Posts

Posted on

RIO Journal 5 years on: over 300 published outcomes from all around the research cycle

Five years on, the Open Science-driven journal Research Ideas and Outcomes (RIO) published an editorial that looks back on the 300 research ideas and research outcomes it has published so far.

Since its early days, RIO has enjoyed quite positive reactions from the open-minded academic community for its innovative approach to Open Science in practice: it provides a niche that had long been missing, namely the publication of early, intermediate and generally unconventional research outcomes from all around the research cycle (e.g. grant proposals, data management plans, project deliverables, reports, policy briefs, conference materials) in a cross-disciplinary scientific journal. In fact, several months after its launch, in 2016, the journal was acknowledged with the SPARC Innovator Award.

‘Alternative’ research publications

In times when posting a preprint was seen as a novel and rather bold practice across many fields, RIO facilitated much deeper dives into the research process, in order to unveil scientific knowledge and the process by which it is gathered, well before any final conclusions have been drawn. Long story short, to date, RIO has published 33 Research Ideas, 78 Grant Proposals, 16 Data Management Plans, 33 Workshop Reports and 5 PhD Project Plans, in addition to plenty of other early, interim and final non-traditional research outcomes, as well as conventional articles. Over time, RIO has kept adding additional article types to its list of publication types, with a few more expected in the near future.

What’s more, over the years, we’ve already observed how papers published in RIO successfully followed up on the continuity of the research process. For example, the Grant Proposal for the “Exploring the opportunities and challenges of implementing open research strategies within development institutions” project, funded by the International Development Research Centre (IDRC), was followed by the project’s Data Management Plan a year later.

Five years later, the figures reflecting the usage and engagement with the content published in RIO are evidently supportive of the value of having non-final and unconventional academic publications. For instance, the Grant Proposal for the COST Action DNAqua-Net, a still ongoing project dedicated to the development of novel genetic tools for bioassessment and monitoring of aquatic ecosystems, is the article with the most total views in RIO’s publication record to date. In the category of sub-article elements, whose usage is also tracked at the journal, the most viewed figure belongs to a Project Report and illustrates a sample code meant to be used in future neuroimaging studies. Similarly, the most viewed table ever published in RIO is part of a Workshop Report that summarises ASAPbio‘s third workshop, dedicated to the technical aspects of services related to the promotion of preprints in the biomedical and other life science communities.

Response to societal challenges

A unique and defining staple for RIO since the very beginning has also been the pronounced engagement with the Sustainable Development Goals (SDGs), as formulated by the United Nations right around the time of RIO’s launch. In order to highlight the societal impact of published research, RIO lets authors map their articles to the SDGs relevant to their paper. Once published, the article displays the associated badge(s) next to its title. Readers of the journal can even search RIO’s content by SDG, in the same way they would filter articles by subject, publication types, date or funding agency. Next on the list for RIO is to add another level of granularity to the SDGs mapping. The practice has already been piloted by mapping relevant RIO articles to the ten targets under SDG14 (Life below water).

Taking transparency, responsibility and collaboration in academia and scholarly publishing up another notch, RIO requires for reviews to be publicly available. In addition, the journal supports post-publication reviews, where peers are free to post their review anytime. In turn, RIO registers each review with its own DOI via CrossRef, in order to recognise the valuable input and let the reviewers easily refer to their contributions. A fine example is a Review Article exploring the biodiversity-related issues and challenges across Southeast Asia, which currently has a total of three public peer reviews, one of which is provided two years after the publication of the paper.

Public, transparent and perpetual peer review, pre- and/or post-publication

What’s more striking about peer review at RIO, however, is that it is not always mandatory. Given that the journal publishes many article types that have already been scrutinised by a legitimate authority – for instance, Grant Proposals that have previously been evaluated by a funder or defended PhD Theses – it only makes sense to avoid withholding these publications and duplicating associated evaluation efforts. On such occasions, all an author needs to do is provide a statement about the review status of their paper, which will be made public alongside the article.

On the other hand, where the article type of a manuscript requires pre-publication review, to avoid potential delays caused by the review process and editorial decisions, RIO encourages the authors to post their pre-review manuscript as a preprint on the recently launched ARPHA Preprints platform, subject to a quick editorial screening, which would only take a few days.

Further, RIO has now abandoned the practice of burdening the journal’s editors with the time-consuming task of finding reviewers, and instead requiring the submitting author to invite suitable reviewers upon submission, who are then immediately and automatically invited by the system. While significantly expediting the editorial work on a manuscript, this practice doesn’t compromise the quality of peer review in the slightest, since the reviews go public, while the final decision about the acceptance of the paper lies with the editor, who is also overlooking the process and able to intervene and invite additional reviewers anytime, if necessary.

Project-driven knowledge hub

The most significant novelty at RIO, however, is perhaps the newly assumed role of the journal as “a project-driven knowledge hub“, targeting specifically the needs of research projects, conference organisers and institutions. For them, RIO provides a one-stop source for the outputs of their scientists, in order to comply with the requirements of their funders or management, or simply to facilitate the discoverability, reusability and citability of their academic outputs and to highlight their interconnectedness.

Unlike typical permanent article collections, already widely used in scholarly publishing, with RIO, collection owners can take advantage of the unique opportunity to add a wide range of research outputs, including such published elsewhere, in order to provide even greater context to the assembled research outputs in their project- or institution-branded article collection (see the Horizon 2020 Project Path2Integrity‘s project collection as an example).

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

For example, a project coordinator could open a collection under the brand of the project, and start by publishing the Grant Proposal, followed shortly by Data and Software Management Plans and Workshop Reports. Thus, even at this early point in the project’s development, the funder – and with them everyone else – would already have strong evidence of the project’s dedication to transparency and active science communication. Later on, the project’s participants would all be able to easily add to the project’s collection by either submitting their diverse research outputs straight to RIO and having it accepted by the collection lead editor, or providing metadata and link to their publication from elsewhere, even preprints. If the document is published outside of RIO, its metadata, i.e. author names and affiliations, article title and publication date, show up in the collection, while a click on the item will lead to the original publication. As the project progresses, the team behind it could add more and more outputs (e.g. Project Reports, Guidelines and Policy Briefs), continuously updating the public and the relevant stakeholders about the development of their work. Eventually, the collection will be able to provide a comprehensive and fully transparent report of the project from start to finish.

###

Follow RIO Journal on Twitter, Facebook and LinkedIn.

Subscribe to RIO Journal’s blog for news updates.

Posted on

Centrally-managed collections & Peer review flexibility: what’s new at RIO

In 2015, Research Ideas and Outcomes (RIO) was launched to streamline dissemination of scientific knowledge throughout the research process, recognised to begin with the inception of a research idea, followed by the submission of a grant proposal and progressing to, for example, data / software management plans and mid-stage project reports, before concluding with the well-known research and review paper.

In order to really expedite and facilitate access to scientific knowledge, the hurdles for engagement with the process need to be minimized for readers, authors, reviewers and editors alike. RIO aims to lay the groundwork for constructive scientific feedback and dialogue that would then lead to the elaboration and refinement of the research work well in its early stage. 

Recently, RIO published its 300th article – about a software for analyzing time series data from a microclimate research site in the Alps – and at that occasion, the RIO team wrote an editorial summarizing how the articles published in RIO so far facilitate engagement with the respective research processes. One of the observations in this regard was that while providing access to the various stages of the research cycle is necessary for meaningful engagement, there is a need for the various outcomes to be packed together, so that we can provide a more complete context for individual published outcomes.

Read the new editorial celebrating RIO’s 5th anniversary and looking back on 300 publications.

RIO introduced updates to its article collection approach to evolve into a “project-driven knowledge hub”, where a project coordinator, research institution or conference organiser can create and centrally manage a collection under their own logo, so that authors can much more easily contribute. Further, research outputs published elsewhere – including preprints – are also allowed, so that the collection displays each part of the ‘puzzle’ within its context. In this case, the metadata of the paper, i.e. title, authors and publication date, are displayed in the article list within the collection, and link to the original source.

Apart from allowing the inclusion of the whole diversity of research outcomes published in RIO or elsewhere, what particularly appeals to projects, conferences and institutions is the simplicity of opening and managing a self-branded collection at RIO. All they need to do is pay a one-time fee to cover the setup and maintenance of the collection, whereas an option with an unlimited number of publications is also available. Then, authors can add their work – subject to approval by the collection’s editor and the journal’s editorial office – by either starting a new manuscript at RIO and then assigning it to an existing collection; pasting the DOI of a publication available from elsewhere; or posting an author-formatted PDF document to ARPHA Preprints, as it has been submitted to the external evaluator (e.g. funding agency). In the latter two cases, the authors are charged nothing, in order to support greater transparency and contextuality within the research process.

Buttons on RIO Journal’s homepage allow users to create a new collection or add a document to an existing collection by either submitting a new manuscript via RIO Journal or pasting a DOI link of a publication from elsewhere, thus allowing for the collection to link to the original source and display the article’s metadata, i.e. title, authors and publication date.

Find more information about how to edit a collection at RIO and the associated benefits and responsibilities on RIO’s website.

Another thing we have revised at RIO is the peer review policy and workflow, which are now further clarified and tailored to the specificity of each type of research outcome.

Having moved to entirely author-initiated peer review, where the system automatically invites reviewers suggested by the author upon submission of a paper, RIO has also clearly defined which article types are subject to mandatory pre-publication peer review or not (see the full list). In the latter case, RIO no longer prompts the invitation of reviewers. Within their collections, owners and guest editors can decide on the peer review mode, guided by RIO’s existing policies.

While pre-publication peer review is not always mandatory, all papers are subject to editorial evaluation and also remain available in perpetuity for post-submission review. In both cases, reviews are public and disclose the name of their author by default. In turn, RIO registers each review with its own DOI via CrossRef, in order to recognise the valuable input and let the reviewers easily refer to their contributions. 

Both pre- and post-publication reviews at RIO are openly published alongside the paper and bear their own DOI. All papers in RIO remain available for post-publication review in perpetuity (see example).

For article types where peer review is mandatory (e.g. Research Idea, Review article, Research Article, Data Paper), authors are requested to invite a minimum of three suitable reviewers upon the submission of the paper, who are then automatically invited by the system. While significantly expediting the editorial work on a manuscript, this practice doesn’t compromise the quality of peer review in the slightest, since the editor is still overlooking the process and able to invite additional reviewers anytime, if necessary. 

For article types where peer review is not mandatory (e.g. Grant Proposal, Data Management Plan, Project Report and various conference materials), all an author needs to do is provide a statement about the review status of their paper, which will be made public alongside the article. Given that such papers have usually already been scrutinised by a legitimate authority (e.g. funding agency or conference committee), it only makes sense to not withhold their publication and duplicate academic efforts.

By the time it is submitted to RIO, a Grant Proposal like this one has often already been assessed by a legitimate funder, so it only makes sense to not undergo the process again at RIO and thereby slowing down its public dissemination.

Additionally, where the article type of a manuscript requires pre-publication review, RIO encourages the authors to click a checkbox during the submission and post their pre-review manuscript as a preprint on ARPHA Preprints, subject to a quick editorial screening, which would only take a few days.

***

Follow RIO Journal on Twitter, Facebook and LinkedIn.

***

Further reading:

Posted on

RIO shifts gears to serve as project-driven knowledge hub

Research Ideas and Outcomes (RIO Journal) upgrades its unique concept to appeal to scientific projects, conference organisers and research institutions

Over the last few years, we’ve been increasingly observing how major funders of research around the world, including the likes of the European Commission, Wellcome, U.S. National Institutes of Health (NIH), Deutsche Forschungsgemeinschaft (DFG) and the Japan Society for the Promotion of Science (JSPS) recognise the research cycle as a continuum, rather than scattered standalone conclusions and reports. 

Hence, as a forward-looking, open science-driven journal Research Ideas and Outcomes (RIO) took it as its own responsibility to encourage scientific project teams, conference organisers and research institutions to bring together unconventional research outputs (e.g. grant proposals, data management plans, project deliverables, policy briefs, conference materials) as well as traditional (e.g. research or review papers, monographs, etc.), including such published elsewhere. To do so, RIO now provides the platform ready to be used as a research knowledge hub, where published outcomes are preserved permanently and easier to share, disseminate, reference and reuse.

Hence, RIO stepped up its game by turning permanent article collections into a one-stop source of diverse research items, where project coordinators, conference organisers or research institutions can not only publish early, interim and conclusive research items as they emerge within a research project, a series of events or the continuous scientific efforts at their lab, but also link relevant publications (i.e. preprints, articles or other documents, published elsewhere) available elsewhere through their metadata. As a result, they will receive a one-stop source under their own branding for every piece of scientific contribution ready to present to funding bodies or prospective collaborators and future research teams.

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

Apart from bringing contextually linked research outcomes together, thus prompting findability, readership and citability en masse, RIO’s approach to collections ensures further accessibility by not only having RIO-published articles available in traditional PDF, semantically enriched HTML and minable XML format. The open-science journal has now made it possible for users to add to their collections preprints from ARPHA Preprints, as well as author-formatted PDFs (e.g. project deliverables, reports, policy briefs, etc.) and linked metadata to documents published elsewhere. Thanks to the integration of the journal with the general-purpose open-access repository Zenodo, all items in a collection are archived, and additionally indexed, disseminated and cited.

By focusing on article and preprint collections coming out from a research project, institution or conference, RIO provides a quite specific and unique combination of benefits to all actors of the research process: scientists, project coordinators, funders and institutions: 

  1. Project, institution or conference branding and promotion.
  2. One-stop point for outputs of a research project, institution or conference.
  3. Free publication of author-formatted project outputs (i.e. grant proposals, deliverables, reports, policy briefs, conference materials and others).
  4. Inclusivity through adding articles, preprints and other documents published elsewhere as easy as entering the DOI number of the document.
  5. Credit and recognition for the Collection and Guest editors, who take care to organise and manage the article collection.
  6. Easier discoverability and usability of topically related studies to benefit both authors and readers.
  7. Increased visibility of related papers in a collection, even when these might otherwise not have much exposure.
  8. Simultaneous citation of multiple articles related to a certain subject.
  9. Citation and referencing of the whole collection as a complete entity.
  10.  DOI and citation details for collections and individual articles.

Furthermore, RIO Journal maps all publications to the Sustainable Development Goals  (SDGs), in order to emphasise the real-world impact of each published contribution, by displaying the corresponding badge within the article list. 

Last, but not least, both collections and individual publications in RIO enjoy the variety of default and on-demand science communication services, provided by Pensoft.  

How do project coordinators, funders and institutions benefit from a collection in RIO?

At the time a grant proposal is submitted to a research funder for evaluation, the team behind the proposed project has already put in considerable efforts, resulting in a unique idea with the potential to make a great stride towards the resolution of an outstanding problem in science, if only given the chance. However, too many of these ideas are bound to remain locked away in the archives of those funders, not because they are lacking in scientific value, but due to limited funds.

So, with its launch back in 2015, RIO Journal made it possible to publish and shed light on grant proposals and research ideas in general, similar early research outputs regardless of whether they are eventually funded or not, a novelty in scholarly publishing which earned RIO the SPARC Innovator Award Winner in 2016. To date, the journal has already published 75 grant proposals. 

Then, imagine what a contribution to science it would make to bring together the whole continuum of knowledge and scientific work all the way from the grant proposal to data  and software management plans, workshop reports, policy briefs and all interim and final deliverables produced within the span of the project!

On the other hand, funders are increasingly evaluating a prospective project’s impact based on its communication strategy. So, why not publish a grant proposal at the time of the submission of your proposal, in order to prove to the funding body that your project is serious about optimising its outreach to both the public and academia? Furthermore, by having an academic journal host any subsequent project deliverable, as a coordinator, you can rest assured that the communication activities of your project remain consistent and efficient.

In an excellent example of a project collection, the EU-funded ICEDIG (Innovation and Consolidation for Large Scale Digitisation of Natural Heritage), led by several major natural history institutions, including the Natural History Museum of London, Naturalis Biodiversity Center (the Netherlands), the French National Museum of Natural History and Helsinki University, brought together policy briefs, project reports, research articles and review papers, in order to provide a fantastic overview of their own research continuum. As a result, future researchers and various stakeholders can easily piece together the key components within the project, in order to learn from, recreate or even build on the experience of ICEDIG.

Explore the ICEDIG Project Outcomes collection on RIO’s website.

Similarly, conference organisers can make use of their own branded collections to overcome the ephemerality of presented research by collating virtually all valuable conference outputs, including abstracts, posters, presentations, datasets and full-text conference talks. For further convenience, a collection can be divided into subcollections, in order to organise the contribution by type or symposium. What particularly appeals to conference participants is the ARPHA Writing Tool, an intuitive collaborative online environment, which practically guides the user through each step: authoring, submission and pre-submission review, within a set of pre-designed, yet flexible templates available for each type of a conference output, thus sparing them the hassle to familiarise themselves with specific and perplexing formatting requirements

For institutions, RIO offers the opportunity to continuously provide evidence of the scholarly impact of their organisation. To better serve the needs of different labs or research teams, an institution can easily organise their outputs into various subcollections, and also customise their own article types, as well as the available usage tracking systems. Furthermore, by making use of the available pre-paid plans, institutions can support their researchers by covering fully or partially the publication charges at a discounted rate.

***

Find more information regarding the submission and review process, policies and pricing, visit RIO Journal’s website.

Follow RIO Journal on Twitter and Facebook.

Posted on

Recursive language and modern imagination were acquired simultaneously 70,000 years ago

The lion-man sculpture from Germany (dated to 37,000 years ago) must have been first imagined by the artist by mentally synthesizing parts of the man and beast together and then executing the product of this mental creation in ivory. The composite artworks provide a direct evidence that by 37,000 years ago humans have acquired prefrontal synthesis.
Image by JDuckeck
[Public domain, https://commons.wikimedia.org/wiki/File:Lion_man_photo.jpg, Wikimedia Commons]

A genetic mutation that slowed down the development of the prefrontal cortex (PFC) in two or more children may have triggered a cascade of events leading to acquisition of recursive language and modern imagination 70,000 years ago.

This new hypothesis, called Romulus and Remus and coined by Dr. Vyshedskiy, a neuroscientist from Boston University, might be able to solve the long-standing mystery of language evolution. It is published in the open-science journal Research Ideas and Outcomes (RIO).

Numerous archeological and genetic evidence have already convinced most paleoanthropologists that the speech apparatus has reached essentially modern configurations before the human line split from the Neanderthal line 600,000 years ago. Considering that the chimpanzee communication system already has 20 to 100 different vocalizations, it is likely that the modern-like remodeling of the vocal apparatus extended our ancestors’ range of vocalizations by orders of magnitude. In other words, by 600,000 years ago, the number of distinct verbalizations used for communication must have been on par with the number of words in modern languages.

On the other hand, artifacts signifying modern imagination, such as composite figurative arts, elaborate burials, bone needles with an eye, and construction of dwellings arose not earlier than 70,000 years ago. The half million-year-gap between the acquisition of the modern speech apparatus and modern imagination has baffled scientists for decades.

While studying acquisition of imagination in children, Dr. Vyshedskiy and his colleagues discovered a temporal limit for the development of a particular component of imagination. It became apparent that modern children who have not been exposed to full language in early childhood never acquire the type of active constructive imagination essential for juxtaposition of mental objects, known as Prefrontal Synthesis (PFS).

Dr. Vyshedskiy explains:

“To understand the importance of PFS, consider these two sentences: “A dog bit my friend” and “My friend bit a dog.” It is impossible to distinguish the difference in meaning using words or grammar alone, since both words and grammatical structure are identical in these two sentences. Understanding the difference in meaning and appreciating the misfortune of the 1st sentence and the humor of the 2nd sentence depends on the listener’s ability to juxtapose the two mental objects: the friend and the dog. Only after the PFC forms the two different images in front of the mind’s eye, are we able to understand the difference between the two sentences. Similarly, nested explanations, such as “a snake on the boulder to the left of the tall tree that is behind the hill,” force listeners to use PFS to combine objects (a snake, the boulder, the tree, and the hill) into a novel scene. Flexible object combination and nesting (otherwise known as recursion) are characteristic features of all human languages. For this reason, linguists refer to modern languages as recursive languages.”

Unlike vocabulary and grammar acquisition, which can be learned throughout one’s lifetime, there is a strong critical period for the development of PFS and individuals not exposed to conversations with recursive language in early childhood can never acquire PFS as adults. Their language is always lacking understanding of spatial prepositions and recursion that depend on the PFS ability. In a similar manner, pre-modern humans would not have been able to learn recursive language as adults and, therefore, would not be able to teach recursive language to their own children, who, as a result, would not acquire PFS. Thus, the existence of a strong critical period for PFS acquisition creates a cultural evolutionary barrier for acquisition of recursive language.

The second predicted evolutionary barrier was a faster PFC maturation rate and, consequently, a shorter critical period. In modern children the critical period for PFS acquisition closes around the age of five. If the critical period in pre-modern children was over by the age of two, they would have no chance of acquiring PFS. A longer critical period was imperative to provide enough time to train PFS via recursive conversations.

An evolutionary mathematical model, developed by Dr. Vyshedskiy, predicts that humans had to jump both evolutionary barriers within several generations since the “PFC delay” mutation that is found in all modern humans, but not in Neanderthals, is deleterious and is expected to be lost in a population without an associated acquisition of PFS and recursive language. Thus, the model suggests that the “PFC delay” mutation triggered simultaneous synergistic acquisition of PFS and recursive language.

This model calls for:

  • two or more children with extended critical period due to “PFC delay” mutation;
  • these children spending a lot of time talking to each other;
  • inventing the recursive elements of language, such as spatial prepositions;
  • acquiring recursive-conversations-dependent PFS;
  • teaching recursive language to their offsprings.

The hypothesis is named after the celebrated twin founders of Rome, Romulus and Remus. Similar to legendary Romulus and Remus, whose caregiver was a wolf, the real children’s caregivers had an animal-like communication system with many words, but no recursion. Their parents could not have taught them spatial prepositions or recursion; children had to invent recursive elements of language themselves. Such an invention of a new recursive language has been observed in contemporary children, for example among deaf children in Nicaragua.

“The acquisition of PFS and recursive language 70,000 years ago resulted in what was in essence a behaviorally new species: the first behaviorally modern Homo sapiens,” concludes Dr. Vyshedskiy. “This newly acquired power for fast juxtaposition of mental objects in the process of PFS dramatically facilitated mental prototyping and led to fast acceleration of technological progress. Armed with the unprecedented ability to mentally simulate any plan and equally unprecedented ability to communicate it to their companions, humans were poised to quickly become the dominant species.”

Humans acquired an ability to trap large animals and therefore gained a major nutritional advantage. As the population grew exponentially, humans diffused out of Africa and quickly settled in the most habitable areas of the planet, arriving in Australia around 50,000 years ago. These humans were very much like modern humans since they possessed both components of full language: the culturally transmitted recursive language along with the innate predisposition towards PFS, enabled by the “PFC delay” mutation.

###

Original source:

Vyshedskiy A (2019) Language evolution to revolution: the leap from rich-vocabulary non-recursive communication system to recursive language 70,000 years ago was associated with acquisition of a novel component of imagination, called Prefrontal Synthesis, enabled by a mutation that slowed down the prefrontal cortex maturation simultaneously in two or more children – the Romulus and Remus hypothesis. Research Ideas and Outcomes 5: e38546. https://doi.org/10.3897/rio.5.e38546

Posted on

FIT Project turns to interdisciplinarity to understand injury factors in youth football

To address the alarming injury rate in youth footballers in Sweden, the project Injury-Free Children and Adolescents: Towards Better Practice in Swedish Football (FIT project) seeks to fill in the knowledge gaps by bringing biomedical and social science together.

With its multi-angled and interdisciplinary approach, the project involves a sample of male and female Swedish football players aged 10 to 19, in order to provide concrete, evidence-based recommendations for injury prevention strategies for the use of sporting federations, sport education institutions, coaches, sport support staff, as well as players.

Strength sub-study

Having received funding by the Swedish Research Council for Sport Science, the grant proposal is published in the open-access journal Research Ideas and Outcomes (RIO Journal). Currently finalising its data collection stage, FIT project is being conducted at the Department of Food and Nutrition, and Sport Science, University of Gothenburg, Sweden, by PhD student Solveig Hausken, Dr Natalie Barker-Ruchti, Dr Astrid Schubring and Prof Stefan Grau.

While injuries in youth athletes could potentially instigate injuries later on in their careers or even force them to drop out of sport, so far, research has focused almost exclusively on the biomedical perspective and the identification of clinical and mechanical risk factors. However, little is known about the role of socio-cultural risk factors.

Image 1

In contrast, FIT Project turns simultaneously to the disciplines of biomechanics, sport medicine, sport coaching and sport sociology. The researchers conducted laboratory tests to determine the physical and sport-specific dispositions of each player; handed out questionnaires to register details about experienced injury; performed interviews with both coaches and players to shed light on the coaching-training dynamics; and made direct observations on the coaching methods and coach-athlete relationships within the sporting context. Each of these sub-studies is meant to produce a separate dataset to be subjected to an interdisciplinary analysis.

“The FIT project is a rare example of how injury research can integrate biomedical and social science disciplines to produce multiple data sets and an interdisciplinary data analysis procedure,” the team explains.

The researchers expect to identify injury risk factors including: growth and maturation; injury history and general health; biomechanical and clinical parameters; training factors such as training intensity and recovery time between trainings; and contextual factors such as pressure to perform, athletic ideals and knowledge of coaches about injury prevention.Movement analysis sub-study

Starting in January 2019, a pilot analysis including the multiple datasets will be conducted. The team will be publishing updates on the FIT project’s progress on its website.

###

Original source:

Hausken S, Barker-Ruchti N, Schubring A, Grau S (2018) Injury-Free Children and Adolescents: Towards Better Practice in Swedish Football (FIT project). Research Ideas and Outcomes 4: e30729. https://doi.org/10.3897/rio.4.e30729

Posted on

Advancing the science and management of European intermittent rivers and ephemeral streams

A COST Action set to bring together scientists and stakeholders from across 14 countries within Europe

Intermittent rivers and ephemeral streams (IRES) are waterways that cease to flow and sometimes dry. However, there is much left to learn about them, including their occurrence in the landscape, ecology, economic and societal values and incredible biodiversity. For efficient and adequate management and protection actions, these knowledge gaps need to be closed sooner rather than later.

In a call for a better understanding of IRES and their vital role in nature, a large international team, led by Dr. Thibault Datry, a freshwater ecologist working at IRSTEA, Lyon, France, has initiated the “Science and Management of Intermittent Rivers and Ephemeral Streams (SMIRES)” project. Their grant proposal, as approved for funding by the European framework COST, is published in the open science journal Research Ideas and Outcomes (RIO).

This COST Action brings together hydrologists, biogeochemists, ecologists, modellers, environmental economists, social researchers and stakeholders from 14 countries from around the continent. The aim of the interdisciplinary team is to develop a research network for synthesising the fragmented knowledge on IRES. In turn, improved understanding of IRES will translate to a science-based, sustainable management of river networks.

Along with networking between scientists and stakeholders, the Action will accommodate a whole set of good practices, including data sharing, technology development and citizen science.

The Calavon River, a Mediterranean IRES, during flowing (left) and dry phases (right).
The Calavon River, a Mediterranean IRES, during flowing (left) and dry phases (right).

Amongst the goals of the project are the creation of two meta-databases providing open data about IRES research activities and flow stations with intermittent flows; a proposal for novel indicators and technologies to assess changes and associated ecological responses in IRES; and the development of a European-scale network of citizen scientists to monitor, locate and map river flow states with the help of smartphone technology.

Having been ignored in conservation policies and initiatives, IRES are being degraded at an alarming rate. Water extraction, flood harvesting, river impoundment, channel modification, land-use change and mining are only part of the threats faced by IRES across Europe. In many areas, they are even used as disposal areas. For others, they are channelled underground or connected to larger water bodies as a means of flow augmentation, which could potentially lead to the spread of invasive species.

The researchers point out that lack of recognition and understanding lead to the rapid degradation of IRES.

###

Original source:

Datry T, Singer G, Sauquet E, Jorda-Capdevilla D, Von Schiller D, Subbington R, Magand C, Pa?il P, Miliša M, Acuña V, Alves M, Augeard B, Brunke M, Cid N, Csabai Z, England J, Froebrich J, Koundouri P, Lamouroux N, Martí E, Morais M, Munné A, Mutz M, Pesic V, Previši? A, Reynaud A, Robinson C, Sadler J, Skoulikidis N, Terrier B, Tockner K, Vesely D, Zoppini A (2017) Science and Management of Intermittent Rivers and Ephemeral Streams (SMIRES). Research Ideas and Outcomes 3: e21774. https://doi.org/10.3897/rio.3.e21774

Posted on

Pilot Project provides findings and advice on data sharing in development research

Launched just ahead of last year’s FORCE11 conference devoted to the utilisation of technological and open science advancements to communication of scholarship, the data sharing pilot project of Prof. Cameron Neylon, Centre for Culture and Technology, Curtin University, Australia, and his collaborators has published its final outcomes days before FORCE2017.

The project made use of the innovative open science RIO Journal, which allows for the publication of various research outcomes and sorting them into dedicated collections. The collection, “Exploring the opportunities and challenges of implementing open research strategies within development institutions: A project of the International Development Research Center” now features the project’s grant proposal as approved by the IDRC, a review article, several data management plans and case studies, and the final report as a research article.

The pilot project looked into the current state and challenges of data management and sharing policies and practices, as shown by case studies of seven IDRC-funded development research projects.

Having worked with the projects selected from across a range of geographies, scales and subjects over the course of 16 months, the data sharing initiative began with an introduction to data management and sharing concepts, as well as helping the projects to develop their own data management plans. Then, they carefully monitored and observed the implementation of those plans.

Over the course of the project, it became apparent that simply developing and implementing funder policies is not enough to change research culture. The question of how funder policy and implementation could support culture change both within research communities and within the funder itself became the focus of the initiative.

Data management plans have become a mandatory part of grant submission for many funders. However, they are often not utilised by researchers or funders later in the project, becoming “at best neutral and likely counter productive in supporting change in research culture.”

While the pilot project managed to identify a number of significant bottlenecks within both research institutions and for grantees that impede efficient data sharing practices, including, expectedly, lack of resources and expertise, the researchers specifically point out issues related to structural issues at the funder level.

“The single most productive act to enhance policy implementation may be to empower and support Program Officers,” says the author.

“This could be achieved through training and support of individual POs, through the creation of a group of internal experts who can support others, or via provision of external support, for instance, by expanding the services provided by the pilot project into an ongoing support mechanism for both internal staff and grantees.”

Amongst the findings of the pilot project are also the importance of language barriers and the need for better suited data management platforms and tools.

Furthermore, the study identified a gap between the understanding of “data” amongst cultures, pointing out that the concept of data is “part of a western scientific discourse which may be both incompatible with other cultures, particularly indigenous knowledge systems.”

In conclusion, the research article outlines a set of recommendations for funders, particularly those with a focus on development, as well as recommendations specific to the IDRC.

Original source:

Neylon C (2017) Building a Culture of Data Sharing: Policy Design and Implementation for Research Data Management in Development Research. Research Ideas and Outcomes 3: e21773. https://doi.org/10.3897/rio.3.e21773

Posted on

The first microbial supertree from figure-mining thousands of papers

While recent reports reveal the existence of more than 114,000,000 documents of published scientific literature, finding a way to improve the access to this knowledge and efficiently synthesise it becomes an increasingly pressing issue.

Seeking to address the problem through their PLUTo workflow, British scientists Ross Mounce and Peter Murray-Rust, University of Cambridge and Matthew Wills, University of Bath perform the world’s first attempt at automated supertree construction using data exclusively extracted by machines from published figure images. Their results are published in the open science journal Research Ideas and Outcomes (RIO).

For their study, the researchers picked the International Journal of Systematics and Evolutionary Microbiology (IJSEM) – the sole repository hosting all new validly described prokaryote taxa and, therefore, an excellent choice against which to test systems for the automated and semi-automated synthesis of published phylogenies. According to the authors, IJSEM publishes a greater number of phylogenetic tree figure images a year than any other journal.

An eleven-year span of articles dating back to January, 2003 was systematically downloaded so that all image files of phylogenetic tree figures could be extracted for analysis. Computer vision techniques then allowed for the automatic conversion of the images back into re-usable, computable, phylogenetic data and used for a formal supertree synthesis of all the evidence.

During their research, the scientists had to overcome various challenges posed by copyrights formally covering almost all of the documents they needed to mine for the purpose of their work. At this point, they faced quite a paradox – while easy access and re-use of data published in scientific literature is generally supported and strongly promoted, common copyright practices make it difficult for a scientist to be confident when incorporating previously compiled data into their own work. The authors discuss recent changes to UK copyright law that have allowed for their work to see the light of day. As a result, they provide their output as facts, and assign them to the public domain by using the CC0 waiver of Creative Commons, to enable worry-free re-use by anyone.

“We are now at the stage where no individual has the time to read even just the titles of all published papers, let alone the abstracts,” comment the authors.

“We believe that machines are now essential to enable us to make sense of the stream of published science, and this paper addresses several of the key problems inherent in doing this.”

“We have deliberately selected a subsection of the literature (limited to one journal) to reduce the volume, velocity and variety, concentrating primarily on validity. We ask whether high-throughput machine extraction of data from the semistructured scientific literature is possible and valuable.”  

 

Original source:

Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589

 

Additional information:

The research has been funded by the BBSRC (grant BB/K015702/1 awarded to MAW and supporting RM).

Posted on

Legitimacy of reusing images from scientific papers addressed

It goes without saying that scientific research has to build on previous breakthroughs and publications. However, it feels quite counter-intuitive for data and their re-use to be legally restricted. Yet, that is what happens when copyright restrictions are placed on many scientific papers.

The discipline of taxonomy is highly reliant on previously published photographs, drawings and other images as biodiversity data. Inspired by the uncertainty among taxonomists, a team, representing both taxonomists and experts in rights and copyright law, has traced the role and relevance of copyright when it comes to images with scientific value. Their discussion and conclusions are published in the latest paper added in the EU BON Collection in the open science journal Research Ideas and Outcomes (RIO).

Taxonomic papers, by definition, cite a large number of previous publications, for instance, when comparing a new species to closely related ones that have already been described. Often it is necessary to use images to demonstrate characteristic traits and morphological differences or similarities. In this role, the images are best seen as biodiversity data rather than artwork. According to the authors, this puts them outside the scope, purposes and principles of Copyright. Moreover, such images are most useful when they are presented in a standardized fashion, and lack the artistic creativity that would otherwise make them ‘copyrightable works’.

image 3

“It follows that most images found in taxonomic literature can be re-used for research or many other purposes without seeking permission, regardless of any copyright declaration,” says Prof. David J. Patterson, affiliated with both Plazi and the University of Sydney.

Nonetheless, the authors point out that, “in observance of ethical and scholarly standards, re-users are expected to cite the author and original source of any image that they use.” Such practice is “demanded by the conventions of scholarship, not by legal obligation,” they add.

However, the authors underline that there are actual copyrightable visuals, which might also make their way to a scientific paper. These include wildlife photographs, drawings and artwork produced in a distinctive individual form and intended for other than comparative purposes, as well as collections of images, qualifiable as databases in the sense of the European Protection of Databases directive.

In their paper, the scientists also provide an updated version of the Blue List, originally compiled in 2014 and comprising the copyright exemptions applicable to taxonomic works. In their Extended Blue List, the authors expand the list to include five extra items relating specifically to images.

“Egloff, Agosti, et al. make the compelling argument that taxonomic images, as highly standardized ‘references for identification of known biodiversity,’ by necessity, lack sufficient creativity to qualify for copyright. Their contention that ‘parameters of lighting, optical and specimen orientation’ in biological imaging must be consistent for comparative purposes underscores the relevance of the merger doctrine for photographic works created specifically as scientific data,” comments on the publication Ms. Gail Clement, Head of Research Services at the Caltech Library.

“In these cases, the idea and expression are the same and the creator exercises no discretion in complying with an established convention. This paper is an important contribution to the literature on property interests in scientific research data – an essential framing question for legal interoperability of research data,” she adds.

###

Original source:

Egloff W, Agosti D, Kishor P, Patterson D, Miller J (2017) Copyright and the Use of Images as Biodiversity Data. Research Ideas and Outcomes 3: e12502. https://doi.org/10.3897/rio.3.e12502

Additional information:

The present study is a research outcome of the European Union’s FP7-funded project EU BON, grant agreement No 308454.

Posted on

Guidelines for scholarly publishing of biodiversity data from Pensoft and EU BON

While development and implementation of data publishing and sharing practices and tools have long been among the core activities of the academic publisher Pensoft, it is well-understood that as part of scholarly publishing, open data practices are also currently in transition, and hence, require a lot of collaborative and consistent efforts to establish.

Based on Pensoft’s experience, and elaborated and updated during the Framework Program 7 EU BON project, a new paper published in the EU BON dedicated collection in the open science journal Research Ideas and Outcomes (RIO), outlines policies and guidelines for scholarly publishing of biodiversity and biodiversity-related data. Newly accumulated knowledge from large-scale international efforts, such as FORCE11 (Future of Research Communication and e-Scholarship), CODATA (The Committee on Data for Science and Technology), RDA (Research Data Alliance) and others, is also included in the Guidelines.

The present paper discusses some general concepts, including a definition of datasets, incentives to publish data and licences for data publishing. Furthermore, it defines and compares several routes for data publishing, namely: providing supplementary files to research articles; uploading them on specialised open data repositories, where they are linked to the research article; publishing standalone data papers; or making use of integrated narrative and data publishing through online import/download of data into/from manuscripts, such as the workflow provided by the Biodiversity Data Journal. Among the guidelines, there are also comprehensive instructions on preparation and peer review of data intended for publication.

Although currently available for journals using the developed by Pensoft journal publishing platform ARPHA, these strategies and guidelines could be of use for anyone interested in biodiversity data publishing.

Apart from paving the way for a whole new approach in data publishing, the present paper is also a fine example of science done in the open, having been published along with its two pre-submission public peer reviews. The reviews by Drs. Robert Mesibov and Florian Wetzel are both citable via their own Digital Object Identifiers (DOIs).

###

Original source:

Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431