ResearchGate, the professional network for researchers, and Pensoft today announced a new partnership that will see a set of Pensoft’s open access journals increase their reach and visibility through ResearchGate – increasing access and engagement with its 25 million researcher members.
As part of this new partnership, 20 journals published by Pensoft – including the publisher’s flagship titles ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal and Research Ideas and Outcomes (RIO Journal) amongst others – will now have their content automatically added to ResearchGate upon publication to benefit from enhanced visibility and discoverability through ResearchGate’s innovative Journal Home offering. These journals will all have dedicated profiles and be prominently represented on all associated article pages on ResearchGate, as well as all other relevant touch points throughout the network.
Journal Home provides a unique opportunity for Pensoft to connect its authors with their readers. The new journal profiles on ResearchGate will provide a central location for each journal, enabling researchers to learn more, discover new article content, and understand how, through their network, they are connected to the journal’s community of authors and editors. Authors of these journals additionally benefit from having their articles automatically added to their ResearchGate profile page, giving them access to metrics, including who is reading and citing their research. These rich insights will also enable Pensoft to build a deeper understanding of the communities engaging with its journals.
“Pensoft is delighted to be working with ResearchGate to provide an even greater service to our authors and readers. ResearchGate offers an innovative way for us to grow the reach and visibility of our content, while also giving us a way to better understand and engage our author and reader audiences.”
said Prof Lyubomir Penev, CEO and founder of Pensoft.
“We couldn’t be happier to see Pensoft embark on this new partnership with ResearchGate. Journal Home will not only enable Pensoft authors to build visibility for their work, but provide them and Pensoft with greater insights about the communities engaging with that research. I look forward to seeing this new collaboration develop”
said Sören Hofmayer, co-founder and Chief Strategy Officer at ResearchGate.
ResearchGate is the professional network for researchers. Over 25 million researchers use researchgate.net to share and discover research, build their networks, and advance their careers. Based in Berlin, ResearchGate was founded in 2008. Its mission is to connect the world of science and make research open to all.
A recent update introduced to the CMSY methodology used to assess the status of fish stocks has proven to more accurately predict the catch that a population can support than highly valued data-intensive models.
In a paper published in the journal Acta Ichthyologica et Piscatoria, the international team of researchers that shaped the improved CMSY++ model noted that its results better correspond with what is, in reality, the highest catch that a fish stock can support in the long-term, given that environmental conditions do not change much.
Now powered by an artificial neural network that has been trained with catch and biomass data of 400 stocks to identify plausible ranges of the initial and final state of the stocks being assessed, CMSY++ allows managers and scientists to input only catch data to estimate how much fish is left in a given stock and how much fishing pressure can be applied.
Maximum sustainable catches or yield (MSY) is a concept developed in the 1950s by US fisheries scientist M.B. Schaefer who proposed that if fishers left in the water a biomass equivalent to at least 50 per cent of the unexploited fish population, that is, of the biomass it had before being commercially exploited, then the highest possible catches could be sustained over time.
“By comparing the results of CMSY++ to models that are considered superior because they require large amounts of initial data inputs, such as the Fox surplus-production model and the Stock Synthesis (SS3) age-structured model, we noticed that these models badly overpredicted the catch that a population can support when previous overfishing has reduced it to a small fraction of its natural size, as is the case with most exploited fish populations in the world.”
Dr. Rainer Froese, lead author of the study and a senior scientist at the GEOMAR Helmholtz Centre for Ocean Research.
In other words, the model underlying the CMSY++ method fitted the observed data, while the predictions of the ‘gold standard’ models were too optimistic in estimating sustainable catches.
“These models tend to estimate the biomass required to produce maximum sustainable yields as less than half of unexploited biomass, which is lower than M.B. Schaefer originally proposed based on the widely observed S-shaped growth curve of unexploited populations or population size that the ecosystem would normally accommodate.
“This finding could explain the often-observed failure of fisheries managers to maintain or rebuild depleted stocks even when the predictions of the gold standard models were followed.”
Daniel Pauly, co-author of the study and principal investigator of the Sea Around Us initiative at the University of British Columbia.
Froese R, Winker H, Coro G, Palomares MLD, Tsikliras AC, Dimarchopoulou D, Touloumis K, Demirel N, Vianna GMS, Scarcella G, Schijns R, Liang C, Pauly D (2023) New developments in the analysis of catch time series as the basis for fish stock assessments: The CMSY++ method. Acta Ichthyologica et Piscatoria 53: 173-189. https://doi.org/10.3897/aiep.53.e105910
Armored catfish (Pterygoplicthys spp.) and microplastics, as invasive species and emerging contaminants, respectively, represent two socio-environmental problems in the globalized world, since both have negative effects on faunistic communities and freshwater habitats, as well as on rural community fisheries and public health.
Non-native invasive species of armored catfish have become numerically dominant in some ecosystems, with efforts to eradicate them a seemingly endless task. Due to this, a possible scenario of biological homogenization in Mesoamerica can be expected, mainly given by the wide dispersion of the Pterygoplichthys species, added to the introduction of other non-native catfish species.
The omnipresence of plastics in terrestrial and aquatic environments is caused by their excessive use and inadequate management of waste. The discarded plastics are fragmented, degraded, and dissolved by solar radiation, wind, and water, among other agents, to be incorporated into the food web in aquatic environments.
Both persist in the aquatic environment, microplastics forming the disproportionate amount of plastic garbage, and catfish thanks to their tolerance to pollution and anoxic environments, and their ability to survive for several hours breeding atmospheric oxygen. What is the relationship between the two? Microplastics, depending on their origin and composition, are sedimented in the wetlands, where they can be ingested by detritus feeders, such as armored catfish, mainly in areas where there is runoff or discharge of liquid waste.
In this context, we ask ourselves, can armored catfish be used as biomonitors of microplastics deposited in wetlands? Taking the above into consideration, the doctoral student Gabriela Angulo-Olmos under the guidance of the researchers Nicolás Álvarez-Pliego, Alberto J. Sánchez, Rosa Florido, Miguel Ángel Salcedo, Allan K. Cruz-Ramírez and Arturo Garrido Mora from the Laboratorio de Humedales, from the División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, decided to answer the aforementioned question based on the numerical dominance of armored catfish recorded in the aquatic ecosystems of the Metropolitan Area of Villahermosa (MAV) in the coastal plain of the Gulf of Mexico.
The stomach contents of the specimens from a lake located in the MAV were reviewed and the results showed that all the specimens had consumed microfibers. This result corroborated that these organisms can ingest sedimented microplastics due to their benthophagous habits.
The use of armored catfish as a resource in the food industry has had positive results, but is still insufficient. Therefore, we propose that another option to control their populations is to subtract and use this organism to verify which are the most frequent and abundant emerging contaminants deposited in the bottoms of urban wetlands.
Angulo-Olmos G, Alvarez-Pliego N, Sánchez AJ, Florido R, Salcedo MÁ, Garrido-Mora A, Cruz-Rámirez AK (2023) Microfibers in the gut of invasive armored catfish (Pterygoplichthys spp.) (Actinopterygii: Siluriformes: Loricariidae) in an urban lake in the floodplain of the Grijalva River basin, Mexico. Acta Ichthyologica et Piscatoria 53: 81–88. https://doi.org/10.3897/aiep.53.102643
Nanopublications complement human-created narratives of scientific knowledge with elementary, machine-actionable, simple and straightforward scientific statements that prompt sharing, finding, accessibility, citability and interoperability.
By making it easier to trace individual findings back to their origin and/or follow-up updates, nanopublications also help to better understand the provenance of scientific data.
With the nanopublication format and workflow, authors make sure that key scientific statements – the ones underpinning their research work – are efficiently communicated in both human-readable and machine-actionable mannerin line with FAIR principles. Thus, their contributions to science are better prepared for a reality driven by AI technology.
The machine-actionability of nanopublications is a standard due to each assertion comprising a subject, an object and a predicate (type of relation between the subject and the object), complemented by provenance, authorship and publication information. A unique feature here is that each of the elements is linked to an online resource, such as a controlled vocabulary, ontology or standards.
Nanopublications associated with a manuscript submitted to BDJ. This workflow lets authors add a Nanopublications section within their manuscript while preparing their submission in the ARPHA Writing Tool (AWT). Basically, authors ‘highlight’ and ‘export’ key points from their papers as nanopublications to further ensure the FAIRness of the most important findings from their publications.
Standalone nanopublication related to any scientific publication, regardless of its author or source. This can be done via the Nanopublications page accessible from the BDJ website. The main advantage of standalone nanopublication is that straightforward scientific statements become available and FAIR early on, and remain ready to be added to a future scholarly paper.
Nanopublications as annotations to existing scientific publications. This feature is available from several journals published on the ARPHA Platform, including BDJ. By attaching an annotation to the entire paper (via the Nanopublication tab) or a text selection (by first adding an inline comment, then exporting it as a nanopublication), a reader can evaluate and record an opinion about any article using a simple template based on the Citation Typing Ontology (CiTO).
Nanopublications for biodiversity data?
At Biodiversity Data Journal (BDJ), authors can now incorporate nanopublications within their manuscripts to future-proofthe most important assertions on biological taxa and organisms or statements about associations of taxa or organisms and their environments.
On top of being shared and archived by means of a traditional research publication in an open-access peer-reviewed journal, scientific statements using the nanopublication format will also remain ‘at the fingertips’ of automated tools that may be the next to come looking for this information, while mining the Web.
Using the nanopublication workflows and templates available at BDJ, biodiversity researchers can share assertions, such as:
So far, the available biodiversity nanopublication templates cover a range of associations, including those between taxa and individual organisms, as well as between those and their environments and nucleotide sequences.
As a result, those easy-to-digest ‘pixels of knowledge’ can capture and disseminate information about single observations, as well as higher taxonomic ranks.
The novel domain-specific publication format was launched as part of thecollaboration betweenKnowledge Pixels – an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing and the open-access scholarly publisherPensoft.
Basically, a nanopublication – unlike a research article – is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists as a reusable and cite-able pieces of a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.
These semantic statements expressed in community-agreed terms, openly available through links to controlled vocabularies, ontologies and standards, are not only freely accessible to everyone in both human-readable and machine-actionable formats, but also easy-to-digest for computer algorithms and AI-powered assistants.
In short, nanopublications allow us to browse and aggregate such findings as part of a complex scientific knowledge graph. Therefore, nanopublications bring us one step closer to the next revolution in scientific publishing, which started with the emergence and increasing adoption of knowledge graphs.
“As pioneers in the semantic open access scientific publishing field for over a decade now, we at Pensoft 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,”
By letting computer algorithms access published research findings in a structured format, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each of those fragmentsof scientific information is interconnected and traceable back to its author(s) and scientific evidence.
By building on shared knowledge representation models, 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 , ready to be reused (as per the R in FAIR) in new contexts.
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.
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.
We encourage you to try the nanopublications workflow yourself when submitting your next biodiversity paper to Biodiversity Data Journal.
Community feedback on this pilot project and suggestions for additional biodiversity-related nanopublication templates are very welcome!
On the journal website: https://bdj.pensoft.net/, you can find more about the unique features and workflows provided by the Biodiversity Data Journal (BDJ), including innovative research paper formats (e.g. Data Paper, OMICS Data Paper, Software Description, R Package, Species Conservation Profiles, Alien Species Profile), expert-provided data audit for each data paper submission, automated data export and more.
Don’t forget to also sign up for the BDJ newsletter via the Email alert form on the journal’s homepage and follow it on Twitter and Facebook.
Earlier this year, Knowledge Pixels and Pensoft presented several routes for readers and researchers to contribute to research outputs – either produced by themselves or by others – through nanopublications generated through and visualised in Pensoft’s cross-disciplinary Research Ideas and Outcomes (RIO) journal, which uses the same nanopublication workflows.
All journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
In support of transparency and openness in scholarly publishing and academia, the scientific publisher and technology provider Pensoft joined the Journal Comparison Service (JCS) initiative by cOAlition S, an alliance of national funders and charitable bodies working to increase the volume of free-to-read research.
As a result, all journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
The JCS was launched to aid libraries and library consortia – the ones negotiating and participating in Open Access agreements with publishers – by providing them with everything they need to know in order to determine whether the prices charged by a certain journal are fair and corresponding to the quality of the service.
According to cOAlition S, an increasing number of libraries and library consortia from Europe, Africa, North America, and Australia have registered with the JCS over the past year since the launch of the portal in September 2021.
While access to the JCS is only open to librarians, individual researchers may also make use of the data provided by the participating publishers and their journals.
This is possible through an integration with the Journal Checker Tool, where researchers can simply enter the name of the journal of interest, their funder and affiliation (if applicable) to check whether the scholarly outlet complies with the Open Access policy of the author’s funder. A full list of all academic titles that provide data to the JCS is also publicly available. By being on the list means a journal and its publisher do not only support cOAlition S, but they also demonstrate that they stand for openness and transparency in scholarly publishing.
“We are delighted that Pensoft, along with a number of other publishers, have shared their price and service data through the Journal Comparison Service. Not only are such publishers demonstrating their commitment to open business models and cultures but are also helping to build understanding and trust within the research community.”
said Robert Kiley, Head of Strategy at cOAlition S.
About cOAlition S:
On 4 September 2018, a group of national research funding organisations, with the support of the European Commission and the European Research Council (ERC), announced the launch of cOAlition S, an initiative to make full and immediate Open Access to research publications a reality. It is built around Plan S, which consists of one target and 10 principles. Read more on the cOAlition S website.
About Plan S:
Plan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. Read more on the cOAlition S website.
By the time authors – who have acknowledged third-party financial support in their research papers submitted to a journal using the Pensoft-developed publishing platform: ARPHA – open their inboxes to the congratulatory message that their work has just been published and made available to the wide world, a similar notification will have also reached their research funder.
This automated workflow is already in effect at all journals (co-)published by Pensoft and those published under their own imprint on the ARPHA Platform, as a result of the new partnership with the OA Switchboard: a community-driven initiative with the mission to serve as a central information exchange hub between stakeholders about open access publications, while making things simpler for everyone involved.
All the submitting author needs to do to ensure that their research funder receives a notification about the publication is to select the supporting agency or the scientific project (e.g. a project supported by Horizon Europe) in the manuscript submission form, using a handy drop-down menu. In either case, the message will be sent to the funding body as soon as the paper is published in the respective journal.
“At Pensoft, we are delighted to announce our integration with the OA Switchboard, as this workflow is yet another excellent practice in scholarly publishing that supports transparency in research. Needless to say, funding and financing are cornerstones in scientific work and scholarship, so it is equally important to ensure funding bodies are provided with full, prompt and convenient reports about their own input.”
comments Prof Lyubomir Penev, CEO and founder of Pensoft and ARPHA.
“Research funders are one of the three key stakeholder groups in OA Switchboard and are represented in our founding partners. They seek support in demonstrating the extent and impact of their research funding and delivering on their commitment to OA. It is great to see Pensoft has started their integration with OA Switchboard with a focus on this specific group, fulfilling an important need,”
adds Yvonne Campfens, Executive Director of the OA Switchboard.
About the OA Switchboard:
A global not-for-profit and independent intermediary established in 2020, the OA Switchboard provides a central hub for research funders, institutions and publishers to exchange OA-related publication-level information. Connecting parties and systems, and streamlining communication and the neutral exchange of metadata, the OA Switchboard provides direct, indirect and community benefits: simplicity and transparency, collaboration and interoperability, and efficiency and cost-effectiveness.
Pensoft is an independent academic publishing company, well known worldwide for its novel cutting-edge publishing tools, workflows and methods for text and data publishing of journals, books and conference materials.
All journals (co-)published by Pensoft are hosted on Pensoft’s full-featured ARPHA Publishing Platform and published in a way that ensures their content is as FAIR as possible, meaning that it is effortlessly readable, discoverable, harvestable, citable and reusable by both humans and machines.
Somatic growth rate is a central life-history parameter, especially in species like fishes or invertebrates which grow throughout their lives. It is needed in conservation and fisheries management but it can sometimes be tricky to estimate.
Dr. Froese presents two new data-limited methods to estimate somatic growth from maximum length combined with either length or age at maturation or with maximum age. They are applicable to a wide range of species, sizes, and habitats. Using these new methods, growth parameter estimates were produced for the first time for 110 fish species.
“The growth estimates derived with the new methods presented in this study appear suitable for consideration and preliminary guidance in applications for conservation or management,” Dr. Froese points out in his study.
He goes on to suggest that journals accept growth estimates performed with the new methods as new knowledge, if they are the first for a given species.
In order to facilitate the conservation and management of natural resources, FishBase will continue to compile growth parameters, including results obtained with these new methods.
For the first time, scientists report a vampire fish attached to the body of an Amazonian thorny catfish. Very unusually, the candirus were attached close to the lateral bone plates, rather than the gills, where they are normally found. Since the hosts were not badly harmed, and the candirus apparently derived no food benefit, scientists believe this association is commensalistic rather than parasitic. The research is published in the open-access journal Acta Ichthyologica et Piscatoria.
Guest blog post by Chiara C. F. Lubich, André R. Martins, Carlos E. C. Freitas, Lawrence E. Hurd and Flávia K. Siqueira-Souza
The Amazon River Basin is home to about 15% of all freshwater fish species known to science, and an estimated 40% yet to be named. These include some of the most bizarre fishes: the vampire fishes, locally known as candiru, members of the catfish subfamily Vandelliinae.). They survive by attaching themselves to the bodies of other fish and sucking on their blood, hence their common name. Yet, it was only recently that we found out that one candiru species, belonging to the genus Paracanthopoma,seems to be making use of its host in quite a different way.
During a sampling study of freshwater fish fauna in a lake of the Demeni River Basin, a left bank tributary of the Negro River, we found candirus attached to the surface of the body of an Amazonian species of a thorny catfish. By the end of the survey, we had observed a total of twenty candirus attached to the outside of the bodies of nine larger Doras phlyzakion, one or two per host. Very unusually, the candirus were attached close to the lateral bone plates, rather than the gills, where these fish are normally found.
As a result of these observations, we recently published the first record of a candiru attached to the body surface of an Amazonian thorny catfish in an article in the open-access scholarly journal Acta Ichthyologica et Piscatoria.
Vampire fish have long and robust snouts, with strong dentary teeth that help them stay attached to the epidermis of their host and feed on its blood. However, when we performed a macroscopic analysis of the stomach contents of the preserved Paracanthopoma specimens, we were surprised to find no coagulated blood, nor flesh, skin or mucus. This might indicate an interaction between parasite and host that is more benign than usually attributed to vampire fish.
We believe the association between candiru and host in this case might be commensalistic (where one organism benefits from another without harming it), rather than parasitic, because the hosts were not badly harmed, and the candiru apparently derived no food benefit.
But what else would they seek on the back of Amazonian thorny catfish? One explanation could be that, since candirus are tiny and nearly transparent, they might be avoiding getting noticed by visual predators by riding on larger fish. Another hypothesis is that they could be using their big cousins to transport them over longer distances that they wouldn’t be able to cover themselves, eventually making it to safety or new food sources.
Lubich CCF, Martins AR, Freitas CEC, Hurd LE, Siqueira-Souza FK (2021) A candiru, Paracanthopoma sp. (Siluriformes: Trichomycteridae), associated with a thorny catfish, Doras phlyzakion (Siluriformes: Doradidae), in a tributary of the middle Rio Negro, Brazilian Amazon. Acta Ichthyologica et Piscatoria 51(3): 241-244. https://doi.org/10.3897/aiep.51.e64324
The scholarly publisher and technology provider Pensoft welcomes the latest addition to its diverse portfolio of scholarly outlets – the open-access, peer-reviewed journal Acta Ichthyologica et Piscatoria (AIeP), which publishes research in the fields of ichthyology and fisheries.
AIeP is an international scientific journal publishing articles in any aspect of ichthyology and fisheries concerning true fishes (fin-fishes), including taxonomy, biology, morphology, anatomy, physiology, pathology, parasitology, reproduction and zoogeography. The academic outlet, which was launched in 1970, favours research based on original experimental data or experimental methods, or new analyses of already existing data. AIeP is indexed by all major indexers, including Web of Science and Scopus. The journal’s first Impact Factor was released in 2010, and currently stands at 0.629 (2019).
In joining the Pensoft portfolio, AIeP gets a brand-new user-friendly website with improved design and access to Pensoft’s self-developed full-featured platform ARPHA, which offers an end-to-end publishing solution from submission to publication, distribution and archiving. With features, such as papers available in semantically enhanced HTML and machine-readable XML formats, automated data export to aggregators, and web-service integrations with major global indexing databases, the easy-to-use, open-access platform ensures that published research is easy to discover, access, cite and reuse by both humans and machines all over the world.
ARPHA is the first end-to-end, narrative- and data-integrated publishing solution that supports the full life cycle of a manuscript, from authoring to reviewing, publishing and dissemination. ARPHA provides accomplished and streamlined production workflows that can be customized according to the journal’s needs. The platform enables a variety of publishing models through a number of options for branding, production and revenue models to choose from.