Author Archives: Lillienne Zen

Looking back: Toxic PCB levels in European orcas and other dolphins

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Guest blog by Paul Jepson, Institute of Zoology at the Zoological Society of London (ZSL), UK

Earlier in 2016 Scientific Reports celebrated its fifth anniversary. You can view our interactive infographic and blogs marking this occasion here.

As this fifth anniversary year draws to a close, we’ve got back in touch with authors from two popular papers from recent years.

Now that some time has passed, we wanted to know about their experience publishing with the journal, what impact they felt their research has had and if there’s been any surprises along the way.
Last week we posted an interview with Alex Greenwood, author of the study “Anti-NMDA Receptor Encephalitis in the Polar Bear (Ursus maritimus) Knut”.

In this blog, we’ve spoken another Scientific Reports author: Paul Jepson. In January 2016, Dr Jepson and his colleagues published the study “PCB pollution continues to impact populations of orcas and other dolphins in European waters” in Scientific Reports.

Here’s what he had to say about the research.

Could you give a brief overview of your study?

The few remaining killer whale populations in European waters have very low, or zero rates of reproduction, and are close to extinction in industrialised parts of Europe. Polychlorinated biphenyls (PCBs) are chemical pollutants which were banned in the EU in the mid-1980s, but after an initial drop in concentrations following the ban, they have now stabilized across Europe in humans, fish and wildlife.

The goal of the study was to assess the exposure to — and likely effects of — specific chemical pollutants including PCBs in European whales, dolphins and porpoises (cetaceans). We found that PCBs were at excessively high concentrations in the blubber of several marine apex predator species across Europe, including killer whales and bottlenose dolphins, and were associated with long-term and on-going population declines.

Our results suggest that much more work is needed to mitigate PCB contamination of the marine environment, and to comply with the Stockholm Convention that requires the reduction and eventual elimination of large sources of PCBs and other persistent organic pollutants.

What impact would you say your paper has had?

The paper was only recently published but it has been widely reported in newspapers and by other media, globally. The PCB issue — as based on our paper — also featured on the BBC current affairs programme Newsnight.

A public meeting about PCBs in killer whales and dolphins in Europe was held at the Zoological Society of London (ZSL) in March, where I spoke along with two other speakers. The meeting had the second largest audience for a ZSL public meeting ever and, after a lively Q&A session, Professor Ian Boyd, Chief Scientific Adviser at the Department of Environment, Food and Rural Affairs, closed the event.

This new cetacean PCB data has quickly fed into various international scientific and policy forums, including the Working Group for Marine Mammal Ecology (WGMME) of the International Council for the Exploration of the Seas (ICES). The recent ICES WGMME report (2016) concludes that PCBs pose the greatest threat to bottlenose dolphins and killer whales throughout the Northeast Atlantic region. The ICES also provide rigorous scientific advice to the Convention for the Protection of the Marine Environment of the North-East Atlantic (OSPAR) — including EU compliance with the Stockholm Convention.

Were any of your findings unexpected?

The main finding that very high PCB concentrations still persist in Europe — over three decades after the EU ban on PCB use / manufacture — has surprised a lot of people, including scientists who thought the ban would result in a gradual decline in PCBs in all biota. In fact, Europe has the highest PCB exposures in the marine environment globally. The very low reproductive rates in some of the highly PCB-contaminated resident/coastal bottlenose dolphins and killer whales are highly consistent with known PCB effects on reproduction. This is a very depressing finding, because if an apex predator population effectively stops reproducing, it will eventually disappear.

Another surprise was the very high PCB exposures in bottlenose dolphins and killer whales around the Iberian Peninsula. We have known that the Mediterranean Sea has been a pollution hotspot for many years, but the very high PCBs levels in bottlenose dolphins and killer whales on the Atlantic side of the peninsula also rather surprised us. Clearly action is urgently needed to dispose of large stocks of PCB-contaminated materials, especially in France and Spain.

Was there a particular reason you chose to publish in Scientific Reports?

The journal is highly respected and open access.  It also takes longer papers and so we were able to include more results and a longer discussion. After submission, the Scientific Reports review process was very rigorous but fair. The referee’s comments improved the final manuscript, including the statistical treatment of the data. Shortly before publication, the journal Press Office held an international telephone conference for science journalists to attend — this undoubtedly helped the paper to obtain the excellent and high-quality media coverage that followed publication.

Dr Paul Jepson is a Reader at the Institute of Zoology at the Zoological Society of London (ZSL) and is the main grant holder for the UK Cetacean Strandings Investigation Programme (CSIP) funded by the UK Government. He is a European Veterinary Specialist in Wildlife Population Health and has worked on pathological and other investigations into stranded marine mammals since 1993 and stranded marine turtles and basking sharks at ZSL since 2002.

Looking back: The mystery of Knut, the famous polar bear

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Guest blog by Alex Greenwood, Leibniz Institute for Zoo and Wildlife Research (IZW), Germany

Knut the polar bear

{credit}Berlin Zoological Garden{/credit}

Earlier in 2016 Scientific Reports celebrated its fifth anniversary. You can view our interactive infographic and blogs marking this occasion here.

As this fifth anniversary year draws to a close, we’ve got back in touch with authors from two popular papers from recent years.

Now that some time has passed, we wanted to know about their experience publishing with the journal, what impact they felt their research has had and what’s surprised them.

First up, here is an interview with Alex Greenwood, an author of the study in Scientific Reports that suggested Knut, the famous hand-reared polar bear from the Berlin Zoological Gardens, suffered from anti-NMDA receptor (NMDAR) encephalitis. The study “Anti-NMDA Receptor Encephalitis in the Polar Bear (Ursus maritimus) Knut” is available here.

We spoke to Professor Greenwood about the research.

Alex Greenwood

Could you give a brief overview of your paper in Scientific Reports?

Our study in Scientific Reports was the culmination of our efforts to determine what caused the death of Knut, the world famous polar bear. A necropsy performed at the Leibniz Institute for Zoo and Wildlife Research (IZW) determined that Knut had inflammation of the brain (encephalitis) and suggested the cause was an infectious agent. However, intensive, cutting-edge pathogen diagnostics immediately after necropsy did not identify any causal pathogen. The negative results required completely new thinking and approaches; among the candidates was an autoimmune disease.

Similar to Knut’s case, many human medical cases went undiagnosed for decades because a causative pathogen could not be linked to the symptoms of encephalitis. In 2007 it was revealed that many of these patients suffered from an autoimmune disease (where the patient’s antibodies attack their own brain as foreign material). The most common among these diseases is anti-NMDA disease — where the patient’s antibodies attack the N-methyl-D aspartate receptor in the brain, leading to severe inflammation. The team of Dr. Harald Prüß at Charité/German Center for Neurodegenerative Diseases (DZNE) Berlin, who are experts on these diseases, reasoned that this could potentially explain Knut’s case. After extensive testing, the teams at the IZW and Charité determined that this in fact is what explained Knut’s encephalitis.

What sort of impact have your findings had?

Anti-NMDA disease is now more broadly recognized among the public because of its association with Knut. This will hopefully lead to improvements in diagnosis of this and related diseases, particularly because in humans the presentation of the disease can be quite variable.  Zoo and wildlife veterinarians have realized that not all diseases, even those where a pathogen is suspected, will necessarily be the result of infectious diseases and that management practices may have to take this into consideration. For example, the counterintuitive management strategy in such an encephalitis case would be to suppress the immune system — not a therapeutic intervention one would necessarily consider in the case of a pathogen caused disease. At the very least, it is quite likely that new cases in more species will be identified, expanding this disease’s occurrence to mammals in general. Others have already seen rarer neuronal receptor diseases in domestic cats. These diseases are unlikely to be restricted to cats and polar bears.

Was there anything surprising about this research?

Upon taking on Knut’s case, the flood of expert opinions, all supporting an infectious pathogen as the cause of Knut’s symptoms, was deafening. It was interesting to see how this guided so many of the contributions from collaborators and spectators. In many ways this narrowed the number of avenues initially investigated. We tried to keep an open mind but some of the ideas we had — including an aberrant immune reaction — were beyond what we thought is amenable to study in wildlife diseases, given that so much less is known about wildlife biology than human or laboratory animal biology.  Many of the techniques we considered would have likely yielded data difficult to interpret, without the fundamental knowledge of, for example, which proteins are expressed where in a polar bear.

Their sharp eyes and the constructive collaboration with Dr. Harald Prüß and his team made it possible to consider the improbable — and demonstrate that the improbable was in fact the answer. The ability to transfer the techniques from human medicine to a polar bear case was both unusual and extremely fortunate.

Was there a particular reason you chose to publish in Scientific Reports?

The study performed, in essence, represents a case report. Scientific Reports recognized that the findings in this case go well beyond Knut as an individual and allowed it to be peer reviewed. The identification of this disorder, which before Knut was only recognized as a human disease, must now be considered a disease of mammals with consequences for diagnosis and management in veterinary medicine in particular. Because Scientific Reports is open access this means anyone who is confronted with a similar case and suspects an autoimmune disease can refer to our study and our methods with no barriers to access. This was an important element in our consideration of where to submit the manuscript.

Professor Alex D. Greenwood is the Head of the Department of Wildlife Diseases at the Leibniz Institute for Zoo and Wildlife Research (IZW) and Professor of Wildlife Diseases in the Department of Veterinary Medicine of the Freie Universität Berlin, both institutions in Berlin, Germany. His work has focused on evolutionary virology, primarily on retroviruses and more recently herpes viruses in wildlife. He integrates ancient DNA, evolutionary and ecological analyses in most of his work and also has an interest in high throughput diagnostic methods. His work with Knut the polar bear intersected with the latter interest.

On Friday (23 December) we will post a second guest blog from another Scientific Reports author. 

The astrophysicist on a mission to get more women into physics

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Guest post by Alex Jackson

Professor Jo Dunkley

Professor Jo Dunkley{credit}Wadham College{/credit}

“Very often the famous names we know and read about in science are not those of women,” says Professor Jo Dunkley. “To get more young girls studying the subject, we must change cultural perceptions and have more visible female role models.”

As we sit discussing the women who have inspired Dunkley, a professor of physics and astrophysical sciences at Princeton University, to study the universe, the mood is rather sombre. On a morning when the first female frontrunner for US presidency has missed out at the final hurdle, and the impacts of that decision on science, are yet unknown, there is a strong sense of disbelief.

“I was really hoping to see the first female president and that in itself is a disappointment,” she says. “I don’t see it as a positive turn of events in terms of funding for science, although I hope there’ll be enough influence to keep ongoing projects running.”

Dunkley admits to being shocked at the result. Having moved from the UK, just shortly after Brexit, she was already starting to see the effects of political uncertainty on European grants. “Uncertainty is not we need right now in science,” she says.

However, the astrophysicist has plenty occupying her mind other than politics. This week, she will receive the Royal Society’s Rosalind Franklin Award and present a public lecture in London. Named after the great English chemist and crystallographer, the award recognises both her research in the cosmic microwave background, and her work encouraging more young women to study physics.

“I see a really important part of my work is not just doing the research I love, but also encouraging others to pursue a career in science,” she says. Dunkley became aware of Franklin’s story when she was an undergraduate at Cambridge University. Sadly, Franklin died at just 37 years old, the age Dunkley has recently turned. “She’s such a wonderful role model, who achieved so much in a very short life.”

Our window on the universe

Dunkley’s own research has gained her much attention. As a research fellow at Princeton, she worked on NASA’s WMAP satellite, before analysing data on the European Space Agency’s Planck satellite. Interrogating rich and complex data, her research group made large strides in furthering our understanding of the universe’s origins.

Studying the evolution of the universe is, however, becoming easier as technology rapidly develops. “Our telescopes have become so sophisticated in recent decades, we are now able to see out into the far reaches of the universe,” Dunkley says. “We’ve been able to put together a fairly successful cosmological model that explains how we got here over the 14 billion year history of the universe.”

A large focus of Dunkley’s work involves turning recorded maps of the most distant light we can see—an image of the universe when it was born—into properties such as age, weight, and the rate of expansion.

“We measure the faint light by capturing a little snapshot of what the universe looked like when it was only 400,000 years old,” she explains. Her team then compare the experimental data to millions of theoretical universes, until they find one which matches. “We can now see the very beginnings of tiny cosmic structures that over billions of years develop to become the first stars and galaxies. It’s then our job to find out what these structures look like, and how they evolved,” she says.

After analysing more than 15 months’ data from Planck, Dunkley and her colleagues created the most detailed map ever made of the oldest light to shine through the universe. The results confirmed many of the theories cosmologists draw on to explain the evolution of the universe. “We think during the first trillionth of a second of the Big Bang, the universe expanded extremely fast, laying down the seeds for the cosmic structure we see today,” she says.

A view of the cosmic microwave background collected by the European Space Agency’s Planck satellite.

A view of the cosmic microwave background collected by the European Space Agency’s Planck satellite.{credit}European Space Agency, Planck Institute{/credit}

By Dunkley’s own admission, there are still many unanswered questions. Her current research at the Atacama Cosmology Telescope in Chile, and a new five-year project at the same site in the Atacama Desert called the Simons Observatory, hope to make the next big steps forward in measuring cosmic microwave background.

“We keep looking for new physics, complexities and extra particles that could have existed when the universe was very young,” notes Dunkley. “Yet, the more data we collect, the simpler the universe’s behaviour looks, which is exciting, but we still have all these unanswered questions.”

After the breakthrough LIGO discovery earlier this year, which detected gravitational waves, Dunkley believes there’s much optimism in now finding a signal from the big bang. She also hopes through another development, gravitational lensing, scientists will soon be able to understand and map out where all the dark matter is in our universe.

Role models

Her optimism and love for physics is affable and evident in her responses. Yet, there is one area she believes cultural changes are needed: role models. This is a theme she will address in her lecture and one that will feature in her first popular science book out late next year, Our Universe: An Astronomer’s Guide.

“There really aren’t enough women role models in physics, and many of the great female astronomers are not often that well known, or talked about in education,” says Dunkley. “I think it is so important. The ability to see someone you can imagine being, is everything, and gives you the confidence to try things out and aim for something. And often that will mean having someone, as a woman, showing a woman can do it.”

Galaxies in our universe

Galaxies in our universe{credit}NASA, Hubble{/credit}

As she enthuses through the great achievements of Henrietta Swan Leavitt, “an incredible woman” who made it possible for Edward Hubble to determine that the universe is expanding; Cecilia Payne-Gaposchkin who figured out how stars were formed; and Vera Rubin whose work led to the theory of dark matter, it’s easy to forget Dunkley has become a star in her own right.

Dunkley may feature on shows such as BBC’s Science Club and Stargazing Live, yet she believes the industry must do better. “The media must do more to get visible female role models on television to change perceptions,” she says. “I’d love to get to the stage where young people knew it was normal to be a female scientist, and expect to be able to have a family too, whether it be in physics or engineering.”

Time for change

On academia, Dunkley is keen to express some sanguinity. “We’re definitely seeing more women now at senior level, which makes a huge difference, and has a direct influence on female students,” she says.

At Princeton, she notes there are growing numbers in female students pursuing astrophysics. It was a similar trend at Oxford University, where until this summer, Dunkley taught for more than eight years.  However, it is the drop-out rate at colleges that worries her.

“In the UK, for example, only 20 percent of physics students aged 16-18 are girls, and this figure continues through to degree, PhD, and researcher level,” she explains. It is a target she’d like to see change. “Consciously or unconsciously, there is often still a common assumption that science, particularly physics, is more for boys than girls. To effect change, we need to influence both teachers and parents.”

Through her book release, she is a planning a series of workshops, talks and videos for students, as well as a public lecture tour of the UK. She hopes to raise awareness of women’s contribution to astronomy, as well as break down the idea that the universe is too difficult to understand.

“I want to promote the many remarkable women who have been central to our biggest discoveries in space,” she says. “We have an incredible group of women currently working in the field, but to answer our world’s most pressing questions and challenges, we need more.”

Professor Jo Dunkley’s Rosalind Franklin award lecture will be streamed live on Thursday, 6.30pm GMT / 1.30pm EST.

The Power of Data: Notes from the STEM Summit 4.0

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By James Cola, Communications Manager, Springer Nature

The STEM Summit 4.0 – The Power of Data was held by Scientific American and Macmillan Learning at the New York Academy of Sciences on October 14, 2016. Hosted by Susan Winslow, Managing Director, Macmillan Learning, and Mariette DiChristina, Editor in Chief, Scientific American, the summit aimed to further collaboration between educators, entrepreneurs and public policy leaders, and to highlight how data can impact and transform the way that people teach and learn.

Across the United States, there are kindergartens, schools and colleges that are using data analytics, adaptive learning platforms, apps, video streaming, images, gaming, and more to help inspire student curiosity, tailor content, enable students to work in ways that suit them and change the way students approach STEM subjects.

At the STEM Summit 4.0, real-life stories reinforced the view that using data in teaching and learning is vital — and is already making a huge difference by helping educators to not only just name challenges and problems, but to go underneath to the root of the problems to solve them. Several presenters noted that data will continue to be key in encouraging greater participation in science, technology, engineering and mathematics (STEM).

The summit championed the increased use of data in education, as well as focusing on specific strengths and weaknesses of data.  Through discussions about different types of data — and interactive breakout sessions that included “How do we get educators past phobias (the fear of teaching STEM)?” and “How Do We Use Technology and STEM to Create Globally Competent Citizens?” — attendees developed strategies to help educators and further encourage students to study STEM topics.

STEM summit image

The day’s highlight, an address from Paul Krugman, the renowned Nobel Laureate and New York Times columnist, captivated the audience. His talk, “Technology, Globalization, and Skills”, discussed how STEM represents 6% of the workforce in the United States (excluding healthcare), and the role that STEM education plays in countries’ ability to compete and succeed globally.

However, speakers were clear that the United States faces challenges.

Dr. Rosemarie Truglio, Senior Vice President, Curriculum and Content, Sesame Workshop, said: “The data are in. We know we have a problem, and students are underperforming in science compared to children in other developed countries.”

Terri McCullough of the Clinton Foundation also noted the fact that there are fewer women studying STEM subjects now compared to 30 years ago.  While Krishanti Vignarajah, Director of Policy and International Affairs, The White House, Office of the First Lady, discussed how a girl’s earning potential increases by 15-20% for every year of secondary school education.

Dr. Adam Black, Chief Learning Officer, Macmillan Learning, gave a presentation on “The Promises and Pitfalls of Big Data”. He suggested that there is a digital renaissance in education and we can start to measure many things empirically due to the growing use of digital and more touchpoints with the learner. These touchpoints include apps, websites, games, and other interfaces where information is recorded about the learner.

Elsewhere during the summit, a particularly joyous and charming presenter talked about “Tactics to Build Engaged Learners”. Renton Prep School 10th grade student Jennifer Fernandez energized the crowd by showing how she and her classmates benefitted from cutting-edge ideas and innovative teachers who use technology in the classroom.

Ms. Fernandez said that for her and her classmates: “Today, we have faster ways to share with each other and there is a community of other people collaborating. For example, when a CEO of a company responds to your app, no matter how young you are, you are challenged and you have to step up your game.”

For more information, the full list of presenters and to continue the conversation about the STEM Summit, visit www.community.macmillan.com/community/stemsummit.

For STEM resources and to find out how Scientific American engages citizen scientists, children, and adults with STEM topics, visit https://www.scientificamerican.com/education/.

Sharing research in three minutes: A shorter timeframe to see the bigger picture

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Joshua Chu-Tan

Joshua Chu-Tan{credit}Jane Duong{/credit}

Joshua Chu-Tan is a second-year PhD student in the Provis Group at the John Curtin School of Medical Research at the Australian National University (ANU).

His presentation of his thesis, “Targeting the Root of Vision Loss”, won him top prize at the ANU’s Three Minute Thesis (3MT) competition. This event challenges PhD students to present their research in three minutes to a non-specialist audience. Joshua also went on to win the 2016 Asia-Pacific 3MT, which drew 50 contestants from six countries.

We ask him about his research and his experience competing in the 3MT.

1. Tell us about your research. What is its significance and what are your main findings?

Age-Related Macular Degeneration (AMD) is the leading cause of blindness in developed countries with a global cost of over US$340 billion per year. Our group looks at the dry form of AMD, which accounts for 90% of all AMD cases. This happens when light-sensitive cells deteriorate, causing a loss in central vision. There is currently no cure.

We work on gene therapies for dry AMD using microRNA. These molecules are masters in gene regulation: a single microRNA molecule can bind to multiple targets, all of which often work within the same cellular pathway. In this way, we can theoretically regulate entire pathways, rather than single genes. This could prove fruitful for complex, multifactorial diseases such as AMD.

I’ve been able to characterise a number of microRNA in our AMD model and through injections of a specific anti-inflammatory microRNA into the eye, we’ve seen a decrease in inflammation, as well as a slowing in the damage progression of the retina, which has been very promising.

Joshua Chu-Tan speaking at the 2016 Asia-Pacific 3MT competition

Joshua Chu-Tan speaking at the 2016 Asia-Pacific 3MT competition{credit}University of Queensland{/credit}

2. How did you hear about the Three Minute Thesis (3MT) competition and why did you choose to enter?

In 2015, I went to watch the ANU 3MT finals. The experience was phenomenal: hundreds of people came to watch students from all departments and faculties condense years of work into a three minute pitch. The interest that people outside of academia showed was inspiring and as I listened to all these brilliant students talk about the bigger impact of their work, I was enthralled. The whole time I was there, I kept thinking of ideas for my own 3MT—I knew I had to give it a crack.

3. Why do you think events like the 3MT are important? What did you gain from your involvement?

I believe the value of science communication is often overlooked in research, especially medical research. As researchers, we’re often invested in a single aspect of a holistic problem, which can result in tunnel vision within our niche. The work we publish uses highly specialised jargon, which is necessary for us to discuss specific problems, but isn’t very accessible for the general public.

Participating in events like the 3MT give us an avenue to convey our work to people outside of our field. We can take a step back and look at the bigger picture: Why should people outside of this field care about our work? What’s the real goal? Even the process of writing a speech for something like the 3MT is rewarding in that it gets us to consider these questions.

The ANU and Asia-Pacific events were also incredible opportunities for me to find out about other people’s research from around the world and consider new ways of looking at a problem. I really think the future of research will be interdisciplinary. We’re all trained to look at a problem in our particular way, but there’s only so much we can achieve within our specialties. Having experts from different fields approach a challenge together will greatly benefit research.

Winning the Asia-Pacific 3MT

Winning first prize at the Asia-Pacific 3MT{credit}Joshua Chu-Tan{/credit}

4. Do you have advice for other students preparing for a 3MT event?

  1. Enjoy it! It’s not an easy task and there will be nerves but really enjoy the moment, be confident in yourself, and take pride in your research.
  2. Only mention the key points of your work and make the audience relate to it. Write it like a story with a beginning, middle and end, and be true to yourself and how you would like to present it.
  3. At the events, truly listen to everyone’s work. Soak in all the amazing research that’s being conducted by your peers. This journey wouldn’t have been as rewarding if it wasn’t for everyone I met along the way.

5. What’s next for you?

With the Asia-Pacific win, I now have the incredible opportunity to attend and present at the Falling Walls Lab/Conference in Berlin. It’s a chance to rub shoulders with the world’s brightest minds so I intend to make the most of it.

After this remarkable 3MT journey ends, it’s full steam ahead to complete my PhD with a bang. I intend to stay in the field and attain fellowships that will allow me to complete my postdoctoral training overseas. Hopefully I can then return to Australia to contribute towards the strong research environment here.

You can watch Joshua’s winning 3MT speech, “Targeting the Root of Vision Loss”, here.

Founded by the University of Queensland in 2008, 3MT events are now hosted by over 400 institutions across six continents. The 2016 Asia-Pacific 3MT was sponsored by Springer Nature.

Winners of the Scientific American Innovators Award Turn Trash into Water Filters [Video]

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Guest post by Andrea Gawrylewski, collections editor at Scientific American

After 50 hours in a lab, three Ohio eighth graders convert Styrofoam food containers into a patent-worthy new water filter

SA-innovators-award

Scientific American Innovators Award winners (from left to right) Julia Bray, Luke Clay and Ashton Cofer
Credit: Andrew Weeks

World-changing ideas may just come from our youngest scientists. This year’s winners of the annual Google Science Fair—including the winners of the Scientific American Innovators Award—were announced this week at Google headquarters in Mountain View, Calif. The event is the largest online science fair in the world, and since its inception in 2011 more than 30,000 teenagers have submitted projects in almost every country.

“Kids are born scientists,” says Scientific American Editor in Chief Mariette DiChristina, who served as head judge at the fair. “They ask great questions and we should foster their efforts to learn the answers firsthand.”

For the past five years Scientific American has partnered with Google to award the Scientific American Innovator Award, which honors an experimental project that addresses a question regarding the natural world. This year’s award went to three eighth graders from Ohio who were particularly disgusted with the amount of Styrofoam (polystyrene foam) trash they saw in their everyday lives—the material accounts for 25 percent of landfill space, and is exceptionally difficult to recycle or reprocess.

The team of Julia Bray, Luke Clay and Ashton Coffer, all age 14, analyzed the chemical structure of Styrofoam and determined that it is composed of over 92 percent carbon. This sparked their idea: They hypothesized that they could use heat to convert the Styrofoam into activated carbon—which could then be used to filter water. After 50 hours of experimental work, the team successfully converted the polystyrene into carbon with over 75 percent efficiency by heating the material to 120 degrees C. They then treated the carbon with a set of chemicals to increase the surface area of the material, and tested it against commercially available water filters. Their results showed that their carbon successfully filtered many of the same compounds that commercials filters remove from water.

“Styro-Filter is just the beginning of an innovation to take dirty waste and make clean water,” Bray explains in her team’s video summary of the project. The team has filed for a provisional patent for its filter-making process.

The winners of the Scientific American Innovators Award share a $15,000 cash prize. The grand prize of the Google Science Fair went to Kiara Nirghin, a 16-year-old from South Africa who used orange peels and avocado skins to devise a superabsorbent material that can absorb and hold 300 times its weight in water. She hopes that the nontoxic material can be used to boost agriculture in water-scarce regions.

“All of the finalists produced inspiring work,” DiChristina says. “It’s thrilling that the judges chose such exciting candidates from all around the globe.”

This article originally appeared at Scientific American on 28 September 2016 and was republished with permission.

Peer review: Nature’s variations

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Heike-LangenbergBy Heike Langenberg, Chief Editor, Nature Geoscience

The week from 19 to 25 September 2016 marks the second round of Peer Review Week with the theme of “Recognition for Review”. The topic is obviously close to our hearts at Nature Research: after all, peer review is much of what we do.

We greatly appreciate the role our reviewers play in the publication process, and we try to help them to convert the time and effort they spend on scrutinising and often improving our authors’ papers into professional recognition.

For their personal use—for example in job applications or career negotiations—reviewers have been able to download a certified record of all their reviewing activities across the Nature-branded titles for several years now. We hope that this information is helpful in our reviewers’ career development.

We also offer a free online subscription to a Nature-branded journal for one year to those who have either reviewed three or more manuscripts across all Nature-branded titles in a year, or to referees who have been nominated by our editors for the outstanding quality of their reviews.

Peer Review Week Recognition for Review

But we are always looking into making peer review better, and offering more choice. In response to popular demand in reader surveys, we have introduced the option of double-blind peer review. Initiated at Nature Geoscience and Nature Climate Change in June 2013, authors are now able to opt to be anonymous to referees—just as referees are usually anonymous to authors—at all the Nature-branded journals since February 2015. Providing this option is now part of our routine workflow.

Uptake has been essentially stable since this option was extended to all Nature-branded journals. It seems that ignorance of the double-blind option is not the reason that the proportion of authors who choose it for their own manuscript is substantially lower than those who support the idea in reader surveys. In the social sciences, double-blind peer review is more widespread, and we note that in journals with a significant social science component, such as Nature Climate Change, Nature Energy and Nature Human Behaviour, acceptance is higher than in most journals.

The next step in this particular direction could be triple-blind peer review: in this version, editors, too, do not know the authors’ identities when they record their initial impression of a paper. This offering is but a glimpse in our eye at this stage, largely for administrative reasons, but we are thinking about it. Unconscious biases may lurk in everyone’s brain, even in the most conscientious editors, and they shouldn’t make a difference. We would like to make sure that papers submitted to the Nature-branded journals are judged by their scientific content only. Nothing else.

Celebrating Peer Review Week at Springer Nature

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By Steven Inchcoombe, Chief Publishing Officer, Springer Nature

Peer review is at the heart of the research process. Academics generously dedicate hours of their week, to examine each other’s work, offer much-valued constructive criticism and improve the published science (or maths, or social science, etc.). Reviews take time, but peer review is mostly anonymous, meaning it is difficult for reviewers’ colleagues, publishers, institutions or funders to recognise it properly.

Of course, peer review has its faults. Regardless, it is the best system we have right now for maintaining high standards and accuracy. In an age when information is everywhere, plagiarism is sadly too common and a stamp of quality is highly valued, peer review is still celebrated as a kitemark for rigor.

peer-review-week

To celebrate peer review, a group of organizations including Springer Nature is working collaboratively to plan a week of activities and events. Today marks the first day of Peer Review Week 2016. This year’s theme is Recognition for Review, exploring all aspects of how those participating in review activity – in publishing, grant review, conference submissions, promotion and tenure, and more – could be better recognized for their contribution.

At Springer Nature we’re constantly looking to improve our peer review systems, and to find new and better ways of recognizing peer reviewers for their hard work. Our existing methods of recognition might take the form of monetary reward in the case of monographs, or incentives such as free subscriptions or discounts on Article Processing Charges. The methods of recognition researchers most commonly ask for are those which simply acknowledge the name of the reviewer, as the process is so often anonymous.

In a recent survey completed by 3886 of our reviewers, only 26% of reviewers agreed that they would like to be paid. Many expressed concerns that a monetary reward would introduce bias into the process. 67% of reviewers believed they should receive non-monetary compensation, and, rather inspirationally, 68% agreed that the knowledge of the contribution they have made to the body of scientific research is enough compensation for their time as a reviewer, confirming what we’ve always thought: academics are a generous lot.

We believe their work shouldn’t go unnoticed. Many of our journals publish lists celebrating our most frequent reviewers. At BioMed Central, 70 of our journals offer open peer review, encouraging transparency. Open peer review is also a valuable educational resource for training future peer reviewers. In the last year, BioMed Central have published over 40,000 open peer review reports, allowing 24,000 peer reviewers to be recognized for their contribution to research.

Nature Editor-in-Chief Philip Campbell writes a letter of thanks to anyone that has peer-reviewed three papers or more for the combined Nature Research portfolio. Since 2015 all of the Nature-branded research journals have offered authors the option to choose double-blind peer review. In 2016 we have additionally piloted the following initiatives: optional publication of peer-reviewer reports in Nature Communications; optional publication of peer-reviewer identities in Nature; optional transfer of peer-reviewer reports and identities from Nature Communications to other selected Springer Nature academic journals.

Another way we’re experimenting is through partnering with Publons, a network of over 75,000 experts showing their commitment to speeding up science through superior peer review. Publons is a free service for academics that lets you effortlessly track, verify and showcase your peer review activity across the world’s journals. This month we’ve started a Publons pilot across 13 of our journals. We’re also proud sponsors of their Sentinels of Science Awards which celebrate frequent peer reviewers.

We have two more pilots launching this week, experimenting with two very different types of peer review; one from BioMed Central is exploring removing potential bias from the system, the other from Springer experimenting with a new type of recognition. Watch this space for more information!

And finally, to all our reviewers around the world: in case we haven’t said it recently, thank you from the team at Springer Nature.

Genetic variants in ‘red hair gene’ associated with increased number of skin cancer mutations

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Carla Daniela Robles Espinoza, author on the Nature Communications paper

Carla Daniela Robles Espinoza {credit}Mamun Rashid{/credit}

Melanoma patients with genetic variants in the ‘red hair gene’, MC1R, have more mutations in their cancers compared to patients without such variants, found a study published in Nature Communications last week. Carla Daniela Robles Espinoza, one of the authors on the paper, takes us through the findings.

What were your main findings?

In this study, we wanted to investigate whether having common genetic variants in the red hair gene (called MC1R) can influence the number of mutations found in melanoma tumours. It has long been known that redheads are more prone to developing melanoma.

A woman with red hair using a camera, taking a photograph, adjusting the lens.

Melanoma patients with genetic variants in the ‘red hair gene’, MC1R, have more mutations in their cancers. {credit}Getty Images{/credit}

This is thought to be because they burn more easily in the sun, as exposure to UV light is one of the main risk factors for developing this cancer. However, there seems to be more to the story of how MC1R genetic variants increase the risk of developing melanoma. For example, previous studies have shown that, in mice, there is a sunlight-independent contribution to melanoma risk via the synthesis pathway of the red pigment1, and that there is an association between MC1R and melanoma risk which occurs independently of sun exposure in humans2.

Here, we analysed the melanoma tumours from more than 400 patients and observed an increase in the number of mutations in patients carrying variants in MC1R. This effect was observed also in individuals that are not necessarily red-headed (those with only one variant copy of the MC1R gene as opposed to two), which means that these people might also be highly susceptible to the mutagenic effects of UV light. However, we observed this increase in all types of tumour mutations, not only the ones associated to UV damage.

We could also quantify this contribution, noting that the expected number of sun-related mutations associated with an MC1R variant is comparable to the number gained in about 21 additional years of age. Therefore, our study provides evidence of the existence of additional mutagenic processes in melanoma patients with MC1R variants, which make up about 26-40% of the patient population3.

How does this work link melanoma and the gene MC1R?

Many studies had noted that people carrying MC1R variants are more susceptible to developing melanoma, but only recently we have started to fully understand the reasons. We provide evidence that there may be additional mechanisms, beyond the effects of UV alone, that contribute to elevating the risk of melanoma in patients with MC1R genetic variants. MC1R has important roles in DNA repair and cell survival; thus, processes that increase the risks of developing cancer might include the generation of DNA-damaging stress when making up the red pigment or a decreased ability to repair DNA in carriers of MC1R variants.

In this study we also report that primary melanocytes (the cells where melanoma originates) with incomplete MC1R function show defects in survival and DNA repair, suggesting this might be one of the mechanisms through which MC1R function impacts melanoma risk.

The distribution of mutation counts in melanoma tumours grouped by the presence of MC1R variants.

The distribution of mutation counts in melanoma tumours grouped by the presence of MC1R variants.{credit}Carla Daniela Robles Espinoza et al., Nature Communications{/credit}

What is the significance of this research for melanoma patients and for the general population?

The conclusion of our study is important because it has relevance for people who are MC1R carriers (for example, about 21% of the British and Irish population, 10% of the French population and 16% of the population in the United States4). This means that the majority of these people, who will not have red hair, are still more susceptible to the effects of melanoma mutagens than people with no MC1R variants, with UV light the most established environmental risk factor.

The results suggest that MC1R carriers should take care in the sun following established guidelines (for example: https://www.cancerresearchuk.org/about-cancer/causes-of-cancer/sun-uv-and-cancer/ways-to-enjoy-the-sun-safely).

Can you outline any future research steps?

Future research will aim to understand the different processes through which MC1R can increase the risk of developing melanoma, and also to look for other genetic contributors to skin cancer predisposition. This will hopefully help us to identify the people who are at increased melanoma risk and allow us to better inform patient management and public health campaigns.

References:

1. Mitra D et al. An ultraviolet-radiation-independent pathway to melanoma carcinogenesis in the red hair/fair skin background. Nature. 2012 Nov 15;491(7424):449-53. doi: 10.1038/nature11624. Epub 2012 Oct 31.
2. Wendt J et al. Human Determinants and the Role of Melanocortin-1 Receptor Variants in Melanoma Risk Independent of UV Radiation Exposure. JAMA Dermatol. 2016 Apr 6. doi: 10.1001/jamadermatol.2016.0050. [Epub ahead of print]
3. Williams, P. F., Olsen, C. M., Hayward, N. K. & Whiteman, D. C. Melanocortin 1 receptor and risk of cutaneous melanoma: a meta-analysis and estimates of population burden. Int. J. Cancer 129, 1730–1740 (2011).
4. Gerstenblith MR et al. Comprehensive evaluation of allele frequency differences of MC1R variants across populations. Hum Mutat 2007 May;28(5):495-505. doi:10.1002/humu.20476

Journal metrics: handle with care

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We have recently updated the journal metrics page for Nature Research to include an array of additional bibliometric data (www.nature.com/npg_/company_info/journal_metrics.html).  In addition to the traditional 2-year impact factor, we are now providing the 5-year impact factor, the immediacy index, the Eigenfactor score and the Article Influence Score. Whilst it is a measure that reflects a journal’s citations, the 2-year impact factor as an arithmetic mean of the citations per article can be disproportionately skewed by a minority of highly cited outliers.

For Nature, the Nature-branded research and reviews journals, and Scientific Reports, we have also provided the 2-year median, defined as the “the median number of citations received in 2015 for articles published in in 2013 and 2014.” Although the median citation is not subject to distortion by outliers like the 2-year impact factor, it should be noted that the median does not address another concern: that for multidisciplinary journals, such indicators measure across a broad swath of disciplines which have their own distinct citation rates. Nevertheless, we consider it to be a useful complement to the 2-year impact factor.

Given that this citation median is not a standard indicator, it is important to explain its derivation. To calculate the median, datasets for individual journals were downloaded from Web of Science in the third quarter of 2016.

  • For Nature and the Nature-branded research journals, articles published in 2013 and 2014 and categorized as “Article” or “Review” in Web of Science were selected.
  • For Nature Reviews journals, articles published in 2013 and 2014 and categorized as “Review” in Web of Science were selected. In addition, a small number of review articles that are categorized as “Article” in Web of Science were also included.
  • For Scientific Reports, articles published in 2013 and 2014 and categorized as “Article” in Web of Science were selected. In addition, a small number of research articles that are categorized as “Review” in Web of Science were also included.

For each dataset, (1) duplicated items were removed, (2) items that were not genuine Articles or Reviews were removed and  (3) items that were published outside the 2013-2014 timeframe as determined by issue date (for Nature and Nature-branded journals with issues) or date of online publication (for Nature Communications and Scientific Reports) were also removed. For each curated dataset (i.e. following steps 1-3 outlined above), the number of citations in 2015 to each item was taken from Web of Science and the median value calculated accordingly.

Thus, the median represents the midpoint number of citations that articles published in 2013 and 2014 received during 2015.

We believe that a broader array of citation-based metrics including the 2-year median citation will provide a more balanced perspective on journal performance and will be helpful to authors, readers and the community at large in assessing the quality of our journals.  At the article level, we have provided article-level metrics and Altmetric data since October 2012 for Nature journals. Our ambition for the future is to add alternative metrics at a journal level, to complement the citation-based metrics and the article level metrics.

We would emphasise that although this wider suite of metrics at the journal and article-level might provide interest and context, there can be no substitute for assessing each article on its own merits.

The Nature journals have a long record of publishing editorials on the limitations of the traditional journal impact factor.  The journal metrics page also provides links to a selection of these editorials from Nature journals and to the Nature special collection on Metrics (Nature 2010).

For better or worse, in survey upon survey, our authors cite impact factor as a primary consideration in driving decisions about where to publish their work, and whether to write for a journal.  This is despite  increasing calls for due caution in using the journal impact factor and a growing recognition that the over-reliance on the journal impact factor as an indicator for the quality of individual articles is damaging to the practice of science. There is no question that decreasing a reliance on the impact factor as an assessment metric is proving to be exceedingly challenging for journals, publishers, funders, research institutions and researchers.

Nevertheless, we hope to see increasing efforts from the community at large to develop mechanisms that  credit best practice in reproducible, robust research, putting the attention squarely where it belongs: on the researchers and their contributions to their fields.

Philip Campbell, Editor-in-Chief, Nature and Nature Research
Sowmya Swaminathan, Head of Editorial Policy, Nature Research