered what factors may shape the interactions we have in online chatrooms? With the advent of the Internet 20+ years ago, the ways in which we communicate have drastically changed, allowing us to easily interact nonverbally or anonymously. Whether it’s in a chatroom, email thread, or an online forum, most of us have taken part in some form of group communication on the Internet. Maybe, unbeknownst to us, we became a part of the group’s collective intelligence, a form of group intelligence that can surface after collaboration and competition among individuals in the group. But some scientists are wondering, how can we measure the ability of others to communicate in a group, and how can we quantify the effectiveness of a group?

Two traits that make us “distinctly human” are our abilities to empathize and to interact well in social settings with others. These traits are usually measured in face-to-face situations, and may be more difficult to measure online, away from in-person social cues.

One factor that correlates to overall collective intelligence is “Theory of Mind” (ToM), or the ability of one individual to understand the mental state of another and recognize it as distinct from their own; what some may consider “mind reading.” In a recent PLOS ONE study, MIT researchers tested the hypothesis that ToM, which can be used to predict collective intelligence in collaborative face-to-face tasks, can almost equally predict collective intelligence in online collaboration. One individual’s ability to “read” the behavior of another individual can help contribute to successful communication and overall group intelligence. More than that, this ToM ability may exist even where verbal communication is prohibited, and may contribute to successful communication within an online group.

The researchers in this study recruited around 270 individuals to participate in a series of tasks online or in person. For individual tests, the participants completed the Reading the Mind in the Eyes (RME) exercise, which requires an individual to estimate the mental state of a face based on an image they are given. This test was performed in addition to several online tasks, some group-based, and some individual.

Figure 1

The researchers structured the online tasks similarly to previous in-person studies of collective intelligence. The group tasks for the individuals online included solving a Sudoku puzzle using a group chat function (see image above), unscrambling words, performing memory tasks, or typing large text pieces with the help of the group. The individual personalities of each participant were also used to contextualize their unique place in the group dynamic.

This group data, in combination with individual RME results, provided a statistical factor that was used to measure the “general intelligence” among the online group. The amount of communication, and the ToM abilities of the group, were strongly correlated with high collective intelligence.  More importantly, the medium of communication (online) did not hinder any abilities to contribute to group tasks or to interpret the emotions of others.

In an age where we rely on the Internet for rapid communication, it can be comforting to know that our collective intelligence may not diminish. These interactions could be as productive and as stimulating as many of the group conversations we have on the phone or in person. The ability to communicate and perceive group dynamics may transcend the limitations of the Internet and allow us to continue to understand and collaborate well with our fellow human.

Citation: Engel D, Woolley AW, Jing LX, Chabris CF, Malone TW (2014) Reading the Mind in the Eyes or Reading between the Lines? Theory of Mind Predicts Collective Intelligence Equally Well Online and Face-To-Face. PLoS ONE 9(12): e115212. doi:10.1371/journal.pone.0115212

Image 1: Official GDC by Jesse Knish Photography

Image 2: Figure 1 from the article

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Flight of the Bats: Exploring Head Shape and Aerodynamics

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It’s a bird…it’s a plane…it’s a bat! All three may be soaring through the sky, but their shapes vary greatly, which affects their aerodynamics during flight. Birds typically have streamlined head profiles that strongly contrast with the appendages featured on echolocating bats. For example, birds do not rely as bats do on external pinnae, the visible part of the ear outside the head, to localize sound during echolocation, or the use of sound waves to locate objects in space. Some bat species also have a large noseleaf, or nose ornament, which allows them to vocalize through their nostrils and direct the echolocation call. While pinnae and noseleaves allow a bat to perform echolocation for hunting and foraging, they are often large in comparison to the bat’s body, and this could potentially slow the bats down by creating a large amount of drag, or resistance, as the bat flies.

To better understand how the structure of a bat’s head might affect its ability to fly, the authors of this PLOS ONE study tested seven different bat species with varying head shapes, including a bat species with a noseleaf, an appendage which hadn’t been tested previously.

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The researchers conducted micro-computerized tomography scans (CT scans) on previously deceased bat heads collected from labs, and then 3D-printed models of the heads. They then created a standardized bat body profile for these models based off of photos of different species of bats in flight, such as the pale spear-nosed bat and the hairy big-eared bat flight poses shown in B and C in the image above. As there were no high-quality flight images available for the common big-eared bat, the authors used images of the hairy big-eared bat, a close relative, to approximate its head posture.

Each of the bat models were placed in a wind tunnel for aerodynamics testing. The models were tested at angles of attack, or the angles a bat flies toward its prey, between −30° and +30°, at air speeds of 5 m/s and 10 m/s, to measure factors such as drag and lift. The graphs below show that while the bat heads generate a large amount of both lift and drag, the lift-to-drag ratio is high for all bat species. This means that the bats experience slightly more lift than drag, and since an increased lift-to-drag ratio helps aid in flight, the authors suggest that the bats’ head shapes may not be hindering their flight as much as previously thought.

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The authors conducted additional testing with the long-legged bat model, to determine whether a bat possessing both pinnae and a noseleaf would also experience more lift than drag in the wind tunnel.  The graphs below show that the bat model with pinnae and noseleaf attached experiences high lift and drag, and when these are removed, those forces mostly decrease.

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Since the bat pinnae generate more lift than drag in most cases, the authors suggest that the shape and features on the bats’ heads do not produce a heavy aerodynamic cost, but may actually aid their flight.

While these researchers aren’t the first to suggest that pinnae may also create lift, they expand on this result with more detailed models of a range of bat species, with different pinnae lengths, and by including a species that has a noseleaf. Furthermore, since the researchers tested bat species from a wide variety of ecological niches, or the ways in which the bats function within the ecosystem, their findings may be more easily generalized across the bat taxa than previous research.

While the authors acknowledge that there are limitations to testing static models for bat aerodynamics, their results suggest that pinnae and noseleaves may not affect bat aerodynamic capability as was previously thought. Looks like the shape of the bats’ faces might not slow down their nighttime flight after all!

Citation: Vanderelst D, Peremans H, Razak NA, Verstraelen E, Dimitriadis G (2015) The Aerodynamic Cost of Head Morphology in Bats: Maybe Not as Bad as It Seems. PLoS ONE 10(3): e0118545. doi:10.1371/journal.pone.0118545

Gardiner J, Dimitriadis G, Sellers W, Codd J (2009) The aerodynamics of big ears in the brown long eared bat plecotus auritus. Acta Chiropterologica 10: 313–321. doi: 10.3161/150811008X414881

Images: Image 1: Bernard Dupont on Flickr, Images 2, 3 and 4: Figures 1, 2 and 4 from published article.

Category: Aggregators, Ecology, Fun, Images, Worth A Thousand Words | Tagged , , , , , | Leave a comment

Small Talk: When Bacterial Chatter Gets Invasive

Sticks and stones may break our bones but microbes’ “words” may hurt us.

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Breast cancer is a threat to men and women worldwide. Like all cancers, the known causes are attributed to genetics and carcinogens, but recently, scientists have begun to recognize the microbiome as another contributing factor. Historically, breast tissue had been thought to be sterile, but it has become increasingly evident that microbes may both move to and reside in the breast tissue and nipple ducts.

Building on the recent discovery of Escherichia and Bacillus bacteria in the breast tissue, researchers published a study in PLOS ONE illustrating the role bacterial communication may play in breast tumor progression.

Bacteria have a system of communicating with each other called quorum sensing, where they may release hormones, lactones, or peptides that act as chemical signals to elicit a specific response in other bacteria. Quorum sensing peptides and bacteria themselves can travel in the blood stream, and this may allow for both the peptides and bacteria from other areas of the body to invade breast tissue.

The authors of this study investigated the relationship between blood vessel formation and quorum sensing peptides, and how these entities may promote breast tumor cell invasion in vitro. To assess the effects that the presence of these bacteria and peptides may have on breast tumor evolution, researchers evaluated signaling peptides released from three different bacterial strains common to the human microbiota: Bacillus subtilis, Streptococcus mitis, and Escherichia coli. Using cancerous cells derived from human tissue, researchers looked at how much protein was produced, what genes were affected, and visual changes in the human tumor cells after cells were exposed to the quorum sensing bacterial peptides.

The researchers found that exposing these cells to quorum sensing peptides caused an increase in the production of specific proteins by the cells related to oncogenes, specific genes associated with cancer spread and growth. One of these oncogenes results in angiogenesis, the process by which new blood vessels are formed so that blood can reach the tumor and deliver nutrients necessary for growth. Additionally, the researchers noted a drop in the expression of an important anti-tumor protein in the human cells, p53, which could result in further tumor growth and progression.

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Next, the researchers used an established assay for tumor invasion, called chick chorioallantoic membrane assay, or CAM, to monitor blood supply, or vascularization, a possible indicator of angiogenesis. As depicted in the image above, after 6 days of exposure to the peptides, the researchers observed neovascularization—the growth and formation of blood vessels—in the embryonic membrane of a chick egg. This increase in vascularization may be a route of transportation for the quorum sensing bacteria and peptides to enter the breast tissue.

The researchers were then able to use microscopy to observe how peptide treatment caused the tumor cells to disrupt the chorionic membrane and spread, the latter through a process called metastasis. They saw that the exposure to quorum sensing peptides appeared to promote tumor cell invasion through the chorionic layer into the mesoderm. The black arrows in the image below point to the aggressive invasion of the tumor cells through the chorionic tissue layers and disruption of the membrane. Although this experiment was performed on chick chorionic epithelial cells and not human breast tissue cells, the results from this tumor invasion assay may indicate what might happen during breast tissue invasion.

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Microbes are the yin to the human yang, and are vital for survival. It is becoming increasingly evident that microbial diversity within our bodies plays a role in not only our daily lives, but also in the progression and or prevention of disease. Although more work needs to be done to map the mechanisms by which the peptides interact with the tumor cells, the authors of this study have taken strides forward to suggest a link between bacterial communication and the growth and spread of breast tumors. With this information, researchers may look at microbial therapy and alternative preventative measures for a variety of diseases and cancers.

Citation: De Spiegeleer B, Verbeke F, D’Hondt M, Hendrix A, Van De Wiele C, Burvenich C, et al. (2015) The Quorum Sensing Peptides PhrG, CSP and EDF Promote Angiogenesis and Invasion of Breast Cancer Cells In Vitro. PLoS ONE 10(3): e0119471. doi:10.1371/journal.pone.0119471

Image 1: Staphylococcus epidermidis Bacteria by NIAID

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

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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:

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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?

Twitter

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

Images:

 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.

 

Citations:

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

Images:

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