An Interview with Biogeochemist Alex Cory

Posted on March 18, 2022 by Natasha McDonald

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/CH₄production 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

Posted on March 1, 2022 by Natasha McDonald

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

Posted on January 27, 2022 by Natasha McDonald

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.**

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 CO₂concentrations. 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

Posted on December 14, 2021 by Carla Pegoraro

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 ID – 0000-0002-3634-6973.

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 ID – 0000-0001-7260-2447

Affective Computing and Human-Computer Interactions Collection

Submit now to PLOS ONE

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Amphibians and reptiles on the edge: An interview with intrepid PLOS ONE authors

Posted on April 9, 2021 by Jamie Males

Amphibians and reptiles are among the world’s most extraordinary and most threatened animals. In this post, we highlight work recently published in PLOS ONE by Rivas and colleagues, which probes the diversity of species in an understudied region at the northernmost extremity of South America. We spoke with the authors about their research and its broader context.

What was the motivation for your study?

Initially, the study aimed to understand the composition of the reptiles and amphibians of a region in northeastern Venezuela, namely the Paria Peninsula and surrounding mountains. However, along the way, many other questions stared emerging concerning the composition and faunal relationships of the whole region, so we aimed to compare the herpetological composition of all the northernmost coastal mountains of South America, ranging from northeastern Colombia through Venezuela to the Caribbean islands of Trinidad and Tobago, totaling about 1000 km east to west.

Map of northern South America showing locations of the sampling sites. pone.0246829

How did you get to the sampling locations? Were there any challenges with the fieldwork?

We sampled in eastern Venezuela (Paria Peninsula), which had already been visited by some of us for about 20 years. We visited some locations in central and western Venezuela, and we had exhaustive literature records and museum revisions at our hands. Similarly, records from Trinidad and Tobago were available from three decades of field trips carried out by some of us as well as through the University of the West Indies and Glasgow University students and staff members. This study was only possible though decades of expeditions and fieldwork in the region by several of the authors of this paper. There were many challenges, especially in Venezuela, such as those related to transport, lack of fuel, increased travel costs, insecurity and remoteness of some of the sampling sites. Fortunately, safety was always supported by local agencies and communities in eastern Venezuela. In addition, funding was at the time lacking or limited for fieldwork in Venezuela and Trinidad, and travel expenses at times were privately funded by ourselves.

Could you briefly describe the key findings of your study and their importance? Were there any surprises?

This is the first study to address the biogeographic patterns of any vertebrates in the region at this scale. We ultimately recorded a total of 294 native species distributed above 200 m in elevation along all the mountain systems. The biogeographic composition supports close species associations for both reptiles and amphibians within regions, such as western areas (northeastern Colombia and western Venezuela) versus eastern localities (eastern Venezuela and Trinidad and Tobago). Our biogeographical findings support the geological history, with the whole region once being a mountain chain that connected all the way up to Tobago, and biogeographical patterns following a natural topographic disposition. However, when we compared species at high elevations, the arrangements were more unstable, with lower numbers of species shared between areas and a minimal association between areas. This suggests that faunal patterns at higher elevations represent more exclusive species which are less useful to assess biogeographic relationships in the region. Overall, the high diversity of reptile species found throughout the study area reflects their dispersal capability and the presence of habitat generalists when compared to the more restricted and ecologically constrained amphibians.

Vegetation in Venezuela’s northernmost montane coastal systems. pone.0246829

What are the main threats to species and ecosystems in the region?

In northern Venezuela the habitat loss is mostly due to logging, illegal crops, and livestock, and to a lesser degree mining, particularly in lower and medium elevations in some mountains. In eastern Venezuela, the most threatened environments are the cloud forest, and it’s increasingly common to find local crops, even within protected areas, putting pressure on the very much depleted hydric resources of some areas. We have encountered small-scale crops at elevations of up to 1500 m. More worrisome is the fact that several illegal crops do not even belong to local villagers but to farmers from the lowland towns, which are increasingly looking for higher and fresher locations for their crops. Low altitude tropical cloud forests such as those found in the Paria Peninsula and in Trinidad are among the most vulnerable terrestrial ecosystems to climate change. Some cloud forests have exceptional low altitudinal ranges and require detailed species inventories, population assessments, and the establishment of new, well-run national parks to protect biodiversity. In addition the lack of scientific funding in the region is limiting the understanding of this biodiversity hotspot.

How can scientific research help us better understand and protect biodiversity in this region?

This and previous studies undertaken by some co-authors are increasingly important to understand the importance of these ecosystems on a wider scale. These mountains can be viewed as the northeastern natural extension of the Andes chain, but due to their relatively low altitude, they have been undervalued in terms of their biodiversity and biogeographical relevance. In addition, surveys help establish species checklists and report on endemism in the region. Taxonomic studies based partly on phylogenetic analyses are key to assess the high rate of cryptic species in the region. Through species descriptions, understanding of population ranges and biogeographic barriers can help establish new areas that need protection. Furthermore, there seems to be little research on ecological studies at a broader scale in the region. In addition, little is known in this region compared to that of The Guianas or Brazil.

Future research should have an important conservation component, as well as the involvement of citizen research. Environmental education with a strong conservation focus must be a priority and be consistently delivered to local communities, which also applies to most Venezuelan national parks. Finally, ecotourism could help establish new sources of income in the region, although the political, economic and safety situation in Venezuela, and to a lesser degree in Trinidad, are obstacles to its development. An important contribution to the preservation of the national parks would be to finish the zoning rules and increase the expansion of some parks. New surveys and effective and consistent monitoring of the parks and other areas are urgently needed in Venezuela.

Some Trinidad amphibians and reptiles. pone.0246829

What is the importance of Open Access for your field of research and the regions where you work?

Without Open Access this research would be visible to a limited audience, mostly within academic institutions in the developed world, and not to local policymakers and scientists.

What should be the priorities for future research in this area?

As mentioned earlier the understanding of species distributions and identification is key to understand if the national parks’ delimitations are correct and if new areas should be protected. Application of molecular techniques will be a priority as much local research is based on the more traditional sciences, and there seems to be a lack of capacity in molecular techniques in Trinidad and Tobago and Venezuela. Universities should benefit from a new generation of researchers that are specialized in contemporary ecological, conservation and molecular techniques. Throughout the elaboration of this study, we had to compile a great amount of available literature on the region and it soon became apparent that most works from Venezuela were on average several decades old and some pioneering works in the region had no follow-ups since their publication. This is a reminder of the poor understanding of biodiversity in the region, in part due to the challenging socioeconomic circumstances.

Reference

Rivas GA, Lasso-Alcalá OM, Rodríguez-Olarte D, De Freitas M, Murphy JC, Pizzigalli C, et al. (2021) Biogeographical patterns of amphibians and reptiles in the northernmost coastal montane complex of South America. PLoS ONE 16(3): e0246829. https://doi.org/10.1371/journal.pone.0246829

Featured image:
El Tucuche, Trinidad- Jamie Males.

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From Collecting Sediment Cores in Iceland to Mentoring Students: The Busy Life of an Early Career Researcher

Posted on April 1, 2021 by Natasha McDonald

Have you ever wondered what life as an early career researcher entails?

From managing a lab group and mentoring PhD students, to applying for funding and leading intensive fieldwork campaigns, scientists in the early stages of their career do it all.

Here, we chat with Dr. Margit Simon from NORCE Climate and Bjerknes Centre for Climate Research and recent PLOS ONE author to find out more about her exciting work.

PLOS: Your recent work, published in PLOS ONE, investigated stable isotope data from a new marine core collected off of Iceland – how did using data with such a high temporal resolution (1-2 years) impact what we know about water mass changes?

MS: Marine sediment cores that have such high-resolution are still a quite rare finding globally. For that specific area, it was a new finding that the upper core section – the youngest sediment part – could resolve the historic time interval so well. Mostly, that is only possible with schlerochronological records, of which there are a few around Iceland actually. We found a good correspondence with the measured phosphate concentrations within the water column – a comparison only possible because we have such high temporal resolution. Stable carbon isotopes in planktonic foraminifera are influenced by a variety of factors and are normally not so easy to interpret. By constraining the influences on the carbon isotopes by comparing to modern measurements, we were able to detect an intermittent 30-year cycle over the entire time series length, that is likely reflecting the ocean response to atmospheric variability, presumably the East Atlantic Pattern. That was not known or found before in that area.

PLOS: Has your data highlighted changes in climate over the past 150 years? What impact have these changes had on ocean variability?

MS: What I was intrigued to see was the long-term trend in benthic δ18O, a proxy recording the water mass properties in the intermediate waters at that location. It suggests that Atlantic-derived waters are expanding their core within the water column, from the subsurface into deeper intermediate depths, towards the present day. That there is greater Atlantic-derived water mass influence in the surface waters offshore of NW Iceland over the past 150 years is well known by now. However, until now, we did not know that this process is also influencing the deeper realms in the water column contemporaneously. That was a new finding.

PLOS: What are some of the challenges of being an Early Career Researcher? Do you feel that these are mitigated by the specific opportunities for ECRs?

MS: Well, securing funding short-term and long-term for my position itself, but also for my research activities is challenging, as the field becomes more and more competitive. Basic research has to be very innovative and impactful to get funding these days. Hence, I am wondering how sustainable the system is over time. I would wish for some more basic funding security or baseline funding in the private research institute section in Norway.

PLOS: You’ve done fieldwork in a number of exciting locations – from Iceland all the way to Southern Africa. Do you have a favorite location? Were there any sampling campaigns that were particularly challenging?

MS: They were all very special and exciting. Despite the Greenland Ice sheet probably being the most ‘exotic’ one that I have been to, my favourite place remains Africa, or specifically South Africa. The most challenging sampling campaign was in Mozambique as part of a wider trip from Zambia to South Africa with the aim to collect modern day river sediments.

PLOS: Field work in many research areas has been delayed or postponed in 2020 due to the Covid-19 pandemic. Were your fieldwork plans affected? And if so, how did you regroup?

MS: I was part of a marine sediment coring campaign offshore South Africa in the beginning of 2020 and retrospectively, I am very happy that we managed to do everything as planned. How little did we know then what was coming! Parallelly on land in South Africa, my project partners did field work, field experiments and excavated archaeological sites that had to be stopped due to COVID-19. This affected me in the sense that I could not get the samples I had hoped for, and we will need to postpone that to approximately Nov/Dec. of this year (2021). It is obviously still unclear if then we can operate again with a kind of normalcy.

PLOS: Now that you have PhD students of your own, is there a particular strategy you take in mentoring them? How do you prepare them for to be Early Career Researchers themselves?

MS: Well, I don’t have a rocket science strategy in place, but I think it is important to be there for them for questions, reviewing and to bounce ideas. I think nothing is worse than when you don´t have someone that you can frequently go to and ventilate ideas and perhaps also frustration. I think when you are in your PhD yourself you might underestimate the value of someone actually taking the time to read your work and give thoughtful feedback back. I think further down the line of your career path that becomes rarer and you think back on those times where your supervisor always gave comments.

PLOS: The University of Bergen and NORCE are hubs of scientific research – how has being in such a diverse group of expertise helped your own work? Do you find yourself collaborating with people in different fields from your own?

MS: Definitely. Before moving to Norway and becoming a part of the Bjerknes Centre for Climate Research, I worked in smaller groups that are more specialised in one field. That is, of course for your own work, very beneficial. However, I recognised that the centre here and the diverse groups and topics really offer new opportunities to merge and reach out and broaden your topic. I have very much benefited and used that platform for my science ever since.

PLOS: What new projects do you have on the horizon?

MS: As much as I am fascinated by the ocean and reconstructing its past variability on various timescales, I am excited about my new project ideas that aim to reveal past climate information from land or specifically from South Africa itself. What is new is that I target specifically archaeological cave sites where we can extract environmental information from the same layer that the material culture information comes from. Key behavioural innovations emerged among Homo sapiens in South Africa around 120 ka ago and the drivers of this development remains debated. One hypothesis is centred around climate changes.

PLOS: As you know, PLOS ONE is an open access journal, and is devoted to promoting open science. We would be curious to know your thoughts and opinions on open access and/or open data and the importance of these concepts for researchers, particularly early career scientists.

MS: I think both are extremely important especially for ECRs, for different reasons.

It might be rather difficult if you are an “unknown scientist” to get access to data if that is not stored at an open access source. That might of course also cost you more time and delay the activity you are working on, while a more known scientist might have asked the same question and might have gotten the data already the next day. Especially currently, during COVID-19 times, universities are conducting more and more data synthesis projects as e.g., master’s projects for students since laboratories are closed. Hence, it is of vital importance to have access without barriers to this. I think data storage facilities like PANGEA are crucial and I think the movement in the community in the last years to use these platforms more and more is great and should be pursued. In this respect, I also appreciate and used recently myself the opportunity to publish data sets only in peer-reviewed journals. It ensures good quality control on the data published but does not force one to interpret the data. Still, one can gain credit for the work. Importantly, data such as this is also available to the community that otherwise might have been hidden in a drawer.

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Author Interview: Sacha Gómez Moñivas on student learning despite COVID-19 confinement

Posted on March 18, 2021 by Jack Kennedy

Using prior academic years as a control group, Sacha Gómez Moñivas and a group of fellow teachers and researchers found that despite the confinement caused by COVID-19, the learning habits of students became more continuous and ultimately led to better scores during assessments. Their study “Influence of COVID-19 confinement on students’ performance in higher education” was one of the highest viewed PLOS publications of 2020 with over 150,000 views. Read our interview with Sacha about his team’s initial response to the surprising results, the importance of providing details to replicate a study and the difficulties in collecting data on student learning.

Would you say this study is outside the scope of your normal research? How did you get involved in this study and why do you believe this research is important?

Our main research line since 2015 is related to new learning methodologies. Within this topic, we study in detail distant learning, among others. When the COVID-19 pandemic forced most of the students stay at home and change their learning strategies, we were completely prepared for this scenario because, by that time, we had already developed different tools and methods of distance learning already applied in our subjects.

We were involved in this study by analyzing and comparing the huge amounts of data obtained in previous years in our pilot experiences applying distant learning with the new data obtained during the COVID-19 pandemic. We were following the same research line as before, but in a new scenario.

This research is important because it is related to the Sustainable Development Goal 4 of UNESCO. More specifically, this research helps us understand the impact of COVID-19 in education and students’ capability to change their learning strategies. It is also important because COVID-19 pandemic has many specific factors that can interact with the previously detected relevant characteristics of distant learning. For example, does student motivation behave in the same way in the pandemic as in a traditional distance learning setting?

I want to send an optimistic message in this case. We have demonstrated that, even in this very difficult situation, students and teachers were able to adapt their strategies in the learning process successfully

Read Sacha’s article

Did you find the results to be generally surprising, or were they relatively in line with your expectations?

Some results were in line with our expectations since, ultimately, distant learning is distant learning. For example, the limited access to technology by the students is a problem that was well-known before. Of course, it also appeared in the COVID-19 confinement. The problems that appear when preparing assessment tools are indeed also present in the pandemic.

There are, however, other elements that appeared and were a huge surprise. For example, the improvement in students’ performance was unbelievable. We spent a lot of time trying to justify it with arguments related to fraudulent behaviors, such as cheating or copying in different forms. For that reason, we discarded many subjects where we considered that we could not fully exclude the possibility of cheating. After that, we still had three subjects where we could be sure that only confinement was related to the increase in students’ performance.

Your Results state that “the new learning methodology is the main reason for the change in students’ performance during the confinement.” How important is it for leadership bodies at institutions and schools to provide teachers with resources to properly implement new teaching practices adapted for less face-to-face interactions?

It is crucial. The first step for a good teaching practice is having a good communication between teachers and students. If that fails, everything fails. In distant learning, teachers should have good multimedia resources and connectivity, at least. If not, it does not matter the amount of material developed by the teacher or how good the teacher is when explaining a lesson. I have seen a lot of very good attempts of developing new and very well-organized online courses that failed at the very beginning due to not having the adequate resources.

I note that you opted to publish a preprint when you initially submitted this paper for review, and that you published your peer review history alongside your PLOS ONE publication. What led you to these decisions and how important is scientific transparency to you?

We believe that scientific advances must follow FATE principles: fairness, accountability, transparency and ethics. Transparency is, actually, a key factor in the scientific method itself. If a scientific result must be replicable, it should include all details about experimental procedures, materials, etc. Obviously, transparency is a must. In the case of scientific publications, the whole peer review history is very important for two reasons. First, it demonstrates that the article followed a rigorous peer review process. Second, it gives valuable information about the questions raised by the reviewers and how they were answered by the authors, which could lead in additional criticism by the readers, which can be also valuable.

Do you think your study could be easily reproduced in other parts of the world by other researchers interested in using your methodologies, or were there specific pre-existing conditions that allowed for this study to take place? How helpful would it be to have data from classrooms in other parts of the world?

The bigger problem is getting data. There are many factors that must be considered. Because of potential cheating by the students when working at home, we had to discard 80% of our data to be sure that this did not influencing in the study. This is the first and maybe more important problem, but there are others. For example, researchers must also take into account the differences between countries in the sense that different countries faced the pandemic with varying levels of confinement. This is important because conclusions should be related to those conditions.

At the very beginning, when we did our study, not many groups had the opportunity to collect and analyze reliable data. Now, there are more and more very interesting studies from many different countries. Soon we will have enough data to get conclusions about the success of different strategies, which will be very helpful for planning distant learning at all levels in the future.

If the general public were to take one lesson from your study, what should that be?

I want to send an optimistic message in this case. We have demonstrated that, even in this very difficult situation, students and teachers were able to adapt their strategies in the learning process successfully. We are going through some very difficult times, but we have been able to adapt and we must have the courage and energy to continue fighting until we overcome this pandemic.

Thank you to Sacha and his research team for their important work and taking the time to answer these questions. Their work was founded by CRUE, CSIC and Banco Santander.

Citation

Gonzalez T, de la Rubia MA, Hincz KP, Comas-Lopez M, Subirats L, Fort S, et al. (2020) Influence of COVID-19 confinement on students’ performance in higher education. PLoS ONE 15(10): e0239490. https://doi.org/10.1371/journal.pone.0239490

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International Day of Women and Girls in Science 2021

Posted on February 11, 2021 by Jamie Males

Today, 11 February, marks the International Day of Women and Girls in Science. To celebrate, we speak to some recent PLOS ONE authors about their research and their experiences as women in science. Our interviewees study very different aspects of agriculture and food security, but all their work contributes to the development of more efficient and sustainable food systems for the future.

Kirsten Ball (KB)- Postdoctoral Research Associate, Department of Environmental Science, University of Arizona, USA

Author of “High-throughput, image-based phenotyping reveals nutrient-dependent growth facilitation in a grass-legume mixture”

Amaia Albizua (AA)- Associate Professor, Department of Didactics & School Organization, University of the Basque Country, Spain

Author of “Social networks influence farming practices and agrarian sustainability”

Matema Imakumbili (MI)- Independent Researcher, Tanzania

Author of “Plant tissue analysis as a tool for predicting fertiliser needs for low cyanogenic glucoside levels in cassava roots: An assessment of its possible use”

Paula Rendón (PR)- PhD Student & Research Assistant, Institute of Physical Geography & Landscape Ecology, University of Hannover, Germany

Author of “Assessment of the relationships between agroecosystem condition and the ecosystem service soil erosion regulation in Northern Germany”

Inderjot Chahal (IC)- Postdoctoral Fellow, School of Environmental Sciences, University of Guelph, Canada

Author of “Cover crop and crop residue removal effects on temporal dynamics of soil carbon and nitrogen in a temperate, humid climate”

Laura Van Eerd (LVE)- Professor, School of Environmental Sciences, University of Guelph, Canada

Author of “Cover crop and crop residue removal effects on temporal dynamics of soil carbon and nitrogen in a temperate, humid climate”

Could you tell us a bit about your research interests and what attracted you to your field of study?

KB: My research is driven from a desire to understand the impacts of agricultural management on soil health, and to increase industry adoption of sustainable production practices. I very much take a plant-soil feedback approach to that goal; I think it is difficult to examine soil health and plant health without considering the interaction between the two.

AA: I am a multidisciplinary scientist studying terrestrial social-ecological systems mitigation and adaptation options to global change. I aim to answer complex sustainability questions such as land use planning accounting for optimizing ecosystem services and social wellbeing under human-driven and environmental crises. I have a special interest in the nexus between land use decision-making processes and the multi-scale connections of land and water governance and other socioeconomic factors.

MI: I have been particularly drawn to research focused on soil fertility and on how it influences crop quality. This is because I believe that soils greatly influence the nutritional quality of all produced food and hence our nutritional well-being. My research on cassava and my work experience on a nutrition project also got me interested in the food and nutrition security of subsistence farming communities in rural parts of Africa.

PR: I am interested in sustainability, resilience and human-nature relationships. Since a very young age, I started to show an interest in environmental issues. But it was later during my studies that I became more aware of the importance of nature in humankind’s survival. I came across the concepts of “ecosystem services” and “ecosystem condition”, and I have been studying them since then.

IC: I study the impacts of sustainable soil management practices on enhancing soil health, soil biogeochemistry (C and N cycling), and crop productivity while minimizing nutrient losses to the environment from vegetable and grain cropping systems. I always had a passion for agriculture, specifically for soil health and fertility. Over the years, I had the pleasure to work and learn from experts in sustainable agriculture, which significantly contributed in strengthening my interest and developing expertise in this area.

What were the key findings of your recent PLOS ONE paper? Why are they interesting and important?

KB: My study used high-throughput, image-based phenotyping (HTP) to distinguish growth patterns, detect facilitation and interpret variations in nutrient uptake in a model mixed-pasture system in response to factorial low and high nitrogen (N) and phosphorus (P) application. HTP has not previously been used to examine pasture species in mixture; it was a useful tool to quantify growth trait variation between contrasting species and to this end is highly useful in understanding nutrient-yield relationships in mixed pasture cultivations.

AA: We found that most farmers were aware of their co-production of nature Contribution to People (NCP) through their land management decisions. We also found that farmers’ awareness about NCP co-production and their land management decisions were correlated with the structure of the social networks among the farming community. Rural network analysis can be useful for understanding the network configuration of rural farming communities to improve rural policy development since it permits understanding interactions between awareness, land management decisions, and knowledge/advice sharing at the landscape level. Considering that those modern farmers’ perceptions and their management practices are significant factors for the creation of the advice network structure, we should incentive structures that make farmers more aware of their contribution to climate regulation to take a more active role within their networks.

MI: In the article, which reports on a research project that I really enjoyed developing and writing up, we showed that cyanogenic glucoside production in cassava is influenced by plant nutritional status, similar to crop yields and well-known crop quality characteristics like fruit colour and taste. Amongst many other things, the study managed to highlight the important role of plant nutritional status (and soil fertility) in producing cassava that is safe to consume for the millions of people that depend on it for their staple food.

PR: We wanted to analyse the relationship between ecosystem condition and services in a regional case study. For this, we used the indicators proposed by the Mapping and Assessment of Ecosystems and their Services (MAES) group of the European Commission to assess the condition of agroecosystems, and compare them against the supply of the ecosystem service erosion control. We identified some correlations between the indicators but also some limitations in the framework, as some indicators cannot explain to what extent ecosystems can provide specific services. These results are interesting because they trigger further research to find better ways to integrate ecosystem condition and services. Additionally, they highlight the need to make temporal and spatially-explicit data available at national and regional scales, that provide more thorough information for policy and decision making.

IC: The key findings of our paper were (a) cover crop adoption in the medium-term (6-yrs) enhanced surface C and N storage in a horticultural cropping system, and (b) cover crop and crop residue retention had an integrative positive effect on increasing soil C and N fractions. This study advanced our understanding of the synergistic effect of cover crop and crop residue retention on the mechanism of soil C and N cycling and increasing soil health in the medium-term.

What are you working on now?

KB: I am currently working at the University of Arizona on an NRCS arid soil health program for cropping systems. I am prioritizing expanding understanding of what constitutes a ‘healthy’ arid soil, paying particular attention to the interaction of soil organic matter with soil carbonates. If we can describe a soil as healthy, what does that look like for arid systems? Further, if there is an achievable goal for soil health in arid systems, how do we quantify it? I currently have a variety of field trials in cropping systems including forage cropping and viticulture.

AA: I am currently Associate Professor at the University of the Basque Country, but the classes I am performing are quite far from my expertise. The way the system works to get a place at the university here demands you have good research background but also teaching experience and I am now getting such experience. At the same time, I’m collaborating with a colleague at the Autonomous University of Barcelona in a meta-analysis to understand the effectiveness of interventions to adapt to climate change in developing countries.

MI: I recently developed a tool that can be used to assess a subsistence farming community’s vulnerability to cassava cyanide intoxication. The tool is a decision support tool that will help highlight the risk of cassava cyanide intoxication in communities, and will also guide the selection of interventions. Since I had only conducted a pilot study, I am currently planning to have the tool validated using a larger study population.

PR: I am working on a similar study to the one we published in PLOS ONE, but this time at the European scale. We are looking at the condition of agroecosystems and erosion control and the variations of the indicators and their relationships in environmental zones with similar climatic and topographic characteristics.

IC: I am currently working on quantifying soil health and understanding the mechanisms regulating soil C and N dynamics in sustainable cropping systems. I am particularly interested in cover crops, crop rotation, tillage, crop diversification, and fertilizer N management. The major goal of my research is to provide valuable information for developing resilient cropping systems.

What has your experience as a woman in science been like?

KB: I had three female supervisors/mentors throughout graduate school; that representation helped me to build the confidence I needed to know I could succeed. As an early career researcher, a conventional avenue of elevating your position in academia is to align yourself (either in project or manuscript collaboration) with highly established and successful researchers: often white men. Unfortunately, this behavior reinforces and amplifies the underrepresentation of women and BIPOC folk, particularly women of color in STEM. I actively seek non-traditional avenues to create research partners, instead creating respectful, mutual, and equitable working relationships that enhance my knowledge and progression while elevating my peers; namely women of color and early career, female researchers.

AA: My experience has been pretty good but sometimes I have had the feeling of not being heard in the way a man would be. I am very aware of the fact that women tend to hold lower positions, have a less active and visible voice in scientific congresses and in the media and sometimes even charge less (perhaps because we demand less) for the same work. For this reason, I participate in networks that give women visibility into science as well as programs to empower and encourage girls to be scientific. The experience of working previously in Montreal, at McGill University, with a woman as a supervisor and a laboratory group in which most of us were women has been very stimulating and has given me a lot of confidence.

MI: I must say that it is difficult to say whether the challenges I have faced in science have been due to me being a woman or due to me being seen as a younger, less experienced researcher. But both women and younger researchers come up with great ideas and must be given credit, as well as support.

PR: So far, I have had a good experience in science. I found many inspiring women working in my field that have done great work and contributed considerably to science. I have not felt any rejection linked to my background or gender; on the contrary, I feel supported and encouraged by my supervisors and colleagues.

LVE: Fortunately, for 99.2% of the time my gender is inconsequential, as it should be. I could tell you about experiences that would make you wince and would surprise many male scientists. Many people like to think that things are better for the next generation of women in science and that is likely be true, but in my experience sexist, inappropriate comments or micro-aggressions still persist. What has improved, in my opinion, is that many people are better at calling out these behaviours.

Photo by S. Hermann & F. Richter on Pixabay

Has Covid-19 affected your work?

KB: I actually started my postdoc at the UofA from my kitchen bench!! I am mostly meeting people via Zoom, which is lucky because I almost always have pyjama pants on! While I have been able to be very productive working from home (I don’t have any small children to worry about) the social isolation creates a lot of stress. I was lucky enough to fit in some fieldwork at the end of 2020 which should tide me over for a few more months. I also hope to be able to get home and see my family in Australia within the next year, I miss them more than ever at the moment!

AA: Motherhood and Covid-19 have arrived at once so I wouldn’t know how Covid-19 has affected me but motherhood. When you become a mother, it is a year in which producing is done at a high price (physical, mental and emotional). Thanks to my mother’s help I’ve managed to keep publishing and pushing my research but sometimes it’s been really hard. I believe that women scientists who want to be mothers need greater protection so that maternity years are not penalized when it comes to getting scholarships or finding jobs. The first few years, or at least the first year, the time a woman must dedicate to the baby cannot be comparable to that of a man even if we are given the same amount of parental leave.

MI: While writing a research proposal I came to realise that I could not easily design a research project that could be carried out in another country, because of the Covid-19 travel restrictions. Covid-19 has also made within-country movements a challenge; one has to carefully think before planning to conduct a research in a rural area, for fear of carrying the disease there. Drawing up research budgets has also been impossible, as prices keep changing due to the economic disruption.

PR: I have been able to work remotely, so I did not experience a strong interruption in my research. In my institute, we try to keep in touch through informal virtual coffee breaks and weekly meetings. However, I miss the exchange of ideas I had with my supervisor and colleagues in the office. An aspect that I somehow underestimated before is the importance of keeping good mental health. The uncertainty of the situation and having family and friends seriously ill with the virus have taken a toll on my mental health and productivity.

LVE: Yes, like many across the world, my research, teaching and extension work has been greatly impacted. Let me be clear, that I am extremely grateful to be healthy and be employed. I have noticed that the requests for presentations, video and audio interviews have more than doubled, not to mention the additional paperwork. Remote teaching is an onerous time commitment that really limits the opportunities for feedback. I worry about my students well-being and learning experience. Mostly I miss the meaningful connections within my research team, as well as colleagues and industry partners.

What change do you hope to see in the future of agriculture and food systems?

KB: There needs to be a recognition of the intrinsic connection between plants and soil, and a more holistic management framework that accounts for both. Further, we (white folk) need to recognise how detrimental it is that Indigenous knowledge and motivations of local communities have historically been taken for granted by scientists with a lack of reciprocity in relationships. As agricultural researchers we need to deconstruct historical understanding of agricultural development that ignored native principles of land stewardship, and pledge to seek knowledge from- and develop research programs alongside- indigenous farmers and researchers that recognizes the primacy of native values if we are truly going to look after our productive lands.

AA: I would like to see local, seasonal and respectful production systems. I would like governments to manage markets to regulate global competition.

MI: I would like to see subsistence farming communities able to produce enough nutritious food to feed themselves adequately throughout the year. I would like to see them well-supported with things like good agricultural extension, farming inputs and with access to markets. I feel that while they struggle to feed so many of us, they themselves are left with little as they cannot properly balance household food and income needs.

PR: I would like to see a system of agricultural production that is sustainable in the long term. One that is resilient to future pressures and the impacts of climate change, that considers local knowledge and practices, and that is beneficial for farmers, consumers and the environment.

IC: I hope that future food production becomes environmentally and economically sustainable. I hope the general public becomes more aware of the numerous agroecosystem benefits provided by sustainable land management practices. Growers adopting agricultural practices which enhance agroecosystem resiliency and minimize environmental degradation will be financially compensated. These changes will contribute to developing healthy soils, providing safe and nutritious food to people, and increasing environmental quality.

LVE: I hope to see a time when the majority of consumers understand considerably more about agriculture and where food comes from. My dream would be an agri-food system where practices that enhance ecosystem services are valued and become the norm. With this knowledge, there could be great advances towards healthy soil, agroecosystems, and people.

The post International Day of Women and Girls in Science 2021 appeared first on EveryONE.

Meet the PLOS ONE Cancer and Oncology Authors

Posted on February 4, 2020 by plos

Today is World Cancer Day — a day for raising the voices of cancer survivors, loved ones, and the people who are working endlessly to find solutions. This year’s theme is “I am and

Meet the PLOS ONE Cancer and Oncology Authors

Posted on February 4, 2020 by plos

Today is World Cancer Day — a day for raising the voices of cancer survivors, loved ones, and the people who are working endlessly to find solutions. This year’s theme is “I am and I will:” a recognition of the power each individual has to make an impact.

Each year, PLOS ONE publishes more than 1000 new research articles in cancer and oncology from authors who have dedicated their careers to studying this disease. In celebration of this years’ theme, we’re sharing their stories which inspired the science we use to understand and fight this disease.

Meet the researchers…

“My research group is mainly focused on the study of lung and pancreatic cancers, which are associated with high morbidity and mortality rates, worldwide. We use high throughput methods to identify new biomarkers and regulatory pathways and functional assays to improve our understanding of disease biology.

Our ultimate goal is to improve patient survival, through better diagnosis, prognosis and treatment.”

— Patricia Pintor dos Reis, Faculty of Medicine, São Paulo State University – UNESP Botucatu, SP, BRAZIL.

MicroRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma. Tainara F. Felix, Rainer M. Lopez Lapa, Márcio de Carvalho, Natália Bertoni, Tomas Tokar, Rogério A. Oliveira, et al

“Bioinformatics is my tool and cancer research is my subject. My dad and many other people died of cancer and I want to uncover what causes cancer. And I love math and computers, which attracted me to become a bioinformatician. Now I am working for NCI initiative Ras program at Frederick National Lab for Cancer Research, which tries to tackle the most critical and ancient gene in cancer biology: Ras genes.

My last paper on PLOS ONE is about common pitfalls often seen in the survival analysis in the field. We wish to first alert researchers about the pitfalls when they perform survival analysis and to provided a novel method that shall help avoid the pitfalls.

The curiosity in biology and the desire to make life better drives my career in science.”

— Ming Yi, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America

GradientScanSurv—An exhaustive association test method for gene expression data with censored survival outcome. Ming Yi, Ruoqing Zhu, Robert M. Stephens

“The goal of my research is to develop an agent that promotes apoptosis in cancer cells but not in normal cells. To accomplish this goal, I explored different protein targets and pathways that included but are not limited to matrix type-I metalloprotease I (MT1-MMP), tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), and oxidative stress.

I believe that the results and proposed future strategies will help to design potent and safe cancer treatments.”

— Dmitri Rozanov, Department of Molecular and Medical Genetics, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America

Targeting mitochondria in cancer therapy could provide a basis for the selective anti-cancer activity. Dmitri Rozanov, Anton Cheltsov, Aaron Nilsen, Christopher Boniface, Isaac Forquer, et al

“I focus on H&N/Skull base cancers and mechanisms of treatment resistance within HPV positive and negative cancers. Understanding mechanism of treatment resistance will enable us to target new pathways for improving patient outcomes.

It is a privilege to work with folks and help the individual patient, but just as important is work on research that can possibly help the many.”

— Dukagjin Blakaj, The James Cancer Center, Ohio State University, Columbus, OH, United States of America

Association of an intact E2 gene with higher HPV viral load, higher viral oncogene expression, and improved clinical outcome in HPV16 positive head and neck squamous cell carcinoma. Nicole V. Anayannis, Nicolas F. Schlecht, Miriam Ben-Dayan, Richard V. Smith, Thomas J. Belbin, et al

“My particular area of research is the staging of colon cancer, it is important because colon cancer is a top 3 killer (of all cancer types) and we need new treatment strategies. However without accurate staging (i.e. determining how advanced the tumor is), it is nearly impossible to develop these new strategies.

My goal is to increase this accuracy, or at least shed light on how accurate our current staging is.”

— Elias Nerad, The Netherlands Cancer Institute, Amsterdam The Netherlands.

The Apparent Diffusion Coefficient (ADC) is a useful biomarker in predicting metastatic colon cancer using the ADC-value of the primary tumor. Elias Nerad, Andrea Delli Pizzi, Doenja M. J. Lambregts, Monique Maas, Sharan Wadhwani, et al

“I have always wanted to understand the incredible organization of brain functions and how to cure patients with brain lesions. My research field focuses on brain anatomy, brain functions, neuroimaging and how all these aspects together can improve the treatment of patients with cerebral tumors. My work tried to change the standard topographical classification of brain tumors to a model including more detailed information regarding the tumor infiltration along the white matter fibers.

This model perfectly fits the open access principle because it is not based on expensive technology, rather on a basic idea merging anatomy neuroimaging and oncology. I believe that anyone in the world can reproduce this classification method with standard MRI pictures contributing to a more extensive and shared knowledge in this field.

I want to fully understand the interaction between brain structures and brain tumors to better cure my patients.”

— Francesco Latini, Department of Neuroscience, Neurosurgery, Uppsala University, Uppsala, Sweden

A novel radiological classification system for cerebral gliomas: The Brain-Grid. Francesco Latini, Markus Fahlström, Shala G. Berntsson, Elna-Marie Larsson, Anja Smits, Mats Ryttlefors

Meet PLOS ONE Author Augusto Cardoso-dos-Santos

Posted on November 26, 2019 by Madison Crystal

Augusto Cardoso-dos-Santos is a PhD student at Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil What first drew you to your field of research? Genetics is

Celebrating Years of Impactful Research and Broad Reach on PLOS ONE

Posted on November 20, 2019 by Joerg Heber

0000-0002-6370-4254 The year is almost over and here on the PLOS ONE team we’ve been reflecting on the tremendous impact our authors’ work has had in the community. Each year, nearly 100,000 researchers (our own

EveryONE: Dr. Zilma Reis

Posted on November 14, 2019 by plos

Dr. Reis: Faculty of Medicine, Universidade Federal de Minas Gerais, Avenida Professor Alfredo Balena, Belo Horizonte, Minas Gerais, Brazil What is your area of study and why is it important? I develop medical devices, electronic health

Meet PLOS ONE Author Elias Nerad

Posted on October 23, 2019 by plos

Elias Nerad works at The Netherlands Cancer Institute, Amsterdam Netherlands. What first drew you to your field of research? Halfway through my residency I did not have any experience with research, but during my

EveryONE: Dr. Harriet Gliddon

Posted on October 15, 2019 by plos

Dr. Gliddon: Department of Reproductive Health and Research, World Health Organization, Geneva, Switzerland, London Centre for Nanotechnology, University College London,London, United Kingdom What first drew you to your field of research? I was drawn to

About Open Science

(All that comes with it, (but not by itself)

Category Archives: Author Spotlight

An Interview with Biogeochemist Alex Cory

An Interview with Palaeoclimate Modeler, Hu Yang

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

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

Amphibians and reptiles on the edge: An interview with intrepid PLOS ONE authors

From Collecting Sediment Cores in Iceland to Mentoring Students: The Busy Life of an Early Career Researcher

Author Interview: Sacha Gómez Moñivas on student learning despite COVID-19 confinement

Citation

International Day of Women and Girls in Science 2021

Meet the PLOS ONE Cancer and Oncology Authors

Meet the PLOS ONE Cancer and Oncology Authors

Meet the researchers…

Our ultimate goal is to improve patient survival, through better diagnosis, prognosis and treatment.”

The curiosity in biology and the desire to make life better drives my career in science.”

I believe that the results and proposed future strategies will help to design potent and safe cancer treatments.”

It is a privilege to work with folks and help the individual patient, but just as important is work on research that can possibly help the many.”

My goal is to increase this accuracy, or at least shed light on how accurate our current staging is.”

I want to fully understand the interaction between brain structures and brain tumors to better cure my patients.”

Read More Cancer Research on PLOS ONE

Meet PLOS ONE Author Augusto Cardoso-dos-Santos

Celebrating Years of Impactful Research and Broad Reach on PLOS ONE

EveryONE: Dr. Zilma Reis

Meet PLOS ONE Author Elias Nerad

EveryONE: Dr. Harriet Gliddon