2026-06-14T19:06:32Z https://riojournal.com/oai.php

10.3897/rio.1.e7462 2015-12-17 rio

Problematic trial detection in ClinicalTrials.gov Hartgerink,Chris George,Stephen clinicaltrials.gov problematic data error data fabrication Research Ideas and Outcomes 1: e7462 Clinical trials are crucial in determining the effectiveness of treatments and directly affect clinical and policy decisions. These decisions are undermined if the data are problematic due to data fabrication or other errors. Researchers have worked on developing statistical methods to detect problematic data. This project aims to develop new methods and apply them to results reported in the ClinicalTrials.gov database. Using both established and and the newly developed statistical methods we will investigate the prevalence of problematic data, trends of problematic data over time, and whether the prevalence of problematic data is predicted by trial characteristics such as funding type. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2015 Small Grant Proposal text/html info:doi:10.3897/rio.1.e7462 https://doi.org/10.3897/rio.1.e7462 https://riojournal.com/article/7462/ https://riojournal.com/article/7462/download/pdf/ en

10.3897/rio.1.e7479 2015-12-17 rio

Heteroatom quantum corrals and nanoplasmonics in graphene (HeQuCoG) Susi,Toma atomic manipulation scanning transmission electron microscopy electron energy loss spectroscopy density functional theory ion implantation Research Ideas and Outcomes 1: e7479 The objective of the Heteroatom quantum corrals and nanoplasmonics in graphene (HeQuCoG) project is to create atomically precise structures made of silicon and phosphorus atoms embedded in the lattice of graphene. This will be achieved by combining proven modeling techniques with sample fabrication via carefully controlled ion implantation, and subsequent manipulation in an atomic resolution scanning transmission electron microscope (STEM). The structures will be computationally designed for interesting nanoplasmonic enhancement and quantum confinement properties, and characterized by electron energy loss spectroscopy mapping in the STEM. The expected outcome is a systematic demonstration of truly atomic-level material design and the creation of freestanding “quantum corral” structures for the first time. The controlled manipulation of matter on the atomic scale has been a long-standing dream of nanotechnology. Pioneering directions towards have already been explored, chiefly with the help of scanning tunneling microscopy. However, compared to the manipulation of surface atoms, graphene heteroatoms have the advantage of being stable at room temperature and even if the sample is taken out of the instrument. Furthermore, the coupling of light to nanostructures via plasmon resonances is an intensively pursued and promising research field, which is awaiting breakthroughs in material design before the field can live up to its expected potential. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2015 FWF Grant Proposal text/html info:doi:10.3897/rio.1.e7479 https://doi.org/10.3897/rio.1.e7479 https://riojournal.com/article/7479/ https://riojournal.com/article/7479/download/pdf/ en

10.3897/rio.1.e7547 2015-12-17 rio

Publishing the research process Mietchen,Daniel Mounce,Ross Penev,Lyubomir Research Ideas and Outcomes 1: e7547 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2015 Editorial text/html info:doi:10.3897/rio.1.e7547 https://doi.org/10.3897/rio.1.e7547 https://riojournal.com/article/7547/ https://riojournal.com/article/7547/download/pdf/ en

10.3897/rio.1.e7576 2015-12-21 rio

Continuous and Focused Developer Feedback on Software Quality (CoFoDeF) Wagner,Stefan Software Quality Information Needs Fast Feedback Research Ideas and Outcomes 1: e7576 Software is intangible and, therefore, difficult to understand and control. Quality problems often creep in unnoticed because the developers do not have a full view of the history and all the consequences of their changes to the system. Therefore, we observe quality decay in many software systems over time. A countermeasure would be frequent quality analyses starting early in the development, e.g. in nightly builds. Frequent quality analyses reduce the problem of quality decay because quality defects are detected soon after they were introduced, but they still allow defects to be introduced. This means that builds might fail, other developers might have already worked with that code revision and changes will result in rework. I propose to apply the detection of quality problems directly before or while they are created. For this, we need continuous and focused feedback about a software's quality to the developers. To give that feedback to the developers without overwhelming them, a main goal of this project is to understand the quality information needs of developers. We will build an information needs theory by empirical analysis and use this theory to investigate diverse quality checks integrated directly into development environments. We will build on advances in test-case generation, static analysis and repository mining to provide this feedback. Finally, we will extensively investigate the impact of the created continuous and focused feedback on the developers in controlled experiments and industrial case studies. We see the main challenges in providing the right feedback to the developer at the right time and in the right context as well as supplying the developers with the necessary explanations to understand and make use of the shown information. We will address these challenges by building focused and learning analyses which understand the context of the change and the developer. The analyses will learn manually and automatically the developer's preferences. Furthermore, we mine and include rationales from detailed quality models, web resources and slicing into the developer feedback. If we succeed, the results will increase the usage of quality analyses in practice, make the developers aware of quality problems, and reduce quality problems and the expenditure they cause. Furthermore, our project will open up possibilities for research to create and integrate new kinds of immediate feedback to the developers. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2015 DFG Grant Proposal text/html info:doi:10.3897/rio.1.e7576 https://doi.org/10.3897/rio.1.e7576 https://riojournal.com/article/7576/ https://riojournal.com/article/7576/download/pdf/ en

10.3897/rio.1.e7573 2015-12-22 rio

Enabling Open Science: Wikidata for Research (Wiki4R) Mietchen,Daniel Hagedorn,Gregor Willighagen,Egon Rico,Mariano Gómez-Pérez,Asunción Aibar,Eduard Rafes,Karima Germain,Cécile Dunning,Alastair Pintscher,Lydia Kinzler,Daniel Virtual Research Environment Wikidata identifiers citizen science collaboration concept mapping ontologies Research Ideas and Outcomes 1: e7573 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2015 H2020 Grant Proposal text/html info:doi:10.3897/rio.1.e7573 https://doi.org/10.3897/rio.1.e7573 https://riojournal.com/article/7573/ https://riojournal.com/article/7573/download/pdf/ en

10.3897/rio.1.e7506 2015-12-28 rio

Determining the direction of a gamma-ray burst's jet in its host galaxy Zou,Yuanchuan GRB relativistic jet galaxy Research Ideas and Outcomes 1: e7506 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2015 Research Idea text/html info:doi:10.3897/rio.1.e7506 https://doi.org/10.3897/rio.1.e7506 https://riojournal.com/article/7506/ https://riojournal.com/article/7506/download/pdf/ en

10.3897/rio.1.e7642 2015-12-29 rio

Mental synthesis involves the synchronization of independent neuronal ensembles Vyshedskiy,Andrey Dunn,Rita mental synthesis imagination binding-by-synchrony independent neuronal ensembles neuronal ensemble synchronization neuronal synchronization  evolution of language Research Ideas and Outcomes 1: e7642 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2015 Research Idea text/html info:doi:10.3897/rio.1.e7642 https://doi.org/10.3897/rio.1.e7642 https://riojournal.com/article/7642/ https://riojournal.com/article/7642/download/pdf/ en

10.3897/rio.2.e7757 2016-01-11 rio

The Open Biodiversity Knowledge Management System in Scholarly Publishing Senderov,Viktor Penev,Lyubomir entomology systematics taxonomy biodiversity informatics evolutionary informatics bioinformatics data visualization data publishing semantically enhanced publication Research Ideas and Outcomes 2: e7757 This project aims to develop and implement novel ways of publication, visualization, and dissemination of biodiversity and biodiversity-related data and thus bring the Open Biodiversity Knowledge Management System closer to fruition. In order to do so, we will develop new types of Enhanced Publications (EP's), which will allow automated data import into the manuscript and export from the manuscript and provide dynamic visualizations. These EP's will enable biodiversity researchers and taxonomists to streamline their work and publish more data-rich species descriptions. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/grantAgreement/EC/H2020/642241 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 PhD Project Plan text/html info:doi:10.3897/rio.2.e7757 https://doi.org/10.3897/rio.2.e7757 https://riojournal.com/article/7757/ https://riojournal.com/article/7757/download/pdf/ en

10.3897/rio.2.e7787 2016-01-19 rio

Unifying European Biodiversity Informatics (BioUnify) Koureas,Dimitris Hardisty,Alex Vos,Rutger Agosti,Donat Arvanitidis,Christos Bogatencov,Peter Buttigieg,Pier Luigi de Jong,Yde Horvath,Ferenc Gkoutos,Georgios Groom,Quentin Kliment,Tomas Kõljalg,Urmas Manakos,Ioannis Marcer,Arnald Marhold,Karol Morse,David Mergen,Patricia Penev,Lyubomir Pettersson,Lars B. Svenning,Jens-Christian van de Putte,Anton P. Smith,Vincent COST Action Biodiversity Informatics Environment Standards Data interoperability Research Ideas and Outcomes 2: e7787 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 COST Grant Proposal text/html info:doi:10.3897/rio.2.e7787 https://doi.org/10.3897/rio.2.e7787 https://riojournal.com/article/7787/ https://riojournal.com/article/7787/download/pdf/ en

10.3897/rio.2.e7869 2016-01-22 rio

Partial synchronization of the colonial diatom Bacillaria "paradoxa" Gordon,Richard colonial diatom Bacillaria paradoxa gliding motility synchrony Research Ideas and Outcomes 2: e7869 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e7869 https://doi.org/10.3897/rio.2.e7869 https://riojournal.com/article/7869/ https://riojournal.com/article/7869/download/pdf/ en

10.3897/rio.2.e8134 2016-02-17 rio

Vertical-Horizontal Regulated Soilless Farming via Advanced Hydroponics for Domestic Food Production in Doha, Qatar Abdullah,Nik-Othman hydroponics soilless farming vertical-horizontal growing large-scale Research Ideas and Outcomes 2: e8134 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Methods text/html info:doi:10.3897/rio.2.e8134 https://doi.org/10.3897/rio.2.e8134 https://riojournal.com/article/8134/ https://riojournal.com/article/8134/download/pdf/ en

10.3897/rio.2.e8424 2016-03-10 rio

ContentMine/Hypothes.is Proposal Martone,Maryann Murray-Rust,Peter Molloy,Jenny Arrow,Tom MacGillivray,Mark Kittel,Chris Kasberger,Stefan Steel,Graham Oppenheim,Charles Ranganathan,Anusha Tennant,Jon Udell,Jon amanuens.is Zika open science open access ContentMine Research Ideas and Outcomes 2: e8424 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Grant Proposal text/html info:doi:10.3897/rio.2.e8424 https://doi.org/10.3897/rio.2.e8424 https://riojournal.com/article/8424/ https://riojournal.com/article/8424/download/pdf/ en

10.3897/rio.2.e8458 2016-03-12 rio

Data Policy Recommendations for Biodiversity Data. EU BON Project Report Egloff,Willi Agosti,Donat Patterson,David Hoffmann,Anke Mietchen,Daniel Kishor,Puneet Penev,Lyubomir open science bidoiversity data policies data mining Research Ideas and Outcomes 2: e8458 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Project Report text/html info:doi:10.3897/rio.2.e8458 https://doi.org/10.3897/rio.2.e8458 https://riojournal.com/article/8458/ https://riojournal.com/article/8458/download/pdf/ en

10.3897/rio.2.e8462 2016-03-14 rio

Paperity Central: An Open Catalog of All Scholarly Literature Wojnarski,Marcin Hanken Kurtz,Debra open access open science open data wiki API Research Ideas and Outcomes 2: e8462 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e8462 https://doi.org/10.3897/rio.2.e8462 https://riojournal.com/article/8462/ https://riojournal.com/article/8462/download/pdf/ en

10.3897/rio.2.e8600 2016-03-23 rio

1st EU BON Stakeholder Roundtable (Brussels, Belgium):  Biodiversity and Requirements for Policy Wetzel,Florian Hoffmann,Anke Haüser,Christoph Vohland,Katrin European environmental policy biodiversity GEO GEOSS EU BON science-policy interface biodiversity data research Research Ideas and Outcomes 2: e8600 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Workshop Report text/html info:doi:10.3897/rio.2.e8600 https://doi.org/10.3897/rio.2.e8600 https://riojournal.com/article/8600/ https://riojournal.com/article/8600/download/pdf/ en

10.3897/rio.2.e8615 2016-03-24 rio

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 Hammond,Chad Indigenous health cancer arts-based methods Research Ideas and Outcomes 2: e8615 Cancer incidence is growing within First Nations, Inuit, and Métis (FNIM) communities, yet research and supportive care is slow to respond to their unique needs and experiences. The proposed project will engage important stakeholders involved in FNIM cancer care within Ontario, including health care professionals, health administrators, and FNIM community leaders. This study builds upon a national study on FNIM cancer survivors. Three objectives drive this research: 1) To identify strengths and needs within FNIM cancer care in Ontario from multiple perspectives; 2) To exchange knowledge of FNIM cancer experiences between stakeholders through arts-based methods, especially photography; 3) To work collaboratively with stakeholders to establish recommendations for improving FNIM cancer care. The project involves early consultations with stakeholders on the most pressing questions and issues in the area. Then, 20 participants (10 health care professionals, 5 health administrators, and 5 FNIM community leaders) will be recruited to use and discuss photos that capture experiences of FNIM cancer care. A report will be generated and dispensed to participants, bringing together various experiences, themes, perspectives, and recommendations for improving the state of care. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e8615 https://doi.org/10.3897/rio.2.e8615 https://riojournal.com/article/8615/ https://riojournal.com/article/8615/download/pdf/ en

10.3897/rio.2.e8616 2016-03-24 rio

2nd EU BON Stakeholder Roundtable (Berlin, Germany): How can a European biodiversity network support citizen science? Vohland,Katrin Haüser,Christoph Regan,Eugenie Hoffmann,Anke Wetzel,Florian Citizen Science biodiversity data data quality Biodiversity Observation Networks EU BON research data European Citizen Science Association Citizen Science Observatories. Research Ideas and Outcomes 2: e8616 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Workshop Report text/html info:doi:10.3897/rio.2.e8616 https://doi.org/10.3897/rio.2.e8616 https://riojournal.com/article/8616/ https://riojournal.com/article/8616/download/pdf/ en

10.3897/rio.2.e8622 2016-03-24 rio

3rd EU BON Stakeholder Roundtable (Granada, Spain): Biodiversity data workflow from data mobilization to practice Vohland,Katrin Hoffmann,Anke Underwood,Evelyn Weatherdon,Lauren Bonet García,Francisco Javier Haüser,Christoph Wetzel,Florian Biodiversity data workflows data integration local and regional biodiversity networks policy support biodiversity portals EU BON test sites data mobilization. Research Ideas and Outcomes 2: e8622 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Workshop Report text/html info:doi:10.3897/rio.2.e8622 https://doi.org/10.3897/rio.2.e8622 https://riojournal.com/article/8622/ https://riojournal.com/article/8622/download/pdf/ en

10.3897/rio.2.e8649 2016-03-30 rio

Roadmap: A Research Data Management Advisory Platform Simms,Stephanie Jones,Sarah Ashley,Kevin Ribeiro,Marta Chodacki,John Abrams,Stephen Strong,Marisa open science data management plans biomedical research funder policies Research Ideas and Outcomes 2: e8649 The DMPTool and DMPonline were developed to meet an emerging need arising from the advent of open data policies and each is now well established as the resource for researchers seeking guidance in creating data management plans (DMPs) in the US and UK respectively. Both services, and their sponsoring organizations, the California Digital Library (CDL) and the Digital Curation Centre (DCC), have succeeded in enabling researchers to comply with funder requirements in producing DMPs. However, this is just one step along the road to advancing open science. We see an opportunity to further leverage DMPs to support open science by integrating them into the broader ecosystem of data management infrastructure. In order to achieve this goal, we must redefine success to include not just adoption of our services by institutions but also widespread adoption by individual researchers, disciplinary communities, and funders. Working together with all stakeholders to make DMPs an essential, open part of the research lifecycle, and not just a matter of compliance, is the next step toward effectively managing and sharing research data. We propose to join forces and build a new, global data management advisory platform that links DMPs to other components of the research lifecycle. The biomedical research community provides an opportunity to adapt the infrastructure and associated educational resources to one specific disciplinary community and plug into new initiatives. We will reposition DMPs as living documents useful for structuring the course of biomedical research activities and integrating with related data management systems to lower the barriers for implementation and promote culture change. Consolidating around a single platform for DMPs extends our reach, keeps costs down, and moves best practices forward, allowing us to participate in a truly global open science ecosystem. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Grant Proposal text/html info:doi:10.3897/rio.2.e8649 https://doi.org/10.3897/rio.2.e8649 https://riojournal.com/article/8649/ https://riojournal.com/article/8649/download/pdf/ en

10.3897/rio.2.e8664 2016-04-05 rio

Data Management Plan for PhD Thesis "Climatic Limitation of Alien Weeds in New Zealand: Enhancing Species Distribution Models with Field Data" Pannell,Jennifer data management plan doctorate ecology Crassulaceae invasions Research Ideas and Outcomes 2: e8664 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Data Management Plan (NSF Generic) text/html info:doi:10.3897/rio.2.e8664 https://doi.org/10.3897/rio.2.e8664 https://riojournal.com/article/8664/ https://riojournal.com/article/8664/download/pdf/ en

10.3897/rio.2.e8720 2016-04-05 rio

A Political Ecology of Value: A Cohort-Based Ethnography of the Environmental Turn in Nicaraguan Urban Social Policy  Fisher,Josh Nading,Alex urban political ecology urban anthropology collaborative anthropology economic anthropology environmental anthropology medical anthropology value Research Ideas and Outcomes 2: e8720 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Data Management Plan (NSF Generic) text/html info:doi:10.3897/rio.2.e8720 https://doi.org/10.3897/rio.2.e8720 https://riojournal.com/article/8720/ https://riojournal.com/article/8720/download/pdf/ en

10.3897/rio.2.e8767 2016-04-07 rio

Towards a biodiversity knowledge graph Page,Roderic biodiversity informatics biodiversity knowledge graph JSON-LD graph databases triple stores RDF linked data Research Ideas and Outcomes 2: e8767 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e8767 https://doi.org/10.3897/rio.2.e8767 https://riojournal.com/article/8767/ https://riojournal.com/article/8767/download/pdf/ en

10.3897/rio.2.e8726 2016-04-07 rio

Tools of Persuasion in Visual Advertisements at Maltese Sites of Cultural Tourism: A Social Science Analysis Toth,Janos small grant proposal marketing research advertising research survey study textual analysis Research Ideas and Outcomes 2: e8726 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e8726 https://doi.org/10.3897/rio.2.e8726 https://riojournal.com/article/8726/ https://riojournal.com/article/8726/download/pdf/ en

10.3897/rio.2.e8758 2016-04-08 rio

Pericardial window operation for malignant pericardial effusion may have worse outcomes for lung cancer than the other cancers Chen,Robert Shen,Ta-Chung Tsai,Kuei-Ton Hu,Chin-Yuan pericardial window malignant pericardial effusion (MPE) lung cancer Research Ideas and Outcomes 2: e8758 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Article text/html info:doi:10.3897/rio.2.e8758 https://doi.org/10.3897/rio.2.e8758 https://riojournal.com/article/8758/ https://riojournal.com/article/8758/download/pdf/ en

10.3897/rio.2.e8760 2016-04-12 rio

Cobweb: A Collaborative Collection Development Platform for Web Archiving Abrams,Stephen Goethals,Andrea Klein,Martin Lack,Rosalie web archives collection development digital library Research Ideas and Outcomes 2: e8760 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e8760 https://doi.org/10.3897/rio.2.e8760 https://riojournal.com/article/8760/ https://riojournal.com/article/8760/download/pdf/ en

10.3897/rio.2.e8815 2016-04-13 rio

Concurrence Topology: Finding High-Order Dependence in Neuropsychiatric Data Klein,Arno Ellis,Steven concurrence topology homology brain imaging adhd high-order dependence statistical analysis Research Ideas and Outcomes 2: e8815 The proposed research develops new computational tools to identify, diagnose, and predict treatment response for different mental illnesses. The research will first be applied to publicly available resting state fMRI BOLD data from patients with attentiondeficit hyperactivity disorder and autism. It will also be applied to existing clinical and biological data concerning suicidality in the context of major depressive disorder. These disorders affect millions of Americans, but these tools can be applied to any mental illness, such as Alzheimer’s disease, bipolar disorder, schizophrenia – indeed to analyze differences in brain, clinical, and biological data between any two populations. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 NIH Grant Proposal text/html info:doi:10.3897/rio.2.e8815 https://doi.org/10.3897/rio.2.e8815 https://riojournal.com/article/8815/ https://riojournal.com/article/8815/download/pdf/ en

10.3897/rio.2.e8814 2016-04-13 rio

Data-Visual Relationships to Subject Performance and Eye Movements Klein,Arno eye tracking eye movements  visualization information graphics Research Ideas and Outcomes 2: e8814 Visual communication is ubiquitous, commanding our attention and commandeering our inattention. The presentation of information can take myriad visual forms, such as bar charts, scatter plots, network diagrams, and tables. These information graphics are attempts to map potentially large amounts of complex data to easily navigable visual form for rapid and accurate knowledge transfer. However, there is not yet a satisfactory formal methodology for selecting the most appropriate visualization method for a given set of data. A data taxonomy and novel visual taxonomy will be used to select visual stimuli from a database of acquired and newly generated information graphics. Oculomotor responses (eye tracking data) and task-based responses (mouse clicks or keyboard input) are recorded; performance on the latter is used to establish an expert subgroup. These results will be used to satisfy the three primary objectives of the proposed research, determining: how the choice of data visualization impacts oculomotor behavior and task performance, if this behavior is discriminable between experts and novices, and an empirically-based taxonomy of visualization based on the results of 1 and 2. Intellectual merit of the proposed activity The proposed research will create a novel taxonomy for and database of acquired and generated information graphics as well as an associated web application to search, organize, and compare entries in the database. Part of this research program is intended to establish the most comprehensive, manually annotated (and taxonomically classified) information graphics database in the world, for use by the public via a web interface. These images will be important for procuring stimuli for other kinds of perceptual and cognitive psychology experiments. The eye tracking and task performance results should help lead to a better understanding of how humans look at data, respond to the relationship between data structures and visual composition, and respond differentially to visualizations of different types. With respect to qualifications, the PI has a background in brain imaging research, image processing, and programming applications for generating graphs. Through his collaborator Dr. Ferrera of Columbia University, he has access to facilities and faculty specialized in eye tracking and psychophysics research. Collaborator Dr. Michelle Zhou, a research manager at IBM T. J. Watson Research Center, has years of experience in the areas of data and visual taxonomies, image databases, and automated generation of information graphics [Zhou and Feiner 1998, Zhou et al. 2002b, Zhou et al. 2002a]. Broader impacts of the proposed activity In addition to contributions the image taxonomy, database, and web application are intended to make to research, they will serve as a rich resource for teaching about the history and scope of visualization methods and design within and across disciplines, and for the general public with an interest in information graphics. The research will be conducted on subjects of varied background and race and will be broadly disseminated via websites in addition to publications. Additionally, defining a visual taxonomy will inform design choices made in information visualization. One implication of this research is a determination of how effective different visualization methods are at conveying information; this understanding will be of profound help to anyone interested in conveying information effectively in a graphical form. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 NSF Grant Proposal text/html info:doi:10.3897/rio.2.e8814 https://doi.org/10.3897/rio.2.e8814 https://riojournal.com/article/8814/ https://riojournal.com/article/8814/download/pdf/ en

10.3897/rio.2.e8796 2016-04-14 rio

Deathcore, creativity, and scientific thinking Angeler,David Sundstrom,Shana Allen,Craig science art music religion creativity inductivism scientific process Research Ideas and Outcomes 2: e8796 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e8796 https://doi.org/10.3897/rio.2.e8796 https://riojournal.com/article/8796/ https://riojournal.com/article/8796/download/pdf/ en

10.3897/rio.2.e8801 2016-04-14 rio

Induced pluripotent stem (iPS) cells and somatic cardiac regeneration — An exploratory bioinformatic analysis Chen,Robert Yu,Yau-Hua induced pluripotent stem (iPS) cells nucleostemin Ingenuity Pathway Analysis Research Ideas and Outcomes 2: e8801 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Conference Abstract text/html info:doi:10.3897/rio.2.e8801 https://doi.org/10.3897/rio.2.e8801 https://riojournal.com/article/8801/ https://riojournal.com/article/8801/download/pdf/ en

10.3897/rio.2.e8867 2016-04-15 rio

Deathcore, creativity, and scientific thinking Angeler,David Sundstrom,Shana Allen,Craig science art music religion creativity inductivism scientific process Research Ideas and Outcomes 2: e8867 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e8867 https://doi.org/10.3897/rio.2.e8867 https://riojournal.com/article/8867/ https://riojournal.com/article/8867/download/pdf/ en

10.3897/rio.2.e8813 2016-04-15 rio

Collection of informatics proposals from 2007 Klein,Arno informatics neuroinformatics Research Ideas and Outcomes 2: e8813 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e8813 https://doi.org/10.3897/rio.2.e8813 https://riojournal.com/article/8813/ https://riojournal.com/article/8813/download/pdf/ en

10.3897/rio.2.e8827 2016-04-15 rio

Coastal Data Information Program (CDIP) McWhorter,Jennifer Wright,Darren Thomas,Julie waves data quality control real-time long-term time series sea-surface temperature Research Ideas and Outcomes 2: e8827 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Data Management Plan (NSF Generic) text/html info:doi:10.3897/rio.2.e8827 https://doi.org/10.3897/rio.2.e8827 https://riojournal.com/article/8827/ https://riojournal.com/article/8827/download/pdf/ en

10.3897/rio.2.e8880 2016-04-18 rio

Exploring the opportunities and challenges of implementing open research strategies within development institutions Neylon,Cameron Chan,Leslie data sharing research data management development data management plan research policy mandate Research Ideas and Outcomes 2: e8880 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Grant Proposal text/html info:doi:10.3897/rio.2.e8880 https://doi.org/10.3897/rio.2.e8880 https://riojournal.com/article/8880/ https://riojournal.com/article/8880/download/pdf/ en

10.3897/rio.2.e8812 2016-04-18 rio

A Million Brains in the Cloud Klein,Arno Ghosh,Satrajit brain imaging data mining Research Ideas and Outcomes 2: e8812 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e8812 https://doi.org/10.3897/rio.2.e8812 https://riojournal.com/article/8812/ https://riojournal.com/article/8812/download/pdf/ en

10.3897/rio.2.e8816 2016-04-19 rio

A game for crowdsourcing the segmentation of BigBrain data Klein,Arno BigBrain brain imaging histology microstructure neurons crowdsourcing game gamify Research Ideas and Outcomes 2: e8816 The BigBrain, a high-resolution 3-D model of a human brain at nearly cellular resolution, is the best brain imaging data set in the world to establish a canonical space at both microscopic and macroscopic resolutions. However, for the cell-stained microstructural data to be truly useful, it needs to be segmented into cytoarchitectonic regions, a challenge no single lab could undertake. The principal aim of this proposal is to crowdsource the segmentation of cytoarchitectonic regions by means of a computer game, to transform an arduous, isolated task performed by experts into an engaging, collective activity of non-experts. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 NIH Grant Proposal text/html info:doi:10.3897/rio.2.e8816 https://doi.org/10.3897/rio.2.e8816 https://riojournal.com/article/8816/ https://riojournal.com/article/8816/download/pdf/ en

10.3897/rio.2.e8817 2016-04-19 rio

Brain Graph Interface Klein,Arno brain imaging graphical display interface interactive GUI Research Ideas and Outcomes 2: e8817 We will analyze variations in brain anatomy and create the first integrated software environment to extract patterns from brains and target differences related to inter-individual variability, pathology, development, or degeneration. We will evaluate how well these differences can help diagnose and predict treatment outcome for major depressive disorder, which affects millions of Americans, but our work is intended to be applied to any mental illness, such as Alzheimer’s disease, bipolar disorder, schizophrenia – indeed to analyze differences in brain anatomy between any two populations. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 NIH Grant Proposal text/html info:doi:10.3897/rio.2.e8817 https://doi.org/10.3897/rio.2.e8817 https://riojournal.com/article/8817/ https://riojournal.com/article/8817/download/pdf/ en

10.3897/rio.2.e8865 2016-04-20 rio

Software quality information needs Graziotin,Daniel information needs software quality process theory affective reactions behavioral patterns Research Ideas and Outcomes 2: e8865 Modern software methodologies, e.g., agile and continuous integration and deployment, rely on frequent feedback loops to respond to sudden changes. Improvements to feedback, development activities, and quality rely on information needs. We found a lack of understanding on the information needs of software engineers when the software quality is the main concern. I propose the term "software quality information needs" to refer to a software engineer’s eagerness to define, locate, obtain, and use information to satisfy a conscious or unconscious concern towards software quality. I want to understand what information about software quality does a developer need while performing code changes or designing new parts of a system. For understanding the broad research question, I propose three sub-questions, namely (1) How can we conceptualize information needs when dealing with software quality? (2) What information is needed when dealing with software quality? and (3) How can software quality information needs be detected unobtrusively through behavioral patterns? I propose a 24 months plan for a research fellowship comprising of three empirical studies, which will involve 120 students in computer science and the companies Daimler, Porsche, and Bosch. The studies will make use of multidisciplinary research in software engineering and behavioral science. The theoretical results of the execution of this proposal are the software quality information needs theory and instances, which will add to the body of knowledge in software engineering. The practical implications might be large. 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. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Grant Proposal text/html info:doi:10.3897/rio.2.e8865 https://doi.org/10.3897/rio.2.e8865 https://riojournal.com/article/8865/ https://riojournal.com/article/8865/download/pdf/ en

10.3897/rio.2.e8861 2016-04-20 rio

Historical analysis of strategies for assimilation and identity maintenance in dispersed groups of overseas Hungarians and their relevance regarding national policy planning Toth,Janos Diaspora Research Hungarian Diaspora National Identity National Policy Planning Research Ideas and Outcomes 2: e8861 Small grant proposal for the period between August 1, 2015 – December 31, 2015 of the Kelemen Mikes Program; for collecting the legacy of the Hungarian diaspora from documents of libraries and archives, and for the historical study of these communities. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e8861 https://doi.org/10.3897/rio.2.e8861 https://riojournal.com/article/8861/ https://riojournal.com/article/8861/download/pdf/ en

10.3897/rio.2.e8835 2016-04-21 rio

Graph-based clinical diagnosis and prediction using multi-modal neuroimaging data Klein,Arno Ghosh,Satrajit graphs brain imaging multimodal data Research Ideas and Outcomes 2: e8835 The proposed research develops new computational tools to identify, diagnose, and predict treatment outcome for different mental illnesses. The research will be applied first to major depressive disorder, which affects millions of Americans, but is intended to be applied to any mental illness, such as Alzheimer’s disease, bipolar disorder, schizophrenia – indeed to analyze differences in brain structure, activity, or connectivity between any two populations. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 NIH Grant Proposal text/html info:doi:10.3897/rio.2.e8835 https://doi.org/10.3897/rio.2.e8835 https://riojournal.com/article/8835/ https://riojournal.com/article/8835/download/pdf/ en

10.3897/rio.2.e8849 2016-04-21 rio

Clinical roles of soluble ST2 for the outcomes of cardiac valve operations Chen,Robert ST2 NT-proBNP heart failure troponin-T biomarker Research Ideas and Outcomes 2: e8849 Soluble ST2 is a novel cardiac biomarker that reflects cardiac injury and the response to treatment. Previous studies showed that ST2 has less confounding and more specific than NT-proBNP. ACCF/AHA has proposed 2013 Guidelines for the Management of Heart Failure that includes ST2 in the recommendations. In the research proposal, we will assess the clinical role of serum ST2 level in cardiac non-coronary valve surgical patients. We will recruit 70 patients who undergo cardiac non-coronary valve operations. Serum levels of ST2 and NT-proBNP and troponin-T will be measured at preoperative baseline, postoperative 24 hours, and postoperative 5 to 10 days in the routine blood sampling. The endpoints include hospital mortality, all-cause mortality, unexpected ICU return, MACE, time to extubation, and total length of stay. We will also collect various preoperative, operative, and postoperative variables, such as EuroScore-II. Their relationships will be analyzed. We expect to demonstrate the superior role of ST2 to NT-proBNP and other variables in risk stratification and outcome prediction and assessment in our cohort. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e8849 https://doi.org/10.3897/rio.2.e8849 https://riojournal.com/article/8849/ https://riojournal.com/article/8849/download/pdf/ en

10.3897/rio.2.e8848 2016-04-22 rio

Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease Klein,Arno mPower Parkinson disease mobile health app voice analysis features crowdsourcing annotation Research Ideas and Outcomes 2: e8848 Mobile phones provide a new way of collecting behavioral medical research data at a scale never before possible – Sage Bionetworks’ mPower Parkinson research app, launched at Apple’s March 9, 2015 ResearchKit announcement, is currently collecting data related to Parkinson symptoms, such as voice recordings, from thousands of registered study participants. Before making such voice data available to any qualified researcher in the world, they need to undergo quality control and editing, which is currently something only a human can do well. To achieve this goal and the required scale, we will crowdsource these tasks through Amazon's Mechanical Turk. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 NIH Grant Proposal text/html info:doi:10.3897/rio.2.e8848 https://doi.org/10.3897/rio.2.e8848 https://riojournal.com/article/8848/ https://riojournal.com/article/8848/download/pdf/ en

10.3897/rio.2.e8860 2016-04-22 rio

The value of statistical tools to detect data fabrication Hartgerink,Chris Wicherts,Jelte van Assen,Marcel data fabrication statistics scientific misconduct integrity Research Ideas and Outcomes 2: e8860 We aim to investigate how statistical tools can help detect potential data fabrication in the social- and medical sciences. In this proposal we outline three projects to assess the value of such statistical tools to detect potential data fabrication and make the first steps in order to apply them automatically to detect data anomalies, potentially due to data fabrication. In Project 1, we examine the performance of statistical methods to detect data fabrication in a mixture of genuine and fabricated data sets, where the fabricated data sets are generated by actual researchers who participate in our study. We also interview these researchers in order to investigate, in Project 2, different data fabrication characteristics and whether data generated with certain characteristics are better detected with current statistical tools than others. In Project 3 we use software to semi-automatically screen research articles to detect data anomalies that are potentially due to fabrication, and develop and test new software forming the basis for automated screening of research articles for data anomalies, potentially due to data fabrication, in the future. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e8860 https://doi.org/10.3897/rio.2.e8860 https://riojournal.com/article/8860/ https://riojournal.com/article/8860/download/pdf/ en

10.3897/rio.2.e9015 2016-04-27 rio

The influence of religion on science: the case of the idea of predestination in biospeleology Romero Jr.,Aldemaro predetermination science and religion biological evolution biospeleology cave biology history of science Research Ideas and Outcomes 2: e9015 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Article text/html info:doi:10.3897/rio.2.e9015 https://doi.org/10.3897/rio.2.e9015 https://riojournal.com/article/9015/ https://riojournal.com/article/9015/download/pdf/ en

10.3897/rio.2.e8834 2016-05-03 rio

Visual Parkinson’s Disease Rating Scale: A Universal Iconic Questionnaire for Epidemiological Studies in India Klein,Arno Parkinson disease UPDRS visual rating scale iconographic representation Research Ideas and Outcomes 2: e8834 There is a great need to gather data from vast populations to better understand the distribution of Parkinson’s disease and the variation in its symptoms, ultimately to aid in its diagnosis, determination of symptom severity, and prediction of disease progression in individuals. Toward these ends, we propose to take the most commonly administered Parkinson’s questionnaire and make it universally intelligible across languages, cultures, and education levels, as well as intuitive and engaging, by creating and evaluating a “Visual Parkinson’s Disease Rating Scale” (VPDRS). To administer a consistent and widely accessible implementation of the VPDRS to Parkinson’s patients in the U.S. and in India, we will deploy it on a mobile phone application, and store the data on server technology that we have developed and will establish in India for managing large-scale data collection from mobile devices in future studies. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 NIH Grant Proposal text/html info:doi:10.3897/rio.2.e8834 https://doi.org/10.3897/rio.2.e8834 https://riojournal.com/article/8834/ https://riojournal.com/article/8834/download/pdf/ en

10.3897/rio.2.e9113 2016-05-08 rio

Open Neuroimaging Laboratory Heuer,Katja Ghosh,Satrajit Robinson Sterling,Amy Toro,Roberto Neuroimaging Collaboration Open Science Co-edition Open Science Prize Magnetic Resonance Imaging Segmentation Research Ideas and Outcomes 2: e9113 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e9113 https://doi.org/10.3897/rio.2.e9113 https://riojournal.com/article/9113/ https://riojournal.com/article/9113/download/pdf/ en

10.3897/rio.2.e9173 2016-05-11 rio

Acoustic biomarkers of Chronic Obstructive Lung Disease Vyshedskiy,Andrey Murphy,Raymond STG16 lung sounds multichannel lung sound COPD Research Ideas and Outcomes 2: e9173 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Poster text/html info:doi:10.3897/rio.2.e9173 https://doi.org/10.3897/rio.2.e9173 https://riojournal.com/article/9173/ https://riojournal.com/article/9173/download/pdf/ en

10.3897/rio.2.e9232 2016-05-16 rio

Unicorn–Open science for assessing environmental state, human health and regional economy Neittanmäki,Pekka Huttula,Timo Karvanen,Juha Frisk,Tom Tuomisto,Jouni Simola,Antti Tuovinen,Tero Ropponen,Janne Open data open models environment human health regional economy Research Ideas and Outcomes 2: e9232 Open data and models are becoming increasingly available, but there are not yet good methods and platforms to turn those into systematic evidence-based decision support. Unicorn will produce such an enviro­­nment based on existing theoretical and practical knowledge about decision support and models. This con­sortium possesses the necessary models, data, and skills to set up an environment and demonstrate its func­tionality and usefulness with several case studies related to the environmental issues, human health, and economy. The Unicorn environment will be built in a generic and systematic way so that it could even be­come an international standard for evidence-based decision support. Developing a technical environment or standard is not enough. Using the Unicorn environment is a large cul­­tural change for both researchers and decision makers, as the current decision support practices do not re­flect the principles of openness, criticism, or reuse. Therefore, this cultural change must be promoted by train­ing to use the environment, by informing the society about its possibilities, and solving a number of practi­cal and technical problems related to current practices in research institutes, ministries, and municipalities. We acknowledge these problems and offer solutions to them with an extensive interaction plan. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Grant Proposal text/html info:doi:10.3897/rio.2.e9232 https://doi.org/10.3897/rio.2.e9232 https://riojournal.com/article/9232/ https://riojournal.com/article/9232/download/pdf/ en

10.3897/rio.2.e9115 2016-05-25 rio

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 Hammond,Chad Indigenous health cancer arts-based methods Research Ideas and Outcomes 2: e9115 Cancer incidence is growing within First Nations, Inuit, and Métis (FNIM) communities, yet research and supportive care is slow to respond to their unique needs and experiences. The proposed project will engage important stakeholders involved in FNIM cancer care within Ontario, including health care professionals, health administrators, and FNIM community leaders. This study builds upon a national study on FNIM cancer survivors. Three objectives drive this research: 1) To identify strengths and needs within FNIM cancer care in Ontario from multiple perspectives; 2) To exchange knowledge of FNIM cancer experiences between stakeholders through arts-based methods, especially photography; 3) To work collaboratively with stakeholders to establish recommendations for improving FNIM cancer care. The project involves early consultations with stakeholders on the most pressing questions and issues in the area. Then, 20 participants (10 health care professionals, 5 health administrators, and 5 FNIM community leaders) will be recruited to use and discuss photos that capture experiences of FNIM cancer care. A report will be generated and dispensed to participants, bringing together various experiences, themes, perspectives, and recommendations for improving the state of care. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e9115 https://doi.org/10.3897/rio.2.e9115 https://riojournal.com/article/9115/ https://riojournal.com/article/9115/download/pdf/ en

10.3897/rio.2.e9268 2016-05-26 rio

Bi-directional immuno-modulation by Matrix Metalloproteinase-7 (MMP-7) and A Disintegrin And Metalloproteinase-17 (ADAM-17) as transplantation rejection-tolerance spectrum Chen,Robert Matrix Metalloproteinase-7 (MMP-7) A Disintegrin And Metalloproteinase-17 (ADAM-17) transplantation rejection allograft Research Ideas and Outcomes 2: e9268 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 PhD Project Plan text/html info:doi:10.3897/rio.2.e9268 https://doi.org/10.3897/rio.2.e9268 https://riojournal.com/article/9268/ https://riojournal.com/article/9268/download/pdf/ en

10.3897/rio.2.e9340 2016-05-26 rio

Defining the Scholarly Commons - Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016 Kramer,Bianca Bosman,Jeroen Ignac,Marcin Kral,Christina Kalleinen,Tellervo Koskinen,Pekko Bruno,Ian Buckland,Amy Callaghan,Sarah Champieux,Robin Chapman,Chris Hagstrom,Stephanie Martone,MaryAnn Murphy,Fiona O`Donnell,Daniel scholarly communication research communication scholarly commons workshop visualization principles Research Ideas and Outcomes 2: e9340 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Workshop Report text/html info:doi:10.3897/rio.2.e9340 https://doi.org/10.3897/rio.2.e9340 https://riojournal.com/article/9340/ https://riojournal.com/article/9340/download/pdf/ en

10.3897/rio.2.e9390 2016-05-31 rio

Data sharing tools adopted by the European Biodiversity Observation Network Project Smirnova,Larissa Mergen,Patricia Groom,Quentin De Wever,Aaike Penev,Lyubomir Stoev,Pavel Pe’er,Israel Runnel,Veljo García Camacho,Antonio Vincent,Timothy Agosti,Donat Arvanitidis,Christos Bonet García,Francisco Javier Saarenmaa,Hannu EU BON GEO BON Interoperability data standards Research Ideas and Outcomes 2: e9390 A fundamental constituent of a biodiversity observation network is the technological infrastructure that underpins it. The European Biodiversity Network project (EU BON) has been working with and improving upon pre-existing tools for data mobilization, sharing and description. This paper provides conceptual and practical advice for the use of these tools. We review tools for managing metadata, occurrence data, and ecological data and give detailed description of these tools, their capabilities and limitations. This is followed by recommendations on their deployment and possible future enhancements. This is done from the perspective of the needs of the biodiversity observation community with a view to the development of a unified user interface to these data – the European Biodiversity Portal (EBP). We described the steps taken to develop, adapt, deploy and test these tools. This document also gives an overview of the objectives that still need to be achieved and challenges to be addressed for the remainder of the project. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/grantAgreement/EC/FP7/308454 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Project Report text/html info:doi:10.3897/rio.2.e9390 https://doi.org/10.3897/rio.2.e9390 https://riojournal.com/article/9390/ https://riojournal.com/article/9390/download/pdf/ en

10.3897/rio.2.e9419 2016-06-06 rio

Boulder Creek Critical Zone Observatory Data Management Plan Fey,Jeri Anderson,Suzanne data management plan hydrology earth sciences critical zone geomorphology meteorology Research Ideas and Outcomes 2: e9419 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Data Management Plan (NSF Generic) text/html info:doi:10.3897/rio.2.e9419 https://doi.org/10.3897/rio.2.e9419 https://riojournal.com/article/9419/ https://riojournal.com/article/9419/download/pdf/ en

10.3897/rio.2.e9580 2016-06-17 rio

Benefits and costs of aphid phenological bet-hedging strategies Joschinski,Jens bet-hedging stochastic polyphenism fluctuating natural selection phenotypic plasticity phenology photoperiodism circadian clocks aphids Acyrthosiphon pisum Rhopalosiphum padi Megoura viciae Research Ideas and Outcomes 2: e9580 Intended readership I am looking for a host institute to research bet-hedging strategies in the seasonal reproductive mode switches of aphids. The intended methods leave room for collaborative side-projects beyond the study question (e.g. molecular control of photoperiodism, or sharing aphid lines from throughout Europe), so this article might be of interest to anyone working with aphids. In addition, I would be happy to receive feedback from experts in bet-hedging theory, phenotypic plasticity and photoperiodism. Summary Global change causes both mean temperature and temperature variability to increase. Organisms can cope with predictable change in means, but increasing variability is less tractable. One strategy to increase survival chances in unpredictable environments is diversified bet-hedging, i.e. spreading the risk by variation in phenotype expression. Despite being considered a general mechanism, definite evidence for bet-hedging is scarce, as it requires both the demonstration that phenotypic variance correlates with environmental variability, and that it maximizes fitness. When assessing fitness, one needs to account for both the benefits and costs of bet-hedging. Bet-hedgers produce suboptimal phenotypes in average years, resulting in decreased arithmetic mean fitness. But this temporary reduction is more than compensated by elevated fitness in harsh years, so this well-known short-term fitness effect is not considered a real cost of bet-hedging. In contrast to the effects on arithmetic mean fitness, I hypothesize that bet-hedging also carries a long-term (geometric mean) fitness costs, in that the ability to generate phenotypic variance is costly per se. With this research idea I seek evidence for bet-hedging and assess its costs and benefits, using aphids and their polyphenism in reproductive modes as model system. I plan to use aphid clones from environments along a gradient of temperature variability, and induce switches in reproductive modes under controlled conditions. To test for bet-hedging, I will correlate variance in phenotype determination with variability of the original environment. To determine the costs of bet-hedging, I will compare population growth of bet-hedgers with non-hedging clones. I will then combine benefits and costs of bet-hedging by calculating the geometric (long-term) mean fitness in predictable and unpredictable environments. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 PostDoc Project Plan text/html info:doi:10.3897/rio.2.e9580 https://doi.org/10.3897/rio.2.e9580 https://riojournal.com/article/9580/ https://riojournal.com/article/9580/download/pdf/ en

10.3897/rio.2.e9342 2016-06-23 rio

Chimeric spider silk production in microalgae: a modular bionanomaterial Dutra Molino,João Vitor Lubiana,Tiago Seno Ferreira Camargo,Livia Croce,Miguel Tanaka,Allan Buson,Felipe Ribeiro,Pedro Campos-Salazar,Antony Padilha Antonio,Eduardo Maizel,André Siratuti,Viviane Costa,Claudia Wlodarczyk,Samarina de Souza Lima,Raquel Mello,Fabio Mayfield,Stephen Carvalho,João Bionanomaterial Silk protein Recombinant protein Microalgae Enzybiotic Research Ideas and Outcomes 2: e9342 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e9342 https://doi.org/10.3897/rio.2.e9342 https://riojournal.com/article/9342/ https://riojournal.com/article/9342/download/pdf/ en

10.3897/rio.2.e9551 2016-06-23 rio

Synthetic epidermal growth factor receptor (EGFR)-mitochondria desired axles-based split green-fluorescent-protein (GFP) could screen for the signaling molecules that overcome the drug resistance to tyrosine kinase inhibitor (TKI) Chen,Robert Yu,Wei-hsuan mitochondria epidermal growth factor receptor tyrosine kinase inhibitor matrix metalloproteinase-7 Research Ideas and Outcomes 2: e9551 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Conference Abstract text/html info:doi:10.3897/rio.2.e9551 https://doi.org/10.3897/rio.2.e9551 https://riojournal.com/article/9551/ https://riojournal.com/article/9551/download/pdf/ en

10.3897/rio.2.e9597 2016-06-24 rio

Speckle Contrast Reduction with a Visible VCSEL Projector Sabuncu,Metin Yilmazlar,İsmail Vertical cavity surface emitting lasers visible VCSEL speckle Research Ideas and Outcomes 2: e9597 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e9597 https://doi.org/10.3897/rio.2.e9597 https://riojournal.com/article/9597/ https://riojournal.com/article/9597/download/pdf/ en

10.3897/rio.2.e9617 2016-06-27 rio

Matrix Proteins and Proteinases Network in Human Cardiovascular Diseases Explored By Cytoscape Chen,Robert Yu,Wei-hsuan Cytoscape matrix proteins metalloproteinase network cardiac disease Research Ideas and Outcomes 2: e9617 Matrix proteins and proteinases altered extracellular matrix that involves in various pathogenesis of cardiovascular diseases. Systematic review selected matrix metalloproteinase-7 (MMP7), a disintegrin and metalloproteinase-17 (ADAM17), type I collagen (COL1), syndecan (SDC), and versican (VCAN). Their network was drawn by Cytoscape and Agilent Literature Search. MMP7, ADAM17, and SDC were grouped together. VCAN and COL1 had inadequate evidence to connect their human potential networks that were more evidence in animal models. The findings may provide clues for further laboratory investigations. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Single-figure Publication text/html info:doi:10.3897/rio.2.e9617 https://doi.org/10.3897/rio.2.e9617 https://riojournal.com/article/9617/ https://riojournal.com/article/9617/download/pdf/ en

10.3897/rio.2.e9632 2016-06-28 rio

Saxifraga aizoides extract: novel potential effects on tumor cell models Pezzani,Raffaele Saxifraga aizoides saxifragaceae cancer cells ethnopharmacology phytotherapy Research Ideas and Outcomes 2: e9632 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e9632 https://doi.org/10.3897/rio.2.e9632 https://riojournal.com/article/9632/ https://riojournal.com/article/9632/download/pdf/ en

10.3897/rio.2.e9648 2016-06-29 rio

A Scoring System for Identifying Severe Cases of Influenza-like Illness by Comorbidity and Age - A Nationwide Cohort Analysis Chen,Robert Fang,Cheng-Chung Shih,Fuh-Yuan King,Chwan-Chuen Influenza-like illness comorbidity ICD-9 risk model Research Ideas and Outcomes 2: e9648 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Presentation text/html info:doi:10.3897/rio.2.e9648 https://doi.org/10.3897/rio.2.e9648 https://riojournal.com/article/9648/ https://riojournal.com/article/9648/download/pdf/ en

10.3897/rio.2.e9774 2016-07-06 rio

EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases Faulwetter,Sarah Pafilis,Evangelos Fanini,Lucia Bailly,Nicolas Agosti,Donat Arvanitidis,Christos Boicenco,Laura Catapano,Terry Claus,Simon Dekeyzer,Stefanie Georgiev,Teodor Legaki,Aglaia Mavraki,Dimitra Oulas,Anastasis Papastefanou,Gabriella Penev,Lyubomir Sautter,Guido Schigel,Dmitry Senderov,Viktor Teaca,Adrian Tsompanou,Marilena biodiversity data legacy literature data archaeology data rescue text mining biogeographic databases data management Research Ideas and Outcomes 2: e9774 The objective of Workpackage 4 of the European Marine Observation and Data network (EMODnet) is to fill spatial and temporal gaps in European marine species occurrence data availability by carrying out data archaeology and rescue activities. To this end, a workshop was organised in the Hellenic Center for Marine Research Crete (HCMR), Heraklion Crete, (8–9 June 2015) to assess possible mechanisms and guideCorrespondinglines to mobilise legacy biodiversity data. Workshop participants were data managers who actually implement data archaeology and rescue activities, as well as external experts in data mobilisation and data publication. In particular, current problems associated with manual extraction of occurrence data from legacy literature were reviewed, tools and mechanisms which could support a semi-automated process of data extraction were explored and the re-publication of the data, including incentives for data curators and scientists were reflected upon. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/grantAgreement/EC/FP7/211372 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Project Report text/html info:doi:10.3897/rio.2.e9774 https://doi.org/10.3897/rio.2.e9774 https://riojournal.com/article/9774/ https://riojournal.com/article/9774/download/pdf/ en

10.3897/rio.2.e9651 2016-07-07 rio

Citation functions revisited: learning from the princes Philipson,Joakim knowledge export relevance citation functions cross-disciplinarity CiTO Research Ideas and Outcomes 2: e9651 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e9651 https://doi.org/10.3897/rio.2.e9651 https://riojournal.com/article/9651/ https://riojournal.com/article/9651/download/pdf/ en

10.3897/rio.2.e9841 2016-07-18 rio

Bibliometric study to assist research topic selection: a case from research design on Jakarta’s groundwater (part 1) Irawan,Dasapta Erwin Priyambodho,Bambang Adhi Rachmi,Cut Wibowo,Dimas Fahmi,Andita Bibliometric literature review groundwater Jakarta Research Ideas and Outcomes 2: e9841 This paper is an example to visualize bibliometric data to extract paper’s topics and their citation relation. It is very important to evaluate the number of documents, the intensity of the paper’s topic, and the relationship between papers. The output can be used to pinpoint suitable research topic. We began with 246 papers, gathered from Google Scholar, Crossref, and Scopus database. We narrowed them down to 70 papers based on language, relevance, pdf availability, and metadata completeness. Open source tools, Vosviewer, Zotero-PaperMachine plugin, were used to visualize the existing reference database. The following paper gives an illustration that a brief bibliometric analysis could assist a researcher to determine our research path. It gives us a glimpse of research landscape in Jakarta area. Therefore for deeper analysis, we will focus our literature review on groundwater and surface water interactions. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Single-figure Publication text/html info:doi:10.3897/rio.2.e9841 https://doi.org/10.3897/rio.2.e9841 https://riojournal.com/article/9841/ https://riojournal.com/article/9841/download/pdf/ en

10.3897/rio.2.e9933 2016-07-20 rio

Community engagement: The ‘last mile’ challenge for European research e-infrastructures Koureas,Dimitris Arvanitidis,Christos Belbin,Lee Berendsohn,Walter G. Damgaard,Christian Groom,Quentin Güntsch,Anton Hagedorn,Gregor Hardisty,Alex Hobern,Donald Marcer,Arnald Mietchen,Daniel Morse,David Obst,Matthias Penev,Lyubomir Pettersson,Lars B. Sierra,Soraya Smith,Vincent Vos,Rutger e-infrastructure Virtual Research Environment Open Science Cloud Europe user engagement research infrastructure Research Ideas and Outcomes 2: e9933 Europe is building its Open Science Cloud; a set of robust and interoperable e-infrastructures with the capacity to provide data and computational solutions through cloud-based services. The development and sustainable operation of such e-infrastructures are at the forefront of European funding priorities. The research community, however, is still reluctant to engage at the scale required to signal a Europe-wide change in the mode of operation of scientific practices. The striking differences in uptake rates between researchers from different scientific domains indicate that communities do not equally share the benefits of the above European investments. We highlight the need to support research communities in organically engaging with the European Open Science Cloud through the development of trustworthy and interoperable Virtual Research Environments. These domain-specific solutions can support communities in gradually bridging technical and socio-cultural gaps between traditional and open digital science practice, better diffusing the benefits of European e-infrastructures. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Policy Brief text/html info:doi:10.3897/rio.2.e9933 https://doi.org/10.3897/rio.2.e9933 https://riojournal.com/article/9933/ https://riojournal.com/article/9933/download/pdf/ en

10.3897/rio.2.e9995 2016-07-27 rio

SCINDR - The SCience INtroDuction Robot that will Connect Open Scientists Smith,Chase Todd,Matthew Patiny,Luc Swain,Christopher Southan,Christopher Williamson,Alice Clark,Alex Open Science Malaria Drug Discovery Electronic Laboratory Notebook Reaction Informatics Chemical Structure Alerts Collaboration Research Ideas and Outcomes 2: e9995 This project will develop a way to connect, in real time, globally disparate researchers who are doing similar science so that they can work better and faster towards the development of new medicines. The scientific literature already fulfills the role of notifying researchers about work that has been done, and social media has recently evolved to alert researchers to what is being done. While these new communication technologies simplify the collaborative process between widely distributed researchers, there still exists a major gap in efficient real time alerting and updating. We aim to automate an alert process so that, as a researcher records what they are doing in a natural way, they are immediately alerted to others around the world in real time who are working on related science. Our system is built on the conceptual model of the machine understanding of human-generated content, used by social media platforms to generate alerts to further relevant content. The system we propose to build will understand the molecular information being recorded in a scientist’s notebook. It will then search both its own records and others in the public domain in order to introduce scientists where there may be mutual advantage - when two laboratories are working on similar molecules, assays or approaches, for example. To achieve this, we will build on a recently developed open source electronic lab notebook (ELN) to create the required component - the automated alerting service we call the SCience INtroDuction Robot, or SCINDR. We foresee wide application of SCINDR in chemical and biological research because it will accelerate research by connecting people. In so doing, SCINDR will provide the incentive for others to take their research into the public domain (Fig. 1). info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e9995 https://doi.org/10.3897/rio.2.e9995 https://riojournal.com/article/9995/ https://riojournal.com/article/9995/download/pdf/ en

10.3897/rio.2.e10266 2016-08-23 rio

Improved understanding of brain morphology through 3D printing: A brief guide Madan,Christopher brain morphology 3d printing structural MRI Research Ideas and Outcomes 2: e10266 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Methods text/html info:doi:10.3897/rio.2.e10266 https://doi.org/10.3897/rio.2.e10266 https://riojournal.com/article/10266/ https://riojournal.com/article/10266/download/pdf/ en

10.3897/rio.2.e10269 2016-08-25 rio

Migration of legacy data to new media formats for long-time storage and maximum visibility: Modern pollen data from the Canadian Arctic (1972/1973) Nichols,Harvey Stolze,Susann data management plan Canadian Arctic surface pollen data modern pollen traps baseline study vegetation climate Research Ideas and Outcomes 2: e10269 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Data Management Plan (NSF Generic) text/html info:doi:10.3897/rio.2.e10269 https://doi.org/10.3897/rio.2.e10269 https://riojournal.com/article/10269/ https://riojournal.com/article/10269/download/pdf/ en

10.3897/rio.2.e10292 2016-09-07 rio

Report on the Managing Impacts of Deep-seA reSource exploitation (MIDAS) workshop on environmental management of deep-sea mining Durden,Jennifer Billett,David Brown,Alastair Dale,Andrew Goulding,Laura Gollner,Sabine Murphy,Kevin Pape,Ellen Purser,Autun Rolin,Jean-Francois Smith,Austin Stewart,Ian Turner,Phillip de Wachter,Tom Weaver,Philip van Dover,Cindy Verlaan,Philomene Jones,Daniel Environmental management deep-sea mining environmental impact assessment marine policy environmental management plan MIDAS project sustainable management European Union Framework 7 deep-sea biology Research Ideas and Outcomes 2: e10292 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/grantAgreement/EC/FP7/603418 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Workshop Report text/html info:doi:10.3897/rio.2.e10292 https://doi.org/10.3897/rio.2.e10292 https://riojournal.com/article/10292/ https://riojournal.com/article/10292/download/pdf/ en

10.3897/rio.2.e10398 2016-09-08 rio

Improved understanding of brain morphology through 3D printing: A brief guide Madan,Christopher brain morphology 3d printing structural MRI Research Ideas and Outcomes 2: e10398 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Methods text/html info:doi:10.3897/rio.2.e10398 https://doi.org/10.3897/rio.2.e10398 https://riojournal.com/article/10398/ https://riojournal.com/article/10398/download/pdf/ en

10.3897/rio.2.e10445 2016-09-12 rio

EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases Faulwetter,Sarah Pafilis,Evangelos Fanini,Lucia Bailly,Nicolas Agosti,Donat Arvanitidis,Christos Boicenco,Laura Catapano,Terry Claus,Simon Dekeyzer,Stefanie Georgiev,Teodor Legaki,Aglaia Mavraki,Dimitra Oulas,Anastasis Papastefanou,Gabriella Penev,Lyubomir Sautter,Guido Schigel,Dmitry Senderov,Viktor Teaca,Adrian Tsompanou,Marilena biodiversity data legacy literature data archaeology data rescue text mining biogeographic databases data management Research Ideas and Outcomes 2: e10445 The objective of Workpackage 4 of the European Marine Observation and Data network (EMODnet) is to fill spatial and temporal gaps in European marine species occurrence data availability by carrying out data archaeology and rescue activities. To this end, a workshop was organised in the Hellenic Center for Marine Research Crete (HCMR), Heraklion Crete, (8–9 June 2015) to assess possible mechanisms and guidelines to mobilise legacy biodiversity data. Workshop participants were data managers who actually implement data archaeology and rescue activities, as well as external experts in data mobilisation and data publication. In particular, current problems associated with manual extraction of occurrence data from legacy literature were reviewed, tools and mechanisms which could support a semi-automated process of data extraction were explored and the re-publication of the data, including incentives for data curators and scientists were reflected upon. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/grantAgreement/EC/FP7/211372 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Project Report text/html info:doi:10.3897/rio.2.e10445 https://doi.org/10.3897/rio.2.e10445 https://riojournal.com/article/10445/ https://riojournal.com/article/10445/download/pdf/ en

10.3897/rio.2.e10451 2016-09-13 rio

World Register of marine Cave Species (WoRCS): a new Thematic Species Database for marine and anchialine cave biodiversity Gerovasileiou,Vasilis Martinez,Alejandro Alvarez,Fernando Boxshall,Geoff Humphreys,William Frank Jaume,Damia Becking,Leontine E. Muricy,Guilherme van Hengstum,Peter J. Dekeyzer,Stefanie Decock,Wim Vanhoorne,Bart Vandepitte,Leen Bailly,Nicolas Illife,Thomas Marine caves anchialine ecosystems biodiversity global species databases biodiversity management Research Ideas and Outcomes 2: e10451 Scientific exploration of marine cave environments and anchialine ecosystems over recent decades has led to outstanding discoveries of novel taxa, increasing our knowledge of biodiversity. However, biological research on underwater caves has taken place only in a few areas of the world and relevant information remains fragmented in isolated publications and databases. This fragmentation makes assessing the conservation status of marine cave species especially problematic, and this issue should be addressed urgently given the stresses resulting from planned and rampant development in the coastal zone worldwide. The goal of the World Register of marine Cave Species (WoRCS) initiative is to create a comprehensive taxonomic and ecological database of known species from marine caves and anchialine systems worldwide and to present this as a Thematic Species Database (TSD) of the World Register of marine Species (WoRMS). WoRCS will incorporate ecological data (e.g., type of environment, salinity regimes, and cave zone) as well as geographical information on the distribution of species in cave and anchialine environments. Biodiversity data will be progressively assembled from individual database sources at regional, national or local levels, as well as from literature sources (estimate: >20,000 existing records of cave-dwelling species scattered in several databases). Information will be organized in the WoRCS database following a standard glossary based on existing terminology. Cave-related information will be managed by the WoRCS thematic editors with all data dynamically linked to WoRMS and its team of taxonomic editors. In order to mobilize data into global biogeographic databases, a Gazetteer of the Marine and Anchialine Caves of the World will be established. The presence records of species could be eventually georeferenced for submission to the Ocean Biogeographic Information System (OBIS) and constitute an important dataset for biogeographical and climate change studies on marine caves and anchialine systems. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Project Report text/html info:doi:10.3897/rio.2.e10451 https://doi.org/10.3897/rio.2.e10451 https://riojournal.com/article/10451/ https://riojournal.com/article/10451/download/pdf/ en

10.3897/rio.2.e10528 2016-09-16 rio

The London Workshop on the Biogeography and Connectivity of the Clarion-Clipperton Zone Glover,Adrian Dahlgren,Thomas Taboada,Sergio Paterson,Gordon Wiklund,Helena Waeschenbach,Andrea Cobley,Amber Martínez,Pedro Kaiser,Stefanie Schnurr,Sarah Khodami,Sahar Raschka,Uwe Kersken,Daniel Stuckas,Heiko Menot,Lenaick Bonifácio,Paulo Vanreusel,Ann Macheriotou,Lara Cunha,Marina R. Hilário,Ana Rodrigues,Clara Colaço,Ana Ribeiro,Pedro Blazewicz,Magdalena Gooday,Andrew Jones,Daniel Billett,David Goineau,Aurélie Amon,Diva Smith,Craig Patel,Tasnim McQuaid,Kirsty Spickermann,Ralph Brager,Stefan Deep-sea biology deep-sea mining biodiversity phylogeography population genetics European Union Framework 7 discussion meeting Research Ideas and Outcomes 2: e10528 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/grantAgreement/EC/FP7/603418 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Workshop Report text/html info:doi:10.3897/rio.2.e10528 https://doi.org/10.3897/rio.2.e10528 https://riojournal.com/article/10528/ https://riojournal.com/article/10528/download/pdf/ en

10.3897/rio.2.e10617 2016-09-23 rio

Online direct import of specimen records into manuscripts and automatic creation of data papers from biological databases Senderov,Viktor Georgiev,Teodor Penev,Lyubomir biodiversity informatics bioinformatics semantic publishing API REST iDigBio Global Biodiversity Information Facility GBIF PlutoF BOLD Systems ecological informatics Ecological Metadata Language EML Darwin Core LTER Network DataONE DwC-SW semantic web Research Ideas and Outcomes 2: e10617 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/grantAgreement/EC/FP7/308454 info:eu-repo/grantAgreement/EC/H2020/642241 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Presentation text/html info:doi:10.3897/rio.2.e10617 https://doi.org/10.3897/rio.2.e10617 https://riojournal.com/article/10617/ https://riojournal.com/article/10617/download/pdf/ en

10.3897/rio.2.e10600 2016-09-27 rio

Data Management Plan for PhD Thesis "Climatic Limitation of Alien Weeds in New Zealand: Enhancing Species Distribution Models with Field Data" Pannell,Jennifer data management plan doctorate ecology Crassulaceae invasions Research Ideas and Outcomes 2: e10600 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Data Management Plan (NSF Generic) text/html info:doi:10.3897/rio.2.e10600 https://doi.org/10.3897/rio.2.e10600 https://riojournal.com/article/10600/ https://riojournal.com/article/10600/download/pdf/ en

10.3897/rio.2.e10593 2016-09-28 rio

Functional characterization of the several splice variants of Fmr1 Abbey,Megha FMRP Fmr1 splice variant alternative splicing CGG repeats protein isoform Research Ideas and Outcomes 2: e10593 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Research Idea text/html info:doi:10.3897/rio.2.e10593 https://doi.org/10.3897/rio.2.e10593 https://riojournal.com/article/10593/ https://riojournal.com/article/10593/download/pdf/ en

10.3897/rio.2.e10610 2016-09-30 rio

Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal Franz,Nico Gilbert,Edward Ludäscher,Bertram Weakley,Alan Aggregation concept taxonomy conflict flora herbarium logic reasoning Region Connection Calculus specimens synthesis Research Ideas and Outcomes 2: e10610 Overview. Taxonomic names are imperfect identifiers of specific and sometimes conflicting taxonomic perspectives in aggregated biodiversity data environments. The inherent ambiguities of names can be mitigated using syntactic and semantic conventions developed under the taxonomic concept approach. These include: (1) representation of taxonomic concept labels (TCLs: name sec. source) to precisely identify name usages and meanings, (2) use of parent/child relationships to assemble separate taxonomic perspectives, and (3) expert provision of Region Connection Calculus articulations (RCC–5: congruence, [inverse] inclusion, overlap, exclusion) that specify how data identified to different-sourced TCLs can be integrated. Application of these conventions greatly increases trust in biodiversity data networks, most of which promote unitary taxonomic 'syntheses' that obscure the actual diversity of expert-held views. Better design solutions allow users to control the taxonomic variable and thereby assess the robustness of their biological inferences under different perspectives. A unique constellation of prior efforts – including the powerful Symbiota collections software platform, the Euler/X multi-taxonomy alignment toolkit, and the "Weakley Flora" which entails 7,000 concepts and more than 75,000 RCC–5 articulations – provides the opportunity to build a first full-scale concept resolution service for SERNEC, the SouthEast Regional Network of Expertise and Collections, currently with 60 member herbaria and 2 million occurrence records.Intellectual merit. We have developed a multi-dimensional, step-wise plan to transition SERNEC's data culture from name- to concept-based practices. (1) We will engage SERNEC experts through annual, regional workshops and follow-up interactions that will foster buy-in and ultimately the completion of 12 community-identified use cases. (2). We will leverage RCC–5 data from the Weakley Flora and further development of the Euler/X logic reasoning toolkit to provide comprehensive genus- to variety-level concept alignments for at least 10 major flora treatments with highest relevance to SERNEC. The visualizations and estimated > 1 billion inferred concept-to-concept relations will effectively drive specimen data integration in the transformed portal. (3) We will expand Symbiota's taxonomy and occurrence schemas and related user interfaces to support the new concept data, including novel batch and map-based specimen determination modules, with easy output options in Darwin Core Archive format. (4) Through combinations of the new technology, enlisted taxonomic expertise, and SERNEC's large image resources, we will upgrade minimally 80% of all SERNEC specimen identifications from names to the narrowest suitable TCLs, or add "uncertainty" flags to specimens needing further study. (5) We will utilize the novel tools and data to demonstrate how controlling for the taxonomic variable in 12 use cases variously drives the outcomes of evolutionary, ecological, and conservation-based research hypotheses.Broader impacts. Our project is focused on just one herbarium network, but the potential impact is as wide as Darwin Core or even comparative biology. We believe that trust in networked biodiversity data depends on open and dynamic system designs, allowing expert access and resolution of multiple conflicting views that reflect the complex realities of ongoing taxonomic research. Taking well over 1 million SERNEC records from name- to TCL-resolution will show that "big" specimen data can pass the credibility threshold needed to validate the substantive data mobilization investment. We will mentor one postdoctoral researcher (UNC), two Ph.D. students (ASU, UIUC), and at least 15 undergraduate students (ASU). Each of our workshops will capacitate 10-15 SERNEC experts, who in turn can recruit colleagues and students at their home collections. We will incorporate the project theme and use cases into undergraduate courses taught at six institutions and reaching an estimated 300-500 students annually (10-40% minority students). At each institution, project members will make a systematic effort to recruit new students from underrepresented groups. Our group's leadership of Symbiota (with close ties to iDigBio), SERNEC, and local biodiversity projects and centers will further promote the new data culture. We will create a feature story "Where do plant species occur?" for ASU's popular "Ask A Biologist" website, and a series of undergraduate student-led "How-To" videos that illustrate the use case workflows, including the creation of multi-taxonomy alignments. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 NSF Grant Proposal text/html info:doi:10.3897/rio.2.e10610 https://doi.org/10.3897/rio.2.e10610 https://riojournal.com/article/10610/ https://riojournal.com/article/10610/download/pdf/ en

10.3897/rio.2.e10708 2016-10-04 rio

Data Management Plan for Moore Investigator in Data Driven Discovery Grant White,Ethan ecology data driven discovery data-intensive research quantitative ecology Research Ideas and Outcomes 2: e10708 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Data Management Plan (Biosciences) text/html info:doi:10.3897/rio.2.e10708 https://doi.org/10.3897/rio.2.e10708 https://riojournal.com/article/10708/ https://riojournal.com/article/10708/download/pdf/ en

10.3897/rio.2.e10714 2016-10-12 rio

Studying the effect of Ruthenium on High Temperature Mechanical Properties of Nickel Based Superalloys and Determining the Universal Behavior of Ruthenium at Atomic Scale with respect to alloying elements, Stress and Temperature Dasari,Sriswaroop Ruthenium superalloy mechanical properties thermomechanical processing creep proposal Research Ideas and Outcomes 2: e10714 Any property of a material is a function of its microstructure and microstructure is a function of material composition. So, to maximize the desired properties of a material, one has to understand the evolution of microstructure which in turn is nothing but the reflection of the role of alloying elements. Research has not been done to understand the universal behavior of a certain base/alloying element. Let’s take the example of Cl- ion in HCl, we all know that in general, chloride ion can only be replaced by Fluoride or oxygen ion and that no other ion can replace it. But when you consider a metal like Ni, Co, Cr, Fe etc. there is no establishment that it behaves only in a certain way. Though I concord to the fact that discovery of universal behavior of Ni is lot complex than chloride ion, I think that future research should be focused in this direction also. Superalloys are the candidate materials required to improve thermal efficiency of a gas turbine by allowing higher turbine inlet gas temperatures. Gas turbines are the heart of local power systems, next generation jet engines and high performance space rockets. Recent research in superalloys showed that addition of some alloying elements in minor quantities can result in drastic change in properties. Such an alloying element is Ruthenium (Ru). Addition of Ruthenium to superalloys has shown improvement in mechanical properties by an order of magnitude. However reasons for such improvement are not known yet. Hence, there is a need to identify its role and discover the universal behavior of ruthenium to utilize it efficiently. In this proposal, we study materials with different compositions that are derived based on one ruthenium containing superalloy, and different thermomechanical history. Based on the evolution of microstructures and results of mechanical testing, we plan to determine the exact role of Ruthenium and prediction of its behavior with respect to other elements in the material such as Ni, Cr, Co, Mo, W etc. and stress and temperature. This helps us to determine the right quantity of ruthenium required for a given composition and operating conditions. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 PhD Project Plan text/html info:doi:10.3897/rio.2.e10714 https://doi.org/10.3897/rio.2.e10714 https://riojournal.com/article/10714/ https://riojournal.com/article/10714/download/pdf/ en

10.3897/rio.2.e11014 2016-11-03 rio

Shuttleworth Fellowship Application 2016 Agosti,Donat fellowship applications Shuttleworth biodiversity open access linked open data TreatmentBank taxonomic treatment Research Ideas and Outcomes 2: e11014 This is the application by Donat Agosti for a Shuttleworth Fellowship with the goal of making scientific data publication an integral part of an open knowledge management system. A successful application will help move TreatmentBank from its current prototype state into a production system that converts and extracts data from taxonomic publications and makes them available as Linked Open Data. The project is about developing the infrastructure and creating a corpus of data, while at the same time serving as a showcase of open access. This is an exemplar approach that hopefully will be adopted by other scientific domains. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Small Grant Proposal text/html info:doi:10.3897/rio.2.e11014 https://doi.org/10.3897/rio.2.e11014 https://riojournal.com/article/11014/ https://riojournal.com/article/11014/download/pdf/ en

10.3897/rio.2.e11065 2016-11-09 rio

A Data Management Plan for Effects of particle size on physical and chemical properties of mine wastes Xu,Hong Ishida,Mayu Wang,Minglu data management plan mine wastes Mojave Desert Souther California NSF Research Ideas and Outcomes 2: e11065 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Data Management Plan (NSF Generic) text/html info:doi:10.3897/rio.2.e11065 https://doi.org/10.3897/rio.2.e11065 https://riojournal.com/article/11065/ https://riojournal.com/article/11065/download/pdf/ en

10.3897/rio.2.e11150 2016-11-25 rio

Physics of Laser in Contemporary Visual Arts: the research protocol Ahmedien,Diaa Laser Art New-Media arts sciences of visual arts holographic art neural holography new aesthetics Research Ideas and Outcomes 2: e11150 This protocol articulates an ongoing PhD thesis in Laser Art as an independent artistic trend including its history, classification criteria, philosophical and aesthetical aspects. Via several analytical studies theoretically and practically, the thesis is going to prove that laser art actively contributes, as an independent artistic trend, to change the conceptual definition of the artistic material. On the other hand, it bridges the gap between the artistic context and the technical issues, in which the conceptual values became fully integrated into the physical properties of the medium (laser beam), therefore it became impossible to separate the idea and the material of the artwork from each other. Besides, the thesis reveals the potential hidden conceptual and philosophical dimensions of the holographic art as one of the most important branches of laser art. In advanced step, the research suggestes a new model of interactive holographic art based on neural controlling system, and how this advanced approach can lead us towards a new kind of the aesthetic values, in which participants effectively contribute neurologically to constituting the artwork. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 PhD Project Plan text/html info:doi:10.3897/rio.2.e11150 https://doi.org/10.3897/rio.2.e11150 https://riojournal.com/article/11150/ https://riojournal.com/article/11150/download/pdf/ en

10.3897/rio.2.e11321 2016-11-29 rio

DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe Leese,Florian Altermatt,Florian Bouchez,Agnès Ekrem,Torbjørn Hering,Daniel Meissner,Kristian Mergen,Patricia Pawlowski,Jan Piggott,Jeremy Rimet,Frederic Steinke,Dirk Taberlet,Pierre Weigand,Alexander Abarenkov,Kessy Beja,Pedro Bervoets,Lieven Bjornsdottir,Snaedis Boets,Pieter Boggero,Angela Bones,Atle Borja,Ángel Bruce,Kat Bursić,Vojislava Carlsson,Jens Čiampor Jr,Fedor Čiamporová-Zaťovičová,Zuzana Coissac,Eric Costa,Filipe Costache,Marieta Creer,Simon Csabai,Zoltán Deiner,Kristy DelValls,Ángel Drakare,Stina Duarte,Sofia Elersek,Tina Fazi,Stefano Fišer,Cene Flot,Jean-François Fonseca,Vera Fontaneto,Diego Grabowski,Michal Graf,Wolfram Guobrandsson,Jóhannes Hellström,Micaela Hershkovitz,Yaron Hollingsworth,Peter Japoshvili,Bella Jones,John Kahlert,Maria Kalamujić Stroil,Belma Kasapidis,Panagiotis Kelly,Martyn Kelly-Quinne,Mary Keskin,Emre Kõljalg,Urmas Ljubešić,Zrinka Macek,Irena Mächler,Elvira Mahon,Andrew Marečková,Marketa Mejdandzic,Maja Mirceva,Georgina Montagna,Matteo Moritz,Christian Mulk,Vallo Naumoski,Andreja Navodaru,Ion Padisák,Judit Pálsson,Snæbjörn Panksep,Kristel Penev,Lyubomir Petrusek,Adam Pfannkuchen,Martin Primmer,Craig Rinkevich,Baruch Rotter,Ana Schmidt-Kloiber,Astrid Segurado,Pedro Speksnijder,Arjen Stoev,Pavel Strand,Malin Šulčius,Sigitas Sundberg,Per Traugott,Michael Tsigenopoulos,Costas Turon,Xavier Valentini,Alice van der Hoorn,Berry Varbiro,Gabor Vasquez,Marlen Ines Viguri,Javier Vitonyte,Irma Vogler,Alfried Vralstad,Trude Wägele,Wolfgang Wenne,Roman Winding,Anne Woodward,Guy Zegura,Bojana Zimmermann,Jonas Research Ideas and Outcomes 2: e11321 The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices for routine application in biodiversity assessments of European fresh- and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Grant Proposal text/html info:doi:10.3897/rio.2.e11321 https://doi.org/10.3897/rio.2.e11321 https://riojournal.com/article/11321/ https://riojournal.com/article/11321/download/pdf/ en

10.3897/rio.2.e11563 2016-12-22 rio

Summary report and strategy recommendations for EU citizen science gateway for biodiversity data Runnel,Veljo Wetzel,Florian Groom,Quentin Koch,Wouter Pe’er,Israel Valland,Nils Panteri,Emmanouela Kõljalg,Urmas citizen science biodiversity observations volunteering motivation data data sharing policy Research Ideas and Outcomes 2: e11563 Citizen science is an approach of public participation in scientific research which has gained significant momentum in recent years. This is particularly evident in biology and environmental sciences where input from citizen scientists has greatly increased the number of publicly available observation data. However, there are still challenges in effective networking, data sharing and securing data quality. EU BON project has analyzed the citizen science landscape in Europe with regards to biodiversity research and proposes several policy recommendations. One of the recommendations is a Pan-European citizen science gateway for biodiversity data with dedicated tools for data collection and management. The prototypes of the gateway components are part of the EU BON biodiversity portal and described in current report. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2016 Policy Brief text/html info:doi:10.3897/rio.2.e11563 https://doi.org/10.3897/rio.2.e11563 https://riojournal.com/article/11563/ https://riojournal.com/article/11563/download/pdf/ en

10.3897/rio.3.e11624 2017-01-05 rio

Data Management Plan for a Biotechnology and Biological Sciences Research Council (BBSRC) Tools and Resources Development Fund (TRDF) Grant Gatto,Laurent Spatial proteomics Bioconductor machine learning mass spectrometry proteomics software Research Ideas and Outcomes 3: e11624 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Data Management Plan (Biosciences) text/html info:doi:10.3897/rio.3.e11624 https://doi.org/10.3897/rio.3.e11624 https://riojournal.com/article/11624/ https://riojournal.com/article/11624/download/pdf/ en

10.3897/rio.3.e11731 2017-01-10 rio

Applying machine learning and image feature extraction techniques to the problem of cerebral aneurysm rupture Chabert,Steren Mardones,Tomás Riveros,Rodrigo Godoy,Maximiliano Veloz,Alejandro Salas,Rodrigo Cox,Pablo Image feature extraction Machine Learning Cerebral Aneurysms Biomedical Engineering Radiology Research Ideas and Outcomes 3: e11731 Cerebral aneurysm is a cerebrovascular disorder characterized by a bulging in a weak area in the wall of an artery that supplies blood to the brain. It is relevant to understand the mechanisms leading to the apparition of aneurysms, their growth and, more important, leading to their rupture. The purpose of this study is to study the impact on aneurysm rupture of the combination of different parameters, instead of focusing on only one factor at a time as is frequently found in the literature, using machine learning and feature extraction techniques. This discussion takes relevance in the context of the complex decision that the physicians have to take to decide which therapy to apply, as each intervention bares its own risks, and implies to use a complex ensemble of resources (human resources, OR, etc.) in hospitals always under very high work load. This project has been raised in our actual working team, composed of interventional neuroradiologist, radiologic technologist, informatics engineers and biomedical engineers, from Valparaiso public Hospital, Hospital Carlos van Buren, and from Universidad de Valparaíso – Facultad de Ingeniería and Facultad de Medicina. This team has been working together in the last few years, and is now participating in the implementation of an “interdisciplinary platform for innovation in health”, as part of a bigger project leaded by Universidad de Valparaiso (PMI UVA1402). It is relevant to emphasize that this project is made feasible by the existence of this network between physicians and engineers, and by the existence of data already registered in an orderly manner, structured and recorded in digital format. The present proposal arises from the description in nowadays literature that the actual indicators, whether based on morphological description of the aneurysm, or based on characterization of biomechanical factor or others, these indicators were shown not to provide sufficient information in order to predict by themselves the risk of rupture. Therefore, our hypothesis is that the risk of rupture lies on the combination of multiple actors. These actors together would play different roles that could be: weakening of the artery wall, increasing biomechanical stresses on the wall induced by blood flow, in addition to personal sensitivity due to family history, or personal history of comorbidity, or even seasonal variations that could gate different inflammation mechanisms. The main goal of this project is to identify relevant variables that may help in the process of predicting the risk of intracranial aneurysm rupture using machine learning and image processing techniques based on structured and non-structured data from multiple sources. We believe that the identification and the combined use of relevant variables extracted from clinical, demographical, environmental and medical imaging data sources will improve the estimation of the aneurysm rupture risk, with respect to the actual practiced method based essentially on the aneurysm size. The methodology of this work consist of four phases: (1) Data collection and storage, (2) feature extraction from multiple sources in particular from angiographic images, (3) development of the model that could describe the risk of aneurysm rupture based on the fusion and combination of the features, and (4) Identification of relevant variables related to the aneurysm rupture process. This study corresponds to an analytic transversal study with prospective and retrospective characteristics. This work will be based on publicly available health statistics data, data of weather conditions, together with clinical and demographic data of patients diagnosed with intracranial aneurysm in the Hospital Carlos van Buren. As main results of this project we are expecting to identify relevant variables extracted from images and other sources that could play a role in the risk of aneurysm rupture. The proposed model will be presented to the physicians of the Hospital Carlos van Buren, to be further implemented in this Institution according to the demonstrated impact of our results. The main results will be published in indexed journals and presented at national and international conferences. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Grant Proposal text/html info:doi:10.3897/rio.3.e11731 https://doi.org/10.3897/rio.3.e11731 https://riojournal.com/article/11731/ https://riojournal.com/article/11731/download/pdf/ en

10.3897/rio.3.e11743 2017-01-13 rio

Mapping Open Access Societal Impact ElSabry,ElHassan open access societal impact of research altmetrics Research Ideas and Outcomes 3: e11743 A proposal to create a comprehensive online resource documenting the usage of Open Access research outside academia including an evidence base, a world map showing instances of impact and a forum for discussing methods to measure the societal impact of Open Access. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Small Grant Proposal text/html info:doi:10.3897/rio.3.e11743 https://doi.org/10.3897/rio.3.e11743 https://riojournal.com/article/11743/ https://riojournal.com/article/11743/download/pdf/ en

10.3897/rio.3.e11825 2017-01-16 rio

Technical aspects of preprint services in the life sciences: a workshop report Chodacki,John Lemberger,Thomas Lin,Jennifer Martone,Maryann Mietchen,Daniel Polka,Jessica Sever,Richard Strasser,Carly Preprints ASAPbio Research Ideas and Outcomes 3: e11825 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Workshop Report text/html info:doi:10.3897/rio.3.e11825 https://doi.org/10.3897/rio.3.e11825 https://riojournal.com/article/11825/ https://riojournal.com/article/11825/download/pdf/ en

10.3897/rio.3.e11875 2017-01-24 rio

4th European Biodiversity Observation Network (EU BON) Stakeholder Roundtable: Pathways to sustainability for EU BONs network of collaborators and technical infrastructure Wetzel,Florian Despot-Belmonte,Katherine Bingham,Heather Underwood,Evelyn Hoffmann,Anke Haüser,Christoph Mikolajczyk,Piotr Vohland,Katrin sustainability biodiversity infrastructure EU BON business plan products and tools biodiversity observation networks Research Ideas and Outcomes 3: e11875 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Workshop Report text/html info:doi:10.3897/rio.3.e11875 https://doi.org/10.3897/rio.3.e11875 https://riojournal.com/article/11875/ https://riojournal.com/article/11875/download/pdf/ en

10.3897/rio.3.e11884 2017-01-25 rio

Advancing marine conservation in European and contiguous seas with the MarCons Action Katsanevakis,Stelios Mackelworth,Peter Coll,Marta Fraschetti,Simonetta Mačić,Vesna Giakoumi,Sylvaine Jones,Peter Levin,Noam Albano,Paolo G. Badalamenti,Fabio Brennan,Ruth Claudet,Joachim Culibrk,Dubravko D'Anna,Giovanni Deidun,Alan Evagelopoulos,Athanasios García-Charton,José Goldsborough,David Holcer,Draško Jimenez,Carlos Kark,Salit Sørensen,Thomas Lazar,Bojan Martin,Georg Mazaris,Antonios Micheli,Fiorenza Milner-Gulland,E.J. Pipitone,Carlo Portman,Michelle Pranovi,Fabio Rilov,Gil Smith,Robert Stelzenmüller,Vanessa Vogiatzakis,Ioannis Winters,Gidon Integrated conservation planning marine biodiversity cumulative impacts biological invasions marine governance maritime spatial planning Research Ideas and Outcomes 3: e11884 Cumulative human impacts have led to the degradation of marine ecosystems and the decline of biodiversity in the European and contiguous seas. Effective conservation measures are urgently needed to reverse these trends. Conservation must entail societal choices, underpinned by human values and worldviews that differ between the countries bordering these seas. Social, economic and political heterogeneity adds to the challenge of balancing conservation with sustainable use of the seas. Comprehensive macro-regional coordination is needed to ensure effective conservation of marine ecosystems and biodiversity of this region. Under the European Union Horizon 2020 framework programme, the MarCons COST action aims to promote collaborative research to support marine management, conservation planning and policy development. This will be achieved by developing novel methods and tools to close knowledge gaps and advance marine conservation science. This action will provide support for the development of macro-regional and national policies through six key actions: to develop tools to analyse cumulative human impacts; to identify critical scientific and technical gaps in conservation efforts; to improve the resilience of the marine environment to global change and biological invasions; to develop frameworks for integrated conservation planning across terrestrial, freshwater, and marine environments; to coordinate marine conservation policy across national boundaries; and to identify effective governance approaches for marine protected area management. Achieving the objectives of these actions will facilitate the integration of marine conservation policy into macro-regional maritime spatial planning agendas for the European and contiguous seas, thereby offsetting the loss of biodiversity and ecosystem services in this region. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Small Grant Proposal text/html info:doi:10.3897/rio.3.e11884 https://doi.org/10.3897/rio.3.e11884 https://riojournal.com/article/11884/ https://riojournal.com/article/11884/download/pdf/ en

10.3897/rio.3.e11997 2017-01-31 rio

Know your insect: The structural backgrounds of regurgitation, a case study on Manduca sexta and Heliothis virescens (Lepidoptera: Sphingidae, Noctuidae) bipspau@gmail.com,Bipana Mikó,István regurgitation herbivory elicitor molecules Research Ideas and Outcomes 3: e11997 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Case Study text/html info:doi:10.3897/rio.3.e11997 https://doi.org/10.3897/rio.3.e11997 https://riojournal.com/article/11997/ https://riojournal.com/article/11997/download/pdf/ en

10.3897/rio.3.e12032 2017-02-01 rio

Data Intensive Science Schmelling,Nicolas OER Learning Open Data Data Management Open Science Reproducibility Data Analysis Python R Research Ideas and Outcomes 3: e12032 A proposal to create a full-semester zero-entry level course about the responsible handling of research data and the associated analyses, storage, and sharing. The syllabus will comprise open science workflows, the creation of data management plans, as well as the addressing issues about reproducibility and data sharing in science. The course and all its materials will be licensed under CC-BY or if possible under CC-0. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Small Grant Proposal text/html info:doi:10.3897/rio.3.e12032 https://doi.org/10.3897/rio.3.e12032 https://riojournal.com/article/12032/ https://riojournal.com/article/12032/download/pdf/ en

10.3897/rio.3.e11827 2017-02-01 rio

Know your insect: Malpighian tubules in Trichoplusia ni (Lepidoptera: Noctuidae) Rivera Vega,Loren Mikó,István cabbage looper caterpillars urinary bladder uric acid Research Ideas and Outcomes 3: e11827 Malpighian tubules are mainly known to be involved in excretion. However, recent studies have begun to look into other potential roles including detoxification, immunity, host establishment, etc. In this case study, we observed the Malpighian tubules of the cabbage looper (Trichoplusia ni) using confocal laser scanning microscopy. We also discuss other functions that Malpighian tubules are known for (i.e. silk-like and gall-inducing secretions) as well as the similarities between Malpighian tubules and salivary glands in endoparasitic Hymenoptera. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Case Study text/html info:doi:10.3897/rio.3.e11827 https://doi.org/10.3897/rio.3.e11827 https://riojournal.com/article/11827/ https://riojournal.com/article/11827/download/pdf/ en

10.3897/rio.3.e11931 2017-02-01 rio

Can video improve grant review quality and lead to more reliable ranking? Doran,Mike Barnett,Adrian Leach,Joan Lott,Bill Page,Katie Grant,Will research funding grant writing video grant review peer review meta-research research policy Research Ideas and Outcomes 3: e11931 Multimedia video is rapidly becoming mainstream, and many studies indicate that it is a more effective communication medium than text. In this project we AIM to test if videos can be used, in place of text-based grant proposals, to improve communication and increase the reliability of grant ranking. We will test if video improves reviewer comprehension (AIM 1), if external reviewer grant scores are more consistent with video (AIM 2), and if mock Australian Research Council (ARC) panels award more consistent scores when grants are presented as videos (AIM 3). This will be the first study to evaluate the use of video in this application. The ARC reviewed over 3500 Discovery Project applications in 2015, awarding 635 Projects. Selecting the “best” projects is extremely challenging. This project will improve the selection process by facilitating the transition from text-based to video-based proposals. The impact could be profound: Improved video communication should streamline the grant preparation and review processes, enable more reliable ranking of applications, and more accurate identification of the “next big innovations”. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Small Grant Proposal text/html info:doi:10.3897/rio.3.e11931 https://doi.org/10.3897/rio.3.e11931 https://riojournal.com/article/11931/ https://riojournal.com/article/11931/download/pdf/ en

10.3897/rio.3.e12029 2017-02-06 rio

Cartograms tool to represent spatial uncertainty in species distribution Rocchini,Duccio Garzon-Lopez,Carol X Uncertainty species distribution models cartogram GBIF sampling effort Research Ideas and Outcomes 3: e12029 Species distribution models have become an important tool for biodiversity monitoring. Like all statistical modelling techniques developed based on field data, they are prone to uncertainty due to bias in the sampling (e.g. identification, effort, detectability). In this study, we explicitly quantify and map the uncertainty derived from sampling effort bias. With that aim, we extracted data from the widely used GBIF dataset to map this semantic bias using cartograms. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Policy Brief text/html info:doi:10.3897/rio.3.e12029 https://doi.org/10.3897/rio.3.e12029 https://riojournal.com/article/12029/ https://riojournal.com/article/12029/download/pdf/ en

10.3897/rio.3.e12095 2017-02-07 rio

Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software Ioanas,Horea-Ioan Saab,Bechara Rudin,Markus gentoo portage linux software management repository dependency management dependency resolution neuroscience flexible scalable rolling-release live software versioning source-based gnu gnu/linux Research Ideas and Outcomes 3: e12095 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Software Management Plan text/html info:doi:10.3897/rio.3.e12095 https://doi.org/10.3897/rio.3.e12095 https://riojournal.com/article/12095/ https://riojournal.com/article/12095/download/pdf/ en

10.3897/rio.3.e12259 2017-02-14 rio

Semi-automated Robust Quantification of Lesions (SRQL) Toolbox Ito,Kaori L Anglin,Julia Liew,Sook-Lei stroke neuroimaging software neuroanatomy robust MRI analysis Research Ideas and Outcomes 3: e12259 Quantifying lesions in a robust manner is fundamental for studying the effects of neuroanatomical changes in the post-stroke brain on recovery. However, the wide variability in lesion characteristics across individuals makes manual lesion segmentation a challenging and often subjective process. This makes it difficult to combine stroke lesion data across multiple research sites, due to subjective differences in how lesions may be defined. We developed the Semi-automated Robust Quantification of Lesions (SRQL; https://github.com/npnl/SRQL; DOI: 10.5281/zenodo.267213) Toolbox that performs several analysis steps: 1) a white matter intensity correction that removes healthy white matter voxels from the lesion mask, thereby making lesions slightly more robust to subjective errors; 2) an automated report of descriptive statistics on lesions for simplified comparison between or across groups, and 3) an option to perform analyses in both native and standard space to facilitate analyses in either space, or comparisons between spaces. Here, we describe the methods implemented in the toolbox and demonstrate the outputs of the SRQL toolbox. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Project Report text/html info:doi:10.3897/rio.3.e12259 https://doi.org/10.3897/rio.3.e12259 https://riojournal.com/article/12259/ https://riojournal.com/article/12259/download/pdf/ en

10.3897/rio.3.e12249 2017-02-14 rio

The cyanide gland of the greenhouse millipede, Oxidus gracilis (Polydesmida: Paradoxosomatidae) Pearsons,Kirsten Mikó,István Tooker,John Oxidus gracilis cyanide gland Diplopoda Polydesmida CLSM Research Ideas and Outcomes 3: e12249 Although the greenhouse millipede, Oxidus gracilis, is distributed worldwide, there is little work using modern tools to explore its morphology. We used confocal laser scanning microscopy (CLSM) to image the cyanide glands of Oxidus gracilis. Glands from adult millipedes were dissected out before imaging, and we were able to image glands of juveniles through the cuticle due to the strong autofluorescence of the gland extract. We can report that CLSM is a promising technique to non-invasively investigate the development and mechanisms of polydesmid cyanide glands. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Case Study text/html info:doi:10.3897/rio.3.e12249 https://doi.org/10.3897/rio.3.e12249 https://riojournal.com/article/12249/ https://riojournal.com/article/12249/download/pdf/ en

10.3897/rio.3.e12165 2017-02-14 rio

Biodiversity data provision and decision-making - addressing the challenges Despot-Belmonte,Katherine Neßhöver,Carsten Saarenmaa,Hannu Regan,Eugenie Meyer,Carsten Martins,Eline Groom,Quentin Hoffmann,Anke Caine,Alessandra Bowles-Newark,Nadine Bae,Haejin Canhos,Dora Ann Lange Stenzel,Stefanie Bowler,Diana Schneider,Aline Weatherdon,Lauren Martin,Corinne biodiversity data knowledge products science-policy interface GEO BON EU BON EBVs EKLIPSE mechanism Research Ideas and Outcomes 3: e12165 Essential Biodiversity Variables (EBVs) are measurements required for study, reporting, and management of biodiversity change. They are being developed to support consistency, from the collection to the reporting of biodiversity data at the national, regional and global scales. However, "EBV stakeholders" need to strike a balance between 'doing innovative research' and 'having positive impact' on biodiversity management decisions. This paper reports on a workshop entitled Identifying joint pathways to address the challenges of biodiversity data provision and decision-making and presents the main workshop’s output, a “researcher’s brief” entitled Guiding principles for promoting the application of EBVs for current and future needs of decision-makers. These guiding principles are: Speak with a common voice; Clearly define what is an EBV and how it relates to indicators; Engage beyond the research world; Be realistic about what can be done now and later; Define criteria for good EBVs; Use EBV as a clearing house; Convey the limitations of EBVs; Clarify what impact EBVs should have; Be salient, credible, legitimate, iterative; Don't put an EBV skin on everything you do; Don't create too many EBVs; and Don't reduce EBVs to building blocks of indicators. This brief is of relevance to the wider GEO BON (Group on Earth Observation Biodoversity Observation Network) community, and in particular those scientists/researchers interested in the application of EBVs. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Workshop Report text/html info:doi:10.3897/rio.3.e12165 https://doi.org/10.3897/rio.3.e12165 https://riojournal.com/article/12165/ https://riojournal.com/article/12165/download/pdf/ en

10.3897/rio.3.e12276 2017-02-15 rio

Mindcontrol: Organize, quality control, annotate, edit, and collaborate on neuroimaging processing results Keshavan,Anisha Madan,Christopher Datta,Esha McDonough,Ian Brain Interactive Visualization Curation Segmentation Research Ideas and Outcomes 3: e12276 Mindcontrol is an open-source web-based dashboard to quality control and curate neuroimaging data. At Neurohackweek 2016, a group assembled to add new features to the Mindcontrol interface. Contributors used Python, Javascript, and Git to configure Mindcontrol for the ABIDE and CoRR open datasets, and add new types of plots to the interface. All contributions are freely available online, and the code is being actively maintained at http://www.github.com/akeshavan/mindcontrol. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Project Report text/html info:doi:10.3897/rio.3.e12276 https://doi.org/10.3897/rio.3.e12276 https://riojournal.com/article/12276/ https://riojournal.com/article/12276/download/pdf/ en

10.3897/rio.3.e12265 2017-02-15 rio

From Open Access to Open Science from the viewpoint of a scholarly publisher Penev,Lyubomir open access open data open science scholarly publishing semantic publishing XML tagging data re-use science communication Research Ideas and Outcomes 3: e12265 info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Research Presentation text/html info:doi:10.3897/rio.3.e12265 https://doi.org/10.3897/rio.3.e12265 https://riojournal.com/article/12265/ https://riojournal.com/article/12265/download/pdf/ en

10.3897/rio.3.e12358 2017-02-23 rio

Interactive online brain shape visualization Keshavan,Anisha Klein,Arno Cipollini,Ben three.js VTK morphometry d3.js Research Ideas and Outcomes 3: e12358 The open-source Mindboggle package improves the labeling and morphometry estimates of brain imaging data. At the 2015 Brainhack event, we developed a web-based, interactive, brain shape visualization of Mindboggle outputs. The application links a 3D brain visualization with boxplots that describe shape measures across a selected cortical label. The code is freely available at http://www.github.com/akeshavan/roygbiv and a demo is online at http://roygbiv.mindboggle.info. info:eu-repo/semantics/altIdentifier/eissn/2367-7163 info:eu-repo/semantics/openAccess CC BY 4.0 Pensoft Publishers 2017 Project Report text/html info:doi:10.3897/rio.3.e12358 https://doi.org/10.3897/rio.3.e12358 https://riojournal.com/article/12358/ https://riojournal.com/article/12358/download/pdf/ en cGFnZT0xJnNldD1yaW8mZnJvbT0mdW50aWw9Jm1ldGFkYXRhX3ByZWZpeD1vYWlfZGM=