Interviews with the lab protocol community — insights from an Academic Editor and a reviewer

PLOS ONE has published a Lab Protocols Collection to highlight this new article type launched in early 2021. This collection showcases a set of peer-reviewed lab protocols across our broad scope, including cell biology, molecular biology, biochemistry, biotechnology, structural biology, and archaeology. We interviewed Academics Editors and reviewers from the community, in order to learn more about the importance of lab protocols in their field and their thoughts on the benefits of this article type for open science. We also discussed the future development of open science to conclude this community engagement.

Academic Editor Ruslan Kalendar (RK)


Dr. Ruslan Kalendar is an Adjunct Professor of Genetics at University of Helsinki (Helsingin Yliopisto), Finland. His interests are molecular genetics, with a particular focus on the evolution of the genome, and, in particular, mobile genetic elements.

Reviewer Alison Forrester (AF)


Dr. Alison Forrester is post-doctoral researcher at Institute Curie (Paris, Île-de-France), France. Her interests are autophagy, endoplasmic reticulum, ER-phagy and membrane trafficking.

What do you think are the benefits of lab protocols for open science?

RK: PLOS ONE journal in collaboration with protocols.io has developed a unique and state-of-the-art platform for publishing lab protocols. This is a well-timed and useful innovation. The development of scientific knowledge is based on a variety of methodological approaches bordering on art. Because of the increasing complexity of scientific methods and their diversity, an appropriate forum or open science platform is needed, where the research community can present the best solution and point out the problems that may be encountered in other laboratories. Such a platform should of course be open, and in this form, it is really effective.

AF: Improving data reproducibility in research is one of today’s most important issues to address. Providing clear and detailed protocols, without limitation of words or space, is an effective way to communicate optimized protocols. This will directly help to improve data reproducibility between labs, as well as provide a thorough record of procedures that have been published in parallel. Improving communication of optimized protocols helps to drive robust research, allowing people to build their own research on already thorough studies, and not spend excessive time optimizing protocols based on poorly executed or explained protocols. 

How important are lab protocols in your field?

RK: In my research, I often encounter new problems for which solutions can be found in similar resources from other scientific publishers. Various publishers offer standard solutions for sharing laboratory methods and protocols. However, most of these solutions are only open to subscribers of a given publisher. PLOS ONE in collaboration with protocols.io offers a truly unique resource for open science for laboratory methods and protocols. This is a consistent step in promoting open science in all directions, sharing experiences and new knowledge for the research community.

AF: Having robust and reliable lab protocols on which to base our own research is of high importance to the field of cell biology. A good protocol can be the difference between efficient replication of a known experiment, leading to fast progress in a new direction using the protocol, and wasting months on trying to replicate a known experiment, sometimes leading to the unnecessary abandonment of threads of research.

Finally, Academic Editor Ruslan Kalendar provides his visions for future development in open science:

RK: The next step for open science, I see, is dynamic (as opposed to today’s static resource), updatable protocols and methods, and most importantly, directly updatable research results.  Working on a given problem is always a team effort. Therefore, researchers from different parts of the world can work together on a given problem, and add new ideas, knowledge, and new approaches to the overall mega-work. To this purpose, it would be more consistent to have a platform for mega-articles, with updated content, which is regularly improved by adding new results from different labs and researchers. Including methodological approaches and protocols could also be updated. In this way, each individual researcher’s work and contribution would be visible. The scientific activity would move to a new level of scientific data exchange and the number of scientific papers would move to a new quality. We would go from the number of publications to their quality.

Image credit: Megan Rexazin, Pixabay License (Free for commercial use, No attribution required)

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

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An interview with Ben Brown, Guest Editor of the PLOS ONE-COS Cognitive Psychology Collection

PLOS ONE, in collaboration with the Center for Open Science, recently launched a Cognitive Psychology Collection. It includes submissions to a Call for Papers in cognitive developmental psychology across the lifespan, with an emphasis on open science—transparent reporting practices such as pre-registration or iterative registration; data, code, and material sharing; and preprint posting. 

Ben Brown was one of three Guest Editors for this project, along with Nivedita Mani and Ramesh Kumar Mishra. Ben is Associate Professor of Psychology at Georgia Gwinnett College in Georgia, USA. Ben’s research interests are in developmental psychology: he has worked on autobiographical memory in populations, for instance in populations with autism spectrum disorder, and on children’s susceptibility to suggestion. 

Benjamin Brown, Guest Editor for the Cognitive Psychology Collection

Ben also has a long-standing interest in open science and the reproducibility and replicability of psychology research: he is a founding member of PsyArXiv, the preprint repository for the psychological sciences hosted by COS, and is a Senior Editor at Collabra: Psychology, the open-access journal of the Society for the Improvement of Psychological Sciences

I asked Ben about his editorial experience for this collection and his advocacy for open science more broadly.

Can you tell us about your interest in open science, what drew you to it and how that affects your own research?

My interest in scientific rigor and transparency began during my graduate training. During this time, I struggled to replicate well-known and highly regarded findings and found myself frustrated with the lack of transparent reporting in psychological research. As a result, I was eager for opportunities to contribute to improving psychological science.

When I learned of community efforts to address these same challenges I had faced in my own work, I happily and without reservation got involved. In doing so, I found a strong sense of camaraderie with other psychologists working on the issues that I felt so isolated grappling with in graduate school.

Preregistrations, including any modifications, help reviewers contextualize results and consider matters such as researchers’ degrees of freedom. I honestly would find it difficult to go back to a more traditional editorial experience.

Ben Brown, PLOS ONE Guest Editor

Throughout my involvement in the open science movement, I have been pleasantly surprised to find that helping to enable scholars to conduct science in more open and transparent ways can be just as if not more rewarding than conducting original research itself. 

A rationale for this Cognitive Psychology Call for Papers, with its emphasis on transparent reporting and pre-registration, was to help address difficulties in recruitment and planning that are particularly relevant to that field of research. Can you tell us more about it? How do these concerns affect your editorial work more generally?

Transparent communication about the process of scientific research – recruitment, protocol, data analysis – is central to the credibility of science as a field. Unfortunately, many factors make this challenging across subdisciplines within psychology.

With regard to cognitive development, scholars working in this area are often tasked with understanding how processes and abilities change over time and doing so often necessitates responsiveness to the practical demands of samples that inherently change over the course of their involvement in a given research project. Further, measuring cognitive processes is quite challenging and trial and error is often necessary to generate sound, reliable research protocols even in the best of scenarios. This is magnified when such protocols need to be adjusted to the needs of a sample whose abilities are also growing and changing. Thus, it can be very difficult to decide at the outset of large longitudinal studies, for example, every decision that will need to be made along the course of the project and to rigidly adhere to such decisions.

Transparently describing and reporting when decisions regarding research methods and analysis were made—at study outset, during data collection, after data analysis had begun—enables others to better contextualize and understand study findings.

Ben Brown, PLOS ONE Guest Editor

Nevertheless, transparent and complete reporting remains important. Given the challenges I described, some scholars working in this area have been hesitant to adopt preregistration due to concerns that this practice may reduce their ability to be creative, flexible, and responsive to their needs or the needs of their samples. What I am so excited about with regard to preregistration, however, is that I see it as actually enabling those things but doing so in a way that improves the interpretability of research findings as well as the cumulative nature of science. Transparently describing and reporting when decisions regarding research methods and analysis were made—at study outset, during data collection, after data analysis had begun—enables others to better contextualize and understand study findings. Further, preregistration and subsequent documentations of deviations from an original plan helps other scholars working in that area better plan their own research by being able to anticipate and proactively address challenges.

SIPS logo
SIPS

I have had some previous experience editing more transparent submissions at outlets like Collabra: Psychology and find it quite refreshing. Open data and code allow for easy verification of results. Preregistrations, including any modifications, help reviewers contextualize results and consider matters such as researchers’ degrees of freedom. I honestly would find it difficult to go back to a more traditional editorial experience.

How do you think some of the papers in this Collection illustrate good open science practices that can improve rigor and reliability in psychological research? For instance, the Collection includes a Registered Report Protocol on improving the diagnostic accuracy of Alzheimer’s disease, a hotly debated research topic, or another Registered Report Protocol on a user-friendly mobile application to assess inhibitory control (see an interview with the authors of this protocol on the COS blog). What role do you think a more transparent planning and reporting process can play?

I was delighted to see the open, transparent practices exemplified by the articles in this collection. I was particularly encouraged to see the Registered Report examining Alzheimer’s disease within the collection. Like I mentioned previously, I believe that preregistrations are among the best things we can be doing as a field and research area to improve rigor and transparency.

PsyArXiv
PsyArXiv

I was also happy to be able to suggest additional ways in which contributing authors might share their science openly. Namely, I personally suggested that we encourage all submitting authors to share their manuscripts as preprints on PsyArXiv. Sharing manuscripts in this way further ensures that findings are transparently disseminated, even if the work is ultimately less appealing to publishing outlets, such as when studies report null findings or when work is considered less novel. These studies are important components of the scientific record and sharing them openly can contribute to a more complete and cumulative science.

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An Interview with Biogeochemist Alex Cory


Alex Cory is a final-year PhD student in the department of Earth, Ocean, and Atmospheric Science at Florida State University. She received her B.A. in geology (and music) at Lawrence University before pursuing a post-bachelors Research Associateship at Pacific Northwest National Laboratory (PNNL). Before entering grad school, she took a one-year break to travel around Southeast Asia. While in Indonesia, she witnessed some of the destructive impacts that agriculture was having on the natural landscape. The beautiful, diverse forests of Indonesia were being ripped up and replaced with rows of palm trees. The locals hated it. She would later come to learn that these alterations cause devastating effects on the climate because peatlands scrub C out of the atmosphere (and palm plantations do not). Now, as a PhD student, her job is to understand what drives the changes in peatland-climate interactions.


In this interview, we chat with Alex about her recent publication in PLOS ONE, life as an early career researcher, and the important role that peatlands play in sequestering CO2.

Your recent paper focuses on the biogeochemical components and processes involved in peatlands. Can you explain the role of peatlands in global climate change and why these carbon sinks (reservoirs that store carbon) are so critical? How much carbon do these bogs sequester?

AC: As carbon sinks, peatlands have a critical influence on the climate. Their ability to scrub carbon dioxide from the atmosphere has facilitated the formation of mind-boggling amounts of organic carbon (60% – 134% of the current atmospheric carbon pool!). Throughout most of the Holocene, this C sink function enabled peatlands to effectively cool the planet. Unfortunately, this cooling effect has lessened over the last ~150 years due to a combination of rising decomposition rates and, in some regions, increasing production of methane (which is a far more potent greenhouse gas than carbon dioxide). This phenomenon can be attributed to rising temperatures and permafrost thaw (among other factors). Determining the extent of this change (and future change) is a top priority to peatland researchers like myself.

You have mentioned that in your travels you’ve witnessed the impact of deforestation on local communities. Do you think that industry-related climate change disproportionately affects certain regions and communities more than others?

AC: Absolutely. Communities with less money/fewer resources are typically the last to receive aid after extreme weather events (such as hurricanes), which are expected to increase in frequency as a result of climate change. Poorer communities also tend to have higher rates of chronic obstructive pulmonary disease (COPD), which can be exacerbated by heat waves. Combined with the dearth of healthcare among these communities, these effects can be devastating. These are just a few examples of the inequities at play.

You’re investigating a number of really important questions regarding Earth’s carbon stores, but the day to day experimentation involves a lot of tedious processing. Did you expect so much of your PhD to entail sampling and filtering?

AC: I spent two years as a research associate before entering graduate school, wherein most of my day-to-day work involved weighing out samples on the microgram scale. (I listened to an impressive number of audiobooks during this time.) Because of this experience, the tedious aspects of lab-work did not come as a surprise to me. While they certainly do tend to lose their charm over time, I definitely find myself missing the lab more and more now that I am spending most of my time at a computer! I would advise anyone in the early stages of their career to embrace the hands-on nature of their work.

Alex in the lab in the early days of the COVID-19 pandemic. Image courtesy of Alex Cory.

Your latest work found that soluble phenolic compounds may be a crucial reason that peat bogs are so recalcitrant (unchanging). Can you tell us a bit more about these important findings?

AC: While the ability for soluble phenolics to inhibit enzyme activity is well established, the importance of phenolics in regulating carbon mineralization in peatlands has been heavily contested. For example, some studies demonstrated that removal of phenolics resulted in significantly elevated rates of enzyme hydrolysis (which is the first stage of peat decomposition). Others, on the other hand, found no significant relationship between phenolic content and rates of hydrolysis.

In our study, we found evidence that the regulatory impact of soluble phenolics varies significantly between bogs and fens (which are two types of peatland habitats). Bogs have a topic of interest for decades due to their extraordinary recalcitrance—which becomes evident when you take a look at the perfectly preserved facial features of humans bodies that were buried in the bog subsurface thousands of years ago. This recalcitrance, combined with the generally high (relative to other peatland habitats) CO2/CH4 production ratios significantly lowers the global warming potential of bogs relative to fens.

In our study, we determined that soluble phenolics could contribute to bogs’ recalcitrance and relatively high CO2/CH4 ratios—at least at our study site (Stordalen Mire, Sweden).

Our evidence for this claim was threefold. First, we noted higher soluble phenolic content in the bog. Second, we found that removal of soluble phenolics results in a far more significant uptick in bog carbon mineralization rates. Third—we noted that while the impact of soluble phenolic content on methane production was negligible in the fen, it was significant in the bog.

A typical sample incubation. Image courtesy of Alex Cory.

You have mentioned that you are part of a research institute called EMERGE. Can you tell us more about that?

AC: EMERGE (“EMergent Ecosystem Response to ChanGE”) is an NSF-funded research institute that works to understand (and predict) how ecosystems will respond to change. This is a tall order given the complexity of such interactions. To effectively carry it out, EMERGE brings in a diverse group of scientists, with expertise in 15 different subdisciplines (including, but not limited to biogeochemistry, ecology, remote sensing, modeling, and genetics). We all work on our ability to (1) communicate outside our areas of expertise and (2) function as effective team members.

One of the coolest aspects of EMERGE (in my opinion) is that we all get to learn about current research on team science (the study of teams). Through EMERGE workshops/meetings, I’ve learned that trust is a cornerstone to team success. I’ve had the opportunity to participate in a number of activities aimed at building that trust. These experiences, combined with the supportive culture within EMERGE, have helped me to speak up more at meetings and enjoy my work that much more.

We have to ask! In addition to your undergraduate and PhD studies in the Geosciences, you have a degree in Music. Can you tell us more about that? Do you see any parallels between music and science?

AC: What I love most about music and science is that they both offer the opportunity to explore one’s curiosity. For me, this always comes back to the mysteries of nature. The more analytical approach that I employ during scientific exploration is nicely complemented by the world-building narrative that I get to create when writing songs. Engaging in both strengthens my drive to understand (and even help protect) natural habitats.

Here is an example of one of my favorite nature-based songs: “Trees are like icebergs, they sit on a mirror, reflecting the secrets beneath the veneer..”

As you may know, PLOS is a huge proponent of Open Science – including Open Access publications, open peer review, open data/code sharing, etc. How do you think Open Science plays a role in Earth Sciences and Climate research?

AC: The aims of climate research—to predict future change and discern viable methods to prepare for that change—can only be effectively approached if the community of climate researchers are able to stay up to date on one another’s research. Open Science does just that! It prevents redundant research (which wastes valuable time and resources) AND offers new questions/ideas for the research community. For these reasons, I am a HUGE proponent of open science. Thank you PLOS One for being a part of that movement!


Citation: Cory AB, Chanton JP, Spencer RGM, Ogles OC, Rich VI, McCalley CK, et al. (2022) Quantifying the inhibitory impact of soluble phenolics on anaerobic carbon mineralization in a thawing permafrost peatland. PLoS ONE 17(2): e0252743. https://doi.org/10.1371/journal.pone.0252743

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

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An Interview with Palaeoclimate Modeler, Hu Yang

Here, we chat with Dr. Hu Yang about his recent publication in PLOS ONE and his predictions of the future of the Greenland Ice Sheet – the second largest body of ice on Earth, which has the potential to dramatically raise global sea level.



Dr Hu Yang is a research scientist in the Paleoclimate Dynamics group at the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research. His research interests include climate dynamics, sea-level change and paleoclimate change. To gather his results, he is particularly focused on combining observations with numerical model simulations. Dr Yang’s studies, including the discovery of a poleward shift in major ocean currents, the interpretation of tropical expansion and reconstruction of the Greenland ice sheet evolution have gained widespread attention and recognition.


Your recent paper published in PLOS ONE focuses on the Greenland Ice Sheet (GrIS) – can you tell us a bit about the ice sheet, how it is changing and what this means for global climate change? 

HY: The GrIS holds a huge amount of ice which has the potential to raise sea level by 7.3 m if it completely melts away. Understanding the GrIS’s response to climate change, therefore, is critically important for us to understand how future sea level will rise. In our study, we revisited the past evolution of the GrIS using numerical model simulations and compared it with geological reconstruction. The results show that the ice volume response of the GrIS (the amplitude of the melting and sea level rise) strongly delayed climate change, which is on the order of thousands of years. That means if we warm our planet within 100 years, the sea level rise within our generation will be minor. However, the rising sea level can last for quite a long period of time, with a much larger amplitude.

Could you explain, how does the response of the Greenland ice volume delay climate change?

HY: The Greenland ice sheet has been standing there for at least 3 million years. The mass balance of the ice sheet is determined by the surface mass gain (snowfall) and mass loss (melting and ice discharge) at its margin. Ice melt usually only takes place at the margins of the ice sheet during a few months in summer. The inner portion or the summit of the ice sheet almost never melts, because of high elevation and cold temperature. When climate warms, it removes the ice from the margin, then more ice will flow down to the margin and begin to melt. This process takes time – not a few decades, but hundreds or even thousands of years. According to the latest IPCC report, in the worst warming scenario, sea level rise within this century will be around 1-2 meters. But geological evidence suggests that the Greenland and Antarctic Ice Sheets will both be melted away if that kind of worst warming stabilized. So, there is a delay for the melt of the ice sheet and sea level rise.

How does an understanding of past climates help us to better understand future changes to the Earth’s environment? 

HY: As a human-being, most of us believe what we see within our lifetime, which is usually less than 100 years. But, 100 years relative to Earth’s history is only equivalent to a minute of time in a person’s life. If we only check one minute’s behavior of a person, we will not be able to get a comprehensive understanding of his personality. For the same reason, an understanding of past climates informs us about the current status, and how it could evolve under the forcing of rapidly rising greenhouse gases.

In the case of the Greenland ice sheet, the past ice evolution tells us that the GrIS is currently at its biggest size within at least the past 7000 years. It will shrink in response to the committed warming. And this shrinking could continue for a long period of time, even if the warming stabilized at the current level.

We have recently seen examples where the unprecedented rate of change to a number of environments has in turn made it more difficult to study those environments – for example, ice breaking off of the Thwaites glacier in the Antarctic is preventing research ships from accessing it. Do you foresee similar challenges in studying the GrIS, as it continues to melt? 

HY: The Antarctic ice sheet is different from the GrIS. The Antarctic ice mostly terminates into the ocean, but most of the margins of the GrIS stop on land. So, I don’t see similar challenges. But unlike the Antarctic ice sheet, which has almost no surface melt, the surface melt of the Greenland ice sheet may produce large river discharge, which may cause problems, perhaps.

Your study utilized openly available models and data to simulate changes to the ice sheet – do you think that Open Data and code/model sharing is important for our improved understanding of global environmental change? 

HY: Definitely, open sharing of data, models and research outputs, accelerate the advance of science.  I can hardly imagine how scientists did research one century ago. I hope in the future, all the journals could make their publications open access, like PLOS ONE, to promote the transformation of knowledge.

Dr Yang holds ocean sediment, from which researchers can extract information about past climates.

Given new and unpredicted changes that have arisen on the GrIS – for example, last year, rain fell on the ice sheet for the first time that we know of – how will existing models account for this? Or do we need ever-changing models? 

HY: There is no best model, but always a better model. Model developing takes decades. Development of climate models started more than half a century ago, and are still developing with higher resolution and new physical parameterizations. Ice sheet modelling is relatively new compared to climate modelling. A lot of processes have not been taken into account, such as rain and the meltwater pool. However, the current ice sheet model can already simulate the general geometry and ice velocity resembling observations. And with more and more processes included in the system, we could expect to have more and more accurate results.  

Have you had an opportunity to do fieldwork on the Ice Sheet yourself? 

HY: Unfortunately, not yet. This seems odd for a scientist doing ice sheet research without ever doing fieldwork on it. But today, scientific research is so specialized. For example, in our team, we have colleagues who have a background in geology. We also have experts on climate dynamics and ice sheet dynamics and computer science. Cooperation between multidisciplinary fields will fill the knowledge gaps and make research easier.

What do you find to be the most challenging aspect of being an Early Career Researcher? 

HY: Currently, I find the most challenging aspect is to find a good balance between funding and doing research. The best science is not planned, it needs time not only for developing the idea, but also for publishing. The newest idea usually takes more time to get published. But, a common working contract for an Early Career Researcher usually lasts for only 2-3 years. When I got my Greenland paper published, the project that supported this study had already been expired for two years already.


Reference: Yang H, Krebs-Kanzow U, Kleiner T, Sidorenko D, Rodehacke CB, Shi X, et al. (2022) Impact of paleoclimate on present and future evolution of the Greenland Ice Sheet. PLoS ONE 17(1): e0259816. https://doi.org/10.1371/journal.pone.0259816

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

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Physical Oceanography – a chat with the Guest Editors of our upcoming collection

PLOS ONE has an open Call for Papers on Physical Oceanography, for which selected publications will be showcased in a special collection. This call for papers aims to highlight the breadth of physical oceanography research across a wide range of regions and disciplines. We welcome submissions including those that feature multidisciplinary research and encourage studies that utilize Open Science resources, such as data and code repositories.

The upcoming collection will be curated by three accomplished researchers in the field, all of whom additionally serve as Editorial Board Members for PLOS: Dr. Maite deCastro (University of Vigo, Spain); Dr. Isabel Iglesias Fernandez (CIIMAR, University of Porto, Portugal); and Dr. Vanesa Magar (CICESE, Mexico).


Here, we chat with Profs. deCastro and Iglesias to learn more about their research, their thoughts on the future of Physical Oceanography and how advances in this field can provide a better understanding of future environmental change.

Tell us about your research.

MdC: My research is clearly aligned with Climate and Renewable Energy, especially on the impact of climate change on marine ecosystems and on wind and wave renewable energy resources. It is also aligned with Food, Bioeconomy, Natural Resources, and Environment, especially in the relationship between climate and species of commercial value.

II: I’d like to say that my research interests are multidisciplinary but always with something in common, and this nexus is physical oceanography. My main research topic is related with estuarine hydrodynamics. I work with numerical models, which are versatile tools that help to unravel the hydrodynamic patterns in these complex areas. Once these models are implemented for a specific region, they can be used for multiple purposes such as representation of sediment, contaminant and marine litter transportation patterns, forecasting the effects of extreme events, anthropic activities or climate change conditions, or even calculating the potential of hydrokinetic energy production. These are some works that I have performed in collaboration with several colleagues and in the scope of national and international research projects.

At the same time, I am also interested in coastal and oceanic dynamics. I have conducted research that related long-term variability sea level anomalies in the North Atlantic with teleconnection patterns; I supervised a study related with wave forecast, and I am collaborating in the generation of a tool to forecast the dispersion patterns of sediment plumes generated by potential deep-sea mining activities in the Atlantic region.

What new finding or growing research topic in the field of physical oceanography are you currently excited about?

MdC: I am very enthusiastic about the research I have carried out in recent years, as it has allowed us to delve into the effect of climate change on historical trends in coastal upwelling, sea surface temperature, and mixed layer, among others, and to analyze its biological impact on species such as sea bream, tuna, and algae. We have also analyzed the future projections of these variables under different climate change scenarios and their possible impacts on bivalves such as mussels, different clam species, and cockles in the Galician estuaries. This approach will allow us to know both the evolution of these ecosystems in the future and to determine what measures will be necessary to mitigate the effect of climate change in order to make these ecosystems more resilient.

II: Ecoengineering. In recent decades, the focus of coastal and estuarine engineering research has shifted from technical approaches towards the integrated combination of technical, ecological, and nature-orientated solutions to reduce environmental impacts. Practical ecoengineering solutions for estuarine regions should be based on numerical modelling tools, which can provide the necessary knowledge of the relevant hydrodynamic processes and an understanding of natural processes, hydrodynamic–ecological interactions, and the impacts of structures on the environment.

At the same time, deep-sea mining is a hot topic. In recent years, deep-sea mining has become an attractive and economically viable solution to provide metals and minerals for the worldwide industry. Although promising, a large proportion of these resources are located in the vicinity of still poorly studied and understood sensitive ecosystems. The generated sediment laden plumes and the trace elements released to the water column that are associated with the extraction procedures can change the biogeochemical equilibrium of the surrounding area. This can alter deep-sea life-support services, damaging the local ecosystems with potential impacts that can persist through decades. Reliable ocean numerical models reproducing the dynamics of deep-sea areas can help to mapping the potential scale of deep-sea mining effects, being one of the key technological advances needed to implement risk assessment and better anticipate possible impacts.

For each of you, your research features an exploration of the effects of wind and the role it plays in ocean and climatological processes. Can you discuss the close link between atmospheric and ocean sciences?

MdC: A part of my most recent research is closely related to the development of renewable energies as an alternative to burning fossil fuels in the fight against climate change. Specifically, my research analyzes future offshore wind and wave energy resources under different climate change scenarios. This research field is an example of the close link between atmospheric and ocean sciences.

II: The atmosphere and the ocean are two different parts of the same system, jointly with the lithosphere, the biosphere and the cryosphere. The atmosphere and the ocean are in contact, constantly exchange mass, momentum and energy between them. The wind is one clear example of this link between the atmosphere and the ocean, generating waves and currents and affecting the sea surface temperature. But there are many others: evaporation, precipitation, heating, cooling, … And these links are the bases of short- (meteorological) and long-term (climatological) processes as winter rainfall, hurricanes or ENSO events, among others.

Many physical oceanographers spend a lot of their time working at a computer – do you ever get to do field work or research cruises?

MdC: At the beginning of my research career, I carried out several oceanographic campaigns in the Galician estuaries to take field measurements that would allow us to characterize their hydrodynamics. These campaigns were carried out jointly with chemists and biologists who analyzed other aspects of the estuaries.

II: Yes! I was in field work in the middle of January and I am expecting to have more campaigns in March and June of this year. Most of the time I am in front of a computer, but numerical models need real data to be calibrated and validated. For that we must go out into the field and measure the physical variables that we need. And although sometimes it hard to start the campaigns at six in the morning, the truth is that it is a breath of fresh air.

There is an undeniable link between anthropogenic pressures on the global environment and changes that we are seeing in marine systems. Can you discuss how you have observed this in your own research and the implications your findings have for the future?

MdC: The enormous increase in global energy consumption, together with the need to avoid the burning of fossil fuels to mitigate climate change, has led the scientific community to make the development of alternative energy sources, such as renewable energies, a priority objective. This has motivated a part of my most recent research where the offshore wind and wave energy resource is analyzed both now and in the near future under different climate change scenarios that take into account different concentrations of greenhouse gas emissions, socioeconomic measures, and land uses. This renewable energy resource analysis is complemented, in some locations, with an economic viability analysis.

II: It is clear that something is happening. Now the effects of the anthropogenic pressures on the global environment are visible. In the Iberian Peninsula we are facing one of the most severe droughts in the last decades. But other recent signals are the floods in western Germany in July 2021, the record-breaking high temperature in Moscow during July 2021, the snowfall in Madrid in January 2021, heavy cyclones and dust storms, or a heavier-than-normal wildfire season. So it is not just something that scientists are saying. It is something that the non-scientific population can see now. And, as the United Nations Secretary General Antonio Guterres has warned, the world is reaching a “point of no return”.

The complex estuarine systems can be considered as one of the most sensitive areas to environmental stressors due to the strong coupling between physics, sediments, chemistry and biology. In this sense, the effects of the climate change conditions in estuaries can be diverse based on changes in river flow, in extreme events frequency, and in water temperature and water level, affecting the circulation, salinity distribution, suspended sediments, dissolved oxygen and biogeochemistry. I used numerical models to forecast the effect of sea level rise inside the estuarine regions. It was demonstrated that the sea level rise can cause more severe floods in some estuaries. However, what should be taken into account is that the sea level rise inside the estuaries will produce a change in the circulation patterns and in the water masses configuration. This will undoubtedly affect the ecological and socio-economic aspects, due to the great value of the estuarine ecosystem services.

Historically, women have had to push for equality, respect and recognition in the field of physics. Do you think that the field is changing to become more inclusive, and what do you think research advisors, university leaders and funding agencies can do to better support women in physical oceanography?

MdC: Personally, I have always felt treated exactly the same as any other colleague throughout my scientific career, both in my closest circle and at an institutional level. I think I’ve had the same opportunities and help. I think that in this sense the field of physics, or at least this is my personal perception, is a privileged field. Despite this, I consider that there are still few women in this field compared to men and any activity aimed at making women feel more attracted to the field of physics is necessary.

II: I must say that I never need to fight more than a “man” to achieve the same respect and recognition for my work neither in my research group, nor in my research institute, country or even internationally. I had the same opportunities as anyone being men or woman. And curiously, we are more women in my research group, which develop research topics that were traditionally associated with “man”, like physics, engineering, mathematics, algorithms, numerical modelling, computational sciences, etc. I know that I am lucky, because other women before me pushed hard for equality and recognition and there are other women in different areas that still need to push to gain respect and visibility.

The term Open Science has been used to highlight the fact that transparency in scientific research goes beyond just Open Access publications. In the field of physical oceanography how do you think that making code and data publicly available can benefit researchers and policy makers?

MdC: In general terms, for the sake of transparency and the progress of the investigation, I consider it important to be able to have all the necessary material (code, data) so that any researcher can reproduce the results of another.  We will move faster and save resources if the data generated by other entities are public and if we all have access to each other’s progress instead of repeating what other researchers have already done. All this, of course, is within a framework of respect for the work of each one.

II: In my opinion, the science needs to be open. We are paying science with public funds, and it is not ethical to keep our research only for us on a long term basis. Of course, there must be some nuances regarding data for articles or patents. But I think that, at the end, the generated research should be public available. And it is not only the Open Access publications, which guarantee the transparency and the replicability of the research methodology, but also the numerical codes, the tools and the data generated in the scope of public funded research projects. Only in this way will we manage to advance faster in science, sharing our knowledge with other researchers and supporting the policy makers with proper tools to ensure the safety of populations and the sustainability of ecosystems and services.

About the Guest Editors


Isabel Iglesias holds a PhD in Climatic Sciences: Meteorology, Physical Oceanography and Climatic Change by the University of Vigo (2010). Since 2011 Isabel is working as an Assistant Researcher at the Interdisciplinary Centre for Marine and Environmental Research (CIIMAR) of the University of Porto, Portugal. Her main research topics are related with physical oceanography, atmosphere-ocean interaction, transport (sediments and marine litter), extreme events and climate change. Particularly she has experience in analysing the hydrodynamic behaviour of the water masses and in applying numerical models at oceanic, including surface and deep-sea areas, coastal and estuarine regions. Other areas of expertise include the performance and analysis of physical data obtained in sampling campaigns and the evaluation and analysis of remote sensing data for numerical modelling calibration/validation.


Maite deCastro is a Professor of Applied Physics at the University of Vigo. She obtained her PhD in Physics from the University of Santiago de Compostela (1998). The main focus of her research deals with (a) the study of hydrodynamics, waves and transport phenomena in shallow waters by means of in situ field data and numerical simulations; (b) the analysis of the variability (inter-annual and inter-decadal) of coastal and oceanic sea surface temperature (SST) using numerical and satellite data; (c) the analysis of the water masses around the Iberian Peninsula using salinity and temperature data obtained from the SODA base or ARGO buoys; (d) The effects of meteorological forcing on the ocean using satellite data or reanalysis such as: wind data, Ekman transport, sea level pressure (SLP), SST, teleconnection indices (NAO, EA, EA-WR, SCA, POL…); (e) The analysis of the plume development of rivers using radiance data from the Oceancolor MODIS base. (f) the influence of climate change on oceanographic variables, both present and in the future and, (h) the analysis of present and future wind, solar and wave resources for renewable energy production.


Vanesa Magar holds a BSc in Physics from UNAM, and a master’s in advanced studies in Mathematics and a PhD in Applied Mathematics from the University of Cambridge, UK. She has been working in coastal and physical oceanography since 2002, and in renewable energy research and development since 2008. She joined the Physical Oceanography Department of CICESE as a senior researcher in 2014, where she co-leads the GEMlab (Geophysical and Environmental Modelling Lab) with Dr Markus Gross. Her research interests include wind energy, marine renewable energy, coastal hydrodynamics, and sustainable development issues in relation to renewable energy project development. She is member of the Energy Group of the Institute of Physics (IOP), UK, and a fellow and chartered mathematician from the IMA. She served in the Mexican Geophysical Union director’s board (as Secretary General, Vice President, and President) from 2016 to 2021. Currently, she is part of the Executive Committee of the National Strategic Programme (PRONACE) in Energy and Climate Change of CONACYT (2018- ).

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

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An Interview with Dr. Travis Courtney – Marine Chemist and PLOS Author

Here, we chat with Dr. Travis Courtney about his newest publication in PLOS ONE, his exciting research on coral reefs, and his thoughts on equity and openness in science.

Dr. Courtney at Red Rock Canyon National Recreation Area. Photo by Lark Starkey.

Travis Courtney (he/him/his) grew up in the coastal city of Wilmington, North Carolina, USA where he gained an intense appreciation for coastal ecosystems. He completed his BS in Geological and Environmental Sciences at the University of North Carolina at Chapel Hill while conducting research on the effects of ocean warming and acidification on a tropical sea urchin. Courtney later attended Scripps Institution of Oceanography for his PhD and postdoctoral research on quantifying the rates and drivers of coral and coral reef calcification. He is currently an assistant professor of marine chemistry in the Department of Marine Sciences at the University of Puerto Rico Mayagüez.


PLOS: You currently head the Biogeochemistry and Ecology Research Group (BERG) at the University of Puerto Rico Mayagüez. Tell us all about your research.

My previous research has largely focused on understanding the drivers of the growth and maintenance of coral reef structures under environmental change. While I plan to continue this research here in Puerto Rico, the BERG lab is also looking to broaden our research goals to include research themes that will be most beneficial to Puerto Rico through conversations with local governmental and non-profit agencies. Climate change, coral diseases, land-use change, fishing practices, and degrading water quality are all potentially important research themes impacting the health and functioning of coastal marine ecosystems here in Puerto Rico. By understanding how these driving forces are influencing coastal ecosystems, we can also work with local agencies and community groups to develop and implement evidence-based conservation, restoration, and remediation efforts.

Travis Courtney setting up a photo quadrat as part of coral reef benthic survey work with Heather Page in Kāne’ohe Bay, Hawai’i. Photo by Andreas Andersson.
Travis Courtney setting up a photo quadrat as part of coral reef benthic survey work with Heather Page in Kāne’ohe Bay, Hawai’i. Photo by Andreas Andersson.

PLOS: Your research has ranged from fieldwork-centric studies (in Bermuda, Belize, etc.) to more data and/or mesocosm-based approaches. Tell us why both types of approaches are needed to create a comprehensive understanding of environmental impacts on coral reefs?

There’s always a trade-off between working in the field vs working in controlled laboratory settings such as mesocosms. On one hand, field-based studies allow us to directly quantify how coral reefs are changing but attributing these changes to individual environmental drivers can be difficult. There are often so many co-varying environmental factors impacting reefs, which makes it challenging to determine the direct and indirect effects of any single variable in the field. On the other hand, mesocosm-based studies allow us to precisely test how selected environmental variables influence coral reefs while keeping all other variables constant. However, controlling for so many variables means that these types of mesocosm studies may not necessarily mimic the true responses of coral reefs occurring in the field. By combining the data and insights gained from these field and mesocosm-based approaches, we can test hypotheses in a controlled setting (mesocosms) and see if those hypotheses are supported in the real world (fieldwork) to increase our understanding for how environmental change impacts coral reef systems.

PLOS: As many researchers know, community-wide adherence to protocols and standards can be critical for temporal research and the intercomparison of results. This is especially true for ocean and atmospheric measurements, where the lack of a uniform approach can impede the identification of long-term trends. In your recent paper, published in PLOS ONE, you discuss the implications of total alkalinity data with respect to salinity. You simulated the potential uncertainties associated with salinity normalization of coral reef total alkalinity data and propose a series of recommendations to reduce these uncertainties in future studies. What was your motivation for pursuing this research, and how do you think it will influence the research community’s approaches to salinity normalization of total alkalinity data on coral reefs?

The original motivation for this study was to develop user friendly tools to rapidly assess coral reef calcification tipping points under climate change as part of a project funded by NOAA’s Ocean Acidification Program. For example, our first ecology-based tool estimates coral reef calcification from coral reef images in CoralNet. When developing the chemistry-based tool, we found a lack of clear guidelines in the literature describing the various assumptions and resulting uncertainties associated with normalizing coral reef total alkalinity data to a common reference salinity. Salinity normalization is an important step that is used to isolate the effects of coral reef calcification on total alkalinity from other processes such as freshwater dilution, evaporation, and mixing. Repeated measurements of coral reef calcification through time are one tool we have as researchers to quantify the impacts of environmental change on the growth of coral reefs so increasing the precision of these measurements is important for detecting any changes in coral reef calcification through time.

The primary goal of this study was to test how the salinity normalization process potentially influences measurements of coral reef calcification derived from seawater total alkalinity data. I hope that by providing a discussion of the uncertainties associated with salinity normalized total alkalinity data and suggestions to reduce these uncertainties, this study will increase our capacity as a research community to reliably detect any potential changes in coral reef calcification under ongoing environmental change.

PLOS: There is a close link between coral reef research and a better understanding of global climate change – how have your findings on reefs contributed to our knowledge of Earth’s rapidly changing climate?

Coral reefs are often called the canaries in the coal mine, owing to the widespread observed declines in global coral cover associated with climate change and other local factors. They can provide unique insights into our knowledge of Earth’s changing climate by quantifying the impacts of climate change on present-day coral reefs as well as historical coral reefs preserved in the geologic record. Additionally, geochemical analysis of calcium carbonate from reef environments can generate useful reconstructions of historical climate change.

For example, my first experiment as an undergraduate researcher cultured sea urchins under various ocean warming and acidification conditions. We quantified changes in growth rates to see how ocean warming and acidification might influence the growth of sea urchins under climate change. Additionally, we quantified how sea urchin skeletal geochemistry was influenced by ocean warming and ocean acidification. This allowed us to develop proxies that could be used to estimate historical seawater temperatures and carbonate chemistry from the skeletal geochemistry of sea urchin spines preserved in the rock record. I’m currently involved in a range of other projects quantifying the impacts of climate change on coral reef calcification and reconstructing historical seawater temperatures from coral skeletons. I hope these ongoing projects will continue to increase our collective understanding for how the Earth’s climate has changed and how these changes influence coral reef structures and the ecosystem services they provide to humanity.

Dr. Courtney setting up instruments to record seawater parameters at the Hawai’i Institute of Marine Biology. Photo by Andreas Andersson.

PLOS: Some people have expressed the belief that the ocean will simply uptake and offset increased carbon emissions, providing a natural solution to the problem of elevated atmospheric CO2 concentrations. Some have even posited that the dissolution of corals and other calcium-rich organisms could create a negative feedback loop, increasing ocean pH and offsetting ocean acidification. Can you discuss the limitations to these theories and why we cannot rely on the ocean to sequester CO2 without making changes to emissions?

While there are a range of feedback mechanisms in the Earth’s climate system that can mitigate climate change, there are also feedback mechanisms capable of accelerating climate change. In the context of global climate change, the current input of CO2 to the atmosphere is more rapid than the rates of CO2 uptake by these naturally occurring CO2 uptake mechanisms. As a result, atmospheric and oceanic CO2 concentrations are currently increasing, and we are experiencing unprecedented ocean warming, acidification, and deoxygenation in response to greenhouse gas emissions. Current estimates suggest we’ve lost approximately 50% of global coral cover in recent decades, and widespread coral bleaching events are expected to continue to intensify in the coming decades and drive further declines in coral reefs. While researchers continue to explore various natural and artificial climate regulatory mechanisms further, the best way to mitigate climate change, and the negative impacts for coral reefs and people around the world, is to reduce emissions of CO2 to the atmosphere as soon as possible. Project Drawdown has many resources for further details on addressing the global climate crisis.

Dr. Courtney sampling a coral core in Bermuda. Photo by Andreas Andersson.

PLOS: The BERG lab’s website has a section titled “We believe” which outlines your support of equity and inclusivity in science (and other realms). Can you talk here in a bit more depth about your views on equity in science and research and how your lab supports efforts to promote this?

I witnessed the “leaky pipeline” throughout my studies with decreasingly diverse classrooms and academic environments as I progressed from high school to undergraduate, graduate, and postgraduate work. How can we, as a research community, promote the importance of diversity for improving success of ecological communities and fail to do the same to promote success within our own research communities? I believe we must do better to promote a more just, equitable, diverse, and inclusive research community.

Maintaining a commitment to these principles of inclusion and equity is an important part of developing a supportive lab environment that actively promotes the success of students to the next stage of their careers. I’m also working on developing relationships with local governmental and non-governmental organizations to identify research needs where our work in the BERG lab can be most beneficial to the coastal ecosystems and people of Puerto Rico. Outside of the lab, I teach a class on ethics that focuses on principles of justice, equity, diversity, and inclusion, where we discuss some of latest scientific literature on these issues within academic science and debate how we can work to improve academic culture.

PLOS: As you may know, PLOS is dedicated to advancing not just Open Access, but Open Science, which includes transparency and equitable access to data, code, protocols, preprints, etc. What are your thoughts on Open Science and how does this ethos fit in with your research?

I believe science should be freely accessible to everyone. Especially since so much research currently remains behind internet paywalls, I think we as a scientific community really need to ask ourselves who this paywalled research benefits and explore Open Science options to share the knowledge and resources we produce. Much of this science is also funded by taxpayer dollars, so I believe publicly funded researchers owe it to those taxpayers to make our research outputs accessible to the people who paid for it. Moreover, the data and code we produce for any given publication or project can often be incredibly useful to other scientific research projects and monitoring efforts for community, non-profit, and governmental organizations so having that data openly available can help to accelerate new discoveries and improve policies. Open science also increases transparency and trust in the scientific process by making everything freely available for review to ensure that any conclusions in the published papers are adequately supported by the data and analyses. Overall, I think that the increased accessibility provided by the Open Science movement has been an incredible step forward in the scientific process and making science more accessible, and I look forward to continuing to educate myself and the students here at UPRM on the latest Open Science best practices.

Citation: Courtney TA, Cyronak T, Griffin AJ, Andersson AJ (2021) Implications of salinity normalization of seawater total alkalinity in coral reef metabolism studies. PLoS ONE 16(12): e0261210. https://doi.org/10.1371/journal.pone.0261210

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Music based brain-computer interfaces – an interview with Stefan Ehrlich and Kat Agres

Music can evoke strong emotions and affect human behaviour. We process music via a series of complex cognitive operations. Consequently, it can be a window to understanding higher brain functions, as well as being used as a diagnostic and therapeutic tool. So how can we understand the way music evokes emotions and effectively use this in healthcare technologies?

Recently PLOS ONE launched a collection on “Affective Computing and Human-Computer Interactions” and we discuss with Stefan Ehrlich from the Technische Universität München and Kat Agres from the National University of Singapore their paper on a music-based brain-computer interface for emotion mediation.


PLOS – In your paper “A closed-loop, music-based brain-computer interface for emotion mediation” you present a Brain-Computer Interface (BCI) pilot study that uses an automatic music generation system to both affect users’ emotional states and allows them to mediate the music via their emotions. What would you say are the key points of your work?

Stefan Ehrlich – Our work focuses on the integration of music with healthcare technology to mediate and reinforce listeners’ emotional states. The key point we see is in providing a novel automatic music generation system that allows a listener to continuously interact with it via an “emotion display”. The system translates the listener’s brain activity, corresponding to a specific emotional state, into a musical representation that seamlessly and continuously adapts to the listener’s current emotional state. Whilst the user listens, they are made aware of their current emotional state by the type of generated music, and the feedback allows them to mediate or to regain control over the emotional state. Many of the neurofeedback applications that have been already proposed often only have one-dimensional feedback provided to the to the subject. For instance, a levitating ball is displayed on the screen, and the subject is asked to control it up or down. The advantage of using music is that it’s possible to map a relatively complex signal, in this case brain activity, in a multi-dimensional manner to a cohesive, seemingly only one- dimensional feedback. It’s possible to embed different information in a single cohesive BCI feedback by using the different features of music, such as rhythm, tempo, the roughness of the rhythm or the harmonic structure.

PLOS – Were there any particular health care applications that you had in mind when designing this pilot study?

Kat Agres – I tend to think of music as being a sort of Swiss army knife where there are lots of features that can come in handy, depending on the scenario or the clinical population. For example, it’s social, it’s engaging, it often evokes personal memories, and it often lends itself to rhythmic entrainment. It’s these properties or features of music that lend itself particularly well to health care applications. Our main focus is on mental health and emotional wellbeing, and teaching people how to control their own emotions. And I think that’s the really interesting part about this study, that the music is a sonification of the listener’s emotional state, as measured via their EEG. It is meant to influence their emotional state, and helps teach the listener how to mediate their emotional states as they interact with the music system. This sonification can show the listener both what’s happening emotionally but it also allows them to mediate the sound of the music by affecting their own emotional state. The music is being created in real time based on the brain activity. We’ve recently been awarded a fairly large grant in Singapore to develop a holistic BCI system that we’re actually calling a Brain-Computer-Brain Interface. The project will cover different aspects, e.g., motor skills, cognition and emotion. We’ve already started developing the 2.0 version of the automatic generation system, and we are about to validate it with a listening study with both healthy adults and depressed patients. Once all these validation steps have been completed and we can effectively say that the system is flexible enough to induce different emotion states in a depressed population, we will be applying this to stroke patients who are battling depression.

PLOS – What do you think the main differences will be in the ability of depressed and healthy populations to affect emotions with this system?

Kat Agres – The number one reason people listen to music is to enhance or modify their emotion state or their mood. There is very significant literature now supporting the use of music for various mental health scenarios and for people who are struggling with various mental health conditions. I think that music is particularly well positioned to help people when other things are not helping them. The first group of depressed patients that we will be testing our system on is made up of many young people who actually think of their identity in part in terms of their music. Based on the literature and unique affordances of music, I think that we have a decent shot at reaching these individuals and helping them figure out how to gain better control of their motion states. In our pilot study, some individuals really got the hang of it and some had a harder time figuring out how to use the system. I think we’ll find the same thing in this population of depressed patients. I’m cautiously optimistic that this system will be effective for this population.

Stefan Ehrlich – When using the system, different psychiatric and neurological populations will probably elicit different patterns of interaction. These will lead to the next steps in understanding how to modify the system in order to better help the patients. At the moment it’s a system that can help them gain awareness of their emotional state and that allows us to measure the variations between the different groups.

Kat Agres –And one of the interesting directions we are exploring with the automatic music generation system is the trajectory of taking someone from a particular (current) emotional state to another, target emotional state. It will be interesting to compare whether the optimal trajectory through emotion space is similar for depressed patients and healthy adults.  

PLOS – Was there anything that particularly surprised you?

Stefan Ehrlich – A surprise for me was that without telling the listeners how to gain control over the feedback, when asked, all of them reported that they self-evoked emotions by thinking about happy/sad moments in their life. I want to emphasise that the system triggered people to engage with their memories and with their emotions in order to make the music feedback change. I was surprised that all of the subjects chose this strategy.

PLOS – What was the biggest challenge for you?

Stefan Ehrlich – The most difficult part was developing the music generation system and the mapping with continuous changes of brain activity. In the beginning we wanted to map brain activity features with musical features and the idea of focusing on emotions as the target only came during the development of the system. Constraining the system to emotional features and target variables helped to reduce the dimensionality and the complexity, while clarifying the main objective (emotion mediation) of the eventual system.

Kat Agres – Creating an automatic music generation system is not as easy as it might sound, especially when it has to be flexible to react to changes in brain state in real time. There’s a lot of structure and repetition in music. So when the participants try to push their emotion state up or down the music has to adapt in real time to their brain signals and sound continuous and musically cohesive.

Stefan Ehrlich – Yes, and there can’t be a big time-lag with the generated music, as this would compromise the sense of agency participants have over the system. If the system does not react or respond accordingly, people would lose faith that the system actually responds to their emotions.

PLOS – This work is very interdisciplinary with researchers from many different backgrounds. What are your thoughts on interdisciplinary research?

Stefan Ehrlich – I think it is more fun to work in an interdisciplinary setting. I’m really excited to hear and learn about the insight or the perspective of the other side on a topic or problem. It can be occasionally challenging. You have to establish a common ground, values and methodological approaches to a problem. You need to be able to communicate and exchange in an efficient way so that you can learn from each other. It’s important that all of the involved parties are willing to understand to a certain degree the mindset of the other side.

Kat Agres – I feel quite passionately about interdisciplinary research, especially as a cognitive scientist working at a conservatory of music. One of the obvious things that comes to mind when you’re working with people from different disciplines is how they use different terms, theoretical approaches, or methods. And yes, that can be a difficulty. But as long as everyone is clear on what the big challenges are, have the same high-level perspectives, values, and a shared sense of what the big goals are, it works well. In order to collaborate, you have to get on the same page about what you think is the most important issue, and then you can decide on the methods and how to get there.

PLOS – Considering your original research backgrounds, how did you end up doing such interdisciplinary research?

Stefan Ehrlich – I have a very non-interdisciplinary background in a way (electrical engineering and computer science). During my masters I attended a lecture called “Introduction to computational neuroscience” and it was really an eye opener for me. I realized that my background could contribute to research in neuroscience, engineering, and medicine. From then I started developing a strong interest in research at this intersection of topics.

Kat Agres – I specifically chose an undergrad institution that allowed me to pursue two majors within one degree programme: cognitive psychology and cello performance. I found it really difficult to choose one over the other and eventually I realised that I could study the cognitive science of music. And then I did a PhD in music, psychology, and cognitive science. I consider health to be yet another discipline that I’m interested in incorporating into a lot of my research. I am very grateful that recently I’ve been able to do more research at the intersection of music, technology, and health.

PLOS – In the field of affective computing and human-computer interactions, what do you think are the biggest challenges and opportunities?  

Stefan Ehrlich – I think one important aspect is the human in the loop. The human is at the centre of this technology, as important as the system itself. Often the transfer from the lab is very difficult to do due to the variables associated with humans. Ultimately, we want to see people using these technologies in the real world, and this is the main challenge. 

Kat Agres – I agree that human data can be messy. Physiological signals, like EEG, galvanic skin response, heart rate variability, etc., are all pretty noisy signals, and so it’s just difficult to work with the data in the first place. We see daily advancements in AI, medical technologies, and eHealth. I think the future is going to be about merging these computational and engineering technologies with the creative arts and music.

PLOS – Do you see Open Science practices, like code and data sharing, as important for these fields?

Stefan Ehrlich – Yes absolutely. When I started working in research there were not many data sets available that would have been useful for my work. I think researchers should upload everything – from data to code to a public repository. I personally use GitHub, which currently has the limitation of not allowing very large files, e.g., EEG data. It’s not an ideal repository for this kind of data at the moment, but there are many other platforms being developed and will hopefully be adopted in the future.

Kat Agres – I wholeheartedly agree that Open Access is extremely important. I am glad that a discussion is happening around not all researchers having access to funds to make their work Open Access. I’m lucky that I’m attached to an academic institution where one can apply for funds for Open Access. My concerns is that policies requiring authors to pay might create elitism in publication. Academic partnerships with journals like PLOS ONE can help researchers publish Open Access.

PLOS – What would be your take home message for the general public?

Stefan Ehrlich & Kat Agres – I think that the public currently perceives music predominantly as a medium for entertainment, but music has a much bigger footprint in human history than this. Historically, music served many important roles in society, from social cohesion, to mother-infant bonding, to healing. In ancient Greece, Apollo was the god of Music and Medicine. He could heal people by playing his harp. They used to think that music had healing properties. The same is found in Eastern cultures, where for example the Chinese character for medicine is derived from the character for music. There is a very long-standing connection between these areas. In more recent years music has taken this more limited role in our society, but now more and more people are beginning to realise that music serves many functions in society, including for our health and wellbeing. We hope that music interventions and technologies such as our affective BCI system will contribute to this evolving landscape and provide a useful tool to help people improve their mental health and well-being.

References:

1. Ehrlich SK, Agres KR, Guan C, Cheng G (2019) A closed-loop, music-based brain-computer interface for emotion mediation. PLOS ONE 14(3): e0213516. https://doi.org/10.1371/journal.pone.0213516


Author Biographies


Stefan Ehrlich is a postdoctoral fellow in the Dystonia and Speech Motor Control Laboratory at Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, USA. His current research is focused on brain-computer interfaces (BCIs) for the treatment of focal dystonia using non-invasive neurofeedback and real-time transcranial neuromodulation. Formerly, he was a postdoctoral researcher at the Chair for Cognitive Systems at the Technical University of Munich, where he also obtained his PhD in electrical engineering and computer science in 2020. His contributions comprise research works on passive brain-computer interfaces (BCI) for augmentation of human-robot interaction as well as contributions to the domain of easy-to-use wearable EEG-based neurotechnology and music-based closed-loop neurofeedback BCIs for affect regulation.

ORCID ID0000-0002-3634-6973.


Kat Agres is an Assistant Professor at the Yong Siew Toh Conservatory of Music (YSTCM) at the National University of Singapore (NUS), and has a joint appointment at Yale-NUS College. She was previously the Principal Investigator and founder of the Music Cognition group at the Institute of High Performance Computing, A*STAR. Kat received her PhD in Psychology (with a graduate minor in Cognitive Science) from Cornell University in 2013, and holds a bachelor’s degree in Cognitive Psychology and Cello Performance from Carnegie Mellon University. Her postdoctoral research was conducted at Queen Mary University of London, in the areas of Music Cognition and Computational Creativity. She has received numerous grants to support her research, including Fellowships from the National Institute of Health (NIH) and the National Institute of Mental Health (NIMH) in the US, postdoctoral funding from the European Commission’s Future and Emerging Technologies (FET) program, and grants from various funding agencies in Singapore. Kat’s research explores a wide range of topics, including music technology for healthcare and well-being, music perception and cognition, computational modelling of learning and memory, automatic music generation and computational creativity. She has presented her work in over fifteen countries across four continents, and remains an active cellist in Singapore.

ORCID ID0000-0001-7260-2447

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15 Years of PLOS ONE – Author Perspectives

This December marks 15 years since PLOS ONE published its first papers. As we celebrate this milestone, we invited authors of some of the first papers to be published, as well as an author of a more recent paper, to share information about their careers, their perspectives on Open Science, and their experiences as PLOS ONE authors.

We spoke with Miriam Kolko (University of Copenhagen), Matthew Goddard (University of Lincoln), Andrej A Romanovsky (Arizona State University) and Seppo Ylä-Herttuala (University of Eastern Finland).

Their perspectives provide a fascinating insight into how their research careers have progressed in the past fifteen years, as well as the changes the research world has experienced. We hear about the importance of open science practices, and how open access publishing has gone from a relatively new idea fifteen years ago to an almost ubiquitous endeavor in the present day. They also discuss their experiences of both expected and unexpected discoveries, how they have stayed on track in pursuing their research goals, and the importance of being a good collaborator and keeping flexible in a dynamic research landscape.


Miriam Kolko


Miriam Kolko is a chief physician and glaucoma specialist at the Copenhagen University Hospital, Rigshospitalet-Glostrup and an author of the PLOS ONE paper “The Prevalence and Incidence of Glaucoma in Denmark in a Fifteen Year Period: A Nationwide Study [1]”.

Could you tell us a bit about what you are working on at the moment? What does your lab group look like?

MK: I am in the fortunate situation of leading the research group Eye Translational Research Unit, EyeTRU. We work with different aspects of glaucoma. All our research projects have the patient in mind and we thus have preclinical and clinical models to explore the pathophysiology behind glaucoma. In addition, we work to stratify and optimize existing treatments for glaucoma patients. We are particularly aware of the inappropriate side effects that occur with preservative-containing eye drops as well as the sparse regulation of generics. Finally, we work with big data to identify predictive factors for risk assessment and earlier detection of sight-threatening diseases, such as glaucoma. Currently, EyeTRU consists of 2 postdocs, 8 PhD students, a laboratory technician and several master’s and bachelor’s students.

It is essential to share knowledge, including sharing data, so that the most knowledge is obtained that can benefit patients

Miriam Kolko

What does a typical day at work look like for you?

MK: I am a clinician-scientist and spend half my time with patients and half time with teaching and research. I treat patients with glaucoma medically and surgically twice a week. The remaining time goes with research teaching and multicenter studies.

In your field, how important are open science practices? Do you have any success stories of having shared or re-used data, code, a preprint, or something else?

MK: Transparency is really important and creates the environment for original ideas and collaborations. The ability to publish preprints is one of many ways to share research at an early stage. Another very important prerequisite for knowledge sharing and innovative research is a safe working environment. Sure, competition is important, but teamwork is the key to ground-breaking research. In general, I believe that it is essential to share knowledge, including sharing data, so that the most knowledge is obtained that can benefit patients.

Can you tell us about an important moment in your career as a scientist, which helped shape you as a researcher?

MK: My research career started in the United States as a Fulbright scholar and later as a PhD student Under Professor Nicolas G Bazan. I spent a total of 5 years in the USA, which shaped me as a basic science researcher and has since given me the foundation to create a translational research environment in my research group Eye Translational Eye Research, EyeTRU.

PLOS ONE is celebrating 15 years as a journal this year. Can you tell us where you were in your career 15 years ago? If you could give advice to your former self as a researcher, what would you say?

MK: Believe in the impossible and keep going. Life as a clinician-scientist or full researcher is fantastic, but you face challenges along the way. The environment is harsh and the best advice is to stay behave as one would like others to behave.


Matthew Goddard


Matthew Goddard is a professor at the University of Lincoln and an author of the PLOS ONE paper “Invasion and Persistence of a Selfish Gene in the Cnidaria [2].”

Looking back at your paper, which was one of the first papers published in PLOS ONE, what did you learn from this study? Did you continue to work in this field and build on these findings?

MG: This paper was the first report inferring the dynamics of the evolution of homing endonuclease genes (HEGs: a type of ’selfish’ gene or non-Mendelian element) in metazoans. The surprising finding was they appear to have horizontally transferred between Cnidarian species. This was one of the final papers in my line of enquiry into HEGs and I moved on to other areas after this.

To meaningfully translate science done in university labs to the outside world is a hard but rewarding activity.

Matthew Goddard

Do you remember when you first heard of PLOS ONE? What made you first interested in publishing with PLOS ONE?

MG: This was back in the days before the explosion of journals occurred and most were still only accessible via subscriptions. I recall hearing the news of a new type of journal that was completely open access being suggested and I liked the idea of this very much. It was a gamble publishing in a new journal with a new format with no impact factor etc. but this was worth it as the ethos of the open access idea sat well with us.

Could you tell us a bit about what you are working on at the moment? What does your lab group look like?

MG: Mostly studying the effects of agricultural management (i.e. conservation agricultural approaches) and land-use change on soil biology (using DNA and classic methods) and physiochemical attributes (mainly C-sequestration and water retention). These are important areas, especially for the UK, to help understand how to best manage land given climate change and the desire to move to more sustainable agricultural approaches. There is a lack of data in this area.

In your field, how common are open science practices? Do you have any success stories of having shared or re-used data, code, a preprint, or something else?

MG: Very common, and pre-prints of any publication must be available to evaluated via the UK Research Excellence Framework (REF) system. I tend to conduct studies that generate data but we have used whole genome DNA sequence data from various microbes that are publicly available to better understand the genomes that we have sequenced. Such resources are invaluable to help understand the larger ecological and genetic picture.

PLOS ONE is celebrating 15 years as a journal this year. Can you tell us where you were in your career 15 years ago? If you could give advice to your former self as a researcher, what would you say?

MG: I had just completed my first post-doctoral position at the NERC centre for population biology at Imperial College’s Silwood Park in the UK. I am not sure about advice to my former self, but to someone at the first post-doc stage of their career it would be to expose yourself to and learn from as wide a diversity of scientists, ideas and places as possible.

Publishing papers is crucial to a career in research. Can you tell us of an event or memory that was not a paper, which influenced your career as a researcher?

MG: Hard: probably moving from the ‘blue-skies’ area where I mostly just interacted with other researchers during my PhD and post-doc to interacting with farmers/agricultural workers and gaining an appreciation of how to attempt to meaningfully translate science done in university labs to the outside world is a hard but rewarding activity.


Andrej A Romanovsky


Andrej A Romanovsky is a founder of Zharko Pharma and an Adjunct Faculty member at Arizona State University, and author of the PLOS ONE paper “Neural Substrate of Cold-Seeking Behavior in Endotoxin Shock [3]”.

Looking back at your paper, which was one of the first papers published in PLOS ONE, what did you learn from this study?

AAR: Actually, that was the very first paper published by PLOS ONE [3]. That study was conducted by two brilliant researchers, Camila Almeida and Alex Steiner, who at that time were postdocs in my FeverLab. Both were trained by Professor Guillermo Branco, a patriarch of Brazilian thermophysiology, and both have become highly productive independent scientists. Camila, who played a leading role on that study, and Alex made a remarkable discovery by showing that behavioral thermoregulation does not require the integrity of the brain structure called hypothalamus. Many textbooks on thermoregulation state that body temperature is controlled by a “central government” located in the hypothalamus. This widely spread erroneous view is allegedly supported by the fact that rats with lesions in a certain part of the hypothalamus cannot defend their body temperature against heat or cold. Camila and Alex reproduced these experiments. They found that rats with lesioned hypothalami indeed could not defend themselves against thermal challenges – but only when they were restrained in little cages and could not use behavioral thermoregulation. When the same rats were allowed to move freely and select a warmer or cooler environment, they exhibited fully competent thermoregulatory responses – no weakness whatsoever! That study was a blow to the idea that the hypothalamus is the “chief commander” of thermoregulation. If the readers of this blog are interested to learn more about how this idea was discrowned and what replaced it, please go to my review [5].

But most importantly, we enjoyed – and still enjoy and are proud of – being a part of the open access revolution.

Andrej A Romanovsky

Do you remember when you first heard of PLOS ONE? What made you first interested in publishing with PLOS ONE?

AAR: The history of science is the history of illusions (like the one about the hypothalamus controlling body temperature)… In 2006, we published in PLOS Biology a study conducted in FeverLab by Alex Steiner (mentioned above) and Andrei Ivanov (now Professor at Cleveland Clinic), with the help of multiple collaborators [6]. This study, which found that fever is initiated outside of the brain, in the lungs and liver, was well-received. Encouraged by this success, we submitted our next study to PLOS Biology – again! Soon we received good reviews and an invitation to move the paper to … PLOS ONE. At that time, PLOS ONE did not exist, and this is where illusions enter our story. Listen, everybody knows that there are many Nature journals, right? Nature Neuroscience, Nature Immunology, Nature This, Nature That… But among all the Nature journals, there is one that stands like Gulliver among the Lilliputians: Nature! Camila, Alex, and I tried to imagine what type of journal PLOS ONE would be. And we came to the conclusion, or should I say illusion, that PLOS ONE would be the same to the PLOS journals as Nature was to the Nature journals! It was due to this illusion that we accepted the invitation, and this is how the very first PLOS ONE article [3] was born! And although PLOS ONE did not turn into the most prestigious PLOS journal (and was not designed to do so), our article seeded what has grown to become the Gulliver of all Gullivers in scientific publishing – the journal that has published more papers than any other academic journal in the history of mankind. But most importantly, we enjoyed – and still enjoy and are proud of – being a part of the open access revolution.

Could you tell us a bit about what you are working on at the moment?

AAR: I retired from laboratory research in 2019 to dedicate my remaining professional life to making several new drugs. The ideas for all these drugs came from or are closely related to my past research. Together with my colleagues, we have launched a couple of startups, including my favorite, Zharko Pharma. The name is a transliteration of the Russian adverb жарко (žárko), which means hot, like in feeling uncomfortably hot. Zharko’s goal is to develop a drug for treating the thermal discomfort experienced by menopausal women – hot flashes. Hot flashes are a widely spread condition that are debilitating in some women, and no effective non-hormonal treatment is currently available.

Publishing papers is crucial to a career in research. Can you tell us of an event or memory that was not a paper, which affected your research?

AAR: Yes, I can tell you about a silly event in FeverLab’s life that gave us a cover of the Journal of Neuroscience. When Andras Garami (now Head of Thermophysiology Department at University of Pécs Medical School in Hungary) worked with me as a postdoc, we were studying the role of the so-called TRPV1 channel in thermoregulation. The latest Nobel Prize in Physiology or Medicine was given to David Julius and Ardem Patapoutian “for their discoveries of receptors for temperature…”, including TRPV1. This channel is expressed on sensory nerves and is responsible for the burning sensation we have while eating chili peppers. Being a Hungarian, Andras was not a stranger to spicy foods, but he wanted to experience first-hand how spicy “spicy” can be and was looking in grocery stores for the hottest peppers. Eventually he found a habanero so spicy that blisters covered his lips after he tasted it. Not a surprise that many mammals avoid eating spicy peppers! Soon thereafter we needed to confirm the absence of the TRPV1 channel in TRPV1-knockout mice. We realized that these mice should not feel the hotness of habanero and would be expected to be able to eat this pepper, whereas “normal” mice (those with a functional TRPV1) should avoid this blister-inducing “poison”. Andras then ran experiments in mice, and these experiments confirmed our expectations. We later published an article about thermoregulation in TRPV1-knockout mice in the Journal of Neuroscience [7], a knockout mouse devouring a habanero stares out at you with hungry eyes from the cover of this issue.


Seppo Ylä-Herttuala


n Academy Professor at the University of Eastern Finland and author of PLOS ONE paper “Short and Long-Term Effects of hVEGF-A165 in Cre-Activated Transgenic Mice [4]”

Looking back at your paper, which was one of the first papers published in PLOS ONE, what did you learn from this study? Did you continue to work in this field and build on these findings?

SYH: We have a long history in therapeutic angiogenesis studies and this PLOS ONE paper was one of the first to realistically study long-term safety concerns of VEGF-A overexpression in vivo. The results were very important since they showed that even a low-level VEGF-A expression in vivo for an extended period of time (> one year) can cause significant side effects, such as cancer, thus preventing the use of vectors leading to long-term transgene expression in clinical VEGF-A studies. Also, Cre-loxP technology was quite new at that time and the paper showed how useful it is for in vivo safety and efficacy studies. We still use this mouse model for retinal angiogenesis studies.

Do you remember when you first heard of PLOS ONE? What made you first interested in publishing with PLOS ONE?

SYH: I think that it was from PLOS website.

For younger researchers, I would say that “Be brave and aim high to reach your vision and goals but be also realistic and prepared for sharp turns and surprises in your research”.

Seppo Ylä-Herttuala

Could you tell us a bit about what you are working on at the moment? What does your lab group look like?

SYH: We are continuing our pioneering work in cardiovascular gene therapy. After several advances in vector design, transgene optimization and improved local cardiac delivery methods, we have continued to apply therapeutic angiogenesis for the treatment of severe myocardial ischemia and have now conducted five clinical phase 1 and 2 trials with adenoviral vectors. Our most recent multicenter trial is currently recruiting patients in five cardiology centers in the EU for the treatment of severe coronary heart disease. We also have a very active research program for new vector development and in VEGF signaling mechanisms. My research group currently has 35 members.

In your field, how common are open science practices? Do you have any success stories of having shared or re-used data, code, a preprint, or something else?

SYH: Open access practices are very common in biomedical and clinical research. Most of our papers are now open access. This is also a requirement of EU and ERC grants which we have had during the last 10 years. Also, we have used open access data archives to identify new non-coding RNAs and gene expression profiles in mouse, pig and human heart and other tissues. From these sources we have identified new short hairpin RNAs and miRs which can regulate endogenous VEGF expression.

PLOS ONE is celebrating 15 years as a journal this year. Can you tell us where you were in your career 15 years ago? If you could give advice to your former self as a researcher, what would you say?

SYH: Fifteen years ago I was a just-appointed professor of Molecular Medicine with a very enthusiastic research program in angiogenesis and cardiac ischemia, extending from VEGF signaling studies to translational and clinical studies. Most of these goals have now come through, albeit with several surprises and new turns in the research direction over the years. For younger researchers, I would say that “Be brave and aim high to reach your vision and goals but be also realistic and prepared for sharp turns and surprises in your research”.

Publishing papers is crucial to a career in research. Can you tell us of an event or memory that was not a paper, which influenced your career as a researcher?

SYH: I so well remember the moment in 1996 when we, as the first in the world, did the first adenoviral gene transfer to human arteries with percutaneous catheter technique. This paved the way for my further research career in angiogenesis and cardiac ischemia.


Author biographies

Miriam Kolko

Miriam Kolko is chief physician and glaucoma specialist at the Copenhagen University Hospital, Rigshospitalet-Glostrup. She is also professor in translational eye research at the Department of Drug Design and Pharmacology at the University of Copenhagen. Prof. Kolko is president of the Danish Glaucoma Society and board member of Fight for Sight, Denmark. During medical school Prof. Kolko completed a Fulbright Scholarship at the Neuroscience Center of Excellence, Louisiana State University, US. Here she became interested in basic neuroscience. After medical school, she completed a Ph.D. and a postdoctoral position in the same laboratory. In 2003, Prof. Kolko returned to Denmark after a total period of 5 years in the United States. She completed another postdoctoral position, after which she underwent residency in ophthalmology followed by a 3-year glaucoma fellowship. From 2014 to 2017, Prof. Kolko directed glaucoma in the Region of Zealand until she was assigned to her current position. At the University of Copenhagen, Prof. Kolko is heading the research cluster “Personalised Medicine”. In addition, Prof. Kolko is heading the research group, Eye Translational Research Unit (EyeTRU). The research in EyeTRU concerns cellular, translational, epidemiological and clinical models for understanding glaucomatous neurodegeneration. Prof. Kolko has received more recognitions. Among these, she has received the first “Award of excellence” from the Danish Ophthalmological Association and the Lions Prize. Prof. Kolko is co-chair of the neuroprotection SIG in the EGS and member of the EGS membership and national society committee. Recently, Prof. Kolko was elected to the WGA, Associate Advisory Board and as EVER glaucoma chair. Finally, Prof. Kolko was elected member of the board of directors of ACTA Ophthalmologica. All in all, Prof. Kolko is one of the few clinician-scientists that bridge between a clinical career with medical and surgical treatment of glaucoma patients and basic and translational research models to understand the pathophysiology behind as well as the current management of glaucoma.

Matthew Goddard

Professor Matthew R Goddard, PhD, BSc hons, DIC, FHEA undertook a PhD and post-doctoral fellowship in evolutionary and ecological biology at Imperial College (Silwood Park), then moved to a Faculty position at University of Auckland (New Zealand) in 2004 and then gain a Professorial position at the University of Lincoln (UK) in 2015. Mat has worked extensively with the agricultural sector and spearheaded microbial ecology revealing the differential distribution of microbes associated with agriculture and how this may effect agricultural outputs. Mat now has a strong focus on soils and runs large scale agri-ecosystem projects fusing next-generation DNA sequencing to evaluate biodiversity (not just microbes) with soil physics and chemistry to both understand the effect of agricultural managements and land-use change to provide evidence to inform decisions by land owners that aim to minimise disease and elevate agricultural and ecological health and quality.

Andrej A. Romanovsky

Andrej A. Romanovsky, MD, PhD, FAPS, is a physiologist and neuroscientist with primary expertise in body temperature regulation. In 2019, he left his Professor position at St. Joseph’s Hospital in Phoenix, Arizona, to work on the development of drugs for disorders of thermoregulation and hot flashes. Dr. Romanovsky helped to found the pharmaceutical startups Zharko Pharma, Catalina Pharma, and Synventa and currently works with these companies as an officer, Board member, or consultant. His current primary affiliation is with Zharko Pharma in Olympia, Washington; he also holds an Adjunct Faculty position at Arizona State University. Dr. Romanovsky has published more than 130 articles in peer-reviewed scientific journals. He is the Editor-in-Chief of the journal Temperature and the Editor of two volumes on Thermoregulation: From Basic Neuroscience to Clinical Neurology published by Elsevier within the Handbook of Clinical Neurology series in 2018. In 2019, he was elected as a Fellow of the American Physiological Society. Andrej’s hobby is tree farming. He has co-founded the family partnership Tree Fever: Forestland Conservation and Development and since 2011 has been operating a Douglas-fir tree farm growing timber in western Washington. He is married to Nancy L. Romanovsky, an oil painter, and they have four children and two grandchildren.

Seppo Ylä-Herttuala

Dr. Seppo Yla-Herttuala, MD, PhD, FESC is a world leader in cardiovascular gene therapy for ischemic diseases. His team was the first to use adenovirus-mediated gene transfer to human arteries already in 1996. Since then, he has conducted five phase 1-2 clinical trials in cardiovascular gene therapy. He is also the originator of the concept of epigenetherapy. His group has been widely recognized for basic biology, translational and epigenetic research of the vascular endothelial growth factors (VEGFs), especially focusing on the new members of the VEGF family. Previously he worked with oxidized LDL and atherosclerosis and was the first to show that OxLDL exists in human atherosclerotic lesions. His list of publications includes over 600 peer reviewed scientific articles.


References

1. Kolko M, Horwitz A, Thygesen J, Jeppesen J, Torp-Pedersen C. The Prevalence and Incidence of Glaucoma in Denmark in a Fifteen Year Period: A Nationwide Study. PLoS ONE. 2015;10(7): e0132048. doi: 10.1371/journal.pone.0132048

2. Goddard MR, Leigh J, Roger AJ, Pemberton AJ. Invasion and Persistence of a Selfish Gene in the Cnidaria. PLoS ONE. 2006;1(1): e3. doi: 10.1371/journal.pone.0000003

3. Almeida MC, Steiner AA, Branco LGS, Romanovsky AA. Neural Substrate of Cold-Seeking Behavior in Endotoxin Shock. PLoS ONE. 2006;1(1): e1. doi: 10.1371/journal.pone.0000001

4. Leppänen P, Kholová I, Mähönen AJ, Airenne K, Koota S, Mansukoski H, et al. Short and Long-Term Effects of hVEGF-A165 in Cre-Activated Transgenic Mice. PLoS ONE. 2006;1(1): e13. doi: 10.1371/journal.pone.0000013

5. Romanovsky AA. The thermoregulation system and how it works. Handb Clin Neurol. 2018;156: 3-43. doi: 10.1016/B978-0-444-63912-7.00001-1

6. Steiner AA, Ivanov AI, Serrats J, Hosokawa H, Phayre AN, Robbins JR, Roberts JL, Kobayashi S, Matsumura K, Sawchenko PE, Romanovsky AA. Cellular and molecular bases of the initiation of fever. PLOS Biol. 2006;4: e284. doi: 10.1371/journal.pbio.0040284

7. Garami A, Pakai E, Oliveira DL, Steiner AA, Wanner SP, Almeida MC, Lesnikov VA, Gavva NR, Romanovsky AA. Thermoregulatory phenotype of the Trpv1 knockout mouse: thermoeffector dysbalance with hyperkinesis. J Neurosci 2011;31: 1721-1733. doi: 10.1523/JNEUROSCI.4671-10.2011

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

Featured image: https://doi.org/10.1371/journal.pone.0000009

The post 15 Years of PLOS ONE – Author Perspectives appeared first on EveryONE.

Cancer and Social Inequity: Interview with the Guest Editors

PLOS ONE has an open Call for Papers on Cancer and Social Inequity, with selected submissions to be featured in an upcoming Collection. The aim is to bring together research that highlights the negative impacts of social inequities on health, identifies the effects of social and corporate policies on access to healthcare services, and proposes solutions to promote more equitable cancer outcomes and ultimately, social justice.

We are thrilled to be working with three distinguished researchers in this field as Guest Editors, who helped conceive this Call and will be curating the final Collection: Prof. Vesna Zadnik (Institute of Oncology, Ljubljana, Slovenia), Dr. Nixon Niyonzima (Uganda Cancer Institute, Kampala, Uganda), and Prof. Claudia Allemani (London School of Hygiene and Tropical Medicine, London, UK).

Technological and medical advances have improved cancer survival although the benefits have not trickled down to many developing countries. Social inequity has widened the gap in cancer outcomes between the rich and the poor. Tackling social inequity will significantly improve cancer survival for everyone regardless of socio-economic status. I am excited about this Collection and publishing in PLOS ONE allows easy access to science all over the world.

Dr. Nixon Niyonzima

Prof. Allemani and Prof. Zadnik share their thoughts on why this topic is important, and their motivations for conducting research in this area.

How does social justice fit within the scope of cancer research?
CA:
Universal access to healthcare, and in this particular context to cancer care, should be a human right everywhere in the world. Every cancer patient should have the chance for an early diagnosis and prompt access to optimal treatment, regardless of where they live or their socio-economic status.

VZ: Researchers in the field of cancer epidemiology and public health address challenges in the field of cancer control in a number of national and international research projects, the results of which enable experts and decision-makers to adopt and implement evidence-based programs at the level of primary, secondary, and tertiary cancer prevention. In recent years, a special focus has been given to research on socio-economic inequalities, which can be observed both within populations and globally.

A close-up view of a catheter (a soft thin tube) placed in an African-American woman's arm to deliver chemotherapy.
Image credit: Catheter for Chemotherapy from National Cancer Institute by Rhoda Baer, Public Domain

Please tell us a bit about your current research and how it ties in with these issues?
CA:
My main interests are world-wide comparisons of population-based survival trends, as indicators of the overall effectiveness of health systems in managing cancer (CONCORD program), patterns of care (VENUSCANCER), and on their impact on policy for cancer control. Differences in patterns of care and survival between countries are often driven by inequalities in access to care, due to the lack of life-saving treatment or to the lack of resources to access it.

VZ: I have co-edited the monograph Social environment and cancer in Europe: towards an evidence-based public health policy published by Springer this year. The monograph addresses the link between the social environment and cancer in Europe. It provides a comprehensive overview of social inequalities in oncology from prevention to survival, offers a comprehensive report of the burden of social inequalities in cancer in Europe, assesses the extent of social inequalities in cancer in Europe based on appropriate data and methodology, and takes an epidemiological approach towards an evidence-based public health policy in Europe for tackling social inequalities in cancer.

Further, I am active within the team that further methodologically develops the European Deprivation Index (EDI) for monitoring and understanding inequalities in health, which is also useful a tool outside of oncology and the healthcare system.

What are the biggest challenges to achieving equitable outcomes in cancer?
CA:
To persuade policy-makers about the need to allocate adequate resources for cancer care, including not only adequate machinery (e.g. radiotherapy facilities), but also trained physicians, especially in low- and middle-income countries (LMICs), where infectious diseases still represent the main priority. COVID-19 has led to about 5 million deaths in two years, but about 18 million individuals are diagnosed with an invasive cancer every year, and about 10 million people die from cancer, again, every year: both numbers are increasing steadily. In addition, policy-makers should support cancer registries to enable routine surveillance of the effectiveness of the health system in managing cancer, and to create a registry for their country if they do not already have one. Without reliable information about inequities in cancer outcome, policy-makers are flying blind.

VZ: The main purpose of public health research in oncology is to provide integrated research and evidence-based cancer control. Completeness, reliability, and quality of data constitute the fundamentals in research. In cancer epidemiology, a major part of research is based on data about patients, their disease and treatment, that are collected by population-based cancer registries. Establishing and maintaining population-based cancer registries is essential, and should be supported by the efficient dissemination of results and their incorporation into the national politics (preferably through national cancer control programs).

A linear accelerator (a large piece of medical machinery) is set up to deliver stereotactic radiosurgery.
Image credit: Linear Accelerator from National Cancer Institute by Daniel Sone, Public Domain

How can open science contribute to overcoming these challenges?
CA:
Open access, as currently mainly supported by Article Processing Charges (APCs), has fees that are not sustainable for researchers in LMICs. It is good that colleagues in LMICs can freely access more articles, but it would be better if they were able to share their local experience with the rest of the world.

VZ: This approach guarantees that new knowledge is made available immediately to the widest possible spectrum of readers. Still, publishing open access supported by APCs is the privilege of well financially supported research teams. In order to maximize the potential impact of the activities and results of the projects implemented by economically deprived researchers, new approaches are needed as well.

[Note from PLOS ONE staff: PLOS is establishing new business models beyond the APC to support more equitable and regionally appropriate ways for all authors to practice Open Access publishing. PLOS ONE offers alternatives to author fees through institutional partnerships. Our Global Participation Initiative and publication fee assistance program are also available to authors who lack publication fee support.]

How has the COVID-19 pandemic affected issues in cancer and social inequity?
CA:
Patients affected by COVID-19 have had priority over patients affected by any other disease, including cancer. The long waiting list to access diagnosis, surgery, chemotherapy or radiotherapy will inevitably lead to a higher proportion of missed diagnoses, patients diagnosed at a late stage, and consequently to poorer outcomes. It has already been shown that people who were already struggling economically have been more affected by the pandemic, increasing the “cancer divide”.

VZ: The COVID-19 pandemic has disrupted the provision and use of healthcare services throughout the world. At several consecutive lockdowns all non-essential health care services were put on hold by a government’s decrees; cancer services were mainly listed as an exception. Nevertheless, cancer management depends also on other health services and additionally major changes in people’s behavior occurred – the effect on cancer diagnostics and treatment during the COVID-19 epidemic is already documented. A sharper fall in the number of referrals for oncological examinations and decrease in the number of diagnostic tests performed is projected for the socio-economically deprived population.

How do you see this field of research evolving in the future?
VZ:
We have been aware for years that the burden of cancer to a large extent typically (but not exclusively) falls on the socio-economically deprived. Every year, many cancer patients throughout the world fall ill or die prematurely precisely because of the socio-economic inequalities in our society. Eliminating these inequalities is therefore going to be the focus of attention for specialists, decision-makers, and the general public for several additional years – researchers should be ready to support these decisions with firm evidence.

About our Guest Editors:

A photograph of Prof. Vesna Zadnik

Prof. Vesna Zadnik is a public health specialist and a Doctor of Science in the field of cancer epidemiology. She is the Head of the Epidemiology and Cancer Registry Sector at the Institute of Oncology Ljubljana, Slovenia.

She directs and carries out detailed epidemiological analysis in order to elucidate a certain condition, e.g. cancer incidence, time series, spatial distribution, survival of cancer patients, efficiency of cancer screening programs, etc. Her special interest goes in explaining socio-economic inequalities in cancer burden.

A photograph of Dr. Nixon Niyonzima

Dr. Nixon Niyonzima is currently a cancer researcher at the Uganda Cancer Institute where he heads research and training. Dr. Niyonzima is also the laboratory director of the laboratories at the Uganda Cancer Institute where he is working to improve access to cancer diagnostics. He is an investigator on several studies on the molecular characterization of cancers in Sub-Saharan Africa (SSA) and development of affordable low-cost diagnostics for diagnosis and prognostication of cancers in resource-limited settings. He is also involved in several initiatives to build health system capacity for cancer care in Uganda.

Dr. Niyonzima qualified as a medical doctor from Makerere University and graduated with a Master of Science in Global Health from Duke University. He did his doctoral studies in Cell and Molecular Biology from the University of Washington before returning to work and undertake cancer research at the Uganda Cancer Institute.

A photograph of Prof. Claudia Allemani

Prof. Claudia Allemani is Professor of Global Public Health at LSHTM. Her main interests are in international comparisons of cancer survival (EUROCARE, HAEMACARE, CONCORD), “high-resolution” studies on patterns of care and short-, medium-, and long-term survival, as well as the estimation of avoidable premature deaths, with a focus on their impact on cancer policy. She has 20 years’ experience in this domain. She is co-Principal Investigator of the CONCORD program for the global surveillance of cancer survival and Principal Investigator of a prestigious European Research Council Consolidator grant to carry out a world-wide study on inequalities in survival from cancers of the breast, cervix, and ovary (VENUSCANCER).

She has published over 150 peer-reviewed articles and 10 book chapters, manuals and reports. Her research has been cited over 13,000 times (h-index 51, i-10 index 76; Google Scholar). She collaborates with the Organisation for Economic Co-operation and Development (OECD) and with several other international agencies, including the International Atomic Energy Agency (IAEA), the World Health Organisation (WHO), the US Centers for Disease Control and Prevention (CDC), the American Cancer Society (ACS), and the French National Cancer Institute (INCa), as well as the European Cancer Patient Coalition (ECPC).

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.


Researchers are encouraged to submit their research to the PLOS ONE Call for Papers on Cancer and Social Inequity by February 22nd 2022.

The post Cancer and Social Inequity: Interview with the Guest Editors appeared first on EveryONE.

Job Hunting with an “Invisible” Disability: A Conversation

Today’s guest post — the second in a series of two — is a conversation between Katy Alexander and Sylvia Hunter about job hunting with a disability in the publishing industry. 

The post Job Hunting with an “Invisible” Disability: A Conversation appeared first on The Scholarly Kitchen.

Some Perspectives on Disability Disclosure in the Publishing Industry

Today’s guest post, by Simon Holt and Erin Osborne-Martin, is the first of two looking at the experiences of people with disabilities in scholarly publishing (the second will be published tomorrow).

The post Some Perspectives on Disability Disclosure in the Publishing Industry appeared first on The Scholarly Kitchen.

Meet PLOS ONE’s new Biogeochemistry Section Editor, Professor Lee Cooper


Join us as we chat with our Editorial Board member and new Biogeochemistry Section Editor Dr. Lee Cooper. Here, he discusses his research in marine biogeochemistry, long-running field campaigns to the Arctic and his view on the importance of Open Science.


Lee Cooper is a Professor at the Chesapeake Biological Laboratory, a part of the University of Maryland Center for Environmental Sciences. His work in the Arctic is centered around understanding how the ecosystem and biogeochemical cycles are responding to climate changes such as the disappearance of seasonal sea ice, with approaches that include the use of stable isotope and other biogeochemical tracers.


Biogeochemistry spans a wide range of scientific disciplines – from soil science to oceanography to atmospheric science. Has serving on the PLOS ONE Editorial Board given you an opportunity to learn more about research outside of your own specific field?

LC: Oh, absolutely. Although as a biogeochemist, I work across many fields, I teach a stable isotope applications course for the University of Maryland, and one thing that is always a constant is how fast the field is changing, and how many new applications are published each year. Working with manuscripts that are applying modern biogeochemical tools can be very challenging because you have to know enough about the disciplinary topic, whether it is food web biomagnification or paleoclimate, or atmospheric chemistry, or whatever, that I think that the maxim that learning never ends really applies to handling manuscripts for PLOS.

What has been your favorite part of serving on the PLOS ONE Editorial Board?

LC:  One of the challenges of course is finding good reviewers who want to contribute to open access scientific publishing, and it is a common complaint among editors about how many potential reviewers will turn you down. I can appreciate that everyone’s time is limited, but on the other hand, if you publish in the peer-reviewed literature, you shouldn’t just have a reflex to turn down review requests because multiple people have taken turns reviewing and improving your manuscripts. But I like turning that whole problem around by searching out people who are underrepresented in the reviewer pool. Maybe they are from countries outside western Europe and North America, or they are early career researchers who names are not well-recognized yet. Identifying those individuals and learning about their research and how they might be in a position to contribute is a very satisfying part of being on the editorial board.

Tell us about your research interests. How does biogeochemistry play a role in your own work?

LC: I work in the Arctic, which of course is undergoing a lot of changes due to climate shifts and so we are seeing a lot of surprising things, fish not seen before coming north, sea ice disappearing and biogeochemical shifts in nutrient cycles too. My specialty is stable isotopes, but I also had the chance while working at Oak Ridge National Laboratory in the 1990’s to contribute to the use of natural and anthropogenic radionuclides in understanding cycling of materials in the marine environment. Stable isotopes are a tool, and often need to be combined with other analyses in order to make sense of the biogeochemical processes at work. So, when we go to sea, I am also involved in collecting water samples for chlorophyll and nutrient measurements, and have interests in dissolved organic materials and the links to water masses in the Arctic and beyond. Oceanography is in the end a rather multidisciplinary research endeavor, so when you mix in biogeochemistry with oceanography, you have to know a bit about most everything.

PLOS recently published a curated collection of stable isotope research. Can you describe how you use stable isotopes in your own work? What new information about spatial and temporal changes can these measurements reveal?

LC: This is a fascinating collection of papers and shows the breadth of research published in PLOS. These are also very state of the art papers, and I highly recommend this special collection for anyone wanting to get up to speed on what is happening in stable isotope methodologies and applications. Clumped isotope analysis for example is a new branch of stable isotope geochemistry that is looking at minor heavy isotope distributions—whether they are random or not, and it turns out that diagnostic interpretations that can arise from non-random distributions are helping to fill in uncertainties in paleoclimate and atmospheric processes. I use stable isotopes in varied ways, including looking at biogeochemical cycles of carbon and nitrogen in sediments in the Arctic and understanding how oceanographic processes influence them. Another theme is to use the oxygen isotope composition of surface sea water to understand how melting sea is influencing ecosystems in the Arctic. Sea ice is isotopically distinct from rain and snow that we normally think of as freshwater, but melting sea ice is also primarily freshwater, so the oxygen isotope composition of that melted sea ice can be distinguished easily in Arctic marine systems.

For you, scientific research has been a family affair. You work closely with your wife, Professor Jacqueline Grebmeier and last year your daughter joined both of you on a research cruise to the Arctic. Do you think that long field campaigns in remote locations are easier when the whole family can be together?

LC: Well, the pandemic has been a challenge for everyone, particularly for anyone doing field research because of the requirements for quarantining ahead of time and making sure no one was bringing the virus aboard a shipboard platform. So, costs in funds and time have gone up significantly and we would see less of our family if we weren’t working together. I know with all the disruptions to field research schedules, that the long absences from families have been hard all around. It also helps even in “normal” times when we get back to them, that researcher couples or families who share complementary research interests and who find ways to work together on projects can accomplish a lot. It won’t work for every case and for everyone in this situation, but I feel that when we merge individual goals and take the “me” out of what we do, it seems like we can get more done and use more tools to arrive at more synergistic results.

You began your career as a researcher in Southern California – how did you transition to research in the Arctic?

LC: I grew up in a well-known southern California beach community and was always interested in plants, whether on land in the dry local chaparral, or in the ocean, but I settled on studying seagrasses, which I like to say are the whales of the plant kingdom, as they evolved on land in the pond weed family and went back to the ocean with an odd set of vascular plant characteristics, pollen, seeds, flowers relative to marine algae. Seagrasses have odd carbon isotope compositions, which probably has to do with their evolution on land and submerged photosynthesis, but I got interested in the ecophysiology that is behind the stable isotope ratios in the 1980’s when I was a graduate student, first at the University of Washington, and then at the University of Alaska Fairbanks. Some of the same seagrass species that grow in southern California also grow in Alaska, so to me, it seemed natural to take advantage of that biological connection between Santa Monica Bay, and Izembek Lagoon on the Alaska Peninsula where my advisor, Peter McRoy had worked for many years. Of course, there isn’t chaparral in Fairbanks, but moving south to north, Sitka Spruce grows from northern California to Kodiak, and there are hints of dry chaparral on Vancouver Island with the beautiful madrone trees there, so for me it was an easy transition, and Arctic research has been central to my work ever since. I came back to UCLA for a postdoc with a great advisor, Michael DeNiro, and he helped fill in a lot of knowledge about stable isotope applications, so I feel a tremendous debt for his mentorship.

You are one of the Principal Investigators of the NOAA/NSF funded Distributed Biological Observatory, a long-running Arctic time series. Can you talk about some of the unique challenges of operating a time series? Especially one that involves researchers from numerous backgrounds and institutes?

LC: We started out with interesting scientific problems about how and why the shallow continental shelf of the northern Bering Sea and the Chukchi Sea is so productive but over time that morphed into studies of how the system was changing in response to climate change. So, like most people with time-series studies, I don’t think we envisioned a 30+ year time-series of biological and biogeochemical data when we started, but that is what we have ended up with through cooperation internationally with others working in the Bering Strait region. We can do more if we work with others and it has been to great satisfaction over the years to see what new insights arise from multiple, leveraged efforts we would never have accomplished just by ourselves.

In addition to open access research, people are now interested in ‘open data’. What do you think the benefits of open data are – and how does open data feature in your own research?

LC: One of the challenges is just getting the data out there for people to use and to make sure all the corrections are made and there is also a lot of work in fielding questions from people who send you emails.  So, I don’t think we have incorporated all the costs in open data access, especially for biological and biogeochemical data. Taxonomy changes, as does precision as instrumentation improves, and data entry errors all come back to bite, so to speak. But I absolutely support making data available at the earliest practical opportunity. This is now formally required in our US National Science Foundation grants, and beyond that it is the right thing to do so that we make the best use of data collected to help society in general or to understand and mitigate climate change in our case in the Arctic.

The post Meet PLOS ONE’s new Biogeochemistry Section Editor, Professor Lee Cooper appeared first on EveryONE.

Introducing the PLOS ONE Energy Materials Collection – Author Perspectives, Part 2


New and modified materials for future energy production, storage and use is an active area of research, where the progress made will shape society and support a sustainable future.  In August of 2021, PLOS ONE published a new collection of Energy Materials papers, showcasing state-of-the-art research in this exciting field. We interviewed some of the authors whose research is part of this collection, in order to shed further light on the discoveries they have made and the challenges they continue to tackle.


Sascha Raufeisen


Sascha is currently a PhD student at Institute of Technical and Environmental Chemistry at the Friedrich Schiller University Jena, Germany. B.Sc. in chemistry (topic bachelor’s thesis: “Synthesis of a thiofunctionalized phosphoramidite for DNA synthesis”). M. Sc. in environmental chemistry (topic master’s thesis: “Investigation of the pyroelectrocatalytic oxidation capability of lithium niobate and lithium tantalate in an aquatic system“). Research focus: new advanced oxidation processes (AOP’s) and combinations (e.g. ultrasound with electrochemistry or photocatalysis) and pyrocatalysis (mechanism elucidation, modelling, application, catalyst development/synthesis) analytical chemistry and water analytics.

Sascha Raufeisen’s paper in this collection: Raufeisen S, Stelter M, Braeutigam P (2020) Pyrocatalysis—The DCF assay as a pH-robust tool to determine the oxidation capability of thermally excited pyroelectric powders. PLoS ONE 15(2): e0228644. https://doi.org/10.1371/journal.pone.0228644

Can you tell us a bit about the beginning of this project that led to your PLOS ONE paper? If you weren’t involved in the study from the start, what was your first impression of the study?

SR: In 2014, I worked on a research module on the topic of electrochemical COD determination as part of my master’s degree in environmental chemistry. During my literature research, I read a lot on the topic of new and innovative advanced oxidation processes. By chance, I came across an article by Gutmann et al. In this article, they presented for the first time a wastewater treatment process based on thermally excited pyroelectric materials. I was immediately fascinated by the underlying mechanism and the prospect of exploiting the huge residual heat potentials in industry for the purification of wastewater. When, by chance, the first author of this study was also working in Jena and we exchanged ideas with him about the topic, I was hooked. I decided to change the topic of my master’s thesis and set out on the stony path of working on a completely new topic. After many missteps, corrections, and minor successes, I finished my master’s thesis with ten times more questions than when I started. Consequently, I decided to investigate pyrocatalysis further as part of my doctoral thesis. In the course of this work, I came to the conclusion that the methodology of the DCF assay needs to be fundamentally revised, which eventually resulted in my PLOS ONE paper.

Pyrocatalysis is a very exciting new research area. Do you envision that it will be possible in the future to apply this to energy generation applications of different kinds, in addition to wastewater remediation?

SR: In my opinion, further potential fields of application are H2 generation and the disinfection of (waste)water. Pyrocatalytic H2 generation could contribute to the supply of industry (e.g. steel production) with sustainably produced H2. Pyrocatalytic disinfection may gain importance especially with regard to future pandemic prevention. At the moment, however, the application of pyrocatalysis in all these three fields of application is highly dependent on the further development of pyroelectric catalysts. The DCF assay presented in the PLOS ONE paper can make a valuable contribution here.

As an early career scientist, how did you prepare yourself for the review process when submitting your first few papers? Is there anything you know now that you wish you’d known before that first submission?

SR: In order to prepare myself, I consulted more experienced scientists at our institute. They explained what I had to pay attention to in the cover letter, the abstract and the introduction. They also helped me with the suggestion of reviewers. The communication with the reviewers went smoothly. The most challenging part of my first two publications was choosing the right journal. With such a new topic at the cross section between environmental/water chemistry and materials science, I received many rejections due to the lack of fit.

What hopes do you have for the future of research into sustainable energy solutions? Do you have a clear sense at this point where you would like to go in your career?

SR: I hope that all industrialized countries will finally recognize that we must increase our efforts extremely in order to slow down climate change as much as possible. An essential point here is the conversion of our entire energy demand (electricity and heat) to a regenerative basis. Since this is not possible with current technologies, research in this area must be accelerated. In addition to storage technologies, I believe that concepts for the use of residual heat must also be further developed. One technique could be pyrocatalysis, which could be used for wastewater treatment and H2 generation at the same time. I want to contribute to this transformation with my research.


Jeremi Dauchet


Jeremi Dauchet is a physicist who received his PhD in chemical engineering in 2012. He is expert in transport physics and radiative transfer in particular (including electromagnetic theory applied to the determination of radiative properties), with special emphasis on the Monte Carlo method. Associate professor at Pascal Institute (France), his research is applied to photoreactive processes engineering.

Jeremi Dauchet’s paper in this collection: Supplis C, Dauchet J, Gattepaille V, Gros F, Vourc’h T, Cornet J-F (2021) Radiative analysis of luminescence in photoreactive systems: Application to photosensitizers for solar fuel production. PLoS ONE 16(7): e0255002. https://doi.org/10.1371/journal.pone.0255002

Can you tell us a bit about the beginning of this project that led to your PLOS ONE paper? If you weren’t involved in the study from the start, what was your first impression of the study?

JD: This work was initiated by experimental results obtained by Caroline Supplis during her PhD. We observed unexpected yet significant impact of luminescence when studying bio-inspired H2 production in a benchmark photoreactor. The analysis of those experiments led us to carry the thorough radiative study presented in our PLOS ONE paper.

We noticed that you shared your Monte Carlo algorithm with your PLOS ONE paper. What motivated you to do this? Do you have any experience of using other researcher’s code from publications, or know of anyone who has used the code you’ve shared?

JD: Indeed, we are dedicated to open research and distributing open source codes and databases is part of that approach. We often provide the codes used in our publications as supplementary material or as links directed to our websites. Ensuring that these codes and databases will be available to readers in the long run is a concern. We know that our codes and databases are used by other researchers because they contact us when they need advises (or when it is no longer available at the provided url!). When those codes are mature enough, we work with Meso-Star for software development, support, maintenance, integration and distribution under GNU general public license (www.meso-star.com/projects/misc/about-en.html). Conversely we routinely use other researcher’s codes, for example the famous Mie code for electromagnetic scattering provided by Craig F. Bohren and Donald R. Huffman as an appendix in their book “Absorption and Scattering of Light by Small Particles”.

Was there anything that surprised you during this study, or did everything go exactly according to plan?

JD: This entire study had not been envisaged when Caroline’s PhD research-plan was being drawn up! Photoreactive processes are controlled at different scales by radiative transfer and therefore, we knew that radiative analysis will be an important part of the work. But we did not anticipate such significant effects of luminescence, which led Caroline to 3 years of investigations.

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

Featured image: https://doi.org/10.1371/journal.pone.0243296

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Introducing the PLOS ONE Energy Materials Collection – Author Perspectives, Part 1


It is difficult to overestimate the importance of the role that advances within the science of energy materials may play in our lives over the next few decades. As the world grapples with the challenges of increasing energy demand and dynamic usage patterns, the community of scientists developing materials for future energy production, usage and storage are a vital part of building a sustainable future. In August of 2021, PLOS ONE published a new collection of Energy Materials papers, showcasing state-of-the-art research in this exciting field. We interviewed some of the authors whose research is part of this collection, in order to shed further light on the discoveries they have made and the challenges they continue to tackle.


Rosa Mondragón


I have a PhD in Chemical Engineering from Universitat Jaume I in Castelló (Spain). I defended my PhD thesis about spray drying of nanofluids in 2013 and that was my first experience with the amazing field of nanofluids. I am currently Associate Professor in the Fluid Mechanics area of the Department of Mechanical Engineering and Construction in Universitat Jaume I and I belong to the Multiphase Fluids research group. My research is focused on the synthesis and characterization of nanofluids for heat transfer, thermal energy storage and solar radiation absorption applications. I have been participant member of the COST Action “Overcoming Barriers to Nanofluids Market Uptake – NANOUPTAKE” (2016-2020) whose objectives were the development of a common understanding about nanofluids preparation and characterization and the acceleration of the transfer of knowledge from fundamental research to industrial applications.

Rosa Mondragon’s paper in this collection: Mondragón R, Sánchez D, Cabello R, Llopis R, Juliá JE (2019) Flat plate solar collector performance using alumina nanofluids: Experimental characterization and efficiency tests. PLoS ONE 14(2): e0212260. https://doi.org/10.1371/journal.pone.0212260

Can you tell us a bit about the beginning of this project that led to your PLOS ONE paper? If you weren’t involved in the study from the start, what was your first impression of the study?

RM: I began my research on nanofluids for heat transfer applications in 2010 but after some years doing experimental characterization of thermophysical properties at the lab scale (thermal conductivity, viscosity, specific heat, etc.) we needed to move towards the analysis of its use in real applications. The only difficulty was to find any research group having the suitable facilities to start a joint collaboration. Besides, most of the facilities required quite a big volume of fluids making also a challenge sending the nanofluid to a different research centre. Fortunately, we found out that the Thermal Engineering research group of our department had recently acquired a flat plate solar collector that could be used. That was the beginning of the project that led to the paper published and some lessons learnt.

What is it about nanofluids that make them such a good candidate for use in solar collectors?

RM: The term nanofluid was coined to refer to the mixture of nanoparticles dispersed in a base fluid with improved thermal properties, specifically thermal conductivity. This thermal conductivity enhancement achieved due to the higher thermal conductivity of the solid nanoparticles leads to an increase in the heat transfer capacity of the fluid and the efficiency of the solar collector. However, there are more variables involved in the process such as the decrease in the specific heat capacity or the increase in the viscosity. As a result, a combined experimental analysis of all the nanofluid thermophysical properties is necessary to ensure a better performance of the nanofluid in transferring the thermal energy obtained from the absorbed solar energy, compared to the base fluid. It is also worth mentioning that there exist a wide variety of nanoparticles with good thermal properties, inexpensive and non-toxic that can be selected.

Was there anything that surprised you during this study, or did everything go exactly according to plan?

RM: Of course not everything went exactly according to the plan but it comes with the experimental research. We had a previous experience using the nanofluid in a thermohydraulic loop and we knew that the compatibility with the materials in pipes and pumps was very important to avoid oxidation and corrosion. If the solar collector was made to transport water, the addition of the nanoparticles should not have caused any problem. However, the acidic conditions needed to stabilize the nanoparticles in water promoted the oxidation of the materials and the corrosion of the copper tubes. Moreover, the contact of the concentrated nanofluid with the hot surface of the tubes caused a deposition layer as is shown in the paper. As a result, the enhancement theoretically predicted for the solar collector efficiency was not achieved due to the thermal resistance caused by the nanoparticle layer. The nanofluid initially white became orangish after the tests which confirmed that is highly recommended to check the compatibility of the nanofluid with the materials of the experimental facilities to ensure a good performance and to achieve the best results.


Bernhard Springer


Bernhard Springer, M. Sc. is currently a research associate at University of Applied Sciences Landshut (UAS Landshut) and a PhD student at Technical University Munich (TUM). He studied physics at the TUM from 2011 and finished his Bachelor’s degree in 2015. From 2015 till 2017 he studied Applied and engineering physics at the TUM and finished with a Master’s degree. Since 2017 he is working as a research associate at the Technology Centre Energy affiliated to the UAS Landshut. In 2018 he started with his PhD studies at the chemistry department of the TUM. Since 2019 he is working with his colleagues on the Project “SpinnAP”. His fields of research include Electrospinning, Lithium-Ion-Batteries  and solid-state electrolytes.

Bernhard Springer’s paper in this collection: Springer BC, Frankenberger M, Pettinger K-H (2020) Lamination of Separators to Electrodes using Electrospinning. PLoS ONE 15(1): e0227903. https://doi.org/10.1371/journal.pone.0227903

Can you tell us a bit about the beginning of this project that led to your PLOS ONE paper? If you weren’t involved in the study from the start, what was your first impression of the study?

BS: The project leading to my publication is “Spinning Technologies for Advanced Battery Production” (SpinnAP) and is funded by the Bavarian Research Foundation. The project aims to improve lithium ion batteries, both liquid and solid electrolyte systems, using electrospinning. An example for such an improvement is to enable lamination on different separators using electrospinning, like described in my paper. In addition, suitable production processes as well as an improved nanofiber output for industrial applications are part of our development focus. To achieve this, we also develop our own high-output electrospinning machine within the frame of the project. We are supported by our project partners 3M Dyneon GmbH, AKE Technologies GmbH and Brückner GmbH with their respective expertise.

Electrospinning seems like a very promising method for the future of lithium ion batteries. What do you think are the main advantages this can bring to the consumer or user of lithium ion batteries?

BS: For lithium ion batteries using a liquid electrolyte, lamination can achieve two main advantages: First, lamination is able to improve the charge and discharge capability, as shown by Frankenberger et al (https://doi.org/10.1016/j.jelechem.2019.02.030). Unfortunately, not all separators are capable for lamination. Using electrospinning we want to enable lamination for all types of separators to combine the advantages of lamination with the advantages of the respective separators, e.g. lower production costs or safety enhancement. Second, lamination creates a firm connection between the electrodes and the separator. This can be positive for the production speed of the cells, since the individual layers can not be displaced during the following production steps. This can lead to an increased production output and more inexpensive battery cells.

As an early career scientist, how did you prepare yourself for the review process when submitting your first few papers? Is there anything you know now that you wish you’d known before that first submission?

BS: In preparation to my first submission, I intensely discussed with my colleagues from the Technology Center Energy, a research facility of the University of Applied Sciences Landshut, about their previous experiences. In addition, I read the guidelines provided by PLOS regarding the submission process carefully.

What hopes do you have for the future of research into sustainable energy solutions? Do you have a clear sense at this point where you would like to go in your career?

BS: I do not have a clear sense where I would like to go in my career yet, but I do intend to pursue an industrial career path. At the moment I strongly focus on my dissertation.


David López Durán


David is Professor in the Department of Physics of the University of Córdoba (Spain). He obtained the MSc degree in the Complutense University of Madrid (Spain), and his PhD in the Fundamental Physics Institute (FPI) of the Spanish National Research Council (SNRC) in Madrid. He has developed his work in La Sapienza, University of Rome (Italy), Argonne National Laboratory, IL (USA), and CIC Nanogune, San Sebastián (Spain), among others. His research topics are: weakly bound molecular clusters, collisions of molecules at low and ultralow temperatures, and potential energy surfaces of small molecular aggregates. Some recent scientific contributions are: (1) “The CECAM electronic structure library and the modular software development paradigm”, J. Chem. Phys. 153, 024117-1/024117-23 (2020) article promoted as part of the “Chemical Physics Software Collection” of the Journal of Chemical Physics (September 2021), and (2) interview in TV (May 2021): https://www.youtube.com/watch?v=HJ71JPVdhtw

David López Durán’s paper in this collection: López-Durán D, Plésiat E, Krompiec M, Artacho E (2020) Gap variability upon packing in organic photovoltaics. PLoS ONE 15(6): e0234115. https://doi.org/10.1371/journal.pone.0234115

Can you tell us a bit about the beginning of this project that led to your PLOS ONE paper? If you weren’t involved in the study from the start, what was your first impression of the study?

DL: This article came up as part of the work supported by the “Centre Européen de Calcul Atomique et Moléculaire” (CECAM), which is formed by several institutions in Europe and funds multiple activities, one of them a partnership between some of these institutions, network called “E-CAM”, and to which I belonged. One of the targets of E-CAM was to bring closer the academic and the industrial worlds through several initiatives, for instance a collaboration between two nodes with different profiles. This manuscript came up due to the work developed in my former institutions, CIC Nanogune (San Sebastián, Spain) and University of Barcelona (Barcelona, Spain), and the industrial partner Merck Chemicals Ltd. (Southampton, United Kingdom). The climate change and global warming are, unfortunately, a hot topic in science and we tried to contribute to its solution studying organic photovoltaics. Specifically, we addressed the problem of the arrangement of the molecules in order to maximize the electric current.

How do you think that the results you obtained in this study will impact the development of organovoltaics in the future?

DL: The design of a device to generate energy based in any kind of photovoltaic molecules must include the analysis of several factors in order to obtain the maximum performance. One of them is the HOMO-LUMO band gap of the constituent molecules, which are usually a donor-acceptor pair, magnitude which dramatically depends on the geometry arrangement of these pairs. As this gap becomes smaller, the electronic transference is easier and, therefore, the generation of electric current. But to be small this gap is necessary that the molecules were arranged in a convenient way one with respect to the others, i. e. with their active electronic areas clearly accessible. In this work we study a great number of configurations of an organic donor-acceptor pair in gas phase, as previous step before moving to the solid phase of a real device. Our study will impact the subsequent research because now there are available some hints about the optimal geometry configuration of the molecules.   

Was there anything that surprised you during this study, or did everything go exactly according to plan?

DL: The donor-acceptor pair that we studied is 4modBT-4TIC, molecules which are based on others extensively employed in the organic photovoltaics field. We found several surprises, the first one being that the variation of the gap in all the studied configurations was around 0.3 eV, which is significant considering that the gaps in this context are not larger than 1 eV. The second surprise was the lack of correlation between the binding energy of the pair and the HOMO-LUMO band gap: the arrangement with the maximum binding energy was not that with the maximum gap and, in turn, the configuration with the maximum gap was not that with the maximum binding energy. A third surprise was that the arrangement with the maximum binding energy were much more bound that the rest. All these findings pose new questions and, therefore, further research is needed.

What’s the most unusual or unexpected collaboration you’ve been a part of during your research?

DL: I have never had an unusual or unexpected collaboration during my scientific career. However, I would like to mention that I feel very lucky because I have known people from all over the world. These experiences enrich you and make you think in a more broad and comprehensive way.

Disclaimer: Views expressed by contributors are solely those of individual contributors, and not necessarily those of PLOS.

Featured image: https://doi.org/10.1371/journal.pone.0243296

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An Interview with PLOS ONE Editorial Board Member, Professor Tara Mastren


As we launch our curated collection of Radiochemistry research we chat with Dr. Tara Mastren about her work in nuclear medicine, life as an Early Career Researcher, and Open Science.


Dr. Tara Mastren is an Assistant Professor in the Nuclear Engineering Program at the University of Utah. She obtained her PhD in Nuclear and Radiochemistry at Washington University in St. Louis in December 2014. She then worked in the Radiology Department at the University of Texas Southwestern Medical School as a postdoctoral researcher. In May 2016 she joined Los Alamos National Laboratory, for her second postdoc, in their Isotope Production Program. Dr. Mastren’s interests are focused on the production and use of radionuclides for the targeted treatment of cancer and other diseases.


Radioisotopes are utilized in a vast array of research fields. Do you think the breadth of the applications affects advances/progress in analytical techniques using these elements? Is there opportunity for interdisciplinarity amongst the various radiochemistry-related fields? 

TM: Yes, I believe as the field of radiochemistry and its techniques become more well known more researchers will see the advantage of using radionuclides in their research. There is a lot of opportunity for interdisciplinary research amongst the various radiochemistry-related fields. For instance, radiochemical separations overlap a multitude of fields including medicine, forensics, and fuel reprocessing.

How did you become interested in nuclear and radiochemistry?  

TM: Like many I was not exposed to nuclear and radiochemistry in high school or during my undergraduate study. When I attended graduate school, my original plan was to study biochemistry.  One day, however, I attended a professor’s lecture on nuclear reactions in stars and I was intrigued. I went to speak to him about research and he discussed with me a possible opportunity to apply nuclear research to medicine and I got excited about it. I have been a radiochemist ever since.

For many researchers, the use of radionuclides, especially alpha-emitters, demands a high level of meticulous care. Does your field require this level of fastidiousness and what if any precautions do you take in working with these materials? 

TM: Yes, working with radioactivity is a huge responsibility. We undergo lots of training to work with these materials plus have the appropriate radiation detection and dosimetry in place to make sure we are working safely. Work with radionuclides is highly regulated, requires a lot of training, internal safety audits and regulation at the state and/or national level. 

Your own research focuses largely on the new and emerging field of Targeted Alpha Therapy. Can you explain what this is, how it utilizes radionuclides, and what potential it has as an effective cancer treatment? 

TM: Targeted alpha therapy (TAT) has been of interest to nuclear medicine for decades; however, its popularity has grown significantly in recent years as a methodology of interest for cancer therapy. In TAT a highly energized alpha particle emitted during decay is used to induce cell death in cancer cells. An alpha particle is a fully ionized helium atom that is emitted from the nucleus during decay. These alpha particles travel ~10 cell lengths; depositing their energy and destroying the cells throughout their path. The alpha emitting radionuclide can be attached to a biological molecule that acts as a mailman delivering the radioactivity directly to the cancer sites, which maximizes the dose to cancer cells while minimizing the impact to healthy tissues. TAT has shown great promise in cancer therapy – in a study by Kratochwil and colleagues in the Journal of Nuclear Medicine1 patients with stage 4 prostate cancer have gone into remission after several treatments with TAT. These results have caused a lot of excitement in the field and jumpstarted additional research for the use of TAT in other cancer types.

Can you tell us about any new and exciting projects you’re working on? What do you foresee as the next step in your research journey? 

TM: I am working on projects that involve using nanoparticles for the advancement of TAT. One project is aimed at containing the daughter radionuclides at the cancer site to increase cancer cell killing effectiveness. Several of the alpha emitting radionuclides of interest to nuclear medicine have a cascade of alpha emissions. Each alpha emission results in the formation of a new “daughter” radionuclide. As alpha decay is high in energy, the daughter recoils, traveling ~100nm. This can cause the daughter to be released from the cancer site, increasing the dose to healthy tissues. Encompassing the radionuclides in a nanoparticle can help to mitigate this issue. We have successfully made nanoparticles containing alpha emitting radionuclides, and our next step will be to study them in vitro for their stability and cancer killing abilities.

What are the biggest challenges you currently face as an Early Career Researcher? 

TM: One of my biggest challenges as an Early Career Researcher is learning time and management skills. We aren’t really taught to manage people during our education and becoming an Assistant Professor one of the biggest parts of your job is managing graduate students and postdocs. Additionally, you wear many hats; instructing classes, mentoring students on research, writing grants, creating and using budgets, internal and external service, and making sure all research is conducted safely. It’s a big job that no one prepared you for, but it is also so very rewarding when you observe the progress that is being made as you watch your students evolve into independent scientists.

What are your thoughts on Open Science, and in what ways has your research community embraced this philosophy? (e.g., publishing in open access journals, making data available in public repositories, etc.). 

TM: I think that Open Science is the future of publishing. It grants access to information to students and countries that otherwise would not have access. I believe that increasing access to science and research is important for the betterment of society. As a graduate student and post doc, my advisors embraced open access journals and several of my publications have been in these journals. I also see more and more of my colleagues publishing in these journals. I believe as these journals become more popular more scientists will feel comfortable publishing open access.


1Kratochwil et al., 225Ac-PSMA-617 for PSMA targeting alpha-radiation therapy of patients with metastatic castration-resistant prostate cancer, Journal of Nuclear Medicine, 2016.

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