Sycamore maples destroyed by the Sooty bark disease. Photo by Dr Miloň Dvořák
Especially after the last few COVID-affected years, nobody doubts that emerging infectious diseases can threaten the whole world. But humans are not the only ones at risk! With intensive global trade, many tree parasites are accidently introduced to Europe in packaging or directly on goods. Traveling in the wood, on plants or in the soil of their pots, they can remain undetected for a long time.
“Forms of life of parasitic fungi are extremely diverse and very often practically invisible,” says Dr Miloň Dvořák of the Department of Forest Protection and Wildlife Management at Mendel University in Brno, Czechia. “An infected tree may look completely healthy for some time, which complicates the control of the disease enormously. It reminds me of the ancient Trojan Horse, where European trees are so surprised, defenceless, and later defeated, like the Trojan warriors.”
How can an infected tree look healthy and then suddenly get sick? “Like in the human body, in trees too, the trigger can be stress,” explains Dr Dvořák. The tolerance of trees to a pathogenic fungus turns lower under the conditions of changing climate and so the tree starts to die of the disease.
One typical example of such a disease is the Sooty Bark Disease (SBD) on maples, caused by a microscopic fungus called Cryptostroma corticale. “The fungus was probably introduced to Europe during the Second World War and for the rest of the 20th century we did not hear much about it,” says Dr Dvořák.
Sooty Bark Disease (Cryptostroma corticale) on Sycamore. Photo by gailhampshire used under a CC BY 2.0 license
The situation has changed and over the last twenty years the fungus has been reported more and more often. After dry and hot periods, the trees start to die of the infection, which is accompanied by the creation of brown-black masses of “soot” under the peeling bark of the maples.
The “soot” is in fact spores, which help the fungus spread and infect other trees. It is harmful for wounded trees, but it can also cause hypersensitivity pneumonitis in humans.
So, the species became a target for a group of phytopathologists gathered by an European HORIZON 2020 project entitled “Holistic management for emerging forest pests and diseases (HOMED)”. Scientists from six countries (Czechia, France, Italy, Portugal, Sweden and Switzerland), including Dr Dvořák, decided to develop a precise, DNA based (real-time PCR) diagnostic method to detect and monitor the pathogen in air samples. They published their method, the outcomes of its use, and their new findings about SBD epidemiology in the open-access journal NeoBiota.
Volumetric air sampler installed in Brno, Czech Republic, sampling pollen for allergen forecast. Photo by Aneta Lukačevičová
How to look for DNA in air samples? Simple devices called volumetric air samplers can suck the air against a piece of sticky tape, where every particle gets stuck and can be analyzed. “These devices are not really cheap, moreover, they demand regular maintenance,” explains Dr Dvořák. “But, actually, they are in common and regular use in the whole of Europe – remember the weather forecast, particularly that part about the “pollen report” for allergic people. This forecast is based on data of more than 600 stations united by the European Aeroallergen Network (EAN). Every station permanently maintains one volumetric air sampler and keeps an archive of the samples.”
The HOMED team got in contact with their national EAN collaborators and processed their samples with molecular techniques (real-time PCR).
Thanks to this sensitive detection method, the survey among samples was very successful. The “sooty” fungus was found in air samples from countries where the disease has been reported, and, in a more detailed study in France, the pathogen was found in the air 310km from currently diseased trees! This result suggests that the fungus can disperse long distances by wind.
Black stromata – source of billions of hyper-allergenic spores. Photo by Dr Miloň Dvořák
“Our results show that the SBD disease is at an exponentially increasing phase in France and Switzerland with an increase in the magnitude of the number of disease cases that peaks following a marked water deficit,” the researchers write in their study. They hope that early aerial detection of C. corticale in disease-free countries could help implement more efficient measures for SBD detection and eradication in the field.
“This European experiment fully confirmed the potential of this approach to monitor the pathogen’s outbreaks in early stages of its spread,” concludes Dr Dvořák.
Research article:
Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549
A group of researchers from the Mississippi Entomological Museum taking break after exploring a site in Texas for grasshoppers. Left to right: Brady Dunaway, JoVonn Hill, Matthew Thorn. Photo by JoVonn Hill
The central region of Texas is a known hotspot of biological wonders. For the last five years, Dr. JoVonn Hill, an Assistant Professor and Director of the Mississippi Entomological Museum (MEM) at Mississippi State University, and his colleagues have made scientific expeditions to the area that have now revealed an extraordinary find.
The team uncovered seven previously unknown flightless grasshopper species, six of them endemic to the Edwards Plateau, which underscores the region’s extraordinary biodiversity.
With this discovery, Dr. Hill is paying tribute to two iconic musicians. In recognition of the “immense contributions” of Texas legends Willie Nelson and Jerry Jeff Walker, he has named two of these flightless grasshopper species after them.
Melanoplus nelsoni held by Dr. JoVonn Hill. Photo by JoVonn Hill
“Melanoplus nelsoni and Melanoplus walkeri immortalize the enduring contributions of these legendary musicians and their connection to Texas,” he says.
Melanoplus walkeri.
“After these last few summers [of field studies], just like Mr. Nelson, we too have a little Texas in our souls,” he writes in his study, which was just published in the journal ZooKeys.
On Melanoplus walkeri, he writes: “Walker’s songs such as Hill Country Rain, Leavin’ Texas, and Sangria Wine brought me and my field team joy while traveling between field sites and added to the amazing ambiance of the Edwards Plateau.” In fact, the artist recorded his most influential album not far away from the spot where the new species was discovered.
Additionally, the team acknowledges the cultural heritage and deep connection to the region of the Comanche and Tonkawa tribes, naming two species after them, Melanoplus commanche and Melanoplus tonkawa respectively.
“These designations recognize the profound historical and cultural significance of the tribes in the region,” Dr. Hill explains.
Melanoplus tonkawa.
“These seven newly described species, alongside two preexisting ones, form a cohesive species group, highlighting their shared characteristics and evolutionary relationships,” Dr. Hill says in conclusion. “The formation of this new species group presents a significant contribution to our understanding of the diverse ecosystems present in central Texas,” he adds.
Melanoplus commanche.
The discovery of these seven flightless grasshopper species and the formation of a new species group underscore the ecological uniqueness of central Texas, Dr. Hill says. He and the staff of the Mississippi Entomological Museum remain committed to scientific exploration and understanding, promoting the conservation of biodiversity, and inspiring a sense of wonder and appreciation for the natural world.
Research article:
Hill JG (2023) Diversification deep in the heart of Texas: seven new grasshopper species and establishment of the Melanoplus discolor species group (Orthoptera, Acrididae, Melanoplinae). ZooKeys 1165: 101-136. https://doi.org/10.3897/zookeys.1165.104047
“Not only does it mean that content is persistent in merit and quality, but that innovative research outputs are already appreciated within academia,” says Editor-in-Chief Prof Dr Benjamin Burkhard
Seven years after its official launch in May 2016, the One Ecosystem journal has successfully completed the rigorous quality and integrity assessment at Web of Science.
The news means that One Ecosystem might see its very first Journal Impact Factor (JIF) as early as 2024, following the latest revision of the metric’s policies Clarivate announced last July. According to the update, all journals from the Web of Science Core Collection are now featured in the Journal Citation Reports, and thereby eligible for a JIF.
“Giving all quality journals a Journal Impact Factor will provide full transparency to articles and citations that have contributed to impact, and therefore will help them demonstrate their value to the research community. This decision is aligned to our position that publications in all quality journals, not just highly cited journals, should be eligible for inclusion in research assessment exercises,” said back then Dr Nandita Quaderi, Editor-in-Chief and Editorial Vice President at Web of Science.
“We are happy to learn that Web of Science has recognised the value and integrity of One Ecosystem in the scholarly landscape. Not only does it mean that the scientific content One Ecosystem has been publishing over the years is persistent in merit and quality, but that innovative research outputs are already widely accepted and appreciated within academia.
After all, one of the reasons why we launched One Ecosystem and why it has grown to be particularly distinguished in the field of ecology and sustainability is that it provides a scholarly publication venue for traditional research papers, as well as ‘unconventional’ scientific contributions,”
“These ‘unconventional’ research outputs – like software descriptions, ecosystem inventories, ecosystem service mappings and monitoring schema – do not normally see the light of day, let alone the formal publication and efficient visibility. We believe that these outputs can be very useful to researchers, as well as practitioners and public bodies in charge of, for example, setting up indicator frameworks for environmental reporting,”
“In fact, last year, we also launched a new article type: the Ecosystem Accounting table, which follows the standards set by the the System of Environmental-Economic Accounting Ecosystem Accounting (SEEA EA). This publication type provides scientists and statisticians with a platform to publish newly compiled accounting tables,”
Previously, One Ecosystem has been accepted for indexing at over 60 major academic databases, including Scopus, DOAJ, Cabell’s Directory, CABI and ERIH PLUS. In June 2022, the journal received a Scopus CiteScore reading 7.0, which placed it in Q1 in five categories: Earth and Planetary Sciences; Ecology; Nature and Landscape Conservation; Agricultural and Biological Sciences (miscellaneous); Ecology, Evolution, Behavior and Systematics.
A citizen science project in Italy had high school students monitor the activities of ambrosia beetles, catching them with traps made from recycled plastic bottles.
While invasive alien species (IAS) represent a growing threat to global biodiversity and ecosystems, public awareness of them hasn’t seen a significant increase. Many researchers believe informing people about IAS is an essential long-term investment to counter biological invasions; in particular, “learning by doing” is an extremely effective method for involving new audiences, such as students.
Map of the study area (the Veneto Region) indicating the high school locations.
About 500 Italian students aged 11-18 took part in a citizen science project that led to new geographical records of two alien species of ambrosia beetles considered to be quarantine pests by the European Union. Dr. Fernanda Colombari and Prof. Andrea Battisti of the University of Padova have described the results in a paper in the open-access journal NeoBiota.
The project involved schools located in urban areas in north-eastern Italy and aimed to connect environmental education and experiential outdoor learning through lectures, videos, reports, and large-scale surveillance of ambrosia beetles. The students used plastic bottles and hand sanitizer to trap ambrosia beetles in their school grounds. They then assessed their abundance, looking at the different species. Before and after the educational activities, their knowledge and awareness of IAS were tested using simple anonymous questionnaires.
Schematic representation of a plastic bottle trap filled with hand sanitizer as attractant
“Our study aimed to both educate students and collect scientific data at sites such as schools where surveillance for potentially invasive ambrosia beetles is not usually conducted, or where it is sometimes misunderstood,” Dr. Colombari and Prof. Battisti write in their paper.
Identifying the specimens collected by the students, the authors found that IAS amounted to 35% of total catches. Remarkably, two out of the four alien species caught, Cnestus mutilatus and Anisandrus maiche, were recorded for the first time in Europe thanks to this study.
Furthermore, questionnaire results showed that the students acquired greater knowledge and increased their awareness and interest in IAS by more than 50%. After the experiment, most of them were interested in learning more about the negative effects of the introduction of IAS and practices to limit their spread.
This study shows that citizen science can successfully involve school students, giving them an opportunity to contribute in an effective early detection of IAS, as most first records occur in cities or suburban areas. The results also point to the primary role of education, which is as a major driver of change in tackling sustainability challenges. Moreover, as students bring home the message and share it with their relatives, the process supports intergenerational learning and enlarges public collaboration.
A plastic bottle trap filled with hand sanitizer as attractant. Photo by Dr Fernanda Colombari
“People are often unaware of the role they have in the entire invasive process,” the researchers write in their study. Citizen science projects like this one are more than a reliable tool for collecting scientific data; they also help engage the public and spread awareness of biological invasions, eventually contributing to the creation of more efficient management strategies.
The monitoring programme in this study was conducted in the context of the European project HOMED (Holistic management of emerging forest pests and diseases), which has developed a full panel of scientific knowledge and practical solutions for the management of emerging native and non-native pests and pathogens threatening European forests. The main results of HOMED’s research are publically available in a special issue in the open-access scholarly journal NeoBiota.
Original source:
Colombari F, Battisti A (2023) Citizen science at school increases awareness of biological invasions and contributes to the detection of exotic ambrosia beetles. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 211-229. https://doi.org/10.3897/neobiota.84.95177
Early detection of pest infestation is an important first step in the adoption of control measures that can be tailored to specific local conditions. Remote sensing technology can be a helpful tool, allowing the quick scanning of large areas, but it’s not universally applicable as sometimes items can be hard to detect. Unmanned aerial vehicles (UAVs), or drones, on the other hand, can help by getting closer to individual trees and detecting smaller atypical signals.
The pine processionary moth is an insect infesting trees in gardens and parks, threatening public health because of the hairs released by its larvae, which can cause a stinging or itching sensation. The pest is rapidly growing in numbers and conquering new territories, which makes it a species of concern.
In a new study, researchers tested different deep learning methods to detect the nests made by pine processionary moth larvae on pine and cedar trees. Drones flying over the trees took images, which were then analysed with the help of artificial intelligence (AI) to identify and localise the nests.
Drone images from Portugal.
The use of AI on drone images proved effective to detect pine processing moth nests on trees of different species and sizes, even under variable densities. The method can be successfully used in both forest and urban settings to help detect moth nests. That way, tree health managers can be informed about where the nests are and take appropriate measures to contain the damage and the public health risks.
“The study proved the advantage of using UAVs to document the presence of at least one nest per tree,” the researchers write in their study, which was published in a special issue of the journal NeoBiota dedicated to forest pests in Europe. “It therefore represents a substantial step forward in the integration of the UAV survey with ground observations in the monitoring of the colonies of an important forest defoliating insect in the Mediterranean area.”
image from the ground in daylightimage from the ground in infrared lightimage from drone
Furthermore, they suggest that the method can be extended to other pests.
“This technique can pave new avenues in the surveillance and management of emerging and non-native pests of trees, where early detection and early action should go together to achieve a satisfactory level of protection,” the study authors write in conclusion.
Research article:
Garcia A, Samalens J-C, Grillet A, Soares P, Branco M, van Halder I, Jactel H, Battisti A (2023) Testing early detection of pine processionary moth Thaumetopoea pityocampa nests using UAV-based methods. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 267-279. https://doi.org/10.3897/neobiota.84.95692
Every year, new alien species of insects and fungi invade European forests. Some of them are exotic pests and diseases that can affect the survival and growth of trees.
To help develop strategies for monitoring and managing these non-native forest pests, a consortium of over 50 scientists representing 23 research institutions and 15 countries from across the globe joined their skills in the Horizon 2020 project HOMED “Holistic management of emerging forest pests and diseases.”
Alex Stemmelen during his presentation at the XXVI ICE Congress 2022. He is the first author of a paper on the pests of Douglas fir in NeoBiota‘s special issue.
Between 2018 and 2022, the HOMED consortium developed a full panel of scientific knowledge and practical solutions to better deal with emerging native and alien invasive pests and diseases.
Fruiting bodies of Austropuccinia psidii on Myrtus communis (symptoms of myrtle rust). Photo by Alberto Santini
This includes targeting the successive phases of invasion, and developing innovative methods for each phase: risk analysis, prevention/detection, surveillance, eradication/containment, and control.
To share the results of this cooperation and help researchers further improve the management of emerging forest pests and pathogens, HOMED has made the main outcomes of its research publically available.
They are now published in a special issue in the open-access journal NeoBiota, called “Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests”. The issue comprises 16 articles on various aspects of the ecology and management of invasive alien insects and fungal pathogens in Europe’s forests.
“Because forests provide irreplaceable goods and materials for people and the European economy, because maintaining healthy forests is essential for their contribution to climate change mitigation through sequestration and storage of atmospheric carbon, it is urgent to develop more effective protective measures against the ever-increasing threat of invasive forest pests,” the editors of the special issue write in an editorial.
More tools are needed that can help identify, prevent and monitor invasive alien species and improve early warning methods, which makes the research in this issue so crucial and timely.
The European project Homed, leaded by Hervé Jactel, gave the opportunity to produce a lot of important scientific results, these are just a part! Incredibly happy and proud!https://t.co/VeIK5zvC7I
“The role of researchers is to develop, test and promote the most relevant methods and tools at each stage of the invasion framework, i.e., for the early detection of these invasive alien organisms, for the identification of the species and for the monitoring of their damage and spread, but also for new eradication and control solutions,” the editors continue.
Hervé Jactel, Lukas Seehausen and Martin Gossner at HOMED’s and Pensoft’s stand during the XXVI ICE Congress 2022.
One highlight in the published research is a study exploring how using the methods of citizen science at schools can increase invasive species awareness. Another explores the efficiency of artificial intelligence in pest detection.
“The publications collected in this special issue demonstrate that current conceptual, methodological, and technological advances allow a great progress in the anticipation, monitoring and management of invasive pest species in forests,” the editors conclude.
Follow HOMED on Twitter. Follow NeoBiota on Twitter and Facebook.See the latest tweets on the special issue using the hashtag #HOMED_SI.
One million plant and animal species are threatened with extinction, many within decades, admits the global Convention on Biological Diversity (CBD) on the eve of the adoption of its boldest plan ever, the New Global Agreement to Safeguard Nature.
Europe is a major player in the political response to this global crisis mobilised through its own Biodiversity Strategy for 2030. In recognition of its global responsibilities, the EU has taken bold steps towards global leadership in setting policies and commitments.
However, political commitments are not sufficient to mitigate and reverse biodiversity loss. To secure the future of the planet and society politicians, business leaders, scientists and society leaders must all prioritise the conservation and restoration of ecosystems through strong legislation and smart decisions.
The recently adopted by the CBD Global Biodiversity Framework (GBF) provides the basis for the instruments for conservation and sustainable use of biodiversity and for equitable sharing of their benefits, including the genetic resources.
About the projects
The new Horizon Europe-funded projects CO-OP4CBD (abbreviation for Co-operation for the Convention on Biological Diversity) and BioAgora (or Bio Knowledge Agora) unite experts from renowned European organisations to enhance the coordination and strengthen the EU support for the implementation of the Convention.
Both projects will make more effective use of existing networks of experts with the aim to transform the EU policy-making process by supplying decision-makers with access to top European scientific expertise on biodiversity and social transformation.
CO-OP4CBD
Logo of the Horizon Europe project CO-OP4CBD (abbreviation for Co–operation for the Convention on Biological Diversity).
CO-OP4CBD kicked-off in December 2022 and will be running until 2026 with the grant of EUR 4 million, provided by the European Union’s Horizon Europe programme.
The project will put in place a mechanism for mobilising, engaging and sharing expertise necessary for effective participation of EU member States and bodies in the CBD policy and decision-making processes.
Experts will provide advice to the European Commission, Member States and associated countries’ delegations of negotiators and technical experts.
CO-OP4CBD kick off meeting in Brussels (Belgium), February 2023.
Furthermore, the project will increase access to European expertise through enhanced mechanisms for promoting technical and scientific cooperation not only for negotiations, but also for implementation, monitoring and review of the efforts of the Parties towards thePost-2020 Global Biodiversity Framework and the Convention on Biological Diversity.
The consortium of CO-OP4CBD comprises 9 universities and research centers from across Europe. Together, they bring together experts from various backgrounds with extensive experience in EU projects in the field of biodiversity.
Logo of the Horizon Europe project BioAgora (abbreviation for Bio Knowledge Agora).
BioAgora was launched in July 2022 and is a five-year project with nearly EUR 12 million granted from the European Union’s Horizon Europe programme.
The project is tasked to build the Science Service for Biodiversity platform (SSBD) as the scientific pillar of the EU Knowledge Centre for Biodiversity (KCBD).
The KCBD, the European Commission’s initiative on better knowledge management for policy-making on biodiversity, plays a central role in the EU biodiversity policy landscape, and therefore BioAgora will support orchestrating a harmonious dialogue among scientists, other knowledge holders and policy actors in the biodiversity policy arena.
The project partners believe that science, policy, and society need to work closer together, if they wish to enable the sustainability transformation in Europe.
BioAgora kick-off meeting, Helsinki (Finland), November 2022.
A key part of this transformation will depend on a stronger role of knowledge, whether from science or practitioner experience in decision-making and implementation of decisions on the ground. BioAgora aims to facilitate this interaction.
“Biodiversity and natural capital have to be integrated into public and business decision-making at all levels. Collective actions and pluralistic principles have to be at the core of biodiversity policy-making efforts, which is why the Science Service for Biodiversity is envisioned as a bridge between science, policy, and society.”
comments project coordinator Kati Vierikko from the Finnish Environment Institute (SYKE).
The consortium of BioAgora consists of 22 partnering organisations from thirteen European countries, all of which bring their extensive knowledge of biodiversity policy and decision-making.
As a South American herpetologist, it is inevitable to be absolutely buzzed every time I hear “Germán, you have to go to the Amazon jungle”. Going to the Amazon forest in Peru is perhaps the most joyful way to do your work. The chances to find so many frogs, lizards, snakes, turtles, and even caimans are really high, so one can’t help but get excited.
The Agua Blanca forest. Photo by Germán Chávez
The thing is, to someone like me who focuses their work on describing new species, the expectations shouldn’t be that high. The Amazon has always been a place full of mysteries, so many explorers, seduced by its enigmatic atmosphere, have gone deeper and deeper into the Amazonia. This has resulted in the description of so many species and very few unexplored places left.
So, when Wilmar Aznaran and I found this new species in the Amazon lowlands of central Peru, a well-visited area, we were quite surprised and kind of speechless. I have to confess that my reaction was “Bloody hell!” Externally, the frog is clearly different from any other similar species, and that was evident for us at the very moment we caught it. Indeed, the first option for the title of our new paper in Evolutionary Systematics was “Expect the unexpected: a new treefrog from the Amazon lowlands of Peru.” We could not believe that a medium-sized arboreal frog had passed in front of other researchers’ eyes, and remained unseen.
Scinax pyroinguinis. Photo by Germán Chávez
Soon we found out that it is not a common species in the area: after catching two individuals, we were unable to find more. Not ready to give up, we went once more time to that site a few months later and our efforts to find it were unsuccessful, so we suggest it is not a common frog.
At that point, we knew that we had a new species on hands, but describing it with only two specimens was challenging. Luis A. García-Ayachi went to the area and his efforts were also unsuccessful. That is when Alessandro Catenazzi joined us, so we decided to add an integrative approach to our work, basing our research on morphological and genetic differences. I can only say thanks to all our co-authors: from then on, everything started to work out.
Scinax pyroinguinis. Photo by Germán Chávez
We noticed there were wildfires in the area, are a serious threat to the frog’s habitat. So it is really curious that the orange pattern on the groins, thighs and shanks of the new species, resembles flames, like those threatening its habitat. No better name for our frog than Scinax pyroinguinis, which literally means “groins of fire”.
Scinax pyroinguinis. Photo by Germán ChávezA wildfire in the frog’s habitat. Photo by Luis A. García-Ayachi
We hope that this discovery encourages people and institutions to protect these remnant forests in central Peru, because they may yet harbour unknown species. If these forests disappear, we will probably lose a diversity that we do not even know now yet, and may never will. It is sort of a race against deforestation and habitat loss, but this doesn’t mean there’s nothing we can do. Research like ours is really important to help put the focus on this place, at least in the short term, and try to attract people to join forces in the conservation of Scinax pyroinguinis and its habitat.
Research article:
Chávez G, Aznaran W, García-Ayachi LA, Catenazzi A (2023) Rising from the ashes: A new treefrog (Anura, Hylidae, Scinax) from a wildfire-threatened area in the Amazon lowlands of central Peru. Evolutionary Systematics 7(1): 183-194. https://doi.org/10.3897/evolsyst.7.102425
To bridge the gap between authors and their readers or fellow researchers – whether humans or computers – Knowledge Pixels and Pensoft launched workflows to link scientific publications to nanopublications.
A new pilot project by Pensoft and Knowledge Pixels breaks scientific knowledge into FAIR and interlinked snippets of precise information
As you might have already heard, Knowledge Pixels: an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing by means of nanopublications – recently launched a pilot project with the similarly pioneering open-science journal Research Ideas and Outcomes (RIO), in a first of several upcoming collaborations between the software developer and the open-access scholarly publisher Pensoft.
“The way how science is performed has dramatically changed with digitalisation, the Internet, and the vast increase in data, but the results are still shared in basically the same form and language as 300 years ago: in narrative text, like a story. These narratives are not precise and not directly interpretable by machines, thereby not FAIR. Even the latest impressive AI tools like ChatGPT can only guess (and sometimes ‘hallucinate’) what the authors meant exactly and how the results compare,”
said Philipp von Essen and Tobias Kuhn, the two founders of Knowledge Pixels in a press announcement.
So, in order to bridge the gap between authors and their readers and fellow researchers – whether humans or computers – the partners launched several workflows to bi-directionally link scientific publications from RIO Journal to nanopublications. We will explain and demonstrate these workflows in a bit.
Now, first, let’s see what nanopublications are and how they contribute to scientific knowledge, researchers and scholarship as a whole.
Basically, a nanopublication – unlike a research article – is just a tiny snippet of a scientific finding (e.g. medication X treats disease Y), which exists as a complete and straightforward piece of information stored on a decentralised server network in a specially structured format, so that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.
A nanopublication may also be an assertion related to an existing research article meant to support, comment, update or complement the reported findings.
In fact, nanopublications as a concept have been with us for quite a while now. Ever since the rise of the Semantic Web, to be exact. At the end of the day, it all boils down to providing easily accessible information that is only a click away from additional useful and relevant content. The thing is, technological advancement has only recently begun to catch up with the concept of nanopublications. Today, we are one step closer to another revolution in scientific publishing, thanks to the emergence and increasing adoption of what we call knowledge graphs.
Second time I hear about nanopublications in biodiversity in 3 days -1st by @rdmpage + now by @Pensoft#ECN2016
“As pioneers in the semantic open access scientific publishing field for over a decade now, at Pensoft we are deeply engaged with making research work actually available at anyone’s fingertips. What once started as breaking down paywalls to research articles and adding the right hyperlinks in the right places, is time to be built upon,”
said Prof. Lyubomir Penev, founder and CEO at Pensoft: the open-access scholarly publisher behind the very first semantically enhanced research article in the biodiversity domain, published back in 2010 in the ZooKeys journal.
Why nanopublications?
Apart from enabling computer algorithms with wholesome access to published research findings, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each byte of knowledge is interconnected and traceable back to its author(s) and scientific evidence.
Nanopublications present a complete and straightforward piece of information stored on a decentralised server network in a specially structured format, so that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. Illustration by Knowledge Pixels.
By granting computers the capability of exchanging information between users and platforms, these data become Interoperable (as in the Iin FAIR), so that they can be delivered to the right user, at the right time, in the right place.
Another issue nanopublications are designed to address is research scrutiny. Today, scientific publications are produced at an unprecedented rate that is unlikely to cease in the years to come, as scholarship embraces the dissemination of early research outputs, including preprints, accepted manuscripts and non-conventional papers.
By linking assertions to a publication by means of nanopublications allows the original authors and their fellow researchers to keep knowledge up to date as new findings emerge either in support or contradiction to previous information.
A network of interlinked nanopublications could also provide a valuable forum for scientists to test, compare, complement and build on each other’s results and approaches to a common scientific problem, while retaining the record of their cooperation each step along the way.
A scientific issue that would definitely benefit from an additional layer of provenance and, specifically, a workflow allowing for new updates to be linked to previous publications is the biodiversity domain, where species treatments, taxon names, biotic interactions and phylogenies are continuously being updated, reworked and even discarded for good. This is why an upcoming collaboration between Pensoft and Knowledge Pixels will also involve the Biodiversity Data Journal (stay tuned!)
What can you do in RIO?
Now, let’s have a look at the *nano*opportunities already available at RIO Journal.
The integration between RIO and Nanodash: the environment developed by Knowledge Pixels where users edit and publish their nanopublications is available at any article published in the journal.
Add reaction to article
This function allows any reader to evaluate and record an opinion about any article using a simple template. The opinion is posted as a nanopublication displayed on the article page, bearing the timestamp and the name of the creator.
All one needs to do is go to a paper, locate the Nanopubs tab in the menu on the left and click on the Add reaction command to navigate to the Nanodash workspace accessible to anyone registered on ORCiD.
To access the Nanodash workspace, where you can fill in a ready-to-use, partially filled in nanopublication template, simply go to the Nanopubs tab in the menu of any article published in RIO Journal and click Add reaction to this article (see example).
Within the simple Nanodash workspace, the user can provide the text of the nanopublication; define its relation to the linked paper using the Citation Typing Ontology (CiTO); update its provenance and add information (e.g. licence, extra creators) by inserting extra elements.
To do this, the Knowledge Pixels team has created a ready-to-use nanopublication template, where the necessary details for the RIO paper and the author that secure the linkage have already been pre-filled.
Post an inline comment as a nanopublication
Another opportunity for readers and authors to add further meaningful information or feedback to an already published paper is by attaching an inline comment and then exporting it to Nanodash, so that it becomes a nanopublication. To do this, users will simply need to select some text with a left click, type in the comment, and click OK. Now, their input will be available in the Comment tab designed to host simple comments addressing the authors of the publication.
While RIO has long been supporting features allowing for readers to publicly share comments and even CrossRef-registered post-publication peer reviews along the articles, the nanopublications integration adds to the versatile open science-driven arsenal of feedback tools. More precisely, the novel workflow is especially useful for comments that provide a particularly valuable contribution to a research topic.
To make a comment into a nanopublication the user needs to locate the comment in the tab, and click on the Post as Nanopub command to access the Nanodash environment.
Add a nanopublication while writing your manuscript
A functionality available from ARPHA Writing Tool – the online collaborative authoring environment that underpins the manuscript submission process at several journals published by Pensoft, including RIO Journal – allows for researchers to create a list of nanopublications within their manuscripts.
By doing so, not only do authors get to highlight their key statements in a tabular view within a separate pre-designated Nanopublications section, but they also make it easier for reviewers and scientific editors to focus on and evaluate the very foundations of the paper.
By incorporating a machine algorithm-friendly structure for the main findings of their research paper, authors ensure that AI assistants, for example, will be more likely to correctly ‘read’, ‘interpret’ and deliver the knowledge reported in the publication for the next users and their prompts. Furthermore, fellow researchers who might want to cite the paper will also have an easier time citing the specific statement from within the cited source, so that their own readers – be it human, or AI – will make the right links and conclusions.
Within a pre-designated article template at RIO – regardless of the paper type selected – authors have the option to either paste a link to an already available nanopublication or manage their nanopublication via the Nanodash environment by following a link. Customised for the purposes of RIO, the Nanodash workspace will provide them with all the information needed to guide them through the creation and publication of their nanopublications.
Why Research Ideas and Outcomes, a.k.a. RIO Journal?
Why did Knowledge Pixels and Pensoft opt to run their joint pilot at no other journal within the Pensoft portfolio of open-access scientific journals but the Research Ideas and Outcomes (RIO)?
Well, one may argue that there simply was no better choice than an academic outlet that was initially designed to serve as “the open-science journal”: something it has been honourably recognised for by SPARC in 2016, only one year since its launch.
Innovative since day #1, back in 2015, RIO surfaced as an academic outlet to publish a whole lot of article types, reporting on scientific work from across the research process, starting from research ideas, grant proposals and workshop reports.
After all, back in 2015, when it was only a handful of funders who required Data and Software Management Plans to be made openly and publicly, RIO was already providing a platform to publish those as easily citable research outputs, complete with DOI and registration on Crossref. In the spirit of transparency, RIO has always operated an open and public by default peer review policy.
More recently, RIO introduced a novel collections workflow which allows, for example, project coordinators, to provide a one-stop access point for publications and all kinds of valuable outputs resulting from their projects regardless of their publication source.
Bottom line is, RIO has always stood for innovation, transparency, openness and FAIRness in scholarly publishing and communication, so it was indeed the best fit for the nanopublication pilot with Knowledge Pixels.
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We encourage you to try the nanopublications workflow yourself by going to https://riojournal.com/articles, and posting your own assertion to an article of your choice!
Don’t forget to also sign up for the RIO Journal’s newsletter via the Email alert form on the journal’s website and follow it on Twitter, Facebook, Linkedin and Mastodon.
The latest issue published in African Invertebrates is a special one: it honours the career and achievements of South African entomologist Dr Jason G. H. Londt. In celebration of Londt’s prolific and inspiring work, the issue was published to coincide with his 80th birthday in 2023.
For more than 50 years, Londt has made a notable impact on South African and international entomology, collecting large numbers of Diptera and other insect orders. He has made outstanding contributions to the entomological research on flies, especially assassin or robber flies (Diptera, Asilidae), on hangingflies (Mecoptera, Bittacidae), and field collections of insects, primarily in South Africa.
Throughout his career, he has described more species of Afrotropical Asilidae and Bittacidae (Mecoptera) than any other author.
“Today, some 952 Asilidae species are recognised from southern Africa and thanks to Jason’s exceptional collecting efforts and detailed revisionary taxonomic publications these species can be easily identified,“ write African Invertebrates editors John Midgley and Torsten Dikow in the editorial to the Festschrift.
The Festschrift includes nine articles celebrating Dr Londt’s career by authors from three continents, covering the broad contributions that he has made to Afrotropical entomology. It also introduces five new species described in his honour, one hangingfly and four true flies.
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For updates about African Invertebrates and its latest publications, follow the journal on Twitter and Facebook. You can also sign up for the journal’s newsletter from the Email alert panel accessible from the homepage.
