Article-Level Metrics Highlight: Top 10 of the Summer

summerHaving just published our 100,000th article, the staff at PLOS ONE realizes that easily finding research papers among our wide selection is very important to our diverse community. This is one reason we’ve now joined forces with the PLOS article-level metrics (ALMs) team to regularly identify and present a selection of our recently published papers that demonstrate high ALM activity*. This post will be the first in a series that highlights new content for our readers.

From genetics to paleontology and microbiology to ecology, all the papers featured here have drawn the attention of the general public and scientific community over the past four months. This list is just the tip of the iceberg and if you haven’t already perused these papers, we encourage you to explore the work here and join the rich conversations already ongoing surrounding them.

Without further ado, this month’s top papers include the following:

1. Investigating “knockin” and “knockdown” in a human cell line

IMAGE 1
Using CRISPR/Cas9, a biological gene editing system that has allowed rapid and efficient modification of an organism’s DNA—as well as captured the imagination of biomedical researchers in the last two years—the authors of “CRISPR/Cas9 Allows Efficient and Complete Knock-In of a Destabilization Domain-Tagged Essential Protein in a Human Cell Line, Allowing Rapid Knockdown of Protein Function” were able to add a destabilizing element to “knockdown” an essential gene ( TCOF1) in a human cell line, effectively impairing cell growth and controlling protein levels. This strategy will hopefully allow the authors to investigate this gene further, as it is critical for cell growth and viability and has been associated with Treacher Collins–Franceschetti syndrome.

Published 4/17/2014, Image from the article

2. The shapes of 2.1 billion year-old macroscopic marine biota

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The authors of “The 2.1 Ga Old Francevillian Biota: Biogenicity, Taphonomy and Biodiversity” analyzed the shapes and structures of fossilized material from the Paleoproterozoic Era—when the Earth’s surface and atmospheric environment was still in flux—found in the Francevillian black shale rocks in southeastern Gabon in Central Africa. The results suggest a biota fossilized during the formation of sedimentary rocks, likely following the rise and fall of atmospheric oxygen. These 400 biota may represent the oldest known macroscopic organisms.

Published 6/25/2014, Image from the article

3. Musical training may benefit young brains

IMAGE 3
The authors of “Behavioral and Neural Correlates of Executive Functioning in Musicians and Non-Musicians” put working adult musicians, adults with no musical training, and kids with a couple years of musical training through a series of tasks to measure various cognitive capabilities. They found that the adults and children with musical training showed enhanced performance in working memory and processing speed compared to those without training.

Published 6/17/2014, Image from the article

4. Cheers for the “bugs” in Lambic beers’ (yeast and bacteria)

IMAGE 4
Traditional Lambic sour beers ferment for one to three years before bottling using wild yeast and bacteria from the air of the Senne river valley in Belgium. To dive into the microbial diversity in fermenting Lambic sour beer in a brewery in Belgium, the authors of “The Microbial Diversity of Traditional Spontaneously Fermented Lambic Beer” analyzed over 2000 bacterial yeast isolates. They found a wide variety of bacterial species and only minor variation between batches. The authors also observed a pattern in the way the “bugs” changed during the fermentation process, which started with a mostly Enterobacteriaceae, replaced by Pediococcus damnosus and Saccharomyces spp. in the second month, and finally replaced at 6 months by Dekkera bruxellensis. Understanding the progression of “bugs” might allow breweries from around the world to replicate this region specific fermentation process.

Published 4/18/2014, Image: Brakspear Oxford Gold Organic Beer by Christer Edvartsen

5. Latent virus reactivation in patients with sepsis

virus
Reactivation of latent viruses may occur with prolonged sepsis. The authors of “Reactivation of Multiple Viruses in Patients with Sepsis” analyzed blood samples from critically-ill septic, critically-ill non-septic, and healthy patients to see if certain latent viruses—herpesviruses, polyomaviruses, and the anellovirus TTV—reactivated in these patients. The results suggested latent virus reactivation may be common with prolonged sepsis, consistent with development of an immunosuppressive state.

Published 6/11/2014, Image: Model of a Virus by Tom Thai

6. Prehistoric crocodiles may have dined on each other

fossils
The authors of “An Additional Baurusuchid from the Cretaceous of Brazil with Evidence of Interspecific Predation among Crocodyliformes” have discovered the fossils of a new crocodyliformes (crocodilians), Aplestosuchus sordidus, from the Late Cretaceous in Brazil.  Not only did the researchers find a new species, but they also discovered fossilized remnants of another crocodylian inside its stomach, suggesting that Aplestosuchus sordidus likely feasted on other crocodyliforms.

Published 5/8/2014, Image from the article

7. Microbes hitching a ride on the skin of a humpback whale

microbiome
Humpback whales live in oceans around the world and the authors of “Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?genetically sequenced over 500,000 bacteria collected from humpback whale skin from different geographical areas, as well as in various health conditions to explore the role these microbes play in their health. They found that in general, two bacterial species, Tenacibaculum and Psychrobacter, were hitching a ride on most healthy whales, but the overall composition of the bacterial populations differed depending on their various geographical locations, as well as on whether individual whales were stressed or deceased. These results indicate that scientists may be able to monitor these widespread whales’ health using microbes in the future.

Published 3/26/2014, Image from the article

8. Up close with 3D insects

insect
Scientists working to develop a cost-effective method to create natural-color 3D models of insects in “Capturing Natural-Colour 3D Models of Insects for Species Discovery and Diagnostics” have used “off-the-shelf” equipment to image and model the insects in 3D. The 3D models are compact in size (~ 10 MB each); have excellent resolution; and can be embedded into documents and web pages, as well as mobile devices. The authors report that the system is portable, safe, and relatively affordable; complements existing imaging techniques; and opens up opportunities to use images of these delicate specimens for research, education, and art.

Published 4/23/2014, Image from the article

9. Mass extinction may not have resulted in slow recovery of prehistoric predators

marine
Organism recovery after the end-Permian mass extinction is thought to have been slow, lasting up to eight million years or more. The authors of “Early Triassic Marine Biotic Recovery: The Predators’ Perspective” surveyed the global distribution and size of Early Triassic and Anisian marine predatory vertebrates—fishes, amphibians and reptiles—to take a closer look at organism recovery after the mass extinction event. Scientists observed no significant predator size increase from the Early Triassic to the Anisian, as would be expected with slow or stepwise recovery. These results likely indicate that from the Early Triassic onward, marine ecosystems were comprised of multiple trophic levels.

Published 3/19/2014, Image from the article

10. Let’s study lions, tigers, and bears (and more?)

bear
Scientists work hard to understand the role carnivores play in ecosystems, but all carnivorous species may not receive the same amount of attention. To investigate further the patterns in carnivore research, the authors of “Correlates of Research Effort in Carnivores: Body Size, Range Size and Diet Matter” combined bibliometric information they obtained from ~16,500 published papers on the Order Carnivora, a well-known group of nearly 300 species. The researchers found that scientists tend to study carnivores with large bodies and large geographic ranges, like bears and walruses, moreso than species with greater adaptability and broader diets.

Thank you for taking a moment to enjoy these PLOS ONE papers from the past four months. We’re looking forward to next list and meanwhile, you may explore our ALMs report to make your own lists.

* This list will be selected each month from a report of papers generated based on the following ALMs ratio: PDF downloads/HTML ratios.  Only papers published within the last four calendar months were eligible for inclusion. (This list was pulled from March 15, 2014- July 15, 2014)

First image: Llegó el verano – Summer is here by Guillermo Viciano

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I Smell Green, You Smell Blue

Color Palate

In elementary school, we all learn about our five senses: taste, smell, touch, sight, and sound. Together, they continuously provide us with massive amounts of sensory input. One way we make sense of all this is by forming associations: between sights and smells, feelings and tastes, and so on. For instance, we may associate the sound of waves to the smell of the ocean, the feeling of sand between our toes, or a salty taste. But to what extent do sensory associations change based on where we are from, and to what extent are they universal? It turns out that two people from opposite sides of the globe may draw very different connections from the same stimulus. That’s according to the authors of new research published in PLOS ONE, who investigated how people from different parts of the world associate colors with smells.

The researchers divided study participants into six populations based on geographic categories: Dutch, Netherlands-residing Chinese, German, Malay, Malaysian-Chinese, and US residents. Participants smelled a series of scents—14 total, including smells like “meat,” “soap,” and “burnt”—and were subsequently asked to choose from a palate of colors which one they most closely associated with the smell.

Odor-color associations chosen by the different groups

After the experiments were performed, the researchers compared the smell-color associations of individuals within each groups, and then compared the results between groups. While people from the same geographic group tended to make similar smell-color associations, color choices differed significantly between the cultural groups.  Some smell-color associations were generalizable across groups.  For instance, participants who smelled a “fruity” odor largely picked a pink or red color, and people chose oranges and browns for the “musty” smells.  The most similar groups to each other were the US and Germany, and the Germany and Malay samples.  Overall, the Malay group’s color choices were the most different from all the others. The authors had also predicted that the geographically-close test groups would lead to similar smell-color associations, but that didn’t appear to be borne out by the data.

So, what may be happening when someone smells a scent, and then chooses a corresponding color? The authors offer several possible explanations of what could be at work:

  • There could be an underlying neural basis for the association of reds and pinks with fruity smells that lead people to associate the two. In other words, the associations are inherent and that’s just how our bodies and our brains work.
  • There could also be a statistical correspondence, which means that a particular color and smell often accompany one another. Example: “I see red and I smell fruit… perhaps the two are related.” Over time, these patterns may start to leave their mark on our brains.
  • Sometimes people make strong associations with colors and words (perhaps “sky” and blue), called semantically mediated correspondences. Language and how it is used can influence these associations, so this experiment was designed to use as few words as possible to minimize language-based associations.

In this particular study, the authors suggest that the variation between the different cultural groups may be evidence that color-smell associations are not inherent or universal, but are informed by other factors that could include culture, language, and experience. More work remains to better understand all the factors that influence these connections, but for now, it seems that the color of a smell may depend on where you’re from.

Related links:

The Color “Fruit”: Object Memories Defined by Color

From Understanding to Appreciating Music Cross-Culturally

Which Colors Do You Smell?

Reference: Levitan CA, Ren J, Woods AT, Boesveldt S, Chan JS, et al. (2014) Cross-Cultural Color-Odor Associations. PLoS ONE 9(7): e101651. doi:10.1371/journal.pone.0101651

Images: The images come from Courtney Rhodes via Flickr and Figure 2 of the published paper

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Sharing is Caring: Varied Diets in Dinosaurs Promoted Coexistence

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Everyone loves a good dinosaur discovery. Though they’re few and far between, sometimes we get lucky, finding feather imprints, mohawks, or birthing sites that reinvigorate public interest and provide bursts of insight about how they ruled the Earth before our arrival.

Dinosaurs must have been doing something right because they coexisted for millions of years, much longer than we humans have even been on the planet. In an article recently published in PLOS ONE, University of Calgary researchers studied markings on dinosaur teeth to determine how a diverse group of megaherbivores—plant-eating species whose adults weighed in at over 1,000kg—was able to coexist in Canada for at least 1.5 million years. The authors’ findings suggest that these dinosaurs managed to last so long by eating things that the others didn’t, thereby reducing competition for food and promoting a more harmonious (if dinosaur life could be considered so) coexistence.

The authors of this study started by taking a look at general tooth shape and any markings visible to the naked eye before moving onto examine the microscopic markings on teeth. The presence of certain small shapes or marks on teeth may indicate what type of food an individual ate during its lifetime, and can be analyzed using a technique called microwear analysis. As you might guess, foods with different textures or hardness leave different markings on our teeth. For instance, pits in the teeth suggest consumption of hard foods like nuts, while scratches are linked to the ingestion of tough leaves or meat. A combination of both reflects a varied diet.

The researchers analyzed a group of 76 fossils from 16 species in three ancestral groups, focusing on teeth still connected to skulls to provide more accurate species identification. These three groups lived together during the Cretaceous period in the Dinosaur Park Formation of Alberta, Canada, which at that point was on an island continent called Laramidia.

ankylosaur_teeth

Ankylosaur Teeth

Ankylosauria, whose teeth are seen above, were a group of armored, stocky dinosaurs. One subgroup, the ankylosaurids, had small, cusp-like teeth (marked A) good for eating fruits and softer plant tissues, while another, the nodosaurids (marked B), had blade-like teeth useful for tougher and more fibrous plant tissues. Microwear analysis showed no significant difference between these two subgroups, meaning that, despite differences in general tooth shape, results indicate that their diets did not differ significantly. The evidence of both pits and scratches on their teeth suggests that both ate a variety of fruits and softer foliage.

hadrosaurid_teeth

Hadrosaurid Teeth

Hadrosauridae—identifiable by their duckbill-shaped face—had similar microwear to the Ankylosauria, suggesting that they also had a generalized diet, though their broad teeth, likely used for crushing food, may have made it easier for them to consume all parts of targeted plants, including stems and seeds, than the cusp or blade-like teeth found in the Ankylosauria.

ceratopsidae_teeth

Ceratopsid Teeth

Ceratopsidae, a family of thick-skulled, horned dinosaurs, including the well-known Triceratops, had teeth that functioned as shears, suggesting that they consumed particularly tough plants. Microwear analysis supports this idea, indicating more scratches than pits, and showing that these dinosaurs may have subsisted on mainly rough foliage, like twigs and leaves.

The evidence provided by microwear analysis, incorporated with other known facts about these species, such as height, skull shape, and jaw mechanics, helps paint a broader picture of the dinosaur food scene in Laramidia, and supports previous research suggesting that the varied diets allowed these large species to coexist for 1.5+ million years. Maybe we can take some cues from them to make sure we are at least as successful. Fingers crossed no meteors come along to ruin our chances.

Citation: Mallon JC, Anderson JS (2014) The Functional and Palaeoecological Implications of Tooth Morphology and Wear for the Megaherbivorous Dinosaurs from the Dinosaur Park Formation (Upper Campanian) of Alberta, Canada. PLoS ONE 9(6): e98605. doi:10.1371/journal.pone.0098605

Image 1: Triceratops prorsus skull by Zachi Evenor

Images 2-4: Figures 1, 9, and 6 from article

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The 2014 Ecological Impacts of Climate Change Collection

Ecology ColectionPost authored by Collection Curator Ben Bond-Lamberty

The impacts of climate change on global ecology, in its many forms and fields, were well represented by PLOS publications in 2013-2014. The articles chosen for the Collection were published by PLOS ONE and PLOS Biology and encompass several broad areas: experimental manipulations and observations, modeling, paleoecology, long-term studies, and support for mitigation and adaptation.

Experimental manipulation and observation are fundamental to understanding climate change impacts. For example, Anadon-Rosell et al. used a six-year soil warming experiment to examine how three dwarf shrubs may respond to high-altitude climate change, while Tair and Schiel use laboratory manipulations to study primary production and respiration in algae. Both studies point out that communities may be more severely affected than what might be expected based on the response of individual species. Such species interactions feature in a fascinating study by Pringle et al., who survey a Mesoamerican precipitation gradient and report that trees invest more in ant defenders when water is scarce; they conclude that rare but extreme herbivory events interact with water limitation to reinforce this mutualism. The interactive effects between species are studied in a theoretical setting by Northfield and Ives, who use simple models to show that coevolution can result in feedback loops that either dampen or amplify climate change effects. Modeling is also used by Riordan and Rundel in a very different arena, to examine how land use and climate change may interact in California sage scrub ecosystems across the 21st century.

The ecological past holds many clues for the present and future. For example, paleobotanical evidence has shown rapid post-glacial movements of many tree species, faster than current observed migration rates. Feurdean et al. address this uncertainty using a macrofossil database, literature estimates, and process models to highlight the importance of microrefugia. Migration rates are partly a function of demographic processes, a subject examined by a 2014 PLOS ONE study on growth-mortality relationships in piñon pines of the U.S. southwest. Moving to the Mediterranean, Kaniewski et al. also mine the past for information, using radiocarbon, tree cores, and pollen records to reconstruct millenial changes and vulnerabilities of coastal ecosystems in northern Israel.

Long-term observational datasets are relatively rare and extremely valuable. A 26-year study of Magellanic penguins near Argentina found that climate change–in particular, increased rain–has lowered reproductive success in the world’s largest breeding colony of these birds. The authors conclude that similar patterns may undermine the resilience of other species in the region. The complexity of species’ responses to climate changes is emphasized by Ryan et al., who updated a 42-year-old survey of Costa Rican forest frogs. Population declines were linked with changes in temperature, rainfall, and leaf litter depth, but without any consistent pattern across the sites and species surveyed.

Møller et al. use decadal data on European birds and their parasites to examine how both hosts and parasite populations can change with climate shifts. (We humans are of course hosts as well, as Thomassen et al. emphasize in examining the predicted range shifts of human monkeypox in response to central African climate change.) Striking similar notes, Zografou et al. report on changes in butterfly communities between 1998 and 2012 in Dadia National Park, Greece, which were found to correlate with longer-term environmental change, with different patterns at high and low elevations. Butterflies and elevation effects are also the subject of Roth et al., who report significant community shifts in vascular plants, butterflies, and birds over eight years in Switzerland.

Given that a great deal of climate change is inevitable in the coming century, it is important to understand how we can mitigate and adapt to the inevitable impacts. Writing in PLOS Biology, Mora et al. provide an assessment of changes in future ocean biogeochemical variables, and the broader implications of these changes for marine biota and people. A conceptually similar study in PLOS ONE looks at climate change impacts on terrestrial vertebrate hotspots, emphasizing the threat this poses for conservation of European biodiversity. Amorim et al. examine how monitoring networks can be designed to detect potential range shifts, taking into account species’ occurrence, conservation status, and unpredictable volunteer commitment. Finally, Rout et al. ask how we decide to move species threated by climate change, applying a qualitative decision framework to the case study of tuatara, a New Zealand reptile.

As I wrote a year ago, the broad range of these papers emphasize both the multi-faceted impacts of climate change on natural and human systems, as well as the breadth and depth of research on these subjects being published in PLOS journals.

BBLDr. Bond-Lamberty is a Research Scientist at the Joint Global Change Research Institute, a partnership of the Pacific Northwest National Laboratory (PNNL) and the University of Maryland, College Park. His research focuses on carbon cycling in terrestrial ecosystems, particularly boreal and other northern forests, and their response to natural and human-initiated disturbances. He has extensive experience modeling biogeochemical cycling in these systems, as well as in manipulative field and lab experiments. He also acts as a Section Editor for PLOS ONE.

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“Low T” and Prescription Testosterone: Public Viewing of the Science Does Matter

testosterone_grayOn January 29th 2014, researchers from UCLA, NCI, and Consolidated Research, Inc. published an observational study in PLOS ONE detailing increased cardiovascular risks associated with men taking testosterone therapy. Only three days later, on January 31st, this study in combination with another, published in JAMA in November 2013 with similar findings, triggered a Food and Drug Administration (FDA) Drug Safety Communication and evaluation that is currently ongoing. Since then, lawsuits against testosterone drug makers have been filed in both the US and Canada, and the FDA has set up a joint advisory committee who will meet this fall to evaluate potential health risks associated with testosterone therapies to determine whether any regulatory measures are required.

Why all the commotion around one or two scientific articles? The authors of the PLOS ONE study report that men aged 65 years and older who filled a testosterone prescription had double the risk of heart attack within three months. The study is based on a sample of 55,000 men from a dataset of enrollees in a health market database during the years 2006-2010. For younger men with pre-existing heart disease, the increased risk was two- to three-fold higher within the same period.

For matters relating to public health, this study is both relevant and controversial due to the skyrocketing of testosterone prescriptions to men, an industry now valued at $2 billion USD. Unfortunately, testosterone is often prescribed without a blood test for the medical diagnosis that warrants its use (hypogonadism), as it is also claimed to have other health benefits, including improved sex drive, mood, energy levels, and anti-aging effects.

Testosterone molecule

Testosterone molecule

While it’s clear that this PLOS ONE article impacted the actions of regulatory agencies and issues pertaining to public health, we wondered whether this influence was reflected in the paper’s article-level metrics (ALMs). Or, as Roli Roberts asked in a recent PLOS Biologue post, “how do you know when you’ve published a great paper?” Or even a good paper?

As it turns out, this paper did have an interesting, atypical trajectory post-publication. Rather than gaining traction first in the media, riding a flurry of social media activity, and then eventually attracting the attention of health regulators, immediate action was taken by the FDA within days of publication. Concurrently, the article received an explosion of media coverage within a week post-publication, including news pieces in the New York Times: Well Blog, NPR: Health News, and The Wall Street Journal MarketWatch, among others, and was continuing to receive coverage in the BBC News and NPR as late as April 2014. All of this coverage was recorded by our media tracking tool, which can be found under “Related Content” here.

Is the influence of this article captured in its ALMs? If we glance at individual measures, the article had ~ 21,000 views in the first month of publication, and currently has well over 36,000 HTML page views, 17% of which have resulted in PDF downloads. If we compare this view number to that of all other PLOS ONE articles published in the same timeframe, we see that this article is ranked 12th most-viewed. Additionally, a PDF download percentage of 17% is roughly average for a PLOS ONE article, where a higher percentage may indicate increased scholarly usage relative to other, more mainstream types of usage. On social media, this article was shared well over 100 times, which is substantial but less than occurred for other articles published since, with a few papers currently at well over 1000 shares.

However, if we examine citations and post-publication commentary seven months since publication, the study has already accumulated 20 citations, more than any other article published in this timeframe. In addition to accumulating citations, the article has prompted researchers to call for additional, more definitive studies: an article published in The Lancet Diabetes and Endocrinology cited the PLOS ONE and JAMA articles and declared an urgent need for large clinical trials of testosterone. Last but not least, the article has stimulated significant post-publication commentary from readers who have analyzed and critiqued the methodology and characteristics of the cohort, spurring further discussion and research,   and effectively moving post-publication peer review in a forward direction.

Therefore, the value of this article may not lie strictly in its views, shares, citations, or even saves, or any combination or calculation thereof, but instead in its open access visibility to the public, healthcare providers, federal agencies, and media outlets. Anyone, anywhere in the world with Internet access can read this article and its surrounding discussion and then decide for themselves how to respond and react, and that alone is worth more than any level of metrics combined.

Citations

Finkle WD, Greenland S, Ridgeway GK, Adams JL, Frasco MA, et al. (2014) Increased Risk of Non-Fatal Myocardial Infarction Following Testosterone Therapy Prescription in Men. PLoS ONE 9(1): e85805. doi:10.1371/journal.pone.0085805

Vigen R, O’Donnell CI, Barón AE, et al. Association of Testosterone Therapy With Mortality, Myocardial Infarction, and Stroke in Men With Low Testosterone Levels. JAMA. 2013;310(17):1829-1836. doi:10.1001/jama.2013.280386

Piszczek J, Mamdani M, Antoniou T, Juurlink DN, Gomes T (2014) The Impact of Drug Reimbursement Policy on Rates of Testosterone Replacement Therapy among Older Men. PLoS ONE 9(7): e98003. doi:10.1371/journal.pone.0098003

Images

Rx image from Ano Lobb on Flickr.

Testosterone image from Benjah-bmm27.

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Does the Fox Say, “I Love Living in the City?”

flickr fox Steve K CCBY

 

Most wild animals move away from areas heavily populated by humans, noisy cars, and sparse natural habitat. Some, however, thrive in the city, learning to hustle to provide for themselves and their families just like the rest of us. Urban wildlife like raccoons and turkeys roam my neighborhood in the San Francisco bay area, stealing food from the compost heap and perching on top of administrative buildings. Other parts of the world see monkeys, moose, or even foxes in their urban centers. Recently, researchers teamed up with citizen scientists to investigate the distribution of urban red foxes in Great Britain. They published the results of their survey in an article in PLOS ONE, “Changes in the Distribution of Red Foxes (Vulpes vulpes) in Urban Areas in Great Britain: Findings and Limitations of a Media-Driven Nationwide Survey.”

Keeping track of animal populations in cities is important for wildlife management and public health, but it is by no means an easy task. Cities are crazy quilts of fences, private residential property, public areas, and commercial property, all with varying degrees of accessibility that can make research on animal distribution a challenge. For these reasons, the authors of this study recruited volunteers to help with the fox survey. Utilizing the eyes and attention of citizen scientists allowed the scientists to evaluate a wide urban area without stomping through everyone’s gardens.

The authors recruited participants using television programs about foxes, with each program including information about how to participate in the fox survey. Participants were asked to submit records and locations of fox sightings with photos via a website. Citizen science makes research like this possible, but it does have drawbacks, including that the  data quality relies on the accurate reporting of many untrained individuals who are much more likely to report positive data points (such as the presence of a fox in their area) rather than negative data points (an absence of foxes), which can skew results.

To improve data reliability, researchers double-checked for errors in location and date. They focused on determining how widespread the foxes were, which is easier to gauge with this method, rather than how densely populated the foxes are, which would be more difficult with potentially skewed data.

journal.pone.0099059.g003

 

The results of this study indicated that, compared to their distribution in the 1980s, foxes have further spread out over Britain, with sightings reported in 91% of 65 cities that were previously thought to have few or no foxes. It is unclear why they have expanded their colonization of British urban areas, but according to the authors they do seem to prefer private backyards to public green spaces. More fox sightings were reported in cities with higher human population densities, as can be seen in the graphic above, but the researchers noted that this result could easily be due to increased reporting and not necessarily related to a higher number of foxes. All in all, more research is needed to determine why the distribution of red foxes in Britain is changing, and whether the fox population is increasing or just spreading out. In the meantime, the authors have made their data available for anyone to have a look.

 

Scott DM, Berg MJ, Tolhurst BA, Chauvenet ALM, Smith GC, et al. (2014) Changes in the Distribution of Red Foxes (Vulpes vulpes) in Urban Areas in Great Britain: Findings and Limitations of a Media-Driven Nationwide Survey. PLoS ONE 9(6): e99059. doi:10.1371/journal.pone.0099059

Flickr image “Oops, I woke up the Fox asleep by my backdoor” by Steve K

Fox sightings map figure is from the article

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Supporting Hepatitis Awareness with Open Access Hepatitis Research

World Hepatitis Day was July 28th, and PLOS ONE is observing the day by raising awareness with a few of our many open access articles on viral hepatitis that we’ve published in the past year. According to the World Hepatitis Alliance, despite hepatitis being a widespread illness and having close to the same mortality rate as HIV/AIDS, it seems to lack the same level of awareness among the general population. Below is a sampling of research articles about hepatitis to help broaden our awareness on this important day, including research on how over the counter pain relievers can impact vaccination, on infection of infants born to mothers with hepatitis, and on reinfection and clearance of hepatitis C in people who inject drugs. For more background information on this disease, check out this intro to the hepatitis viruses on the World Hepatitis Day website.

vaccines

Vaccination and Pain Relief

Sometimes vaccinations can cause soreness at the vaccination site and low grade fever. Over the counter (OTC) paracetamol, also known as acetaminophen—the main active ingredient in pain-relieving products like Tylenol—is sometimes used before or after vaccination to prevent or treat this pain and fever. Researchers have previously shown that taking paracetamol during hepatitis B vaccination makes it less effective in babies, and the authors of this PLOS ONE study sought to determine if the same might be true for young adults 18 years old or older receiving the vaccination. In this randomized, controlled clinical trial, researchers compared three groups: one group was given paracetamol before vaccination, one group was given paracetamol after, and the third group received no paracetamol. The results showed that the vaccinated adults experienced modest suppression of their immune systems and lower production of antibodies if they received paracetamol before being given the vaccine, but not if they received it post-vaccine. Due to concerns about reduced effectiveness, the authors recommend further investigation into the timing of taking paracetomol to treat any hepatitis B vaccine side effects.

Hepatitis virions

Hepatitis virions

 

Infants Born to Mothers with Hepatitis B in Cameroon

The World Health Organization recommends vaccinating infants against hepatitis B when they are born to mothers with the disease, and a program to do just that began in Cameroon in 2007. PLOS ONE authors in this study tested pregnant women in North Cameroon between 2009 and 2010 and found that 20% of the women tested positive for hepatitis B even though most of them exhibited no symptoms. Since Cameroon is a high risk area where hepatitis B is common, this study supports previous research and provides further support for the WHO recommendation in favor of routine hepatitis B vaccines at birth for children of at-risk mothers.

hepCneedlework

Hepatitis C Cell Embroidery Art, Flickr

 

Hepatitis C Clearance and Reinfection in People Who Inject Drugs

Researchers have previously shown that 20-40% of people infected with hepatitis C fight off and clear the virus from their body without any medical intervention. This does not mean, though, that these individuals are immune to reinfection. Researchers in Australia report nine confirmed and 17 possible cases of hepatitis C reinfections in 188 drug-injecting study participants in this PLOS ONE study. Additionally, many of those who were re-infected did not clear the virus as they did the first time, suggesting that immunity is incomplete and supporting previous research. The authors therefore suggest public health campaigns may help to inform people who inject drugs about the risk of reinfection.

For more hepatitis research and information, have a look at some of our other articles here.

 

Images

  1. Flickr image: all in a day’s work by Dawn Huczek
  2. Image of hepatitis virions by E.H. Cook, Jr. from the CDC Public Health Image Library is in the public domain.
  3. Flickr image: Hepatitis C Cell Embroidery Art by Hey Paul Studios

References

Doedée AMCM, Boland GJ, Pennings JLA, de Klerk A, Berbers GAM, et al. (2014) Effects of Prophylactic and Therapeutic Paracetamol Treatment during Vaccination on Hepatitis B Antibody Levels in Adults: Two Open-Label, Randomized Controlled Trials. PLoS ONE 9(6): e98175. doi:10.1371/journal.pone.0098175

Ducancelle A, Abgueguen P, Birguel J, Mansour W, Pivert A, et al. (2013) High Endemicity and Low Molecular Diversity of Hepatitis B Virus Infections in Pregnant Women in a Rural District of North Cameroon. PLoS ONE 8(11): e80346. doi:10.1371/journal.pone.0080346

Sacks-Davis R, Aitken CK, Higgs P, Spelman T, Pedrana AE, et al. (2013) High Rates of Hepatitis C Virus Reinfection and Spontaneous Clearance of Reinfection in People Who Inject Drugs: A Prospective Cohort Study. PLoS ONE 8(11): e80216. doi:10.1371/journal.pone.0080216

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If at First You Don’t Succeed, Sit Back and Listen

Brain

Few of us remember how easily we learned language as children. Although the acquisition wasn’t always graceful then—‘awry’ never sounds the same way aloud as the way I read it in my head— using our primary language as an adult is as habitual as tying shoelaces and seemingly as instinctual as smiling. Given how involuntarily we adults use our primary language, it’s shocking how difficult learning new languages as an adult can be. The authors of a recent PLOS ONE paper postulated that the very functions we develop as our brains mature as adults may be what hinder us from mastering language the way a child does. We might, in fact, be “trying” too hard.

Researchers have shown in previous studies that adults outperform children in tasks that require attentional focus and effort. This is because the regions of the brain associated with these abilities—the prefrontal and parietal cortices—develop more slowly, and as a result, these abilities become stronger as we age. In other words, adult brains develop abilities that help us “try harder.” These same capabilities may, however, interfere with our capacity to learn some aspects of language as adults, like the tricky networks that underlie grammar.

To test the limits of our adult brains, the authors of “When it hurts (and helps) to try: the role of effort in language learning” tested participants on how well they learned an artificial language. In the first experiment, participants were instructed to simply listen to the word stream. In the second experiment, participants were told to identify patterns and categories within the artificial language.

The researchers stimulated “effort” in the second experiment by tasking participants with a series of learning drills. Learners pressed buttons to indicate when they thought they had mastered a series of words or a grammar pattern. On the other hand, participants in the first group were explicitly distracted from learning. These participants colored during the experiment.

After the experiment, researchers scored both sets of participants on their ability to identify words, categories of words presented (for example: nouns), and the correct order of words in test sentences.

Based on the results of the test, the participants who were told to learn the language did not outperform the participants who merely listened in all categories. The “learners” were better than the “listeners” at identifying specific words of the artificial language, but both “learners” and “listeners” were equally successful in indicating the order patterns of words in test sentences. When it came to learning categories of words, only the listeners were significantly better than chance. The authors concluded that trying to learn may be a detriment to participants in this aspect of language learning.

Although fully developed prefrontal and parietal cortices endow adults with many advantages (think the ability to plan, reason, and problem solve, among others), according to the authors, these same adult brains may hinder us from learning some aspects of language. To become masters of the murkier depths of grammar, we may want to tap into the more intuitive methodology employed by children. In the meantime, we adults will continue to struggle with the differences between ‘who’ and ‘whom,’ ‘further’ and ‘farther,’ and the best way to retain complex information presented by grammar.

Citation: Finn AS, Lee T, Kraus A, Hudson Kam CL (2014) When It Hurts (and Helps) to Try: The Role of Effort in Language Learning. PLoS ONE 9(7): e101806. doi:10.1371/journal.pone.0101806

Image 1: Exercise Plays Vital Role Maintaining Brain Health by Saad Faruque

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Not Just a Pretty Face: Island Poppies Defend With Prickles

PoppyAlthough the vibrant, waifish petals of the poppy may appear inviting to the casual observer, a closer look reveals a pricklier message: Stay away! To discourage plant eaters like insects and birds from biting into their leafy appendages, many plant species protect themselves with defense mechanisms, like tougher leaves, distasteful latex, and armor made of prickles. Developing these defense features is part of a plant’s natural growth throughout its lifetime. Some plants, however, are able to activate additional protection when faced with attacking herbivores. The authors of a recent PLOS ONE paper investigated these defense mechanisms in two species of poppy currently found in Hawaii, where natural herbivores have long been extinct. The authors’ results reveal that island poppies may have more “nettle” in the face of simulated adversity than previously predicted.

The authors chose two species of poppy for testing, Argemone glauca, a species native to Hawaii, and Argemone mexicana, a species originally hailing from the North American continent and a recent inhabitant of the Hawaiian islands. Both species come pre-equipped with permanent features that may function as defense strategies. However, permanent defenses are costly to maintain for a plant: They divert energy away from other functions, like reproduction and growth, and are therefore an energy investment for the plant. To combat the cost of maintaining a full suite of permanent defenses, some plants respond to attacks from plant eaters only when they occur by activating additional defenses, known as inducible defenses. Unlike defense features that develop throughout the course of a plant’s lifetime, also known as constitutive defenses, inducible defenses are not permanent, only prompted by specific need.

In this study, the researchers simulated the need for additional defenses by subjecting the two species to various “attacks” to see how the poppies would respond. Plants were assigned to one of four random treatment groups:

  1. The control group, which received no treatment
  2. The damage group, where the authors clipped off portions of the leaves
  3. The Jasmonic acid group, where researchers sprayed the leaves with a harmful solution that inhibits growth
  4. And the combination group, where authors defoliated plants first and then sprayed them with Jasmonic acid

The researchers then allowed for two new leaves to grow to ensure that the plants had an adequate amount of time to respond.

Although neither species developed additional leaf toughness or produced more natural latex in response to treatments, both species exhibited increased prickle density on new leaves that grew after treatment. To evaluate prickle density, the authors harvested new leaves and counted all the new prickles on the surfaces of the leaves, excluding prickles found along the leaf edge. They also quantified the leaf area and performed statistical analyses to identify patterns in the various groups.

The authors found that Hawaiian native A. glauca responded more intensely to treatment by developing significantly more prickles than its continental North American counterpart, A. mexicana. The authors report that prickles for A. glauca were 20x more dense and 2.7x higher than A. mexicana.

Plant defenses are selected for over time due to snacking pressures from herbivores. On the Hawaii islands, however, natural herbivores of A. glauca, such as flightless ducks and beetles, are now extinct. The lack of natural predators for island plants has given rise to the idea that island plants have ‘gone soft’ over time. The authors consider A. glauca’s robust response to external attacks evidence that island plants may be better defended than previously thought.

Although it may be impossible to determine whether these island defenses have been selected for by herbivores of the past, no longer present, the inducibility of prickles in A. glauca and A. mexicana demonstrates that these poppies have the mettle to fight back against attackers and snackers.

For more on how herbivores and plants interact, check out this EveryONE blog post on snail mucus.

Citation: Hoan RP, Ormond RA, Barton KE (2014) Prickly Poppies Can Get Pricklier: Ontogenetic Patterns in the Induction of Physical Defense Traits. PLoS ONE 9(5): e96796. doi:10.1371/journal.pone.0096796

Image 1: Agemone glauca by Forest and Kim Starr

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PLOS launches Responding to Climate Change Collection

Today PLOS ONE launches the Responding to Climate Change Collection. At its centre is a paper published last December, “Assessing ‘Dangerous Climate Change’:  Required Reduction of Carbon Emissions to Protect Young People, Future Generations and Nature” by James Hansen and colleagues. The paper presented a disruptive call to action on climate change through cohesive, unified steps to reduce fossil fuel emissions to pre-industrial era levels.

Responding to climate change

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

The publication was accompanied by a call for papers for the PLOS ONE Collection, focussing on research that examines the practicalities of reducing fossil fuel emissions; returning the Earth to a state of energy balance; and climate and conservation management strategies that counter the impact of climate change and preserve natural habitats. Areas covered in the call for papers include atmospheric chemistry, alternative energy research, geoengineering, science policy, behavioural psychology, and ecosystem and habitat conservation.

“Minimizing human-made climate change requires insight across a broad science and policy spectrum, and ready access to knowledge as understanding is gained.  As an Open Access journal, PLOS ONE provides a vehicle to achieve that,” says Hansen.

The launch of the collection coincides with the publication of the first submission to the call. “Climate Exposure of US National Parks in a New Era of Change” by William B. Monahan and Nicholas A. Fisichelli of the U.S. National Park Service describes a variety of recent extreme climates in some of the nation’s most visited parks. Evaluation of data for 289 natural resource parks administered by the National Park Service shows that parks are overwhelmingly at the extreme warm end of historical temperature distributions. The authors call for intensive climate science education, and inclusion of the general public, in order to help steward parks and park resources in the face of the changing climate: “As climate shifts further outside of the historical range of variability, resistance strategies will likely become less effective and extremely difficult management decisions – with input from the public and stakeholder groups – will be required.”

The Collection also includes 8 related papers that have been published in PLOS ONE since the call was issued. The papers cover such diverse topics as stratospheric aerosol geoengineering, energy potential of bioenergy cropping systems and the impact of climate awareness on dietary choices of young adults in Finland.

Grand Canyon - Luca Galuzzi

Grand Canyon National Park has recently experienced extreme high temperatures compared to its historical range of variability and may require new management strategies to manage resources that are sensitive to changes in temperature. Image Credit: Luca Galuzzi CC BY-SA 2.5 – www.galuzzi.it

The “Responding to Climate Change” Collection remains open for new submissions. Few areas can benefit as much from the force of Open Access as climate change research: the combination of public, scientific, and governmental interest with the mounting misinformation, unsubstantiated opinions, and unsourced data make public access to original, well-reported, and peer-reviewed climate change research of utmost importance.

PLOS ONE’s wide scope and broad publication criteria make it a perfect venue to publish and collate relevant articles in these vastly differing areas of research into one place. Our hope is that by encouraging and facilitating further research, replication, and sharing of both positive and negative results, this Collection will become a catalyst for continued climate research and policy formation.

Image 1: (clockwise from top left) Matt Rudge, Flickr.com; Vik Walker, Flickr.com; Vera Kratochvil, PublicDomainPictures.net; NASA Goddard Space Flight Center

Image 2: Luca Galuzzi CC BY-SA 2.5 – www.galuzzi.it

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