RIO Editorial Office

31/05/201610/05/2023

RIO celebrates its 50th publication

We are pleased to announce that RIO published its 50th article!

The milestone paper “Defining the Scholarly Commons – Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016” is a Workshop Report by Bianca Kramer et al., one among many showcasing RIO’s innovative publication types in use. To date, the journal has published outputs in various innovative categories (see chart), including Research Ideas, Workshop Reports, Data Management Plans, Research Posters, Conference Abstracts and PhD Project plans. We are especially proud to host Grant Proposals from a wide variety of funding initiatives worldwide.

See a more detailed breakdown of RIO’s publications in the pie chart above.

17/05/201610/05/2023

Open Science environment Unicorn allows researchers and decision makers to work together

Given that the most important societal needs require multidisciplinary collaboration between researchers and decision makers, a suitable environment has to be provided in the first place. A proposal, prepared by a Finnish consortium and published in the open access journal Research Ideas and Outcomes, suggests a new, open virtual work and modeling platform to support evidence-based decision making in a number of areas, while also abiding by the principles of openness, criticism and reuse.

The Finnish consortium, led by Prof. Pekka Neittaanmäki, University of Jyväskylä, and bringing together Timo Huttula and Janne Ropponen, Finnish Environment Institute, Juha Karvanen and Tero Tuovinen, University of Jyväskylä, Tom Frisk, Pirkanmaa Centre for Economic Development, Transport and the Environment, Jouni Tuomisto, National Institute for Health and Welfare, and Antti Simola, VATT Institute for Economic Research, acknowledge that, “it is not enough that experts push data to politicians.”

“There must be practices for mutual communication: experts must answer policy questions in a defendable and useful way; decision makers must more clearly explain their views using evidence; and there must be ICT tools to support this exchange,” the authors explain. “The focus is on end-users.”

Unicorn is to combine shared practices, tools, data, working environments and concerted actions in order to aggregate open information from multiple databases, and create tools for efficient policy studies.

The consortium have already developed and tested prototypes of such practices and tools in several projects, and insist that they are now ready to apply their experience and knowledge on a larger scale. They are also certain that open data and models are deservedly the “mega trend” nowadays.

“Unicorn directs this trend to paths that are the most beneficial for societal decision making by providing quick, reliable and efficient decision support,” they say.

“Significant saving of resources will be manifested with improved data collection, analyses and modeling. Also, the quality and amount of assessments that can be done to support work.”

“The major challenges related to evidence-based decision making actually are about changing the practices of researchers and decision makers,” according to the authors. Therefore, they see their project as a demonstration of the needed shifts.

Although the approach is applicable in all areas, the researchers are to initially implement them in environment, human health, and regional economy, “as they are complex and challenging enough to offer a good test bed for general development.”

Having already been submitted to the Strategic Funds of Academy of Finland in 2015, the Unicorn environment proposal has been rejected due to overambitiousness and low commercial potential. However, the authors are confident that the Unicorn environment along with its growing community of developers can, in fact, meet a great success. They are currently looking for further funding suggestions and forming new consortiums.

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Original source:

Neittaanmäki P, Huttula T, Karvanen J, Frisk T, Tuomisto J, Simola A, Tuovinen T, Ropponen J (2016) Unicorn-Open science for assessing environmental state, human health and regional economy. Research Ideas and Outcomes 2: e9232. doi: 10.3897/rio.2.e9232

12/05/201610/05/2023

Open neuroscience: Collaborative Neuroimaging Lab finalist for the Open Science Prize

Despite the abundance of digital neuroimaging data, shared thanks to all funding, data collection, and processing efforts, but also the goodwill of thousands of participants, its analysis is still falling behind. As a result, the insight into both mental disorders and cognition is compromised.

The Open Neuroimaging Laboratory framework, promises a collaborative and transparent platform to optimise both the quantity and quality of this invaluable brain data, ultimately gaining a greater insight into both mental disorders and cognition.

The project was submitted for the Open Science Prize competition by Katja Heuer, Max Planck Institute for Human Cognitive and Brain Sciences, Germany, Dr Satrajit S. Ghosh, Massachusetts Institute of Technology (MIT), USA, Amy Robinson Sterling, EyeWire, USA, and Dr Roberto Toro, Institut Pasteur, France. Amongst 96 submissions from all around the globe, it was chosen as one of six teams to compete in the second and final phase of the Prize.

Simply having access and being able to download brain magnetic resonance imaging (MRI) data is not enough to reap all potential benefits. In order for it to be turned into insight and knowledge, it needs to also be queried, pre-processed and analysed, which requires a substantial amount of human curation, visual quality assessment and manual editing. With research being rather patchy, a lot of efforts are currently redundant and unreliable.

On the other hand, the Open Neuroimaging Laboratory aims to aggregate annotated brain imaging data from across various resources, thus improving its searchability and potential for reuse. It is to also develop a tool that will facilitate and encourage the creation of distributed teams of researchers to collaborate together in the analysis of this open data in real time.

“Our project will help transform the massive amount of static brain MRI data readily available online into living matter for collaborative analysis,” explain the researchers.

“We will allow a larger number of researchers to have access to this data by lowering the barriers that prevent their analysis: no data will have to be downloaded or stored, no software will have to be installed, and it will be possible to recruit a large, distributed, group of collaborators online.”

“By working together in a distributed and collaborative way, sharing our work and our analyses, we should improve transparency, statistical power and reproducibility,” they elaborate. “Our aim is to provide to everyone the means to share effort, learn from each other, and improve quality of and trust in scientific output.”

Having already developed a functional prototype of the BrainBox web application, which provides an interactive online space for collaborative data analyses and discussions, the team will now turn it into a first version with an improved user experience, stability and documentation. Planned for the Open Science Prize Phase 2 are furthering the type of analyses and exploring the development of interfaces for database-wise statistical analyses.

In the spirit of the competition, the scientists have decided to release their code open source on GitHub to facilitate bug fixes, extension and maintainability.

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Original source:

Heuer K, Ghosh S, Robinson Sterling A, Toro R (2016) Open Neuroimaging Laboratory.Research Ideas and Outcomes 2: e9113. doi: 10.3897/rio.2.e9113

03/05/201610/05/2023

Influence of religion and predestination on evolution and scientific thinking

Generally seen as antithetical to one another, evolution and religion can hardly fit in a scientific discourse simultaneously. However, biologist Dr Aldemaro Romero Jr., Baruch College, USA, devotes his latest research article, now published in the open access Research Ideas and Outcomes (RIO), to observing the influences a few major religions have had on evolutionists and their scientific thinking over the centuries.

Inspired by the lack of pigmentation and/or eyes in some cave organisms, he focuses on biospeleology to challenge the notions of predetermination and linearity. Although the author makes it clear that fellow scientists do not claim their findings based on religion, he notes that “words matter and that words can hide a lot of the philosophical baggage that sooner or later may influence their ultimate conclusion”.

Using examples from across the centuries, Dr Aldemaro Romero Jr. goes back to the times long before Charles Darwin had started compiling his prominent “The Origin of Species” and then turns once again to his evolutionist successors. Thus, he explores the link between the notion of predestination, underlying in various religions and nations, and the evolutionary theories.

The author notices that despite conclusions that evolution is not a linear process, biologists have never stopped seeing and contemplating “preadaptations” and “regressive evolution”, when speculating on phenomena such as the lack of eyes in some exclusively cave-dwelling animals. Such choice of words can be easily traced back to assumptions of linearity and, therefore, predestination, common for various religions.

FALCON STATE, VENEZUELA - Aldemaro Romero Jr., Executive Director, BIOMA, during cave exploration in Paraguana in 1988. — FALCON STATE, VENEZUELA – Aldemaro Romero Jr., Executive Director, BIOMA, during cave exploration in Paraguana in 1988.

“Since the advent of Modern Synthesis we have a pretty consistent set of evidence that evolution is not linear, that there is not such a thing as direction for evolutionary processes, and that nothing is predetermined since natural selection, the main evolutionary mechanism, is a process that is not moved by any mystical force, nor directs beings toward a particular end,” points out Dr Aldemaro Romero Jr..

“Therefore, I hope this paper serves as a warning to scientists that no matter what reductionist view they have in the way they practice their research, if they do not understand the historical roots and the philosophical framework of their research, they are doomed at presenting only a very partial (and many times biased) view of nature,” he concludes.

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Original source:

Romero Jr. A (2016) The influence of religion on science: the case of the idea of predestination in biospeleology. Research Ideas and Outcomes 2: e9015. doi: 10.3897/rio.2.e9015

21/04/201610/05/2023

New development tool based on ‘software quality information needs’ and 3 case studies

While constantly developing, software takes over more and more aspects of our life at both individual and community level. Thus, software failures and security are easily becoming major concerns which need to be addressed on the spur of the moment.

A way to do so, according to computer scientist Dr Daniel Graziotin, University of Stuttgart, is adopting a new concept, which he terms ‘Software quality information needs’, along with multi-angled extensive empirical evidence to produce a development tool to improve software quality. His Grant Proposal is published in the open access journal Research Ideas and Outcomes (RIO).

The proposed research is in the context of an earlier DFG Grant Proposal, authored by Prof. Dr. Stefan Wagner, University of Stuttgart, and published in the same journal. The earlier project idea suggests novel tools analysing software changes before and during their implementation. Similarly to Dr Daniel Graziotin’s idea, it is based on fast and focused feedback loop.

The presently proposed research, planned to take 24 months, is set to start with establishing the ‘software quality information needs’ construct. The author coins this theory in order to conceptualise and provide deeper understanding of the information essential for a developer when performing code changes or designing new parts of a system.

The project is to then go on to produce metrics to detect and satisfy a developer’s needs. As a result, optimally unobtrusive measurement techniques are to be developed and evaluated in three empirical studies.

About 120 software engineering students from the University of Stuttgart are to be recruited to provide empirical evidence. While they are working on either real-world or university software projects, they are to be observed, regularly interviewed and asked to think aloud. Their insights will be further enriched through a post-task interview. The findings are to answer the question “How can we conceptualise information needs when dealing with software quality?”.

“What information is needed when dealing with software quality?”, is to be covered by the second empirical study, which plans to involve the software engineers of Daimler, Porsche, and Bosch, since the automotive industry is particularly concerned with software quality issues. The engineers are to fill in mostly open-ended surveys and thus, provide a broad view of software quality information needs and their priority from a practitioner’s perspective.

Building on the above case studies, the German multinational engineering and electronics company Robert Bosch GmbH is to be approached for validated questionnaires and behavior patterns tests, such as keystroke frequency and typos detection. Ultimately, the findings are to answer how software quality information needs to be detected unobtrusively through behavioral patterns.

To exemplify the tool, based on the described research and its expected findings, the scientist uses fictional software developer, called Anne. While working on a system routine to be applied in a banking application, she is notified by the integrated development environment (IDE), that there might be some quality issues.

It turns out that she is employing a design pattern that is not frequently employed in similar cases, so the IDE suggests that she browses some StackOverflow.com related questions and answers regarding the design pattern. Because she has also created part of the procedure by cloning code from another part of the project, the tool offers her to help to refactor the cloned code.

“Providing a software developer with the right kind of information about the current state of and the effect of changes on software quality can prevent catastrophic software failures and avoid opening up security holes,” Dr Daniel Graziotin argues.

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Original source:

Graziotin D (2016) Software quality information needs. Research Ideas and Outcomes 2: e8865.doi: 10.3897/rio.2.e8865

19/04/201610/05/2023

Data sharing pilot to report and reflect on data policy challenges via 8 case studies

This week, FORCE2016 is taking place in Portland, USA. The FORCE11 yearly conference is devoted to the utilisation of technological and open science advancements towards a new-age scholarship founded on easily accessible, organised and reproducible research data.

As a practical contribution to the scholarly discourse on new modes of communicating knowledge, Prof. Cameron Neylon, Centre for Culture and Technology, Curtin University, Australia, and collaborators are to publish a series of outputs and outcomes resulting from their ongoing data sharing pilot project in the open access journal Research Ideas and Outcomes (RIO).

Starting with their Grant Proposal, submitted and accepted for funding by the Canadian International Development Research Centre (IDRC), over the course of sixteen months, ending in December 2016, they are to openly publish the project outputs starting with the grant proposal.

The project will collaborate with 8 volunteering IDRC grantees to develop Data Management Plans, and then support and track their development. The project expects to submit literature reviews, Data Management Plans, case studies and a final research article with RIO. These will report and reflect on the lessons they will have learnt concerning open data policies in the specific context of development research. Thus, the project is to provide advice on refining the open research data policy guidelines.

“The general objective of this project is to develop a model open research data policy and implementation guidelines for development research funders to enable greater access to development research data,” sum up the authors.

“Very little work has been done examining open data policies in the context of development research specifically,” they elaborate. “This project will serve to inform open access to research data policies of development research funders through pilot testing open data management plan guidelines with a set of IDRC grantees.”

The researchers agree that data constitutes a primary form of research output and that it is necessary for research funders to address the issue of open research data in their open access policies. They note that not only should data be publicly accessible and free for re-use, but they need to be “technically open”, which means “available for no more than the cost of reproduction, and in machine-readable and bulk form.” At the same time, research in a development context raises complex issues of what data can be shared, how, and by whom.

“The significance of primary data gathered in research projects across domains is its high potential for not only academic re-use, but its value beyond academic purposes, particularly for governments, SME, and civil society,” they add. “More importantly, the availability of these data provides an ideal opportunity to test the key premise underlying open research data — that when it is made publicly accessible in easily reusable formats, it can foster new knowledge and discovery, and encourage collaboration among researchers and organizations.”

However, such openness is also calling for extra diligence and responsibility while sharing, handling and re-using the research data. This is particularly the case in development research, where challenging ethical issues come to the fore. The authors point out the issues, raised by such practice, to be, among others, realistic and cost-effective strategies for funded researchers to collect, manage, and store the various types of data resulting from their research, as well as ethical issues such as privacy and rights over the collected data.

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Original source:

Neylon C, Chan L (2016) Exploring the opportunities and challenges of implementing open research strategies within development institutions. Research Ideas and Outcomes 2: e8880. doi: 10.3897/rio.2.e8880

12/04/201610/05/2023

Open-source collaborative platform to collect content from over 350 institutions’ archives

With the technical and financial capacity of any currently existing single institution failing to answer the needs for a platform efficiently archiving the web, a team of American researchers have come up with an innovative solution, submitted to the U.S. Institute of Museum and Library Services (IMLS) and published in the open-access journal Research Ideas and Outcomes (RIO).

They propose a lightweight, open-source collaborative collection development platform, called Cobweb, to support the creation of comprehensive web archives by coordinating the independent activities of the web archiving community. Through sharing the responsibility with various institutions, the aggregator service is to provide a large amount of continuously updated content at greater speed with less effort.

In their proposal, the authors from the California Digital Library, the UCLA Library, and Harvard Library, give an example with the fast-developing news event of the Arab Spring, observed to unfold online simultaneously via news reports, videos, blogs, and social media.

“Recognizing the importance of recording this event, a curator immediately creates a new Cobweb project and issues an open call for nominations of relevant web sites,” explain the researchers. “Scholars, subject area specialists, interested members of the public, and event participants themselves quickly respond, contributing to a site list that is more comprehensive than could be created by any curator or institution.”

“Archiving institutions review the site list and publicly claim responsibility for capturing portions of it that are consistent with local collection development policies and technical capacities.”

Unlike already existing tools supporting some level of collaborative collecting, the proposed Cobweb service will form a single integrated system.

“As a centralized catalog of aggregated collection and seed-level descriptive metadata, Cobweb will enable a range of desirable collaborative, coordinated, and complementary collecting activities,” elaborate the authors. “Cobweb will leverage existing tools and sources of archival information, exploiting, for example, the APIs being developed for Archive-It to retrieve holdings information for over 3,500 collections from 350 institutions.”

If funded, the platform will be hosted by the California Digital Library and initialized with collection metadata from the partners and other stakeholder groups. While the project is planned to take a year, halfway through the partners will share a release with the global web archiving community at the April 2017 IIPC General Assembly to gather feedback and discuss ongoing sustainability. They also plan to organize public webinars and workshops focused on creating an engaged user community.

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Original source:

Abrams S, Goethals A, Klein M, Lack R (2016) Cobweb: A Collaborative Collection Development Platform for Web Archiving. Research Ideas and Outcomes 2: e8760. doi: 10.3897/rio.2.e8760

12/04/201610/05/2023

Pericardial window operation less efficient in cases of lung cancer than any other cancer

Pericardial window operation, a procedure, where abnormal quantity of malignant fluid, or malignant pericardial effusion (MPE), surrounding the heart, is drained into the neighbouring chest cavity through a surgically placed tube, is commonly applied to patients diagnosed with cancer.

However, researchers from the Taipei Tzuchi Hospital, Taiwan, have now looked into the electronic medical records of 52 cancer patients, including 30 cases of lung-cancer, archived between 2005 and 2015. They conclude that the treatment is not as effective in lung cancer cases when compared to any other cancer patients. In their study, published in the open access journal Research Ideas and Outcomes (RIO), they also suggest a few no inferior alternatives worth of consideration.

The authors retrieved retrospective data of the patients and compared them in terms of hospital stay length, overall mortality and overall length of survival. They also took details such as dates of operations, hospital discharge and death, into account.

As a result, they found out that there was not any significant difference between the treatment’s outcomes in the patients groups at the time of hospital release. On the other hand, over a longer ten-year timeline, it turned out that the lung cancer patients have experienced notably higher mortality rate.

Alternative treatments for MPE, such as less invasive, yet no less efficient, methods relying on needle punctures instead of an “open” approach, where internal organs and tissues are exposed, are proposed by the authors. However, they note that the decision for a treatment needs to be taken strictly individually.

“Since the MPE prognosis is multi-factorial, the superiority of percutaneous versus surgical approach is still controversial,” they explain.

In conclusion, the researchers point out that their survey is a single-institution based one and not quite extensive, so there is still need for research to track the relation between a type of cancer and the MPE treatments.

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Original source:

Chen R, Shen T, Tsai K, Hu C (2016) Pericardial window operation for malignant pericardial effusion may have worse outcomes for lung cancer than the other cancers. Research Ideas and Outcomes 2: e8758. doi: 10.3897/rio.2.e8758

08/04/201610/05/2023

Undergraduates survey cultural tourists’ attitudes and visual advertising in Malta

While advertising and promotion in general, specifically observed within the American society, is a largely researched topic, Dr János Tóth, Kodolányi János University of Applied Sciences, and the undergraduate students from the Karoli Gaspar University of the Reformed Church in Hungary have had their curiosity and attention drawn to a specific non-American and, therefore, underrepresented in such studies environment, namely the Maltese city of Msida.

Their grant proposal, published in the open-access Research Ideas and Outcomes (RIO), was funded under the framework of the New Széchényi Plan, so that the team could travel to the University of Malta, with whose help they surveyed the cultural tourists’ attitudes towards advertising in the Maltese city.

Through their trip to the Mediterranean island country and the additional distance work in collaboration with the University of Malta, the team conducted a two-stage research in the area with a focus on visual advertisements located at popular tourist sites. There, the students applied the knowledge they had acquired in their university modules, such as Research Methods, Marketing Research, and Marketing Communication, to attain original scientific results about both the cultural tourists’ attitudes towards visual advertisements and the used text-level persuasion tools.

In the first phase of the project, the researchers carried out a survey at popular tourist sites, attended by international tourists. In such an environment advertisements need to appeal to visitors with different national and cultural backgrounds.

Then, in the second part of the study, the researchers examined the tools and techniques of persuasive communication in public advertising. They focused on cultural tourist sites, where advertisement is more specifically targeted. Although the visitors at such places are just as highly diverse in terms of their socio-cultural background, they have been drawn there by a relatively common goal. In fact, the researchers refer to these sites as advertisements on their own.

In their paper, the team have also listed a number of benefits they intend to reap as a result of their survey. They have counted knowledge about the cultural tourists in Malta and their attitudes towards the local advertising techniques, as well as the opportunity to compare them with similar findings from Europe. They also intend to formulate empirical research-based recommendations to support decision makers in the marketing field. Moreover, their data and analysis are to build on the available literature concerning advertising communication and tourism research.

In order to make their research activities fully transparent and traceable, not only have they published their grant proposal in the open access Research Ideas and Outcomes (RIO), but they have also included a timeline of their tour in it. During the trip itself, the students took the initiative to give real-time updates about their experience via social media networks, including Facebook, Flickr, Twitter and personal blogs.

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Photos credit:

Dr János Tóth and Karoli Gaspar University of the Reformed Church in Hungary

Original source:

Tóth J (2016) Tools of Persuasion in Visual Advertisements at Maltese Sites of Cultural Tourism: A Social Science Analysis. Research Ideas and Outcomes 2: e8726. doi: 10.3897/rio.2.e8726

01/04/201610/05/2023

Better cancer care for Indigenous Canadians with arts and dialogue in a new proposal

With the number of First Nation, Inuit, and Métis (FNIM) Canadians diagnosed with cancer currently growing, it turns out that little is done to study and address their unique needs in a timely enough manner. In his grant proposal, submitted to the annual Canadian Institutes of Health Research competition for postdoctoral fellowships, Dr Chad Hammond at the University of Ottawa suggests an innovative and inclusive approach to studying the challenges within Indigenous communities in Ontario.

The proposed research, described in the open-access journal Research Ideas and Outcomes (RIO), suggests a collaborative interdisciplinary approach using visual arts and participatory dialogue with stakeholders involved in cancer care for FNIM peoples.

Participants for the project will include 10 health care professionals, 5 health administrators, and 5 FNIM community leaders who will engage with photovoice and photo-elicitation techniques to develop priorities and solutions in FNIM cancer care in Ontario. By the end, a report of recommendations is to be generated and dispensed to participants, bringing together various experiences, themes, perspectives, and recommendations for improving the state of care. The final report will serve as the basis for discussions around implementing the recommendations, for which additional funding opportunities will be sought.

“The use of photography as data and for eliciting data marks an innovative and inclusive approach to studying challenges within FNIM cancer care, while extending the reach of established projects,” explains the author.

“Through strong partnerships and a stakeholder-driven agenda, this research promises to build timely knowledge exchange initiatives between professional stakeholders and to identify viable pathways toward improving cancer care for FNIM peoples in Ontario.”

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Original source:

Hammond C (2016) Widening the circle of care: An arts-based, participatory dialogue with stakeholders on cancer care for First Nations, Inuit,and Métis peoples in Ontario, Canada.Research Ideas and Outcomes 2: e8615. doi: 10.3897/rio.2.e8615