EveryONE

This is my last day as the Publisher of PLoS ONE, and I wanted to mark it with a brief blog post.

When I came to work on PLoS ONE (in March 2008), the journal was in its infancy, but was clearly going places.  At that time it was receiving about 280 submissions, and publishing about 170 articles, per month. The journal is now receiving over 3,100 submissions per month and in May it should exceed 2,000 publications for the first time ever. PLoS ONE now publishes more articles per month than all but about 20 journals worldwide publish in a year, and in 2012 it could publish almost 3% of the STM literature.

But although the publication volume of the journal has made it very visible, it is how it got there which is the truly interesting story. PLoS ONE was a radical concept when proposed by the PLoS Founders – a journal which would judge submissions only on scientific and methodological soundness, leaving any subjective determinations of impact, scope, or relevance to the post-publication phase. As a result, many commentators felt that it could become a dumping ground for otherwise unpublishable work, or would in some way be a vanity press. But this was never the case. In fact, PLoS ONE has applied exemplary standards to its publication practices; it has rigorously enforced global and local ethical standards; it has treated all authors with courtesy and respect; and it has peer reviewed all submitted content to the highest levels – collectively, these are things which have shown that the journal is serious about the ways in which it will evaluate and handle submitted articles. Today, more than 75% of authors who publish in PLoS ONE have selected the journal as their first or second choice publication venue, and the citation activity of published articles is incredibly high (for example, for those articles which are 12 months or older, 88% have 1 or more citations, and 66% have 3 or more). In addition, the journal has won two awards for Innovation from Industry and Community bodies.

Clearly this radical approach to the evaluation and publication of scientific results has been extremely well received. As a result it is my belief that PLoS ONE has caused (and will continue to cause) a seismic shift in the scholarly publication landscape. It represents a real force for positive change in the way in which academic articles are evaluated and distributed.

Therefore, it is with a sense of considerable sadness that today is my last day on the Journal – running PLoS ONE has been the high point of my career. I would like to take this opportunity to thank everyone who has worked on the journal over the years – without the efforts of the Academic Editors (who now number more than 3,000), the Peer Reviewers (who number almost 75,000) and the staff (located in both our offices, and in various partner organizations) PLoS ONE would not have been the success it is. The journal is, of course, in safe hands – we have a strong organization of experienced staff, and dedicated Academic Editors who, I know, will take the journal to new heights in the coming years.

Thank you,

Peter Binfield,

Publisher PLoS ONE

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Filed under:General | Tagged: PLoS ONE

World Malaria Day may have come and gone, but our PLoS ONE authors certainly seem to be keeping in the spirit, with three new malaria-related publications in the last week.

On Friday, we published “Distributed Medical Image Analysis and Diagnosis through Crowd-Sourced Games: A Malaria Case Study,” by a group of authors from University of California, Los Angeles. Today we have two more to add to the list: “Investigation of Host Candidate Malaria-Associated Risk/Protective SNPs in a Brazilian Amazonian Population,” from an international team of authors from Brazil and the UK, and “Algae-Produced Pfs25 Elicits Antibodies that Inhibit Malaria Transmission,” from University of California, San Diego.

I love how these articles all tackle aspects of a single problem, but in such different ways, from the patient to the mosquito host to the causative parasite, and from diagnosis to treatment to prevention. This breadth of coverage highlights the incredible richness and diversity of malaria research, and of the broader scientific research community as well, which is very important for a multidisciplinary – and frequently interdisciplinary – journal like PLoS ONE.

Citations:

Mavandadi S, Dimitrov S, Feng S, Yu F, Sikora U, et al. (2012) Distributed Medical Image Analysis and Diagnosis through Crowd-Sourced Games: A Malaria Case Study. PLoS ONE 7(5): e37245. doi:10.1371/journal.pone.0037245

da Silva Santos S, Clark TG, Campino S, Suarez-Mutis MC, Rockett KA, et al. (2012) Investigation of Host Candidate Malaria-Associated Risk/Protective SNPs in a Brazilian Amazonian Population. PLoS ONE 7(5): e36692. doi:10.1371/journal.pone.0036692

Gregory JA, Li F, Tomosada LM, Cox CJ, Topol AB, et al. (2012) Algae-Produced Pfs25 Elicits Antibodies That Inhibit Malaria Transmission. PLoS ONE 7(5): e37179. doi:10.1371/journal.pone.0037179

Filed under:Aggregators | Tagged: citizen science, Editor's choice, Malaria, Research highlights

Figure 1. Image of one of the corridors of the Catacombs.

Have humans always suffered from the same kinds of health issues? When we age, do we experience the same aches and pains as our ancestors? Did our joints become stiff and painful back in the 1700s, just like they still do today? Researchers in Germany and Italy posed this question and attempted to answer it by scanning the hip bones of Sicilian friars from the 18^th and 19^th centuries. They looked for markers of osteoarthritis in the mummified remains of these former clergymen, and have now concluded that a specific type of bone marker, herniation pits on the femoral neck, should be considered when scientists examine remains for signs of that ailment. The results are published in this paper, “Herniation Pits in Human Mummies: A CT Investigation in the Capuchin Catacombs of Palermo, Sicily.” You can see a larger version of the image here.

Abstract

Herniation pits (HPs) of the femoral neck were first described in a radiological publication in 1982 as round to oval radiolucencies in the proximal superior quadrant of the femoral neck on anteroposterior radiographs of adults. In following early clinical publications, HPs were generally recognized as an incidental finding. In contrast, in current clinical literature they are mentioned in the context of femoroacetabular impingement (FAI) of the hip joint, which is known to cause osteoarthritis (OA). The significance of HPs in chronic skeletal disorders such as OA is still unclear, but they are discussed as a possible radiological indicator for FAI in a large part of clinical studies.

In this paleoradiological study we examined a sample of mummies from the Capuchin Catacombs of Palermo, Sicily, by a mobile computed tomography (CT) scanner. Evaluation of the CT examinations revealed HPs in six out of 16 (37.5%) adult male mummies.

The first aim of this study was to compare the characteristics of HPs shown in our mummy collection to the findings described in clinical literature. Thereby CT evaluation revealed that their osseous imaging characteristics are in accordance, consisting of round to oval subcortical lesions at the anterior femoral neck, clearly demarcated by a sclerotic margin.

The second aim was to introduce HPs to the paleoradiological and paleopathological methodology as an entity that underwent a renaissance from an incidental finding to a possible radiological indicator of FAI in the clinical situation. As FAI plays an important role in the development of OA of the hip, which is a very common finding in human skeletal remains, HPs should always be considered in paleoradiological evaluation of hip joint diseases.

Citation: Panzer S, Piombino-Mascali D, Zink AR (2012) Herniation Pits in Human Mummies: A CT Investigation in the Capuchin Catacombs of Palermo, Sicily. PLoS ONE 7(5): e36537. doi:10.1371/journal.pone.0036537

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The road to a PhD is long and hard, and it’s natural that students’ goals for the future would change over the course of their education. Anecdotal evidence abounds – just ask anyone who’s been through it – and now a study published last week in PLoS ONE shows that students close to graduation are less interested in pursuing faculty careers than are their younger counterparts.

The authors, Henry Sauermann from Georgia Institute of Technology and Michael Roach from University of North Carolina, investigated the attractiveness of different careers to over 4,000 PhD students at different stages in their training in the life sciences, chemistry, and physics at 39 different US tier-one research universities. Across the board, late stage students, defined as those who were looking for jobs or were planning to do so within a year, found faculty jobs less attractive than did early stage students, who had not yet completed their qualifying exam or similar milestones.

There were some interesting distinctions between the responses from chemistry students and the biologists and physicists that caught my attention. My PhD is in chemistry, but I conducted my research in a biology lab, and I felt like the cultures were very different – a distinction that appears to be borne out in the numbers.

From the beginning, the chemistry students in the study were much less interested in faculty positions than were either the biologists or the physicists: only 23% of early stage chemistry students declared a research-focused faculty position to be extremely attractive, as compared to 39% for biologists and 37% for physicists. Furthermore, chemists’ interest in working for either an established firm or a start-up showed huge increases from early to late stage, even though their initial interest in these types of positions was already high relative to their counterparts in biology or physics.

The authors don’t discuss potential reasons for these differences, but my impression is that industry jobs in chemistry are simply more common and more accessible than those in biology. This may not always be the case, but it will be interesting to see how both the academic and industrial cultures evolve as research – and the accompanying funding – goes in new directions.

Citation: Sauermann H, Roach M (2012) Science PhD Career Preferences: Levels, Changes, and Advisor Encouragement. PLoS ONE 7(5): e36307. doi:10.1371/journal.pone.0036307

Filed under:Aggregators | Tagged: Editor's choice, Research highlights, science careers, science education

Fingerprints are as unique as snowflakes – or so we’re taught in elementary school. Identical twins, though, provide an interesting caveat to this rule: Not only do they look alike, they are also more likely than non-twins to have similar fingerprint patterns.

These similarities raise potential complications for biometrics-based security systems and crime solvers, but a PLoS ONE paper published Friday suggests there’s no reason to worry.

The study, conducted by an international team of researchers from the Chinese Academy of Sciences and the University of Iowa, looked at fingerprints from 83 pairs of identical twins. They collected each print six times, rather than the single impression that is usually collected, and used two different identification methods, called P071 and VeriFinger 6.1, and novel analytical methods to evaluate the prints. They found that identical twins’ fingerprints had a 74% probability of being the same type (though not identical), as compared to a 32% probability for a random pair of prints, but they also showed that the fingerprints could be distinguished using the sophisticated identification methods.

Based on these results, it looks like identical twins may not be the perfect criminals after all. Nevertheless, they seem to have a leg up on the rest of us – maybe something to keep in mind the next time you’re trying to solve that thorny art heist.

Citation/Image source: Tao X, Chen X, Yang X, Tian J (2012) Fingerprint Recognition with Identical Twin Fingerprints. PLoS ONE 7(4): e35704. doi:10.1371/journal.pone.0035704

Filed under:Aggregators, Topic Focus | Tagged: Editor's choice, fingerprints, forensics, Research highlights, twin science

Cross-sections of Q. palmeri stems.

Today’s internationally recognized tree holiday was founded in 1872 by J. Sterling Morton, former Secretary of Agriculture to US President Grover Cleveland, and avid tree enthusiast. The holiday is generally observed on the last Friday in April, and today marks over 135 years of tree planting and conservation efforts across the globe. Highlighted below are some of PLoS ONE’s arboreal related articles. Take a moment to read about the  critical role trees have in our global ecosystem.

Sudden Oak Death, caused by a pathogen introduced to California forests, continues to disturb local oak populations. This research explores the clonal reproductive behavior of the pathogen, Phytophthora ramorum.

Researchers at the University of Toronto have collected samples from Panamanian rainforest tree species to estimate total carbon content in tropical ecosystems. Read more here.

The fascinating colonization of Juniper trees, Juniperus brevifolia, a native species to the Azores archipelago, has been explored in the following article.

Recent analysis indicates that although forested areas have declined globally, the overall tree density in such areas has increased. Read more about how this is important in the sequestration of atmospheric carbon.

Logging practices in wood-producing forests pose risks for many endangered flora and fauna. Managing these areas sustainably could help conserve such species, as well as increase carbon storage. Read more here.

To find ways to get involved, or to learn how to plant a tree in your community, visit www.arborday.org

Filed under:Aggregators, Fun, Images, Topic Focus, Worth A Thousand Words | Tagged: Arbor Day, carbon, forestry, PLoS ONE, trees, tropical ecosystems

Today is the fifth annual World Malaria Day, commemorated every April 25 to recognize and encourage global efforts to control malaria. This year’s theme, “Sustain Gains, Save Lives: Invest in Malaria,” alludes to the many important advances against the malaria parasite that have been achieved in recent years, but also includes a warning: we must continue to invest in malaria research and maintain our vigilance to ensure that painstakingly earned gains are not surrendered to complacency.

Based on the 251 malaria-related PLoS ONE papers published since last year’s World Malaria Day, it’s pretty clear to us that the research community is maintaining its commitment to this disease. Instead of trying to provide an overview of all of these articles, which cover perspectives as diverse as public health, ecology, and microbiology, we decided to observe the day by highlighting a single article that, like this year’s theme, emphasizes the importance of continued research as the parasite proves itself to be a constantly evolving target.

The study, published last October, monitors drug resistance in the causative parasite Plasmodium falciparum in Mozambique over five years, from 2006 to 2010, as the recommended drug treatment was adjusted. The researchers, led by Jaishree Raman of the South African Medical Research Council, found that the incidence of parasitic resistance to the originally recommended drug regimen increased significantly over the course of the study, from 56.2% at the start up to 75.8% in 2010. This approximately 20% leap in resistance suggested that the preferred treatment at the time would become much less effective as its use increased.

However, the Mozambican Ministry of Healthy preempted this scenario by changing their recommended front-line drug treatment in 2008. The authors weren’t able to study the full impact of this policy change, though, because it was not fully deployed until 2010, at which point the study was winding down – further highlighting the need for continued careful monitoring as new treatments are introduced.

You can learn more about World Malaria Day at Roll Back Malaria and the World Health Organization, and read about some additional malaria papers from last year’s World Malaria day post.

Citation: Raman J, Mauff K, Muianga P, Mussa A, Maharaj R, et al. (2011) Five Years of Antimalarial Resistance Marker Surveillance in Gaza Province, Mozambique, Following Artemisinin-Based Combination Therapy Roll Out. PLoS ONE 6(10): e25992. doi:10.1371/journal.pone.0025992

Image source: eyeweed on Flickr

Filed under:Aggregators, Featured Image, General, Topic Focus | Tagged: Malaria, Research highlights, WHO, World Malaria Day

Although the nationally celebrated Earth Day has just passed, it’s important to consider our impact on the environment every day.  In their recently published article “Proliferation of Hydroelectric Dams in the Andean Amazon and Implications for Andes-Amazon Connectivity,” authors Matt Finer and Clinton N. Jenkins highlight a constant environmental concern; meeting the world’s growing energy demands. Finer and Jenkins developed a strategic ecological impact assessment of planned dams from the Andes to the Amazon. Their findings point to the need for this kind of heightened environmental awareness every day.

Abstract

Due to rising energy demands and abundant untapped potential, hydropower projects are rapidly increasing in the Neotropics. This is especially true in the wet and rugged Andean Amazon, where regional governments are prioritizing new hydroelectric dams as the centerpiece of long-term energy plans. However, the current planning for hydropower lacks adequate regional and basin-scale assessment of potential ecological impacts. This lack of strategic planning is particularly problematic given the intimate link between the Andes and Amazonian flood plain, together one of the most species rich zones on Earth. We examined the potential ecological impacts, in terms of river connectivity and forest loss, of the planned proliferation of hydroelectric dams across all Andean tributaries of the Amazon River. Considering data on the full portfolios of existing and planned dams, along with data on roads and transmission line systems, we developed a new conceptual framework to estimate the relative impacts of all planned dams. There are plans for 151 new dams greater than 2 MW over the next 20 years, more than a 300% increase. These dams would include five of the six major Andean tributaries of the Amazon. Our ecological impact analysis classified 47% of the potential new dams as high impact and just 19% as low impact. Sixty percent of the dams would cause the first major break in connectivity between protected Andean headwaters and the lowland Amazon. More than 80% would drive deforestation due to new roads, transmission lines, or inundation. We conclude with a discussion of three major policy implications of these findings. 1) There is a critical need for further strategic regional and basin scale evaluation of dams. 2) There is an urgent need for a strategic plan to maintain Andes-Amazon connectivity. 3) Reconsideration of hydropower as a low-impact energy source in the Neotropics.

Filed under:Aggregators, Images, Topic Focus, Worth A Thousand Words | Tagged: Amazon, Andes, energy, environment, hydroelectric dams

Emperor penguin - Credit: British Antarctic Survey

This month in PLoS ONE news: Penguin populations recorded from outer space, super strength bacteria discovered in caves, and much more!

Satellite mapping provides the first comprehensive record of the Emperor Penguin population in Antarctica. Scientists found that the overall population is higher than previously estimated; however, other colonies may have disappeared altogether, most likely due to climate change. Wired Scientific American and BBC covered this article.

Strains of previously undiscovered bacteria found deep in the Lechuguilla Cave of New Mexico, show remarkably strong resistance to modern antibiotics. Scientific American, The Los Angeles Times and National Geographic covered this article.

The commonly used Body Mass Index (BMI) measure may vastly underestimate the ongoing obesity epidemic, according to new research. Read this study and more at The Huffington Post, TIME and The Los Angeles Times.

What makes a good athlete? Traits like problem solving, creativity and quick decision making are commonly referred to as “game intelligence” in sports. According to new research, professional soccer players show increased cognitive abilities, which may be linked to such athletic success. New York Times, Wired and CNN discussed this article.

For more in-depth coverage on news and blog articles about PLoS ONE papers, please visit our Media Tracking Project.

Filed under:Aggregators, Featured Image, Media, Topic Focus | Tagged: Antarctica, athlete, bacteria, BMI, census, Emperor Penguin, game inteligence, Lechuguilla Cave, microbes cave, obesity, penguin, soccer, sports

In paleontology, the fossil is the basic data point for any research, regardless of the amount of technology used. Consequently, descriptions of a fossil’s anatomy are critical for scientists answering a variety of questions. What species is this animal? Look to the fossil. What did it eat? Look at the teeth. Where does the animal fit on the evolutionary tree? Compare its fossil with other fossils. Detailed documentation and description of a specimen isn’t particularly glamorous, but absolutely necessary.

The tiny plant-eating dinosaur Fruitadens scurried through the underbrush of Colorado around 150 million years ago, long before the rise of the Rocky Mountains. First named in a brief article in 2010, Fruitadens made a splash for its diminutive length of less than 1 meter and estimated body mass of under 1 kilogram. Unfortunately, the original publication did not have space for more than a general anatomical description as well as confirmation that Fruitadens’ small size wasn’t because it was “just” a baby of a larger species. Thus, a new paper in PLoS ONE by Richard Butler, Laura Porro, Peter Galton, and Luis Chiappe fills in many of the essential details.

Artist’s reconstruction of Fruitadens. By Smokeybjb, licensed under Creative Commons Attribution-Share Alike 3.0 Unported license.

Fruitadens belonged to an unusual, widespread, and rare group of dinosaurs called heterodontosaurids. They first appeared around 200 million years ago in South Africa, and persisted until around 140 million years ago in England. Heterodontosaurids were small (no more than 2 meters in maximum body length) and characterized by unusual fangs at the front of their jaws. Fruitadens was no exception—although its lower jaw is incomplete, the preserved portion of the teeth shows that it too probaby had fangs. The rest of the teeth are more conventional, similar to those seen in other small plant-eating dinosaurs.

So, how did Fruitadens and other heterodontosaurids use their tiny, fanged jaws? The researchers developed simple two-dimensional models of the jaws in heterodontosaurids, reconstructing the movements associated with the bones and muscles. A basic difference between early and late-surviving heterodontosaurids (including Fruitadens) was identified. Specifically, Fruitadens and its close relatives had simpler jaw anatomy than their ancestors, suggestive of a switch to simpler, weaker, and more rapid jaw movements. Although much more work remains, Butler and colleagues suggest that Fruitadens may have been an ecological generalist subsisting on a variety of plants, insects, and other small organisms. This contrasts with the diet of its ancestors, subsisting primarily on plants.

A reconstruction of the skull of Fruitadens, from Butler et al. 2012.

Because they are so small, heterodontosaurid fossil are pretty scarce, and details of their evolutionary relationships are sketchy. Butler and colleagues carefully documented all of the relevant anatomical details in Fruitadens through photographs, CT scans, and text. In the process, the researchers identify some previously unrecognized features that characterize heterodontosaurids as a whole, and other formerly recognized features that do not. Although much work remains—particularly through the collection and description of new fossils—this new paper is an important step towards better understanding Fruitadens and its enigmatic kin.

REFERENCES

Butler RJ, Galton PM, Porro LB, Chiappe LM, Henderson DM, Erickson GM (2010) Lower limits of ornithischian dinosaur body size inferred from a diminutive new Upper Jurassic heterodontosaurid from North America. Proc Roy Soc B 277: 375–381.

Butler RJ, Porro LB, Galton PM, Chiappe LM (2012) Anatomy and cranial functional morphology of the small-bodied dinosaur Fruitadens haagarorum from the Upper Jurassic of the USA. PLoS ONE 7(4): e31556. doi:10.1371/journal.pone.0031556

IMAGE CREDITS:

Top image from http://en.wikipedia.org/wiki/File:Fruitadens.jpg, licensed under Creative Commons Attribution-Share Alike 3.0 Unported license.

Bottom image from Butler et al. 2012, Figure 1.

About the Author: Dr. Andrew Farke is a vertebrate paleontologist and an academic editor at PLoS ONE. He handled the manuscript described in this post. Andy also has a blog, The Open Source Paleontologist and can be followed via Twitter @andyfarke.

Filed under:Aggregators, Images, Topic Focus | Tagged: Andy Farke, Butler, dinosaur, Fruitadens, PLoS ONE