Category: Uncategorized

Faster, Better, Stronger: New batch of updates now available in ARPHA Writing Tool

Only a couple of months ago, we announced a whole set of exciting features newly applied to ARPHA Writing Tool, based on the feedback we received from our users. Now, we are delighted to announce that we are back with a fresh batch of updates.

Here’s what we recently got in store for all authors in Research Ideas and Outcomes (RIO), Biodiversity Data Journal, One Ecosystem and BioDiscovery, all powered by the innovative end-to-end journal publishing platform ARPHA and making use of the new-age ARPHA Writing Tool:

We have become faster. ARPHA has been optimised, so that it is even easier to prepare your manuscript. Enjoy your references and whole datasets being delivered straight into your draft in the blink of an eye!

Speaking of references, we have updated our Reference Parser. Simply copy-paste a reference in the box and click Parse – ARPHA Writing Tool will have it ready to go on your list momentarily!

Yet, there’s even more to the reference-related updates! To double-check an in-text citation in your manuscript, all you need to do is hover over it to see the full-text reference it is linked to.

Our new toolbar and re-arranged functionalities make up for the better intuitivity of the ARPHA Writing Tool that welcomes you the moment you open a new manuscript.

Hover over the new toolbar and you will notice another new perk we have added for your convenience. Keyboard shortcuts are now implemented to the ARPHA Writing Tool to let you add smart objects as you type.

Get a stronger grip on your figures! Two new buttons let you re-order your figures either by number, or by order of appearance. Alternatively, enter editing mode and simply drag and drop any figure wherever you wish.

We thank you for your continuous feedback which helps us focus on tailoring the ARPHA Writing Tool according to the needs and taste of our clients.

We are already working hard on the next updates, so keep an eye on us!

In the meantime, please feel welcome to test our new features and let us know what you think. We will be happy to address any comments and requests on info@arphahub.com.

RAINBIO: a mega database improves knowledge on distribution of vascular plants in tropical Africa

Last November, PhytoKeys published an exciting paper on the launch of the first-of-its kind RAINBIO mega database of tropical African vascular plant distributions.

The publication is part of the RAINBIO project (African RAIN forest community dynamics: implications for tropical BIOdiversity conservation and climate change mitigation, http://rainbio.cesab.org) funded by CESAB (CEntre de Synthèse et d’Analyse sur la Biodiversité) of the FRB (Fondation pour la Recherche sur la Biodiversité, France). Making use of the innovative data paper format, offered by most Pensoft journals, the project announced is key product – a state-of-the-art high quality mega database of vascular plant species distribution across tropical Africa.

The RAINBIO mega database is a response to the limited knowledge of plant species distribution patterns when it comes to the tropical vegetation of Africa. Africa’s vegetation is characterised by high levels of species diversity. However, it is now undergoing important shifts in response to the challenges of ongoing climate change and increasing anthropogenic pressures. To better foster conservation and preservation of ecosystems, basic knowledge about plant species distribution is an important prerequisite.

To compile a comprehensive collection of data, RAINBIO merged large publicly available datasets, in combination with smaller private databases, resulting in a mega database containing 609,776 unique georeferenced records allowing the exploration and extraction of distributional data for 22,577 plant species across continental tropical Africa.

After announcing the database with us at the end of last year, the project published a companion research article providing a state-of-the-art synthesis about our understanding of vascular plant distribution across tropical Africa. The paper, published in BMC Biology concludes that botanical exploration of tropical Africa is far from complete, stressing the importance of continued field inventories and herbarium digitization of past collections.

Analysing this unique dataset provides some important insights into African biodiversity. For example, the observed number of tree species for African forests was smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. The article also contains a comprehensive list of the total number of plant species for 31 countries across tropical Africa.

The data compiled in the RAINBIO database provides a solid basis for a more sustainable management and improved conservation of tropical Africa’s unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011–2020.

Original Sources:

Dauby G, et al. (2016) RAINBIO: a mega-database of tropical African vascular plants distributions. PhytoKeys 74: 1-18. https://doi.org/10.3897/phytokeys.74.9723

Sosef M S M, et al. (2016) Exploring the floristic diversity of tropical Africa. BMC Biology 15:15. https://doi.org/10.1186/s12915-017-0356-8

Journal publishing platform ARPHA partners with content recommendation engine TrendMD

Thanks to the new collaboration between content recommendation engine TrendMD and journal publishing platform ARPHA, readers of all journals under Pensoft’s imprint, as well as those using the white-label publishing solution provided by the platform, will be given a useful list of recommended articles related to the study they are reading. The new widget is to save the users a great amount of time, by simply pointing them to the most relevant papers on the topic from across a constantly expanding network of of peer-reviewed articles and research news.

While nearly 8,000 new scholarly articles are published each day, it is basically impossible staying up-to-date with the news from a single scientific field, let alone doing cross-disciplinary research. Furthermore, sifting out the quality literature is another painstaking activity no academic is looking forward to. Hence, TrendMD comes as the sensible solution to help a reader find the most relevant and fine studies on a particular topic. The widget’s recommendations are based on the topic a user is currently reading, what papers they have read in the past, and the articles others with similar interests have sought out – all available from the most authoritative and quality journals in the world.

“TrendMD is excited to welcome Pensoft, a highly innovative, open access, online publishing platform, to the TrendMD network! This partnership will bring over 5,000 open access articles and books in the field of natural history, predominantly taxonomy and organismal biology, to TrendMD’s ever expanding network,” says Paul Kudlow, CEO and co-founder of TrendMD.

“In our continuing effort to develop and implement the most novel tools and workflows in academic publishing, at Pensoft we are pleased to have integrated our journal publishing platform ARPHA with the new-age scholarly innovation that is TrendMD’s tool, so that our readers have an easy and constant access to the most relevant and best-quality research,” says Pensoft’s CEO and founder Prof. Lyubomir Penev.

Five new Pensoft journals integrated with Dryad to improve data discoverability

Academic publisher Pensoft strengthens partnership with Dryad by adding its latest five journals to the list integrated with the digital repository. From now on, all authors who choose any of the journals published under Pensoft’s imprint will be able to opt for uploading their datasets on Dryad. At the click of a button, the authors will have their data additionally discoverable, reusable, and citable.

Started in 2011 as one of the first ever integrated data deposition workflows between a repository (Dryad) and a publisher (Pensoft), the partnership has now been reinforced to cover publications submitted to any of Pensoft’s 21 journals, including recently launched Research Ideas and Outcomes (RIO) and One Ecosystem, as well as BioDiscovery, African Invertebrates and Zoologia, which all moved to Pensoft within the last year.

By agreeing to deposit their datasets to Dryad, authors take advantage of a specialised and highly acknowledged platform to easily showcase and, hence, take credit for their data. On the other hand, the science community, including educators and students, can readily access the data, facilitating verification, citability and even potential collaborations.

“Dedicated to open and reproducible science, at Pensoft we have always strived to encourage our authors to make their research as transparent and, hence, trustworthy as possible, by providing the right infrastructure and support,” says Pensoft’s founder and CEO Prof. Lyubomir Penev. “By strengthening our long-year partnership with Dryad, I envision more and more authors, who publish in our journals, adding open data to their list of best practices.”

“Dryad works to promote data that are openly available, integrated with the scholarly literature, and routinely re-used to create knowledge,” said Dryad’s Executive Director, Meredith Morovati. “We are encouraged by the growth of our partnership with Pensoft, one of our earliest supporters. We are honored to provide services to Pensoft authors to ensure their data is openly available, linked to the article, and preserved for future use and for the future of science.”

Articles published in journals on ARPHA indexed by ReadCube for easier discoverability

While research outputs are being published at a rate greater than ever, it is becoming more and more likely to simply pass by the study that is most relevant to your particular interest. This is where ReadCube comes to aid. Now, thanks to the new partnership between ARPHA and ReadCube, all articles in the journals published on Pensoft‘s ARPHA platform, have been indexed and therefore, easily discoverable via ReadCube’s free web, desktop and mobile apps.

“Our mission is to ensure that scholarly literature is not only easily discoverable but also that each article itself is seen as a conduit for deeper discovery, not simply an endpoint,” said Robert McGrath, CEO at ReadCube. “This collaboration with Pensoft supports both these objectives, and we are thrilled to have them as a partner.”

In addition to advanced searchability, all Pensoft articles are also available in ReadCube’s Enhanced PDF format. While maintaining the simple and clean look of a standard PDF at first glance, Enhanced PDFs offer interactive feature connecting the reader to relevant information around the article including supplements, article metric, annotation tools, clickable in-line references and even hyperlinked author names which redirect readers to the author’s historical publications.

“I am pleased to see all journals published on ARPHA, which is to say not only the ones published by Pensoft, but also those that use our white-label journal publishing platform, being indexed by ReadCube,” said Pensoft’s founder and CEO Prof Lyubomir Penev. “As a strictly open-access publisher and technological provider with a strong background in semantic content enrichment, Pensoft has always strived to keep research as accessible and discoverable as possible. We are very pleased to collaborate with like-minded people who have their own innovative view on science to be on hand to anyone who asks for it.”

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Additional information:

About ReadCube:

ReadCube develops software to make the world of research more accessible and connected – serving researchers, publishers, academic and commercial organizations.

ReadCube’s web, desktop, and mobile reference management apps, including the ReadCube and Papers brands, dramatically improve the ways researchers find, organize, read, share, and cite research literature

ReadCube’s publisher solutions, adopted by over 70 partners to date, include indexing via Readcube Discover, enhanced PDF viewing and sharing via ReadCube Connect, and article-level ecommerce via ReadCube Checkout.

About ARPHA:

ARPHA is the first end-to-end journal publishing solution that supports the full life cycle of a manuscript, from authoring through submission, peer review, publication and dissemination. With ARPHA, journals and publishers enjoy a complete set of services, which enable tailored, technologically advanced publishing solutions. The platform enables a variety of publishing models through a number of options for branding, production and revenue models to choose from.

Publishing platform ARPHA partners with Altmetric to track online attention to research

With a research output mentioned online every 1.8 seconds, it only makes sense for the science community to grow curious of how they could access the knowledge of this public interest to better and build on their work.

Journal publishing platform ARPHA, developed by academic publisher Pensoft, has partnered with Altmetric to enable authors, readers and other users to track the online shares and discussions relating to each research output in journals published on ARPHA.

Thanks to the integration, a single click in the top menu of an article reveals the Altmetric donut visualisation, which provides an at-a-glance summary of the attention the item has received. The colours of the donut reflect the source of the attention, and the user can click on the image to be taken to the Altmetric details page, which provides a record of all of the mentions. Data is updated in real-time to provide insight into how the item is being received and shared.

To deliver such detailed information, Altmetric follows 2,000 mainstream media outlets in over 30 languages, social networks, public policy documents, post-publication peer-review forums, online reference managers, blogs, and Wikipedia.

As a result, all authors, readers, editors and funders can easily and immediately track the popularity, reception and impact of each of their studies.

“Having built an extensive portfolio of innovations as a technological provider, we are always looking forward to making yet another effort at providing our users with the best-quality experience. The integration of Altmetric data provides us with another opportunity to do exactly this,” says Pensoft’s founder and CEO Prof Lyubomir Penev.

“Furthermore, the science community has long been in need of a more adequate measure of the influence and engagement of individual research outputs, and Altmetric provides this.”

Altmetric’s Founder Euan Adie adds, “We’re excited to see the Altmetric badges being implemented across the ARPHA platform. Helping researchers get credit for their work and demonstrate its reach and influence is a core part of what we do, and this integration provides new opportunities to do so.”

The Altmetric badges and associated details pages are now available for all articles within Pensoft’s journals, as well as the journals using the white-label publishing available from ARPHA.

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Additional information:

About Altmetric:

Altmetric was founded in 2011 and has made it a mission to track and analyze the online activity around scholarly literature. Altmetric tracks what people are saying about research outputs online and works with some of the biggest publishers, funders, and institutions around the world to deliver this data in an accessible and reliable format. Altmetric is supported by Digital Science. Visit http://www.altmetric.com for more information, and follow on Twitter @altmetric.

About ARPHA:

New open access journal Rethinking Ecology publishes novel ideas under Pensoft’s imprint

Needless to say, it is through sharing new ideas and hypotheses that critical issues such as climate change and biodiversity loss can be addressed. However, few scientists are currently in a position to do so, because publishing bold ideas in peer-reviewed journals is very difficult, especially for those who are not world-renowned scientists in their field. At the same time, scientists sharing novel ideas that have not been published yet, carry the risk of being ‘scooped’. This is probably a scientist’s worst nightmare: seeing someone else publish the idea they have been working on. In this context, many innovative ideas are kept secret and it can take years before they are made available to the scientific community.

This is the niche that the novel open access peer-reviewed journal Rethinking Ecology aims to fill by providing a platform for forward thinking and publication of novel ideas in all aspects of ecology, evolution and environmental science.

Adding to its innovative nature, Rethinking Ecology joins the modern technologically advanced Pensoft journals published on next-generation platform ARPHA (abbreviation standing for Authoring, Reviewing, Publishing, Hosting and Archiving). Not only is the platform to provide fast-track and convenient publishing for the authors, reviewers and editors in Rethinking Ecology, as it takes care of a manuscript through all stages from authoring and reviewing to dissemination and archiving, but it is user-friendly to the readers as well, who enjoy publications in three formats (PDF, XML, HTML) and full of semantic enhancements.

The innovative journal aims to encourage all scientists, regardless of their seniority, publication track record, gender, or country of origin, to publish perspective papers, so that they are put in the open for peers to discuss and build on, while credit is given where credit is due. Publishing these ideas early also draws attention from the scientific community, potential collaborators and potential funders. To further avoid potential bias, Rethinking Ecology implements double-blind peer review, with the journal supporting the notion that it is the content of a manuscript that matters. Moreover, reviewers will not be asked for a formal recommendation. Instead, they will comment and evaluate the work against a set of specific questions. Thus, each paper ends up with a score on Novelty, Feasibility, Scholarship and Literacy, so that only perspective papers with an emphasis on novel hypotheses and bold ideas are accepted for publication.

Another innovative feature applied in the new journal is an Author Contribution Index (ACI), meaning that each publication will include a pie chart pointing to the contribution of each of the authors, estimated in percentage. This is the editors’ answer to the so-called ‘guest authorship’ (i.e. inclusion of authors who did not significantly contribute to the work).

It is no coincidence that Rethinking Ecology has a spiral-shaped unfurling fern leaf as a logo. Called Koru in the language of the indigenous Polynesian people of New Zealand – Māori, it symbolises novelty, new life and new beginning, as well as perpetual movement.

“Each publication in Rethinking Ecology can be seen as the beginning of life for a new idea and its metaphorical unfurling as it reaches out to the scientific community,” explain the journal editors in their very first Editorial at Rethinking Ecology.

“We see Rethinking Ecology as an incubator for novel ideas, and a catalyst for new thinking,” says the journal’s Editor-in-Chief Dr Stephane Boyer, Unitec Institute of Technology, New Zealand.

“In a world where scientific publications are increasingly open source and immediately available, it makes no sense to keep our most innovative ideas hidden from the world for years while we secretly test them,” he elaborates. “Bold ideas and new hypotheses need to be shared, they may or may not turn into world-changing paradigm shifts, but they all have the potential to contribute to new thinking.”

“I am pleased to welcome a groundbreaking journal such as Rethinking Ecology to the Pensoft family, which has already built a nice and extensive portfolio of innovations in scholarly publishing,” says Pensoft’s founder and CEO Prof. Lyubomir Penev. “Seeing genuine ideas and hypotheses yet to be tested, and possibly, yet to revolutionise the ecological science is certainly a thing worthy of eager anticipation.”

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About ARPHA:

The Caucasus as an ‘island’ in the ‘sea’ of steppes: New insights in mosquito evolution

From a geographical point of view, the Caucasus is far from an island or even a peninsula, being a relatively big mountainous region appearing as a fence at the border of Europe and Asia, situated between the Black and the Caspian seas. However, a study into the chromosome structure of mosquito larvae of the species Glyptotendipes salinus, living by a saltwater lake in the foothills of the Caucasus, suggests that the region could be imagined as an “island” in the “sea” of steppes.

Scientists Dr Mukhamed Karmokov, Tembotov Institute of Ecology of Mountain territories, Russian Academy of Science, and Dr Azamat Akkizov, Institute of Biomedical Problems, RAS, and Center of Medico-Ecological Researches, have their paper, where they describe the Caucasian population of the species, published in the open access journal Comparative Cytogenetics.

Earlier, it has been known that in the Tambukan Lake, located at the foothills of the Caucasus Mountains, lives at least one of the representatives of the genus Glyptotendipes, more precisely, the species G. salinus. Actually, the process of studying the fauna of the genus in the Caucasus region has just began and many questions have remained unclear.

During their research, the authors collected a sufficient amount of larvae of G. salinus that made it possible to study the chromosome structure, rearrangements and peculiarities of the Caucasian population of the species. In addition, the authors tried to understand how the population relates to the previously studied ones, living in the Altai region of Russia and Kazakhstan.

Researchers found interesting, some of them even striking, peculiarities in the chromosome structure and morphology of the larvae from Caucasus. Namely, they found four new chromosome rearrangements, likely unique for the Caucasus. Also, some of the chromosome characters were most similar to the mosquitoes from Altai, while others — to the population in Kazakhstan. The most curious difference of the Caucasian larvae in comparison to data from earlier studies was that they were twice as short.

In conclusion, the authors note that from the obtained data it could be deduced that that the Caucasian population had undergone a significant divergence, or even that it represents a subspecies.

Also, it turns out that the Caucasus itself is a relatively isolated and complex region in terms of microevolution. “The Caucasus, in some sense, can be imagined as a relatively isolated territory, a special place, where evolution has made some unexpected twists,” they say.

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Original source:

Karmokov MKh, Akkizov AY (2016) Karyotype characteristics, larval morphology and chromosomal polymorphism peculiarities of Glyptotendipes salinus Michailova, 1983 (Diptera, Chironomidae) from Tambukan Lake, Central Caucasus. Comparative Cytogenetics 10(4): 571-585. https://doi.org/10.3897/compcytogen.v10i4.9400

Business: Theory and Practice journal moves to the ARPHA white label publishing platform

Vilnius Gediminas Technical University and Pensoft launch a new joint pilot project for the open access peer-reviewed journal BTP

In a new joint pilot project, the open access peer-reviewed journal Business: Theory and Practice (BTP), issued by VGTU Press since 2000, runs on the new journal publishing platform ARPHA, developed by Pensoft. ARPHA provides end-to-end technological solution for all peer-review stages starting from submission to fully functional dedicated new website. Publications are also available in semantically enriched HTML and XML formats, as well as the traditional PDF. The journal’s authors and editors enjoy easily manageable peer-review workflow in ARPHA.

Business: Theory and Practice publishes original research articles and reviews that integrate economic development and globalization, interpretations and consequences of entrepreneurship, strategic management and organizational behavior, theoretical questions and empirical questions of industrial organizations. It covers a variety of fields, including business environment, economic development and globalization, entrepreneurial finance, interpretations and consequences of entrepreneurship, strategic management, organizational behavior, theoretical questions and empirical questions of industrial organization, and case studies.

BTP has opted for the ARPHA-DOC publishing workflow, which provides an individually designed website under the imprint and logo of VGTU Press, a document-based article submission, as well as peer review, publication, hosting and dissemination. The manuscripts submitted to BTP will be subject to double-blind peer review.

“It is a great pleasure to work with the Pensoft team on establishing an innovative publishing platform for Business: Theory and Practice. I am sure the new platform will exceed the expectations of all – the authors, the editors and the readers,” says VGTU Press Director Eleonora Dagiene.

“Academic publishing is in a process of disruptive transition. As a result, small journal publishers and society journals are strongly affected and threatened with decline and even extinction. This is because access to high-level publishing technologies is not easy and, in most cases, not affordable. So, we developed ARPHA specially for them! ARPHA is not only an end-to-end journal publishing platform, covering the whole process from website design, authoring, editorial management and peer-review to publishing and dissemination – it also delivers a wide range of easily customizable end-to-end services, on the choice of the journal. I am glad to see Business: Theory and Practice published by VGTU Press as the first Lithuanian journal coming to the ARPHA platform and becoming a member of ARPHA’s growing family of international partners,” says Pensoft’s founder and CEO Prof. Lyubomir Penev.

The articles accepted for the current issue of 2016 in BTP, published via ARPHA, are already available on the journal’s new website.

ARPHA is open to journals looking for a technologically advanced publishing platform plus all associated services, which can be customized to the journal’s preferences.

People can simultaneously give a hand to endangered apes and stay at safe distance

Primates claim the highest proportion of endangered species among all mammals, according to the IUCN Red List. Yet, the substantial conservation interference from humans, which is already in place, could itself lead to even greater losses.

Plenty of studies have proven that while researchers and ecotourists raise vital for ape conservation knowledge and funds, it is actually human presence that compromises primates’ well-being due to extremely similar genetics and, thereby, easily transmittable diseases, ranging from common cold to human tuberculosis and Ebola fever.

In a paper published in the open access journal BioRisk, Rhiannon Schultz, Miami University, seeks the golden mean between giving ape species a hand and keeping safe distance. To showcase the impact human have on primates, the scientist makes example of the Mountain gorilla, an endangered species living in the montane forests of the Democratic Republic of Congo, Uganda and Rwanda.

Simply being in close proximity to primates, humans can easily transmit a wide range of diseases to the animals, including intestinal parasites, hepatitis, tuberculosis, Typhoid fever, Cholera, and Ebola fever. The transmission can occur as easily as having the two species breathing the same air, or the people leaving a banana peel behind.

Furthermore, threats to the gorilla species are also posed by the humans destroying the primates’ habitats. The result is overlapping populations, where a disease is much easier to transmit among the small gorilla populations. For example, normally an ill individual would be put under a ‘natural quarantine’, which is impossible when the habitat has already been reduced.

In the meantime, banning people, both tourists and scientists, from gorilla habitat is not an option, since knowledge about the populations’ dynamics is essential for the conservation of all primate species. On the other hand, ecotourism is what raises a great part of the resources need for conservation work. Income from gorilla trekking is enough to support the Ugandan Wildlife Authority, while also contributing a significant part to the country’s national budget.

The key, Rhiannon Schultz concludes, is to, firstly, promote understanding of the risk for interspecies disease transmission as a conservation threat, and then, improve on current protocols and regulations.

“It may be difficult to ask tourists to wear masks while visiting animals in the wild, and it may be expensive to maintain a veterinary program for wild populations and to improve healthcare systems for local people, but making these improvements could be the key to preventing disease transmission to not only Mountain gorillas but also to other apes,” sums up the scientist.

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Original source:

Schultz R (2016) Killer Conservation: the implications of disease on gorilla conservation.BioRisk 11: 1-11. doi: 10.3897/biorisk.11.9941