2026-05-15T23:05:33Z https://riojournal.com/oai.php

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

Tilburg University, Tilburg, Netherlands author Hartgerink, Chris https://orcid.org/0000-0003-1050-6809 Duke University, Durham, NC, United States of America author George, Stephen https://orcid.org/0000-0002-3625-5852 2015-12-17 2015-12-17 2015 Research Ideas and Outcomes 2367-7163 1 e7462 2015 10.1136/bmj.331.7511.267 10.1136/heartjnl-2013-304262 10.1002/(SICI)1097-0258(19991230)18:243.0.CO;2-O 10.1111/j.1365-2044.2012.07128.x 10.1111/anae.13126 Rapport vervolgonderzoek naar mogelijke schending van de wetenschappelijke integriteit Commissie Vervolgonderzoek author text https://web.archive.org/web/20151027084205/http://www.erasmusmc.nl/5663/135857/3675250/3706798/erasmusmc.commissie.verv.onderzoek.2012 10.1371/journal.pone.0005738 10.1007/s10147-015-0887-3 10.4155/cli.14.116 The Journal of Cell Biology author 2015 About the Journal https://web.archive.org/web/20150911132421/http://jcb.rupress.org/site/misc/about.xhtml 2015 Flawed science: The fraudulent research practices of social psychologist Diederik Stapel Levelt Committee author text https://www.commissielevelt.nl/ 10.1080/08989620212969 10.1080/08989629508573866 10.1186/1751-0473-8-7 R Core Team author 2015 R: A Language and Environment for Statistical Computing http://www.R-project.org/ 2015 Research Integrity Adjudications Panel author 1996 Thereza Imanishi-Kari, Ph.D., DAB No. 1582 (1996) http://web.archive.org/web/20150810164314/http://www.hhs.gov/dab/decisions/dab1582.html 1996 10.1177/0956797613480366 10.1007/s10120-015-0533-9 10.3897/rio.1.e7462 https://riojournal.com/article/7462/ https://riojournal.com/article/7462/download/pdf/ https://riojournal.com/article/7462/download/xml/ 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. text/html en_US Pensoft Publishers clinicaltrials.gov problematic data error data fabrication Problematic trial detection in ClinicalTrials.gov Small Grant Proposal

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

University of Vienna, Vienna, Austria author Susi, Toma https://orcid.org/0000-0003-2513-573X 2015-12-17 2015-12-17 2015 Research Ideas and Outcomes 2367-7163 1 e7479 2015 10.1103/physrevb.83.115424 10.1063/1.4871997 10.1021/nl402812y 10.1119/1.13262 10.1126/science.262.5131.218 10.1021/nl3042799 10.1088/0034-4885/72/1/016502 10.1103/physrevb.71.035211 10.1103/physrevlett.97.187401 10.1038/33823 10.1016/0925-9635(94)90045-0 10.1038/nnano.2014.310 10.1038/nature08879 10.1038/nature13870 10.1103/physrevlett.89.076402 10.1103/physrev.74.1759 10.1063/1.2901147 10.1103/physrevb.71.035109 10.1002/pssb.201451174 10.1103/physrevb.87.205410 Ion implanter schematic. Licensed under CC BY-SA 3.0 via Wikimedia Commons D. Schwen author text http://commons.wikimedia.org/wiki/File:Ion_implanter_schematic.png 10.1103/physrevlett.112.096801 10.1103/physrevlett.113.115501 10.1063/1.4816715 10.1021/nl300985q 10.1038/nnano.2011.252 10.3897/rio.1.e7479 https://riojournal.com/article/7479/ https://riojournal.com/article/7479/download/pdf/ https://riojournal.com/article/7479/download/xml/ 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. text/html en_US Pensoft Publishers atomic manipulation scanning transmission electron microscopy electron energy loss spectroscopy density functional theory ion implantation Heteroatom quantum corrals and nanoplasmonics in graphene (HeQuCoG) FWF Grant Proposal

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

EvoMRI Communications, Jena, Germany author Mietchen, Daniel https://orcid.org/0000-0001-9488-1870 University of Cambridge, Cambridge, United Kingdom author Mounce, Ross https://orcid.org/0000-0002-3520-2046 Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 2015-12-17 2015-12-17 2015 Research Ideas and Outcomes 2367-7163 1 e7547 2015 10.1007/bf01406139 10.3897/zookeys.50.506 10.1038/embor.2012.99 10.1007/s11192-013-1020-x 10.1371/journal.pcbi.0010034 10.1371/journal.pcbi.1000787 10.1037/h0042814 Publish in Wikipedia or perish Declan Butler author text doi:10.1038/news.2008.1312 10.1017/s0140525x00065675 10.1190/1.1822162 10.1261/rna.1200508 10.1002/14651858.mr000003.pub2 10.12688/f1000research.6742.1 10.1093/biostatistics/kxq028 There is but one journal: the scientific literature Richard Gordon author text http://www.plosmedicine.org/annotation/listThread.action?root=16331 Tim Gowers author gowers.wordpress.com/2009/02/01/questions-of-procedure/#comment-1701 10.1038/461879a 10.1371/journal.pbio.1002010 10.1109/MIS.2007.93 10.1161/circoutcomes.115.002415 10.1371/journal.pcbi.1000941 10.1038/520432a 10.1371/journal.pbio.1002027 10.1632/prof.2011.2011.1.169 10.1242/dmm.003285 10.3897/zookeys.90.1369 10.1038/528153a 10.3389/fncom.2012.00019 10.1038/493588a 10.1177/016224398501000309 10.1073/pnas.1418218112 10.3897/bdj.1.e995 10.1073/pnas.1511912112 10.1016/s0140-6736(97)11129-1 10.1371/journal.pcbi.1002446 10.1038/nchem.1149 10.1038/420461c 10.3897/rio.1.e7547 https://riojournal.com/article/7547/ https://riojournal.com/article/7547/download/pdf/ https://riojournal.com/article/7547/download/xml/ text/html en_US Pensoft Publishers Publishing the research process Editorial

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

University of Stuttgart, Stuttgart, Germany author Wagner, Stefan https://orcid.org/0000-0002-5256-8429 2015-12-21 2015-12-21 2015 Research Ideas and Outcomes 2367-7163 1 e7576 2015 10.1145/93548.93576 10.1109/2.796139 D. Binkley author 2007 Proc. Future of Software Engineering (FOSE’07). IEEE 2007 10.1109/tse.2011.105 10.1145/1985793.1985977 10.1109/ms.2008.129 10.1145/1368088.1368172 U. Dekel author 2009 17th International Conference on Program Comprehension (ICPC ’09) 2009 L. Heinemann F. Deissenboeck author 2012 Proc. 16th European Conference on Software Maintenance and Reengineering 2012 10.1002/0471028959.sof359 10.1145/1806799.1806828 10.1109/iwpse.2003.1231205 10.1097/00006199-196807000-00014 10.1007/s11219-013-9217-z 10.1145/1065010.1065036 10.1109/csmr.2009.20 10.1145/2591062.2591068 10.1109/icpc.2011.21 10.1145/1052883.1052895 B Hummel author 2010 Proc. International Conference on Software Maintenance (ICSM’10) 2010 10 10.1007/s10664-013-9268-6 10.1109/ESEM.2007.36 10.1109/icse.2009.5070547 10.1145/1810295.1810308 D Kahneman author 2012 Thinking. Fast and Slow 2012 490 10.1109/tse.2012.70 10.1147/sj.331.0004 10.1109/wcre.2009.36 10.1145/1181775.1181777 10.1007/978-3-642-13881-2_7 10.1145/1287624.1287633 10.1109/seaa.2009.88 10.1016/0164-1212(90)90094-3 10.1109/tse.2006.28 10.1145/2499393.2499404 10.1109/ICSM.2005.63 10.1002/stvr.294 10.1109/icsm.2009.5306381 10.1109/ms.2006.105 10.1145/222124.222136 S. M. Nasehi author 2012 Q&A in StackOverflow. Proc. International Conference on Software Maintenance (ICSM’12) 2012 10.1109/tse.1985.232178 10.1145/2460999.2461010 10.1109/ICSE.2007.37 10.1109/ICSE.1994.296790 10.1109/icse.2013.6606701 A. Pretschner author 2005 Proc. 27th International Confernce on Software Engineering (ICSE’05) 2005 10.1109/icse.2015.82 Tool support for user-defined quality assessment models H Schackmann author 2009 text MetriKon 2009 10.1109/icpc.2013.6613836 10.1109/ESEM.2007.44 10.1016/j.infsof.2010.03.016 10.1007/978-3-642-38571-1 10.1007/11430230_4 10.1109/icst.2008.63 10.1109/esem.2009.5316003 S. Wagner author 2012 Technical Report TUM-I129 2012 10.1109/icse.2012.6227106 10.1016/j.infsof.2015.02.009 10.1109/52.896249 T D Wilson author B C Vicerky author 1994 Fifty Years of Information Progress: A Journal of Documentation Review 1994 10.1109/tse.2004.52 10.1109/icpc.2011.35 10.1109/tse.2006.38 10.1109/tse.2005.72 10.3897/rio.1.e7576 https://riojournal.com/article/7576/ https://riojournal.com/article/7576/download/pdf/ https://riojournal.com/article/7576/download/xml/ 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. text/html en_US Pensoft Publishers Software Quality Information Needs Fast Feedback Continuous and Focused Developer Feedback on Software Quality (CoFoDeF) DFG Grant Proposal

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

Museum für Naturkunde Berlin, Berlin, Germany author Mietchen, Daniel https://orcid.org/0000-0001-9488-1870 Museum für Naturkunde Berlin, Berlin, Germany author Hagedorn, Gregor Maastricht University, Maastricht, Netherlands author Willighagen, Egon https://orcid.org/0000-0001-7542-0286 Universidad Politécnica de Madrid (UPM), Madrid, Spain author Rico, Mariano https://orcid.org/0000-0001-5878-8521 Universidad Politécnica de Madrid (UPM), Madrid, Spain author Gómez-Pérez, Asunción Universitat Oberta de Catalunya, Barcelona, Spain author Aibar, Eduard Inria, Paris, France author Rafes, Karima Université Paris-Sud, Paris, France author Germain, Cécile The European Library, Den Haag, Netherlands author Dunning, Alastair Wikimedia Deutschland e.V., Berlin, Germany author Pintscher, Lydia Wikimedia Deutschland e.V., Berlin, Germany author Kinzler, Daniel 2015-12-22 2015-12-22 2015 Research Ideas and Outcomes 2367-7163 1 e7573 2015 10.3897/rio.1.e7573 https://riojournal.com/article/7573/ https://riojournal.com/article/7573/download/pdf/ https://riojournal.com/article/7573/download/xml/ text/html en_US Pensoft Publishers Virtual Research Environment Wikidata identifiers citizen science collaboration concept mapping ontologies Enabling Open Science: Wikidata for Research (Wiki4R) H2020 Grant Proposal

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

Huazhong University of Science and Technology, Wuhan, China author Zou, Yuanchuan https://orcid.org/0000-0002-5400-3261 2015-12-28 2015-12-28 2015 Research Ideas and Outcomes 2367-7163 1 e7506 2015 10.1038/nature04787 10.1103/revmodphys.76.1143 10.1088/0004-637x/691/1/182 10.3897/rio.1.e7506 https://riojournal.com/article/7506/ https://riojournal.com/article/7506/download/pdf/ https://riojournal.com/article/7506/download/xml/ text/html en_US Pensoft Publishers GRB relativistic jet galaxy Determining the direction of a gamma-ray burst's jet in its host galaxy Research Idea

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

Boston University, Boston, United States of America author Vyshedskiy, Andrey https://orcid.org/0000-0002-1610-8716 ImagiRation LLC, Boston, United States of America author Dunn, Rita 2015-12-29 2015-12-29 2015 Research Ideas and Outcomes 2367-7163 1 e7642 2015 10.1126/science.1099745 Joaquin M. Fuster author 2008 The prefrontal cortex 2008 999 10.1126/science.1164685 D. O. Hebb author 1949 The organization of behavior: A neuropsychological approach 1949 999 10.1038/35042575 10.1126/science.1101864 10.1037/a0016917 10.1016/j.tics.2007.12.003 10.1152/jn.00125.2007 10.1038/nature03687 10.1146/annurev.neuro.18.1.555 10.4249/scholarpedia.1657 I Tattersall author 1999 Becoming Human: Evolution and Human Uniqueness 1999 999 10.2753/rpo1061-040505036 A. Vyshedskiy author 2013 On the origin of the human mind  2013 999 10.1523/jneurosci.2101-06.2006 10.3897/rio.1.e7642 https://riojournal.com/article/7642/ https://riojournal.com/article/7642/download/pdf/ https://riojournal.com/article/7642/download/xml/ text/html en_US Pensoft Publishers mental synthesis imagination binding-by-synchrony independent neuronal ensembles neuronal ensemble synchronization neuronal synchronization  evolution of language Mental synthesis involves the synchronization of independent neuronal ensembles Research Idea

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

Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria author Senderov, Viktor https://orcid.org/0000-0003-3340-5963 Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 2016-01-11 2016-01-11 2016 Research Ideas and Outcomes 2367-7163 2 e7757 2016 project BIG4 - Biosystematics, Informatics and Genetics of the big 4 insect groups: training tomorrow's researchers and entrepreneurs BIG4 642241 funder European Commission 10.13039/501100000780 Why not let the computer save you time by reading the taxonomic papers for you? D Agosti author 2007 text Biologico 2007 69 545 548 10.1038/scientificamerican0501-34 Brill and DANS Launch a New Open Access Journal on Research Data Brill author text http://www.brill.com/news/brill-and-dans-launch-new-open-access-journal-research-data A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadinae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species BUNTIKA AREEKUL Butcher author 2012 text Zootaxa http://www.mapress.com/zootaxa/list/2012/3457.html 2012 1 232 T Catapano author 2010 TaxPub: An Extension of the NLM / NCBI Journal Publishing DTD for Taxonomic Descriptions. Proceedings of the Journal Article Tag Suite Conference 2010 2010 1-6 10.1190/1.1822162 10.1093/sysbio/syu060 10.3897/zookeys.414.7717 10.1371/journal.pone.0114069 10.3897/zookeys.494.9352 10.1073/pnas.1423041112 10.1038/455481a 10.1111/mec.12481 10.1504/ijtel.2011.045454 10.1371/journal.pbio.1002027 10.3897/rio.1.e7573 10.3897/bdj.3.e5063 10.1186/1741-7007-10-87 10.1371/journal.pone.0019491 10.1101/031971 Challenges in Irreproducible Research Nature author text http://www.nature.com/news/reproducibility-1.17552 From Relational to Neo4j Neo4j author text http://neo4j.com/developer/graph-db-vs-rdbms/ The vision thing - it's all about the links R. D.M. Page author text http://iphylo.blogspot.bg/2014/06/the-vision-thing-it-all-about-links.html Putting some bite into the Bouchout Declaration R. D.M. Page author text http://iphylo.blogspot.bg/2015/05/putting-some-bite-into-bouchout.html 10.1093/bib/bbn022 10.17161/bi.v3i0.25 Dark taxa: GenBank in a post-taxonomic world Roderic D. M. Page author text http://iphylo.blogspot.bg/2011/04/dark-taxa-genbank-in-post-taxonomic.html Visualising big phylogenies (yet again) Roderic D. M. Page author text http://iphylo.blogspot.bg/2015/09/visualising-big-phylogenies-yet-again.html 10.1101/016758 10.1016/j.tree.2011.11.001 10.1016/j.tree.2010.09.004 Implementation of TaxPub, an NLM DTD extension for domain-specific markup in taxonomy, from the experience of a biodiversity publisher Lyubomir Penev author 2012 text Journal Article Tag Suite Conference (JATS-Con) Proceedings http://www.ncbi.nlm.nih.gov/books/NBK100351/ 2012 1 1 14 10.3897/zookeys.150.2213 Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples Lyubomir Penev author 2010 text ZooKeys 2010 50 1 16 TDWG Life Sciences Identifiers (LSID) Applicability Statement, Version 2009-09. Biodiversity Information R Pereira author text http://www.tdwg.org/standards/150 Project Final Report pro-iBiosphere author text http://adm.pro-ibiosphere.eu/getatt.php?filename=oo_4751.pdf Open Biodiversity Knowledge Management System (OBKMS) pro-iBiosphere author text http://adm.pro-ibiosphere.eu/getatt.php?filename=oo_4749.pdf 10.1371/journal.pone.0066213 TDWG GUID Applicability Statement, Version 2010-09. Biodiversity Information Standards (TDWG) K Richards author text http://www.tdwg.org/standards/150 10.1087/2009202 10.1186/1742-9994-6-31 10.3897/bdj.1.e995 10.5117/9789089641892 10.3897/rio.2.e7757 https://riojournal.com/article/7757/ https://riojournal.com/article/7757/download/pdf/ https://riojournal.com/article/7757/download/xml/ 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. text/html en_US Pensoft Publishers entomology systematics taxonomy biodiversity informatics evolutionary informatics bioinformatics data visualization data publishing semantically enhanced publication The Open Biodiversity Knowledge Management System in Scholarly Publishing PhD Project Plan

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

Natural History Museum, London, United Kingdom author Koureas, Dimitris https://orcid.org/https://orcid.org/0000-0002-4842-6487 Cardiff University, Cardiff, United Kingdom author Hardisty, Alex https://orcid.org/0000-0002-0767-4310 Naturalis Biodiversity Center, Leiden, Netherlands author Vos, Rutger https://orcid.org/0000-0001-9254-7318 www.plazi.org, Bern, Switzerland author Agosti, Donat https://orcid.org/0000-0001-9286-1200 Hellenic Center for Marine Recearch (HCMR), Heraklion Crete, Greece author Arvanitidis, Christos Research and Educational Networking Association of Moldova (RENAM), Chișinău, Moldova author Bogatencov, Peter HGF-MPG Group for Deep Sea Ecology and Technology Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremen, Germany author Buttigieg, Pier Luigi https://orcid.org/0000-0002-4366-3088 University of Eastern Finland, Joensuu, Finland author de Jong, Yde https://orcid.org/0000-0003-2703-5556 Institute of Ecology and Botany, Centre for Ecological Research, Hungarian Academy of Sciences, Vacratot, Hungary author Horvath, Ferenc College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom author Gkoutos, Georgios Agentschap Plantentuin Meise, Meise, Belgium author Groom, Quentin https://orcid.org/0000-0002-0596-5376 University of Zagreb, Faculty of Geodesy, Zagreb, Croatia author Kliment, Tomas University of Tartu, Tartu, Estonia author Kõljalg, Urmas Information Technologies Institute, Centre for Research and Technology Hellas, Thessaloniki, Greece author Manakos, Ioannis CREAF, Cerdanyola del Vallès, Spain author Marcer, Arnald https://orcid.org/0000-0002-6532-7712 Univerzita Karlova v Praze, Praha 2, Czech Republic author Marhold, Karol https://orcid.org/0000-0002-7658-0844 The Open University, Milton Keynes, United Kingdom author Morse, David Royal Museum for Central Africa, Tervuren, Belgium author Mergen, Patricia https://orcid.org/0000-0003-2848-8231 Pensoft, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 Biodiversity Unit, Department of Biology, Lund University, Lund, Sweden author Pettersson, Lars B. https://orcid.org/https://orcid.org/0000-0001-5745-508X Aarhus University, Aarhus, Denmark author Svenning, Jens-Christian https://orcid.org/0000-0002-3415-0862 OD Nature, Royal Belgian Institute for Natural Science, Bruxelles, Belgium author van de Putte, Anton P. https://orcid.org/0000-0003-1336-5554 Natural History Museum, London, United Kingdom author Smith, Vincent https://orcid.org/0000-0001-5297-7452 2016-01-19 2016-01-19 2016 Research Ideas and Outcomes 2367-7163 2 e7787 2016 10.1186/1472-6785-13-16 Donald Hobern author 2013 Global Biodiversity Informatics Outlook: Delivering biodiversity knowledge in the information age 87-92020-52-6 http://www.biodiversityinformatics.org 2013 44 10.1353/lib.0.0036 10.3897/rio.2.e7787 https://riojournal.com/article/7787/ https://riojournal.com/article/7787/download/pdf/ https://riojournal.com/article/7787/download/xml/ text/html en_US Pensoft Publishers COST Action Biodiversity Informatics Environment Standards Data interoperability Unifying European Biodiversity Informatics (BioUnify) COST Grant Proposal

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

Embryogenesis Center, Gulf Specimen Aquarium & Marine Laboratory, Panacea, Florida, United States of America author Gordon, Richard 2016-01-22 2016-01-22 2016 Research Ideas and Outcomes 2367-7163 2 e7869 2016 クサリケイソウの不思議Mysterious behavior of Bacillaria [movie] ALMuseum author text https://www.youtube.com/watch?v=BDvCkttQPMk クサリケイソウの舞; Dancing Bacillaria [movie] ALMuseum author text https://www.youtube.com/watch?v=PUCSTiwZZ18 Bacillaria paxillifer [movie] D. Basili author text https://www.youtube.com/watch?v=SPfhjazILYA Bacillaria paxillifer - Is Not a Caterpilififer [movie] BirdWhisperer46 author text https://www.youtube.com/watch?v=klMGTnqMwfg Bacillaria Diatomea [movie] F. P. Capilla author text https://www.youtube.com/watch?v=o9zNtXw2JMI Bacillaria paxillifer diatomea - diatom [movie] F. P. Capilla author text https://www.youtube.com/watch?v=lVg0lSKziys Bacillaria paxillifer Diatomea [movie] F. P. Capilla author text https://www.youtube.com/watch?v=xFfQ9piAzDo Bacillaria [movie] Cimellimay author text https://www.youtube.com/watch?v=M2f6y4aiU8s 10.1080/0269249x.2004.9705869 Comparative analysis of light- stimulated motility responses in diatoms S. A. Cohn author 2011 text Molecular Biology of the Cell 2011 22 15 48 Comparative analysis of irradiation-induced direction change in diatoms S. A. Cohn author 2004 text Molecular Biology of the Cell 2004 15 163 Analysis of diatom motility using light avoidance and fluorescent bend assays S. A. Cohn author 1999 text Molecular Biology of the Cell 1999 10 15 27 Bacillaria paradoxa [movie] R. Do author text https://www.youtube.com/watch?v=7ddWMC1KjPc 10.1007/bf01254629 'On weakly coupled diatomic oscillators: Bacillaria's paradox resolved R. W. Drum author 1971 text Journal of Phycology 1971 7 13 14 J. F. Gmelin author 1788 Caroli à Linné Systema naturae 1788 1 3903 10.1016/j.tibtech.2008.11.003 クサリケイソウ（バキラリア）属の一if - Bacillaria sp. [movie] S Gougi author text https://www.youtube.com/watch?v=sQU1nWZk_cE M. D. Guiry author M. D. Guiry author 2015 AlgaeBase http://www.algaebase.org/search/genus/detail/?genus_id=s2335e6205d52bee2&-session=abv4:43E996C81db731E398Rh3AF9EDC0 2015 奇異棍形藻 Bacillaria paxillifera（偏光、穿透光) [movie] A Hsiao author text https://www.youtube.com/watch?v=PD7FKihgAjY 10.1080/09670260701428864 10.1080/0269249x.1992.9705215 Bacillaria paxillifer [movie] D Kersulis author text https://www.youtube.com/watch?v=2np5EhefZKo Gliding Movement - Diatom (Bacillaria paradoxa, Pennales)/Gleitbewegung - Kieselalge (Bacillaria paradoxa, Pennales) [movie] O Kiermayer author text http://www.cells.de/cellseng/medienarchiv/archiv/bp1c1562d/1562_b58.html Bacillaria paradoxa Gmelin: Taxonomic Serial No.: 5302 J. Patrick Kociolek author text http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=5302 11/07/15 Diatom Colony (Bacillaria paxillifer?) [movie] D Laundon author text https://www.youtube.com/watch?v=cWiDIMY_QgM ) Bacillaria: The "carpenter's rule" diatom, easily recognized by the sliding of the cells against one another in the colony. [QuickTime movie] C Lobban author text http://www.uog.edu/classes/botany/474/diatoms/bacillaria.html 10.1016/j.jtbi.2013.03.021 Bacillaria paxillifer - a diatom with a spectacular gliding movement [movie] D. Ott author text https://www.youtube.com/watch?v=NvHF-YjDZBo イカダケイソウのii'ti／Bacillaria sp. [movie] Otyatatemushi author text https://www.youtube.com/watch?v=GUdDI_QhaoI イカダケイソウBacillaria paradoxaのii'ti [movie] Otyatatemushi author text https://www.youtube.com/watch?v=SyYjuMhKU3Y The Amazing Sliding Diatom (Bacillaria paxillifer) [movie] PeacefulProtist author text https://www.youtube.com/watch?v=s5LQbh4dVoM Bacillaria paradoxa [movie] Pierre microscope author text https://www.youtube.com/watch?v=3Mk1xi6FMXE 10.1017/cbo9780511755743 Plankton Theater, Bacillaria paxillifera, a motile, colonial pennate diatom, Narragansett Bay, Rhode Island, Fall [movie] J Rines author text http://thalassa.gso.uri.edu/plankton/theater/alphabetical.html The acceleration noise of motile diatoms Ahmet Can Sabuncu author 2015 text To be submitted 2015 in preparation 10.1111/j.1529-8817.2006.00299.x Carpenters Rule Diatoms (Bacillaria paxillifer) [movie] P Shilov author text https://www.youtube.com/watch?v=DxK7QgD9Oic microlife casco bay unfolding diatoms Bacillaria paxillifer 092914 plant locomotion [movie] J Stetson author text https://www.youtube.com/watch?v=FF9JKX48_fw Tonysharks author https://www.youtube.com/watch?v=N6XV849ZAmQ Bacillaria paradoxa.AVI [movie] uni2さんのチャンネル author text https://www.youtube.com/watch?v=a864NCFBsDs Anne P Ussing author 2005 The colonial diatom "Bacillaria paradoxa": chaotic gliding motility, Lindenmeyer Model of colonial morphogenesis, and bibliography, with translation of O. F. Müller (1783). 'About a peculiar being in the beach-water 2005 139 Bacillaria paxillifera Just Slides Along [movie] Hidden WLanier author text https://www.youtube.com/watch?v=Ol6hbX5mhPc The ground swell produced by gliding motion of diatom, Bacillaria paradoxa (うごめくイカダケイソウ) [movie] R Yanase author text https://www.youtube.com/watch?v=HyGoK7WfoS8 The gliding motion of diatom, Bacillaria paradoxa Part 2 [movie]. R Yanase author text https://www.youtube.com/watch?v=4cJb9jCN2oI The gliding motion of diatom, Bacillaria paradoxa Part 1 [movie]. R Yanase author text https://www.youtube.com/watch?v=j1lCCpZPNH8 10.3897/rio.2.e7869 https://riojournal.com/article/7869/ https://riojournal.com/article/7869/download/pdf/ https://riojournal.com/article/7869/download/xml/ text/html en_US Pensoft Publishers colonial diatom Bacillaria paradoxa gliding motility synchrony Partial synchronization of the colonial diatom Bacillaria "paradoxa" Research Idea

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

Department of Biotechnology, Malaysia University of Science and Technology, Kuala Lumpur, Malaysia author Abdullah, Nik-Othman 2016-02-17 2016-02-17 2016 Research Ideas and Outcomes 2367-7163 2 e8134 2016 10.5772/2215 Water Use Efficiency in Hydroponics and Aquaponics Perry Baptista author text https://www.brightagrotech.com/water-use-efficiency-hydroponics-aquaponics/ 10.1201/b16482 GDP per capita (current US$) World Bank Data author text http://data.worldbank.org/indicator/NY.GDP.PCAP.CD The Five Advantages of Hydroponics Donna Dawson author text http://www.accuweather.com/en/home-garden-articles/gardening/the-five-advantages-of-hydropo/50379 10.1038/nrmicro954 Qatar GDP 1970-2016 Qatar GDP author text http://www.tradingeconomics.com/qatar/gdp Graze Green author http://www.grazegreen.com/systems12-24.html Qatar Banking on Hydroponics as Find New Sources of Food Supply Hydroponeast author text http://hydroponeast.com/en/news/qatar-banking-on-hydroponics-as-find-new-sources-of-food-supply Food and Water Security in Qatar Haweya Ismail author Haweya Ismail author 2015 text Independent Strategic Analysis of Australias Global Interest 2015 1 6 James Jones author 2014 Complete Guide for Growing Plants Hydroponically 2014 1 206 James Jones author 2014 Complete Guide for Growing Plants Hydroponically 978-1-4398-7669-5 2014 1 206: 3-4 James Jones author 2014 Complete Guide for Growing Hydroponically 13: 978-1-4398-7669-5 2014 1 10.17660/actahortic.2004.648.10 John Mason author 1988 Commercial Hydroponics 978-0-9871022-2-5 1988 1 144 John Mason author 2014 Commercial Hydroponics 978-0-9571022-2-5 2014 1 144 Hydroponics system grows crops with less water, no soil Brandon Merrill author text http://swes.cals.arizona.edu/environmental_writing/stories/2011/merrill.html Enhanced strawberry seed germination through in vitro culture of cut achenes A. Miller author 1992 text Journal of the American Society for Horticultural Science 1992 117 2 313 316 10.1016/j.soilbio.2015.07.012 Howard Resh author 2013 Hydroponic Food Production 2013 1 551 10.1201/b13737-6 Howard Resh author 2014 Hydroponic Food Production 978-1-4398-7869-9 2014 1 551 10.1111/j.1469-8137.1998.00194.x Keith Roberto author 2003 How-To-Hydroponics 0-9672026-1-2 2003 1 102 Keith Roberto author 2003 How-To-Hydroponics 978-1-4398-7669-5 2003 1 102: 11-14 Advantages & Disadvantages of Hydroponics Olivia's Solutions author text http://www.oliviassolutions.com/blog/advantages-disadvantages-of-hydroponics/ Diazotroph Diazotrophs in Wikipedia author text https://en.wikipedia.org/wiki/Diazotroph Hydroponics gives 100 times field yields Android World author text http://www.androidworld.com/prod26.htm Where does our food come from? An insight into Qatar’s food industry Kim Wyatt author text http://www.dohafamily.com/Winter-2015/Where-does-our-food-come-from-An-insight-into-Qatars-food-industry/ 10.3897/rio.2.e8134 https://riojournal.com/article/8134/ https://riojournal.com/article/8134/download/pdf/ https://riojournal.com/article/8134/download/xml/ text/html en_US Pensoft Publishers hydroponics soilless farming vertical-horizontal growing large-scale Vertical-Horizontal Regulated Soilless Farming via Advanced Hydroponics for Domestic Food Production in Doha, Qatar Methods

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

Hypothes.is, San Francisco, United States of America author Martone, Maryann https://orcid.org/0000-0002-8406-3871 University of Cambridge, Cambridge, United Kingdom author Murray-Rust, Peter https://orcid.org/0000-0003-3386-3972 ContentMine, Cambridge, United Kingdom author Molloy, Jenny ContentMine, Cambridge, United Kingdom author Arrow, Tom Cottage Labs LLP., Edinburgh, United Kingdom author MacGillivray, Mark ContentMine, Cambridge, United Kingdom author Kittel, Chris ContentMine, Cambridge, United Kingdom author Kasberger, Stefan ContentMine, Cambridge, United Kingdom author Steel, Graham https://orcid.org/0000-0003-4681-8011 ContentMine, Cambridge, United Kingdom author Oppenheim, Charles Cottage Labs LLP., Edinburgh, United Kingdom author Ranganathan, Anusha Imperial College London, London, United Kingdom author Tennant, Jon https://orcid.org/0000-0001-7794-0218 Hypothes.is, San Francisco, United States of America author Udell, Jon 2016-03-10 2016-03-10 2016 Research Ideas and Outcomes 2367-7163 2 e8424 2016 10.1109/thfe2.1960.4503259 10.3897/rio.2.e8424 https://riojournal.com/article/8424/ https://riojournal.com/article/8424/download/pdf/ https://riojournal.com/article/8424/download/xml/ text/html en_US Pensoft Publishers amanuens.is Zika open science open access ContentMine ContentMine/Hypothes.is Proposal Grant Proposal

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

Plazi, Bern, Switzerland author Egloff, Willi www.plazi.org, Bern, Switzerland author Agosti, Donat https://orcid.org/0000-0001-9286-1200 University of Sydney, Sydney, Australia author Patterson, David https://orcid.org/0000-0003-2645-7335 Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany author Hoffmann, Anke EvoMRI Communications, Jena, Germany author Mietchen, Daniel https://orcid.org/0000-0001-9488-1870 Plazi, Bern, Switzerland author Kishor, Puneet https://orcid.org/0000-0002-1746-6195 Pensoft Publishers & Institute for Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 2016-03-12 2016-03-12 2016 Research Ideas and Outcomes 2367-7163 2 e8458 2016 10.3897/zookeys.414.7717 10.1186/1756-0500-7-79 Pensoft Data Publishing Policies and Guidelines for Biodiversity Data. Pensoft Publishers, http://www.pensoft.net/J_FILES/Pensoft_Data_ Publishing_Policies_and_Guidelines.pdf L Penev author text http://www.pensoft.net/J_FILES/Pensoft_Data_ Publishing_Policies_and_Guidelines.pdf 10.1038/461171a 10.7717/peerj-cs.1 10.3897/zookeys.150.1766 10.3897/rio.2.e8458 https://riojournal.com/article/8458/ https://riojournal.com/article/8458/download/pdf/ https://riojournal.com/article/8458/download/xml/ text/html en_US Pensoft Publishers open science bidoiversity data policies data mining Data Policy Recommendations for Biodiversity Data. EU BON Project Report Project Report

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

Paperity, Warsaw, Poland author Wojnarski, Marcin DuraSpace, Beaverton, OR, United States of America author Hanken Kurtz, Debra 2016-03-14 2016-03-14 2016 Research Ideas and Outcomes 2367-7163 2 e8462 2016 10.3897/rio.2.e8462 https://riojournal.com/article/8462/ https://riojournal.com/article/8462/download/pdf/ https://riojournal.com/article/8462/download/xml/ text/html en_US Pensoft Publishers open access open science open data wiki API Paperity Central: An Open Catalog of All Scholarly Literature Small Grant Proposal

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

Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Wetzel, Florian Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Hoffmann, Anke Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Haüser, Christoph Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Vohland, Katrin 2016-03-23 2016-03-23 2016 Research Ideas and Outcomes 2367-7163 2 e8600 2016 10.1080/14888386.2015.1075902 10.3897/rio.2.e8600 https://riojournal.com/article/8600/ https://riojournal.com/article/8600/download/pdf/ https://riojournal.com/article/8600/download/xml/ text/html en_US Pensoft Publishers European environmental policy biodiversity GEO GEOSS EU BON science-policy interface biodiversity data research 1st EU BON Stakeholder Roundtable (Brussels, Belgium):  Biodiversity and Requirements for Policy Workshop Report

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

School of Rehabilitation Sciences, University of Ottawa, Ottawa, Canada author Hammond, Chad https://orcid.org/0000-0001-8715-6793 2016-03-24 2016-03-24 2016 Research Ideas and Outcomes 2367-7163 2 e8615 2016 10.3897/rio.2.e8615 https://riojournal.com/article/8615/ https://riojournal.com/article/8615/download/pdf/ https://riojournal.com/article/8615/download/xml/ 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. text/html en_US Pensoft Publishers Indigenous health cancer arts-based methods 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 Small Grant Proposal

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

Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Vohland, Katrin Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Haüser, Christoph United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntingdon Road, Cambridge, CB3 0DL, United Kingdom author Regan, Eugenie Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Hoffmann, Anke Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Wetzel, Florian 2016-03-24 2016-03-24 2016 Research Ideas and Outcomes 2367-7163 2 e8616 2016 10.3897/rio.2.e8600 10.1080/14888386.2015.1075902 10.3897/rio.2.e8616 https://riojournal.com/article/8616/ https://riojournal.com/article/8616/download/pdf/ https://riojournal.com/article/8616/download/xml/ text/html en_US Pensoft Publishers Citizen Science biodiversity data data quality Biodiversity Observation Networks EU BON research data European Citizen Science Association Citizen Science Observatories. 2nd EU BON Stakeholder Roundtable (Berlin, Germany): How can a European biodiversity network support citizen science? Workshop Report

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

Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Vohland, Katrin Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Hoffmann, Anke Institute for European Environmental Policy (IEEP), 11 Belgrave Road, London SW1V 1RB, United Kingdom author Underwood, Evelyn United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, CB3 0DL, United Kingdom author Weatherdon, Lauren https://orcid.org/0000-0002-3989-027X Laboratorio de Ecología (iEcolab), Centro Andaluz de Medio Ambiente (CEAMA), Universidad de Granada, Avenida del Mediterráneo s/n, 18006, Granada, Spain author Bonet García, Francisco Javier Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Haüser, Christoph Museum fuer Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstr. 43, 10115 Berlin, Germany author Wetzel, Florian 2016-03-24 2016-03-24 2016 Research Ideas and Outcomes 2367-7163 2 e8622 2016 10.3897/rio.2.e8616 10.3897/rio.2.e8600 10.1080/14888386.2015.1075902 10.3897/rio.2.e8622 https://riojournal.com/article/8622/ https://riojournal.com/article/8622/download/pdf/ https://riojournal.com/article/8622/download/xml/ text/html en_US Pensoft Publishers Biodiversity data workflows data integration local and regional biodiversity networks policy support biodiversity portals EU BON test sites data mobilization. 3rd EU BON Stakeholder Roundtable (Granada, Spain): Biodiversity data workflow from data mobilization to practice Workshop Report

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

California Digital Library, University of California Curation Center, Oakland, United States of America author Simms, Stephanie https://orcid.org/0000-0001-9129-3790 Digital Curation Centre, Glasgow, United Kingdom author Jones, Sarah https://orcid.org/0000-0002-5094-7126 Digital Curation Centre, Edinburgh, United Kingdom author Ashley, Kevin Digital Curation Centre, Edinburgh, United Kingdom author Ribeiro, Marta California Digital Library, University of California Curation Center, Oakland, United States of America author Chodacki, John https://orcid.org/0000-0002-7378-2408 California Digital Library, University of California Curation Center, Oakland, United States of America author Abrams, Stephen California Digital Library, University of California Curation Center, Oakland, United States of America author Strong, Marisa 2016-03-30 2016-03-30 2016 Research Ideas and Outcomes 2367-7163 2 e8649 2016 bioCADDIE author https://biocaddie.org/ BioSharing author https://biosharing.org/ DMP Ethics Review CASRAI author text http://dictionary.casrai.org/DMP_Ethics_Review CASRAI author http://casrai.org/ Center for Open Science author https://cos.io/ Open Funder Registry Crossref author text http://www.crossref.org/fundingdata/registry.html Checklist for a Data Management Plan v.4.0 Digital Curation Centre author text http://www.dcc.ac.uk/sites/default/files/documents/resource/DMP/DMP_Checklist_2013.pdf Developing Locale-Aware Support for DMPonline version 4 Digital Curation Centre author text https://dmponline.dcc.ac.uk/files/DMPonline-v4-LocaleSupport.pdf Edinburgh: Digital Curation Centre DMPonline author text https://dmponline.dcc.ac.uk/ The Regents of the University of California DMPTool author text http://dmptool.org/ ELIXIR author https://www.elixir-europe.org/ EZID author http://ezid.cdlib.org/ Identifiers.org author http://identifiers.org/ International Digital Curation Conference author http://www.dcc.ac.uk/events/idcc16 Annual Report and Accounts, 2014/2015 Medical Research Council author text http://www.mrc.ac.uk/publications/browse/annual-report-and-accounts-2014-15/ NIH Awards by Location and Organization National Institutes of Health author text https://report.nih.gov/award/ Center for Open Science Open Science Framework author text https://osf.io/ Research Ideas and Outcomes (RIO) Journal author http://riojournal.com/ NIH Data Sharing Repositories U. S. National Library of Medicine author text https://www.nlm.nih.gov/NIHbmic/nih_data_sharing_repositories.html Wellcome Trust Grants Awarded 2013/14 Wellcome Trust author text http://www.wellcome.ac.uk/Managing-a-grant/Grants-awarded/ Data repositories and database resources Wellcome Trust author text http://www.wellcome.ac.uk/About-us/Policy/Spotlight-issues/Data-sharing/Guidance-for-researchers/WTX060360.htm 10.3897/rio.2.e8649 https://riojournal.com/article/8649/ https://riojournal.com/article/8649/download/pdf/ https://riojournal.com/article/8649/download/xml/ 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. text/html en_US Pensoft Publishers open science data management plans biomedical research funder policies Roadmap: A Research Data Management Advisory Platform Grant Proposal

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

Lincoln University, Lincoln, New Zealand author Pannell, Jennifer 2016-04-05 2016-04-05 2016 Research Ideas and Outcomes 2367-7163 2 e8664 2016 Design and implementation of the Solar Analyst: an ArcView extension for modeling solar radiation at landscape scales P. Fu author 1999 text Proceedings of the Nineteenth Annual ESRI User Conference 1999 1 1 31 A spherical densiometer for estimating forest overstory density P. E. Lemmon author 1956 text Forest Science 1956 2 4 314 320 10.1111/2041-210x.12146 10.1111/2041-210x.12001 Montane outcrop vegetation of Banks Peninsula, South Island, New Zealand S. K. Wiser author 2009 text New Zealand Journal of Ecology 2009 33 2 164 176 10.3897/rio.2.e8664 https://riojournal.com/article/8664/ https://riojournal.com/article/8664/download/pdf/ https://riojournal.com/article/8664/download/xml/ text/html en_US Pensoft Publishers data management plan doctorate ecology Crassulaceae invasions Data Management Plan for PhD Thesis "Climatic Limitation of Alien Weeds in New Zealand: Enhancing Species Distribution Models with Field Data" Data Management Plan (NSF Generic)

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

High Point University, High Point, NC, United States of America author Fisher, Josh University of Edinburgh, Edinburgh, United Kingdom author Nading, Alex 2016-04-05 2016-04-05 2016 Research Ideas and Outcomes 2367-7163 2 e8720 2016 10.3897/rio.2.e8720 https://riojournal.com/article/8720/ https://riojournal.com/article/8720/download/pdf/ https://riojournal.com/article/8720/download/xml/ text/html en_US Pensoft Publishers urban political ecology urban anthropology collaborative anthropology economic anthropology environmental anthropology medical anthropology value A Political Ecology of Value: A Cohort-Based Ethnography of the Environmental Turn in Nicaraguan Urban Social Policy  Data Management Plan (NSF Generic)

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

University of Glasgow, Glasgow, United Kingdom author Page, Roderic https://orcid.org/0000-0002-7101-9767 2016-04-07 2016-04-07 2016 Research Ideas and Outcomes 2367-7163 2 e8767 2016 10.1186/1471-2105-13-211 10.1016/j.jbi.2008.03.004 CrossRef Revises DOI Display Guidelines CrossRef author text http://www.crossref.org/01company/pr/news080211.html 10.3897/zookeys.494.9352 10.1093/nar/gkr1097 10.1186/1756-0500-2-101 10.7717/peerj.190 Rethinking annotating biodiversity data Roderic D. M. Page author text http://iphylo.blogspot.com/2014/03/rethinking-annotating-biodiversity-data.html 10.1007/978-3-319-25010-6_12 10.14778/1453856.1453965 10.1371/journal.pone.0029715 10.3897/rio.2.e8767 https://riojournal.com/article/8767/ https://riojournal.com/article/8767/download/pdf/ https://riojournal.com/article/8767/download/xml/ text/html en_US Pensoft Publishers biodiversity informatics biodiversity knowledge graph JSON-LD graph databases triple stores RDF linked data Towards a biodiversity knowledge graph Research Idea

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

Kodolányi János University of Applied Sciences, Székesfehérvár, Hungary author Toth, Janos 2016-04-07 2016-04-07 2016 Research Ideas and Outcomes 2367-7163 2 e8726 2016 10.1080/00913367.1989.10673140 Advertising Value and Advertising on the Web R. H. Ducoffe author 1996 text Journal of Advertising Research 1996 36 5 21 35 10.1057/palgrave.thr.6040049 10.1002/jtr.346.abs B. McKercher author 2002 Cultural tourism: The partnership between tourism andcultural heritage management. 9780789011060 2002 262 Attitude towards advertising among students at private higher learning institutions in Selangor J. Munusamy author 2007 text Journal of UNITAR 2007 3 1 31 51 10.1080/02650487.1995.11104615 Advertisier to Consumer: How'm I Doing? S. Ogilvy author 1985 text Listening Post 1985 61 2 2 2 10.1108/03090560710728354 10.1002/(sici)1520-6653(199922)13:33.3.co;2-i 10.1177/1470593107083162 10.1080/02650487.1984.11104995 10.3897/rio.2.e8726 https://riojournal.com/article/8726/ https://riojournal.com/article/8726/download/pdf/ https://riojournal.com/article/8726/download/xml/ text/html en_US Pensoft Publishers small grant proposal marketing research advertising research survey study textual analysis Tools of Persuasion in Visual Advertisements at Maltese Sites of Cultural Tourism: A Social Science Analysis Small Grant Proposal

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

Cardiovascular Surgery, Taipei Tzuchi Hospital, Buddhist Tzuchi Medical Foundation, New Taipei City, Taiwan author Chen, Robert https://orcid.org/0000-0001-6892-0602 Cardiovascular Surgery, Taipei Tzuchi Hospital, Buddhist Tzuchi Medical Foundation, New Taipei City, Taiwan author Shen, Ta-Chung Cardiovascular Surgery, Taipei Tzuchi Hospital, Buddhist Tzuchi Medical Foundation, New Taipei City, Taiwan author Tsai, Kuei-Ton Cardiovascular Surgery, Taipei Tzuchi Hospital, Buddhist Tzuchi Medical Foundation, New Taipei City, Taiwan author Hu, Chin-Yuan 2016-04-08 2016-04-08 2016 Research Ideas and Outcomes 2367-7163 2 e8758 2016 10.1510/icvts.2010.232546 10.1186/1477-7819-10-123 10.1378/chest.125.4.1328 10.4061/2011/197838 10.1016/1010-7940(91)90189-Q 10.1016/j.amjcard.2013.05.066 10.1016/j.rmr.2014.02.011 10.4065/75.3.248 10.1016/j.jtcvs.2010.09.015 10.3897/rio.2.e8758 https://riojournal.com/article/8758/ https://riojournal.com/article/8758/download/pdf/ https://riojournal.com/article/8758/download/xml/ text/html en_US Pensoft Publishers pericardial window malignant pericardial effusion (MPE) lung cancer Pericardial window operation for malignant pericardial effusion may have worse outcomes for lung cancer than the other cancers Research Article

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

California Digital Library, University of California Curation Center, Oakland, United States of America author Abrams, Stephen Harvard University, Cambridge, United States of America author Goethals, Andrea University of California, Los Angeles, United States of America author Klein, Martin California Digital Library, University of California Curation Center, Oakland, United States of America author Lack, Rosalie 2016-04-12 2016-04-12 2016 Research Ideas and Outcomes 2367-7163 2 e8760 2016 10.3897/rio.2.e8760 https://riojournal.com/article/8760/ https://riojournal.com/article/8760/download/pdf/ https://riojournal.com/article/8760/download/xml/ text/html en_US Pensoft Publishers web archives collection development digital library Cobweb: A Collaborative Collection Development Platform for Web Archiving Small Grant Proposal

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

Stony Brook University, Stony Brook, United States of America author Klein, Arno https://orcid.org/0000-0002-0707-2889 Columbia University, New York, United States of America author Ellis, Steven 2016-04-13 2016-04-13 2016 Research Ideas and Outcomes 2367-7163 2 e8815 2016 H. Abelson author 1984 Structure and Interpretation of Computer Programs 1984 10.1002/9781119970583 10.1137/1.9780898719246 10.1016/0169-7439(95)80060-m Centers for Disease Control and Prevention. National Center for Injury Prevention and Control, Webbased Injury Statistics Query and Reporting System (WISQARS) CDCP author text www.cdc.gov/injury/wisqars/index.html 10.1371/journal.pcbi.1000205 10.1198/jasa.2009.tm08439 Herbert Edelsbrunner author 2010 Computational Topology: An Introduction 2010 Describing high-order statistical dependence using “concurrence topology”, with application to functional MRI brain data Steven P. Ellis author 2012 text Homology, Homotopy and Applications http://arxiv.org/abs/1212.1642 2012 16 245 264 Trevor Hastie author 2001 The Elements of Statistical Learning: Data Mining, Inference, and Prediction 2001 Exploring the brain network: A review on restingstate fMRI functional connectivity Martijn P van den Heuvel author 2010 text European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology 2010 20 8 519 534 Aapo Hyvarinen author 2001 Independent Component Analysis 2001 The under-recognized public health crisis of suicide T. Insel author text http://www.nimh.nih.gov/about/director/2010/the-under-recognized-publichealth- crisis-of-suicide.shtml 10.1016/j.biopsych.2009.10.008 P. Jezzard author 2002 Functional MRI: An Introduction to Methods 2002 10.3389/fnins.2012.00171 A Klein author 2011 Mindboggle - A neuroinformatics framework for automated anatomical labeling and shape analysis of brain images 2011 1 A Klein author 2011 Mindboggle - An informatics framework for open research in quantifying the shape of the human brain 2011 1 A Klein author 2011 Automated extraction of nested sulcal features from human brain MRI data 2011 1 N Lee author 2011 A graph-based database of hierarchical brain features 2011 1 J. R. Munkres author 1984 Elements of Algebraic Topology 1984 10.1002/wcs.58 10.1002/hbm.20531 10.3897/rio.2.e8815 https://riojournal.com/article/8815/ https://riojournal.com/article/8815/download/pdf/ https://riojournal.com/article/8815/download/xml/ 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. text/html en_US Pensoft Publishers concurrence topology homology brain imaging adhd high-order dependence statistical analysis Concurrence Topology: Finding High-Order Dependence in Neuropsychiatric Data NIH Grant Proposal

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

New School University, New York, United States of America author Klein, Arno https://orcid.org/0000-0002-0707-2889 2016-04-13 2016-04-13 2016 Research Ideas and Outcomes 2367-7163 2 e8814 2016 10.1145/985692.985733 J. Bertin author 1983 Semiology of Graphics 1983 A. F. Blackwell author M. Anderson author 1999 Diagrammatic Representation and Reasoning. London: Springer-Verlag 1999 109-123 10.1109/infvis.2000.885092 10.1109/visual.2004.10 Evaluating models of visual comprehension M. E. Foster author 2003 text Proc. of Eurocogsci '03, The European Cognitive Science Conference 2003 2003 115 6 10.1109/infvis.2004.1 L. Itti author 2006 Advances in Neural Information Processing Systems (NIPS*2005) 2006 19 1-8 10.1109/visual.1990.146374 10.1145/22949.22950 10.1518/hfes.45.1.28.27225 10.1109/visual.1993.398874 10.1145/968363.968368 B. Shneiderman author 1996 The eyes have it: a task by data type taxonomy for information visualizations 1996 336-343 Rethinking visualization: a high-level taxonomy M. Tory author 2004 text Proc. of the IEEE Symp. on Information Visualization 2004 (InfoVis 2004) 2004 151-158 10.1109/visual.2005.1532836 10.1109/visual.1990.146375 10.1109/wsc.2003.1261489 The alignment framework for data visualization: relationships among research goals, data types, and multivariate visualization techniques C. H. Yu author 1995 text Annual Meeting of the American Psychological Society 1995 27 264 271 10.1006/ijhc.1996.0042 10.1145/274644.274698 10.1109/infvis.2002.1173143 10.1147/sj.413.0504 10.3897/rio.2.e8814 https://riojournal.com/article/8814/ https://riojournal.com/article/8814/download/pdf/ https://riojournal.com/article/8814/download/xml/ 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. text/html en_US Pensoft Publishers eye tracking eye movements  visualization information graphics Data-Visual Relationships to Subject Performance and Eye Movements NSF Grant Proposal

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

Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, Uppsala, Sweden author Angeler, David Nebraska Cooperative Fish and Wildlife Unit, School of Natural Resources, University of Nebraska – Lincoln, Lincoln, United States of America author Sundstrom, Shana U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Unit, School of Natural Resources, University of Nebraska -Lincoln, Lincoln, United States of America author Allen, Craig 2016-04-14 2016-04-14 2016 Research Ideas and Outcomes 2367-7163 2 e8796 2016 10.1007/s10021-013-9744-2 Sesame Street breaks Iraqi POWs BBC author text http://news.bbc.co.uk/go/pr/fr/-/2/hi/middle_east/3042907.stm 10.1017/cbo9780511541957 10.1080/14797585.2011.594579 D. Kahneman author 2011 Thinking, Fast and Slow 2011 512 K. Kahn-Harris author 2007 Extreme Metal: Music and Culture on the Edge 2007 224 10.1093/jxb/erp043 Planetary boundaries: exploring the safe operating space for humanity J. Rockström author 2009 text Ecology and Society 2009 14 32 L. J. Savage author 1954 The foundations of statistics 1954 310 10.1073/pnas.1404649111 10.5751/es-07434-200203 A. White author 2009 From Comfort Zone to Performance Management 2009 20 10.1890/070037 10.3897/rio.2.e8796 https://riojournal.com/article/8796/ https://riojournal.com/article/8796/download/pdf/ https://riojournal.com/article/8796/download/xml/ text/html en_US Pensoft Publishers science art music religion creativity inductivism scientific process Deathcore, creativity, and scientific thinking Research Idea

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

Cardiovascular Surgery, Taipei Tzuchi Hospital, New Taipei City, Taiwan author Chen, Robert https://orcid.org/0000-0001-6892-0602 Periodontology, Tuft University School of Dental Medicine, Boston, MA, United States of America author Yu, Yau-Hua 2016-04-14 2016-04-14 2016 Research Ideas and Outcomes 2367-7163 2 e8801 2016 10.1038/452406a 10.1093/bioinformatics/btn336 10.1016/j.ejcts.2008.03.032 10.1634/stemcells.2007-0821 10.1161/CIRCULATIONAHA.108.778795 10.1161/circulationaha.108.769562 Stem-cell-based therapy and lessons from the heart Robert Passier author 2008 text Nature https://doi.org/10.1038/nature07040 2008 453 7193 322 329 Recent advances using stem cell-derived cardiac and vascular cells for cardiomyoplasty , H. Sauer author 2008 text Xenotransplantation https://doi.org/10.1111/j.1399-3089.2008.00488_14.x 2008 15 5 306 306 10.1634/stemcells.2008-0033 10.1161/circresaha.107.169334 10.1016/j.ejcts.2008.03.067 10.1161/CIRCRESAHA.108.179994 10.1161/circulationaha.108.791442 10.1093/bioinformatics/btn277 10.3897/rio.2.e8801 https://riojournal.com/article/8801/ https://riojournal.com/article/8801/download/pdf/ https://riojournal.com/article/8801/download/xml/ text/html en_US Pensoft Publishers induced pluripotent stem (iPS) cells nucleostemin Ingenuity Pathway Analysis Induced pluripotent stem (iPS) cells and somatic cardiac regeneration — An exploratory bioinformatic analysis Conference Abstract

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

Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, Uppsala, Sweden author Angeler, David Nebraska Cooperative Fish and Wildlife Unit, School of Natural Resources, University of Nebraska – Lincoln, Lincoln, United States of America author Sundstrom, Shana U.S. Geological Survey, Nebraska Cooperative Fish and Wildlife Unit, School of Natural Resources, University of Nebraska -Lincoln, Lincoln, United States of America author Allen, Craig 2016-04-15 2016-04-15 2016 Research Ideas and Outcomes 2367-7163 2 e8867 2016 10.1007/s10021-013-9744-2 Sesame Street breaks Iraqi POWs BBC author text http://news.bbc.co.uk/go/pr/fr/-/2/hi/middle_east/3042907.stm 10.1017/cbo9780511541957 10.1080/14797585.2011.594579 D. Kahneman author 2011 Thinking, Fast and Slow 2011 512 K. Kahn-Harris author 2007 Extreme Metal: Music and Culture on the Edge 2007 224 10.1093/jxb/erp043 Planetary boundaries: exploring the safe operating space for humanity J. Rockström author 2009 text Ecology and Society 2009 14 32 L. J. Savage author 1954 The foundations of statistics 1954 310 10.1073/pnas.1404649111 10.5751/es-07434-200203 A. White author 2009 From Comfort Zone to Performance Management 2009 20 10.1890/070037 10.3897/rio.2.e8867 https://riojournal.com/article/8867/ https://riojournal.com/article/8867/download/pdf/ https://riojournal.com/article/8867/download/xml/ text/html en_US Pensoft Publishers science art music religion creativity inductivism scientific process Deathcore, creativity, and scientific thinking Research Idea

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

Columbia University, New York, United States of America author Klein, Arno https://orcid.org/0000-0002-0707-2889 2016-04-15 2016-04-15 2016 Research Ideas and Outcomes 2367-7163 2 e8813 2016 10.1016/j.imavis.2006.06.020 10.1016/j.neuroimage.2006.05.061 10.1007/3-540-45787-9_74 10.1007/3-540-45468-3_31 10.1109/tmi.2003.816961 10.1016/0167-8191(94)00071-h Bayesian Modeling of Facial Similarity Baback Moghaddam author 1998 text Advances in Neural Information Processing Systems 1998 11 910 916 10.1016/j.imavis.2004.06.007 10.1007/11907350_51 10.1109/tmi.2004.828354 10.3897/rio.2.e8813 https://riojournal.com/article/8813/ https://riojournal.com/article/8813/download/pdf/ https://riojournal.com/article/8813/download/xml/ text/html en_US Pensoft Publishers informatics neuroinformatics Collection of informatics proposals from 2007 Research Idea

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

University of California, San Diego, United States of America author McWhorter, Jennifer University of California, San Diego, United States of America author Wright, Darren University of California, San Diego, United States of America author Thomas, Julie 2016-04-15 2016-04-15 2016 Research Ideas and Outcomes 2367-7163 2 e8827 2016 10.3897/rio.2.e8827 https://riojournal.com/article/8827/ https://riojournal.com/article/8827/download/pdf/ https://riojournal.com/article/8827/download/xml/ text/html en_US Pensoft Publishers waves data quality control real-time long-term time series sea-surface temperature Coastal Data Information Program (CDIP) Data Management Plan (NSF Generic)

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

Centre for Culture and Technology, Curtin University, Perth, Australia author Neylon, Cameron https://orcid.org/0000-0002-0068-716X University of Toronto, Toronto, Canada author Chan, Leslie https://orcid.org/0000-0001-7779-2059 2016-04-18 2016-04-18 2016 Research Ideas and Outcomes 2367-7163 2 e8880 2016 10.1002/asi.22634 10.5281/ZENODO.27872 Open Definition v2.0 Open Knowledge author text http://opendefinition.org/od/2.0/en/ 10.1007/978-3-319-00026-8_14 Science as an Open Enterprise Royal Society author text https://royalsociety.org/topics-policy/projects/science-public-enterprise/report/ 10.1016/s0140-6736(10)62234-9 10.3897/rio.2.e8880 https://riojournal.com/article/8880/ https://riojournal.com/article/8880/download/pdf/ https://riojournal.com/article/8880/download/xml/ text/html en_US Pensoft Publishers data sharing research data management development data management plan research policy mandate Exploring the opportunities and challenges of implementing open research strategies within development institutions Grant Proposal

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

Sage Bionetworks, Seattle, United States of America author Klein, Arno https://orcid.org/0000-0002-0707-2889 MIT, Cambridge, United States of America author Ghosh, Satrajit https://orcid.org/0000-0002-5312-6729 2016-04-18 2016-04-18 2016 Research Ideas and Outcomes 2367-7163 2 e8812 2016 10.3897/rio.2.e8812 https://riojournal.com/article/8812/ https://riojournal.com/article/8812/download/pdf/ https://riojournal.com/article/8812/download/xml/ text/html en_US Pensoft Publishers brain imaging data mining A Million Brains in the Cloud Research Idea

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

Sage Bionetworks, Seattle, United States of America author Klein, Arno https://orcid.org/0000-0002-0707-2889 2016-04-19 2016-04-19 2016 Research Ideas and Outcomes 2367-7163 2 e8816 2016 10.1016/j.neuroimage.2013.08.067 10.1007/s00429-005-0025-5 10.1126/science.1235381 10.1016/0006-3223(94)91023-5 10.1126/science.1152882 10.1016/0197-4580(95)00021-6 K. Brodmann author 1909 Vergleichende Lokalisationslehre der Grosshirnrinde 1909 ? CogSci2011 attendees author 2011 CogSci2011 workshop: "How to use Mechanical Turk for Cognitive Science Research" http://cognitivesciencesociety.org/uploads/2011-t4.pdf 2011 ? 10.1145/1822348.1822354 10.1046/j.1528-1157.2003.00448.x 10.1002/cne.23786 H. M. Duvernoy author 1999 The Human Brain: Surface, Three-Dimensional Sectional Anatomy with MRI, and Blood Supply 1999 ? 10.1038/nbt.2109 10.1038/nsmb.2119 10.1016/j.neuroimage.2008.12.037 10.1117/12.844182 BigBrain: Initial Tissue Classification and Surface Extraction L. Lewis author 2014 text 2 0th Annual Meeting of the Organization for Human Brain Mapping (Hamburg, Germany) 2014 1 1 10.2174/187152706778559273 Online Gamers Achieve First Crowd-Sourced Redesign of Protein Jessica Marshall author 2012 text Scientific American 2012 ? ? 10.3758/s13428-011-0124-6 10.1016/j.conb.2006.03.013 10.3389/fninf.2014.00054 10.1038/nrn3085 10.3389/fninf.2013.00027 10.1016/j.neurobiolaging.2003.12.005 10.1002/hipo.20779 10.1016/j.neuroimage.2015.01.004 10.3897/rio.2.e8816 https://riojournal.com/article/8816/ https://riojournal.com/article/8816/download/pdf/ https://riojournal.com/article/8816/download/xml/ 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. text/html en_US Pensoft Publishers BigBrain brain imaging histology microstructure neurons crowdsourcing game gamify A game for crowdsourcing the segmentation of BigBrain data NIH Grant Proposal

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

Columbia Unversity, New York, United States of America author Klein, Arno https://orcid.org/0000-0002-0707-2889 2016-04-19 2016-04-19 2016 Research Ideas and Outcomes 2367-7163 2 e8817 2016 10.1093/brain/120.2.257 10.1016/j.neuroimage.2007.08.049 10.1093/cercor/bhm180 10.1093/brain/awn137 10.1002/ajmg.1569 10.1016/j.tins.2007.12.004 10.1016/j.biopsych.2004.04.007 10.1210/er.17.2.187 10.1093/cercor/bhp127 10.1093/cercor/bhs292 10.1016/j.neuroimage.2011.04.062 Topological morphing using Reeb graphs P. Kanonchayos author 2002 text Proceedings of the First International Symposium on Cyber Worlds 2002 3.2 465 471 10.1109/tmi.2006.886810 10.3174/ajnr.a1417 10.1016/j.neuroimage.2008.12.037 10.1007/978-3-540-85988-8_33 10.1016/s1361-8415(00)00024-4 10.1093/cercor/bhm174 10.1097/wco.0b013e32833a0afc 10.1002/jmri.22806 10.1111/j.1399-5618.2009.00683.x 10.1006/nimg.2001.0975 10.1016/j.cad.2009.02.007 10.1016/j.neuroimage.2010.02.020 10.1176/appi.ajp.160.9.1606 10.1007/s11910-003-0027-8 10.1016/j.biopsych.2007.04.012 10.1176/appi.ajp.163.1.28 10.1523/jneurosci.4154-05.2006 10.1115/1.4001683 10.3897/rio.2.e8817 https://riojournal.com/article/8817/ https://riojournal.com/article/8817/download/pdf/ https://riojournal.com/article/8817/download/xml/ 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. text/html en_US Pensoft Publishers brain imaging graphical display interface interactive GUI Brain Graph Interface NIH Grant Proposal

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

University of Stuttgart, Stuttgart, Germany author Graziotin, Daniel https://orcid.org/0000-0002-9107-7681 2016-04-20 2016-04-20 2016 Research Ideas and Outcomes 2367-7163 2 e8865 2016 John W Creswell author 2009 Research design: qualitative, quantitative, and mixed method approaches 2009 246 10.1109/MS.2008.129 Total quality control A. V. Feigenbaum author 1956 text Harvard Business Review 1956 43 6 93 101 Arlene Fink author 2003 The Survey Handbook 2003 184 10.1145/1806799.1806828 10.1177/1094428113518348 10.7717/peerj.289 10.1002/smr.1673 10.1145/2804381.2804386 10.7717/peerj-cs.18 10.1007/s10664-013-9268-6 10.1109/TSE.2012.70 10.1109/52.476281 10.1109/ICSE.2007.45 10.1177/2158244015601719 10.1016/j.jss.2015.04.084 10.1111/j.1365-2702.2006.01573.x 10.1109/ICSE.2015.82 10.1002/asi.5090130405 10.1177/1077800411409884 10.3897/rio.1.e7576 10.1109/52.896249 10.1109/MC.2003.1204373 T D Wilson author 1994 Information needs and uses: fifty years of progress? 1994 15-51 10.1001/jama.2013.281053 10.3897/rio.2.e8865 https://riojournal.com/article/8865/ https://riojournal.com/article/8865/download/pdf/ https://riojournal.com/article/8865/download/xml/ 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. text/html en_US Pensoft Publishers information needs software quality process theory affective reactions behavioral patterns Software quality information needs Grant Proposal

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

Kodolányi János University of Applied Sciences, Budapest, Hungary author Toth, Janos 2016-04-20 2016-04-20 2016 Research Ideas and Outcomes 2367-7163 2 e8861 2016 Robin Cohen author 2008 Global Diasporas. An introduction. 978-0-203-92894-3 2008 219 10.1353/dsp.1991.0004 10.3897/rio.2.e8861 https://riojournal.com/article/8861/ https://riojournal.com/article/8861/download/pdf/ https://riojournal.com/article/8861/download/xml/ 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. text/html en_US Pensoft Publishers Diaspora Research Hungarian Diaspora National Identity National Policy Planning Historical analysis of strategies for assimilation and identity maintenance in dispersed groups of overseas Hungarians and their relevance regarding national policy planning Small Grant Proposal

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

Columbia University, New York, United States of America author Klein, Arno https://orcid.org/0000-0002-0707-2889 MIT, Cambridge, United States of America author Ghosh, Satrajit https://orcid.org/0000-0002-5312-6729 2016-04-21 2016-04-21 2016 Research Ideas and Outcomes 2367-7163 2 e8835 2016 10.1016/j.socnet.2010.03.006 10.1016/j.neuroimage.2006.09.018 10.1038/nrn2618 10.1097/01.wnr.0000174407.09515.cc 10.1016/j.biopsych.2006.09.018 10.1016/s1053-8119(01)91441-7 10.1016/s1053-8119(01)91491-0 10.1006/nimg.1998.0396 10.1176/ajp.2007.164.4.599 10.1007/978-1-84996-290-2_2 10.1037/0735-7044.121.3.602 10.1093/cercor/bhp127 10.1016/j.biopsych.2009.10.008 10.1001/archgenpsychiatry.2009.62 10.1016/j.biopsych.2009.04.036 10.1007/978-3-540-85988-8_33 10.1016/s1361-8415(00)00024-4 10.1093/cercor/bhm174 10.1109/ICCV.1999.790410 10.1023/b:visi.0000029664.99615.94 10.1016/j.biopsych.2009.02.031 10.1177/002221940103400607 10.1176/appi.ajp.2008.07101682 10.1001/archpsyc.62.7.761 10.1006/nimg.2001.0975 10.1109/tmi.2006.886810 10.1371/journal.pone.0001049 10.1002/hbm.20210 SIFT-Rank: Ordinal description for invariant feature correspondence M. Toews author 2009 text IEEE Conference on Computer Vision and Pattern Recognition. 2009 10.1371/journal.pbio.0060159 10.1016/j.biopsych.2005.11.013 10.1016/j.neuroimage.2009.12.027 10.3897/rio.2.e8835 https://riojournal.com/article/8835/ https://riojournal.com/article/8835/download/pdf/ https://riojournal.com/article/8835/download/xml/ 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. text/html en_US Pensoft Publishers graphs brain imaging multimodal data Graph-based clinical diagnosis and prediction using multi-modal neuroimaging data NIH Grant Proposal

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

Cardiovascular Surgery, Taipei Tzuchi Hospital, Tzuchi University College of Medicine, Buddhist Tzuchi Medical Foundation, New Taipei City, Taiwan author Chen, Robert https://orcid.org/0000-0001-6892-0602 2016-04-21 2016-04-21 2016 Research Ideas and Outcomes 2367-7163 2 e8849 2016 10.1016/j.cardfail.2012.01.008 10.1093/eurjhf/hfr156 10.1586/erm.10.25 10.1016/j.cardfail.2008.06.415 10.1093/eurjhf/hfs006 10.1373/clinchem.2012.191106 10.1016/j.ahj.2010.06.033 10.1016/j.cca.2009.08.010 10.1016/j.jacc.2008.07.045 10.1016/j.jchf.2013.10.005 10.2174/1875318301205010001 10.1007/s12265-013-9459-y 10.1161/CIRCHEARTFAILURE.110.958223 10.1016/j.mayocp.2012.09.016 10.1016/j.amjcard.2010.09.011 10.1159/000338800 10.1016/j.jacc.2009.08.049 10.1586/erm.12.128 10.1373/clinchem.2007.096560 10.1093/eurjhf/hfr047 10.1016/j.jacc.2009.07.041 10.1016/j.athoracsur.2011.07.048 10.1016/j.jacc.2008.07.042 10.1161/CIRCULATIONAHA.107.728022 10.1172/JCI30634 10.1093/eurjhf/hfs130 10.1016/j.immuni.2005.09.015 10.1007/s11897-010-0005-9 10.1161/CIRCHEARTFAILURE.108.833707 10.1016/j.cardfail.2013.01.010 10.1161/01.CIR.0000047274.66749.FE 10.1161/01.CIR.0000038705.69871.D9 10.1016/j.jacc.2009.08.047 10.1111/eci.12022 10.5114/aoms.2013.33344 10.1161/CIR.0b013e31829e8776 10.3897/rio.2.e8849 https://riojournal.com/article/8849/ https://riojournal.com/article/8849/download/pdf/ https://riojournal.com/article/8849/download/xml/ 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. text/html en_US Pensoft Publishers ST2 NT-proBNP heart failure troponin-T biomarker Clinical roles of soluble ST2 for the outcomes of cardiac valve operations Small Grant Proposal

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

Sage Bionetworks, Seattle, United States of America author Klein, Arno https://orcid.org/0000-0002-0707-2889 2016-04-22 2016-04-22 2016 Research Ideas and Outcomes 2367-7163 2 e8848 2016 10.1371/journal.pone.0031461 High-accuracy discrimination of Parkinson’s disease participants from healthy controls using smartphones. S. Arora author 2013 text Movement Disorders 2013 28 10 e12 10.1093/pan/mpr057 Error driven paraphrase annotation using mechanical turk. Olivia Buzek author 2010 text Proceedings of the NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon’s Mechanical Turk. 2010 10.3115/1699510.1699548 Creating speech and language data with amazon’s mechanical turk. Chris Callison-Burch author 2010 text Proceedings of the NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon’s Mechanical Turk. 2010 10.3758/s13428-013-0365-7 10.1145/1837885.1837889 10.1371/journal.pone.0057410 Exploring normalization techniques for human judgments of machine translation adequacy collected using amazon mechanical turk. Michael Denkowski author 2010 text Proceedings of the NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon’s Mechanical Turk. 2010 10.1002/bdm.1753 10.1007/s10683-011-9273-9 Real user evaluation of spoken dialogue systems using amazon mechanical turk. Filip Jurcicek author 2011 text Proceedings of INTERSPEECH. 2011 11 10.1016/j.specom.2009.08.009 10.1145/1357054.1357127 10.3758/s13428-011-0124-6 How to use Mechanical Turk for Cognitive Science Research W. A. Mason author text http://cognitivesciencesociety.org/uploads/2011-t4.pdf Running experiments on Amazon Mechanical Turk. G. Paolacci author 2010 text Judgment and Decision Making 2010 5 411 419 10.1002/mds.10248 10.1145/2390803.2390808 10.4018/ijswis.2013070102 10.1177/2167702612469015 10.1111/j.1749-6632.2009.04497.x 10.1145/1998549.1998550 10.1212/wnl.0b013e31822c9123 10.2196/jmir.2426 10.3897/rio.2.e8848 https://riojournal.com/article/8848/ https://riojournal.com/article/8848/download/pdf/ https://riojournal.com/article/8848/download/xml/ 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. text/html en_US Pensoft Publishers mPower Parkinson disease mobile health app voice analysis features crowdsourcing annotation Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease NIH Grant Proposal

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

Tilburg University, Tilburg, Netherlands author Hartgerink, Chris https://orcid.org/0000-0003-1050-6809 Tilburg University, Tilburg, Netherlands author Wicherts, Jelte Utrecht University, Utrech, Netherlands Tilburg University, Tilburg, Netherlands author van Assen, Marcel 2016-04-22 2016-04-22 2016 Research Ideas and Outcomes 2367-7163 2 e8860 2016 The Law of Anomalous Numbers F. Benford author 1938 text Proceedings of the American Philosophical Society 1938 78 4 551 572 10.1007/s11192-007-1950-2 Bruce D Burns author 2009 Sensitivity to statistical regularities: People (largely) follow Benford’s law 2009 2872-2877 10.1002/(sici)1097-0258(19991230)18:243.0.co;2-o 10.1111/j.1365-2044.2012.07128.x 10.1111/anae.13126 10.1096/fj.11-183988 10.1093/pan/mpr014 10.1080/02664760601004940 Many Labs 3: Evaluating participant pool quality across the academic semester via replication Charles Ebersole author 2016 text Journal of Experimental Social Psychology 2016 NA NA 10.1371/journal.pone.0005738 R. A. Fisher author 1925 Statistical Methods for Research Workers 1925 NA 10.1371/journal.pone.0127502 Flawed science: The fraudulent research practices of social psychologist Diederik Stapel Levelt Committee author text https://www.commissielevelt.nl/ 10.1111/anae.13165 10.1080/03610919608813325 10.1080/08989629508573866 10.1080/08989620212969 10.1045/november14-murray-rust 10.3758/s13428-015-0664-2 B. Rihoux author 2009 Configurational comparative methods: Qualitative comparative analysis (QCA) and related techniques 2009 NA 10.1111/j.1467-9280.2008.02128.x 10.1177/0956797613480366 10.1037/h0054651 10.1371/journal.pone.0114876 10.1016/j.paid.2015.01.024 10.1038/480007a Dynamic documents with R and knitr Y. Xie author 2014 text Journal of Statistical Software 2014 56 NA S. Yamasaki author B. Rihoux author 2009 Configurational Comparative Methods: Qualitative Comparative Analysis (QCA) and related techniques 2009 10.3897/rio.2.e8860 https://riojournal.com/article/8860/ https://riojournal.com/article/8860/download/pdf/ https://riojournal.com/article/8860/download/xml/ 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. text/html en_US Pensoft Publishers data fabrication statistics scientific misconduct integrity The value of statistical tools to detect data fabrication Small Grant Proposal

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

Baruch College, New York, United States of America author Romero Jr., Aldemaro https://orcid.org/https://orcid.org/0000-0002-0409-5241 2016-04-27 2016-04-27 2016 Research Ideas and Outcomes 2367-7163 2 e9015 2016 T. A Appel author 1987 The Cuvier-Geoffroy debate: French biology in the decades before Darwin. 1987 306 10.1007/978-94-015-9259-8_13 L. S. Berg author 1926 Nomogenesis; or, evolution determined by law 1926 477 F. Bourdier author C. C. Gilliespie author 1972 Dictionary of Scientific Biography 1972 5 10.4159/harvard.9780674731363 R. Bushman author 1967 From Puritan to Yankee: character and the social order in Connecticut, 1690-1765. 1967 343 J. -A. N. de C. Condorcet author 1802 Outlines of an historical view of the progress of the human mind being a posthumous work of the late M. de Condorcet. 1802 398 L. Cuénot author 1911 La genesis de las especes animals 1911 284 F. Darwin author 1896 The life and letters of Charles Darwin 1896 576 T. de Chardin author 1955 Le phénomè humain 1955 318 C. de Duve author 1995 Vital dust: life as a cosmic imperative 1995 362 D. de Valencia author 1984 Isaac Vazquez Janeiro, Tratados castellanos sobre la predestinación y sobre la Trinidad y la Encarnación, del Maestro Fray Diego de Valencia OFM (siglo XV). Identificación de su autoría y edición crítica (coll. Bibliotheca Theologica Hispana - Textos, 2) 1984 184 10.5962/bhl.title.1350 T. Eskola author 1998 Theodicy and Predestination in Pauline Soteriology 1998 353 10.1093/jts/XXXIII.1.134 Knowledge, fortune and predestination concerning the discovery of America J. L. Fuertes Herreros author 1992 text Arbor: Ciencia, Pensamiento y Cultura 1992 143 133 160 F. García Martínez author 1999 The Dead Sea Scrolls. Study Edition 1999 1389 10.1111/j.1465-7295.1998.tb01724.x 10.1177/09526950122120989 C. Grimoult author 1998 Évolutionnisme et fixisme en France. Histoire d’un combat 1800-1882 1998 184 W. Haacke author 1893 Gestaltung und Vererbung. Eine Entwicklungsmechanik des Organismus 1893 312 10.1086/649301 10.1007/s10739-004-6509-y M. Howard author 1981 The Franco-Prussian War: The German invasion of France, 1870-1871 1981 536 S. Innes author 1996 Creating the Commonwealth: the economic culture of Puritan New England 1996 416 F. A. James III author 1998 Peter Martyr Vermigli and predestination 1998 304 R. G. Jeannel author 1950 La marche de l’evolution 1950 171 D. H. Kenyon author 1969 Biochemical Predestination 1969 301 10.1093/acprof:oso/9780195308969.001.0001 10.1177/016001799761012307 A. Lange author 1995 Weisheit und Prädestination: Weisheitliche Urordnung und Prädestination in den Textfunden von Qumran 1995 345 E. H. Merrill author 1975 Qumran and predestination: A theological study of the thanksgiving hymns. 1975 71 Emil G. Racovitza: Founder of biospeleology C. Motas author 1962 text National Speleological Society Bulletin 1962 24 3 8 H. F. Osborn author 1934 Aristogenesis, the creative principle in the origin of species 1934 9 Thomas Paine Addresses Calvinist Clergy on Predestination Thomas Paine author text http://www.deism.com/paine_essay_predestination_calvinism.htm L. Plate author 1913 Selektionsprinzip und Probleme der Artbildung.Ein Handbuch des Darwinismus. 1913 650 E. Rabaud author 1941 Introduction aux sciences biologiques 1941 214 Can evolution regress? A. Romero author 1985 text National Speleological Society Bulletin 1985 47 86 88 Between the first blind cave fish and the last of the Mohicans: the scientific romanticism of James E. DeKay A. Romero author 2002 text Journal of Spelean History 2002 36 19 29 10.1017/CBO9780511596841 10.1111/j.0022-1112.2005.00776.x 10.3897/rio.2.e9015 https://riojournal.com/article/9015/ https://riojournal.com/article/9015/download/pdf/ https://riojournal.com/article/9015/download/xml/ text/html en_US Pensoft Publishers predetermination science and religion biological evolution biospeleology cave biology history of science The influence of religion on science: the case of the idea of predestination in biospeleology Research Article

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

Sage Bionetworks, Seattle, United States of America author Klein, Arno https://orcid.org/0000-0002-0707-2889 2016-05-03 2016-05-03 2016 Research Ideas and Outcomes 2367-7163 2 e8834 2016 Node: A Real Time Smartphone Big Data Application for Health Care Epidemiology S. Abiola author 2013 text Princeton University Senior Theses http://arks.princeton.edu/ark:/88435/dsp01sx61dm401 2013 1 1 High-accuracy discrimination of Parkinson’s disease participants from healthy controls using smartphones S. Arora author 2013 text Movement Disorders 2013 28 10 e12 Prevalence of Parkinson's disease in the Parsi community of Bombay, India NE Bharucha author 1988 text Arch. Neurol. http://archneur.jamanetwork.com/article.aspx?articleid=588311 1988 45 12 1321 1323 10.1159/000080090 Neurology: the scenario in India S. V. Khadilkar author 2012 text J Assoc Physicians India http://www.japi.org/january_2012/07_neurology_the_scenario.pdf 2012 60 42 44 New Approaches to Image-based Research and Visual Literacy: A Pilot Project Report. New Horizons in Visual Literacy: Selected Readings of the International Visual Literacy Association S McMaster author text http://www.academia.edu/1487179/New_Approaches_to_Image-based_Research_and_Visual_Literacy 10.2188/jea.je20081034 India had third largest smartphone base with 117M users in 2013; to grow 45% in 2014: Mary Meeker Report A Rai author text http://techcircle.vccircle.com/2014/05/29/india-had-third-largest-smartphone-base-with-117m-users-in-2013-to-grow-45-in-2014-mary-meeker-report/ 10.1002/mds.10248 10.3897/rio.2.e8834 https://riojournal.com/article/8834/ https://riojournal.com/article/8834/download/pdf/ https://riojournal.com/article/8834/download/xml/ 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. text/html en_US Pensoft Publishers Parkinson disease UPDRS visual rating scale iconographic representation Visual Parkinson’s Disease Rating Scale: A Universal Iconic Questionnaire for Epidemiological Studies in India NIH Grant Proposal

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

Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany author Heuer, Katja MIT, Cambridge, United States of America author Ghosh, Satrajit https://orcid.org/0000-0002-5312-6729 EyeWire, Cambridge, United States of America author Robinson Sterling, Amy Institut Pasteur, Paris, France author Toro, Roberto https://orcid.org/0000-0002-6671-858X 2016-05-08 2016-05-08 2016 Research Ideas and Outcomes 2367-7163 2 e9113 2016 10.3897/rio.2.e9113 https://riojournal.com/article/9113/ https://riojournal.com/article/9113/download/pdf/ https://riojournal.com/article/9113/download/xml/ text/html en_US Pensoft Publishers Neuroimaging Collaboration Open Science Co-edition Open Science Prize Magnetic Resonance Imaging Segmentation Open Neuroimaging Laboratory Small Grant Proposal

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

Boston Universit, Boston, United States of America author Vyshedskiy, Andrey https://orcid.org/0000-0002-1610-8716 Brigham and Women’s / Faulkner Hospitals, Boston, United States of America author Murphy, Raymond 2016-05-11 2016-05-11 2016 Research Ideas and Outcomes 2367-7163 2 e9173 2016 10.1155/2012/139395 10.3897/rio.2.e9173 https://riojournal.com/article/9173/ https://riojournal.com/article/9173/download/pdf/ https://riojournal.com/article/9173/download/xml/ text/html en_US Pensoft Publishers STG16 lung sounds multichannel lung sound COPD Acoustic biomarkers of Chronic Obstructive Lung Disease Research Poster

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

University of Jyväskylä, Jyväskylä, Finland author Neittanmäki, Pekka Finnish Environment Institute, Jyväskylä, Finland author Huttula, Timo University of Jyväskylä, Jyväskylä, Finland author Karvanen, Juha Pirkanmaa Centre for Economic Development, Transport and the Environment, Tampere, Finland author Frisk, Tom National Institute for Helth and Welfare, Kuopio, Finland author Tuomisto, Jouni VATT Institute for Economic Research, Helsinki, Finland author Simola, Antti University of Jyväskylä, Jyväskylä, Finland author Tuovinen, Tero Finnish Environment Institute, Jyväskylä, Finland author Ropponen, Janne 2016-05-16 2016-05-16 2016 Research Ideas and Outcomes 2367-7163 2 e9232 2016 MMRF-Green: a dynamic multi-regional applied general equilibrium model of the Australian economoy, based on the MMR and MONASH models. Centre of Policy Studies Working Papers (140) P. Adams author 2003 text Centre of Policy Studies Working Papers 2003 140 M. Airaksinen author 2015 18th Annual Conference on Global Economic Analysis 2015 10.1108/s0573-8555(2001)256 10.1093/acprof:oso/9780199641178.001.0001 10.5194/hess-8-717-2004 10.1002/env.2204 Kalman Filter and Smoother for Exponential Family State Space Models.R package version 1.1.1 J. Helske author 2015 text http://cran.r-project.org/web/packages/KFAS/index.html 2015 10.2139/ssrn.2284665 J. Honkatukia author 2011 VATT Research Reports 2011 10.1016/j.jpolmod.2005.01.008 10.1007/s10666-015-9470-6 R. K. Hydman author 2008 Forecasting with exponential smoothing. The state space approach 2008 forecast:Forecasting functions for time series and linear models R package version 5.9 R. Hyndman author 2015 text Forecast http://CRAN.R-project.org/package=forecast 2015 10.1007/s00267-015-0514-0 COHERENS — A coupled Hydrodynamical-Ecological Model for Regional and Shelf Seas: User Documentation. Version 2.0 P. Lyuten author 2011 text Royal Belgian Institute of the Natural Sciences 2011 10.2166/wst.2015.042 Pragmatic knowledge services M. P. Pohjola author 2011 text Journal of Universal Computer Science 17 2011 17 472 497 10.1016/j.jenvman.2015.01.053 Transport model application in River Vuoksi. In Suito H. (ed.): Project report for cooperative program between Japan and Finland; Assessment Tools for solving Aquatic Problems J. Ropponen author 2014 text Project Report Okayama University http://ousar.lib.okayma-u.ac.jp/metadata/52687 2014 58 68 Testing a river basin model with sensitivity analysis and autocalibration for an agricultural catchment in SW Finland S. Tattari author 2009 text Agricultural Food and Science Vol 2009 18 3 4 Ilmastonmuutoksen ääri-ilmiöihin liittyvän riskienhallinnan kustannus-hyötyanalyysi osana julkista päätöksentekoa - IRTORISKI-hankkeen loppuraportti. H. Virta author 2011 text Ilmatieteen laitoksen raportteja 2011 3 1 97 10.3897/rio.2.e9232 https://riojournal.com/article/9232/ https://riojournal.com/article/9232/download/pdf/ https://riojournal.com/article/9232/download/xml/ 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. text/html en_US Pensoft Publishers Open data open models environment human health regional economy Unicorn–Open science for assessing environmental state, human health and regional economy Grant Proposal

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

School of Rehabilitation Sciences, University of Ottawa, Ottawa, Canada author Hammond, Chad https://orcid.org/0000-0001-8715-6793 2016-05-25 2016-05-25 2016 Research Ideas and Outcomes 2367-7163 2 e9115 2016 10.3897/rio.2.e9115 https://riojournal.com/article/9115/ https://riojournal.com/article/9115/download/pdf/ https://riojournal.com/article/9115/download/xml/ 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. text/html en_US Pensoft Publishers Indigenous health cancer arts-based methods 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 Small Grant Proposal

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

Cardiovascular Surgery, Taipei Tzuchi Hospital, New Taipei City, Taiwan author Chen, Robert https://orcid.org/0000-0001-6892-0602 2016-05-26 2016-05-26 2016 Research Ideas and Outcomes 2367-7163 2 e9268 2016 10.4049/jimmunol.1303441 10.1165/rcmb.2015-0193OC 10.1007/s00251-015-0884-8 10.1093/nar/gku1091 10.1186/1423-0127-19-54 10.1007/978-3-319-18603-0_8 10.1074/jbc.M109.035147 Crosslinking of the human Fc receptor for IgA (FcalphaRI/CD89) triggers FcR gamma-chain-dependent shedding of soluble CD89. G van Zandbergen author 1999 text Journal of Immunology http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=10570263&retmode=ref&cmd=prlinks 1999 163 11 5806 5812 10.1101/gad.925702 10.1186/1423-0127-19-54 10.1074/jbc.275.6.4183 10.1006/abio.2001.5099 10.3897/rio.2.e9268 https://riojournal.com/article/9268/ https://riojournal.com/article/9268/download/pdf/ https://riojournal.com/article/9268/download/xml/ text/html en_US Pensoft Publishers Matrix Metalloproteinase-7 (MMP-7) A Disintegrin And Metalloproteinase-17 (ADAM-17) transplantation rejection allograft Bi-directional immuno-modulation by Matrix Metalloproteinase-7 (MMP-7) and A Disintegrin And Metalloproteinase-17 (ADAM-17) as transplantation rejection-tolerance spectrum PhD Project Plan

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

Utrecht University, Utrecht, Netherlands author Kramer, Bianca https://orcid.org/0000-0002-5965-6560 Utrecht University, Utrecht, Netherlands author Bosman, Jeroen Variable.io, London, United Kingdom author Ignac, Marcin YKON, Berlin, Germany author Kral, Christina YKON, Helsinki, Finland author Kalleinen, Tellervo YKON, Helsinki, Finland author Koskinen, Pekko Cambridge Crystallographic Data Centre, Cambridge, United Kingdom author Bruno, Ian https://orcid.org/0000-0003-4901-9936 University of Chicago, Chicago IL, United States of America author Buckland, Amy Science and Technology Facilities Council, Swindon, United Kingdom author Callaghan, Sarah Oregon Health and Science University, Portland OR, United States of America author Champieux, Robin Pentandra, Logan UT, United States of America author Chapman, Chris https://orcid.org/0000-0001-9770-735X University of California, San Diego, San Diego CA, United States of America author Hagstrom, Stephanie Hypothes.is, San Diego CA, United States of America University of California, San Diego, San Diego CA, United States of America author Martone, MaryAnn University of Reading, Reading, United Kingdom author Murphy, Fiona https://orcid.org/0000-0003-1693-1240 University of Lethbridge, Lethbridge AB, Canada Centre for the Study of Scholarly Communication, Lethbridge AB, Canada author O`Donnell, Daniel https://orcid.org/0000-0002-0127-4893 2016-05-26 2016-05-26 2016 Research Ideas and Outcomes 2367-7163 2 e9340 2016 10.3897/rio.2.e9340 https://riojournal.com/article/9340/ https://riojournal.com/article/9340/download/pdf/ https://riojournal.com/article/9340/download/xml/ text/html en_US Pensoft Publishers scholarly communication research communication scholarly commons workshop visualization principles Defining the Scholarly Commons - Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016 Workshop Report

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

Royal Museum for Central Africa, Tervuren, Belgium author Smirnova, Larissa Royal Museum for Central Africa, Tervuren, Belgium Botanic Garden Meise, Meise, Belgium author Mergen, Patricia https://orcid.org/0000-0003-2848-8231 Botanic Garden Meise, Meise, Belgium author Groom, Quentin https://orcid.org/0000-0002-0596-5376 Royal Belgian Institute of Natural Sciences, Brussels, Belgium author De Wever, Aaike https://orcid.org/0000-0001-8804-8321 Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 National Museum of Natural History and Pensoft Publishers, Sofia, Bulgaria author Stoev, Pavel https://orcid.org/0000-0002-5702-5677 GlueCAD, Haifa, Israel author Pe’er, Israel University of Tartu, Tartu, Estonia author Runnel, Veljo https://orcid.org/0000-0001-5198-8678 CSIC, Spanish Council for Scientific Research, Seville, Spain author García Camacho, Antonio INPA - National Institute for Amazonian Research, Manaus, Brazil author Vincent, Timothy www.plazi.org, Bern, Switzerland author Agosti, Donat https://orcid.org/0000-0001-9286-1200 Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece author Arvanitidis, Christos University of Granada, Granada, Spain author Bonet García, Francisco Javier University of Eastern Finland, Joensuu, Finland author Saarenmaa, Hannu 2016-05-31 2016-05-31 2016 Research Ideas and Outcomes 2367-7163 2 e9390 2016 project EU BON: Building the European Biodiversity Observation Network EU BON 308454 funder European Commission 10.13039/501100000780 10.1186/1756-0500-2-53 10.1371/journal.pbio.1000385 T. Catapano author 2010 TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions. http://www.ncbi.nlm.nih.gov/books/NBK47081/ 2010 0 10.1186/1471-2105-12-s15-s2 10.1525/bio.2013.63.6.3 10.3897/BDJ.2.e4034 10.3897/zookeys.414.7717 10.1890/0012-9623(2005)86[158:mtvoed]2.0.co;2 10.3897/bdj.3.e7318 10.3163/1536-5050.101.3.020 10.1186/1472-6785-13-16 10.1109/ssdm.2002.1029707 Donald Hobern author 2015 Presentation at the 13th global Nodes meeting in Antananarivo, Madagascar, 6 October 2015 http://community.gbif.org/pg/file/read/50950/gnm13-session-1-update-and-strategic-plan-201721 2015 10.3897/natureconservation.6.6498 10.1111/j.2008.0030-1299.16434.x 10.1016/j.tree.2011.09.007 10.1016/j.ecoinf.2007.05.004 Biodiversity and integrated environmental monitoring W. Magnusson author 2013 text INPA https://www.griffith.edu.au/__data/assets/pdf_file/0011/633962/2013-Biodiversity-and-Integrated-Env-Monitoring-BOOK.pdf 2013 1 1 356 10.1890/110154 10.1038/498255a 10.3897/bdj.3.e5063 Publishing sample data using the GBIF IPT (Unpublished Draft) Éamonn Ó Tuama author 2015 text GBIF http://www.gbif.org/sites/default/files/gbif_IPT-sample-data-primer_en.pdf 2015 0 1 10 10.1371/journal.pone.0102623 10.3897/bdj.1.e995 10.12688/f1000research.3-6.v1 10.5061/DRYAD.6T94P 10.3897/rio.2.e8622 10.1371/journal.pone.0089606 The roles and contributions of Biodiversity Observation Networks (BONs) in better tracking progress to 2020 biodiversity targets: a European case study Florian Wetzel author 2015 text Biodiversity 2015 16 137 149 10.4033/iee.2013.6b.6.f 10.1371/journal.pone.0029715 10.3897/rio.2.e9390 https://riojournal.com/article/9390/ https://riojournal.com/article/9390/download/pdf/ https://riojournal.com/article/9390/download/xml/ 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. text/html en_US Pensoft Publishers EU BON GEO BON Interoperability data standards Data sharing tools adopted by the European Biodiversity Observation Network Project Project Report

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

Boulder Creek Critical Zone Observatory/INSTAAR, Boulder, CO, United States of America author Fey, Jeri University of Colorado at Boulder, Boulder, United States of America author Anderson, Suzanne 2016-06-06 2016-06-06 2016 Research Ideas and Outcomes 2367-7163 2 e9419 2016 10.3897/rio.2.e9419 https://riojournal.com/article/9419/ https://riojournal.com/article/9419/download/pdf/ https://riojournal.com/article/9419/download/xml/ text/html en_US Pensoft Publishers data management plan hydrology earth sciences critical zone geomorphology meteorology Boulder Creek Critical Zone Observatory Data Management Plan Data Management Plan (NSF Generic)

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

Department of Animal Ecology and Tropical Biology, Biocentre, University of Würzburg, Würzburg, Germany author Joschinski, Jens 2016-06-17 2016-06-17 2016 Research Ideas and Outcomes 2367-7163 2 e9580 2016 10.1098/rspb.2009.1355 R. L. Blackman author 2000 Aphids on the world's crops 2000 476 10.1002/bies.20436 10.1126/science.1157174 10.1371/journal.pbio.1000357 10.1016/002f2-5193(66)90188-3 10.1016/S0169-5347(97)01274-3 10.1111/j.1744-7348.1971.tb04633.x 10.1002/bies.201500124 10.1086/383618 10.1111/1744-7917.12130 IPCC author 2014 Climate Change 2014: Synthesis Report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change 2014 151 10.1073/pnas.0901644106 10.7717/peerj.1103 10.1007/s10682-015-9786-3 10.1093/jisesa/iew013 10.1038/ncomms1213 10.1016/0022-1910(72)90170-9 10.1016/0022-1910(59)90024-1 10.1016/0022-1910(60)90078-0 10.1016/0022-1910(63)90067-2 10.1111/phen.12021 10.1042/bc20070135 10.1016/j.jinsphys.2012.07.009 10.1146/annurev.en.37.010192.001541 10.1038/hdy.2015.8 10.1016/s0169-5347(01)02331-x 10.1098/rspb.2011.0176 10.2307/3546608 10.1554/05-396.1 10.1093/ee/19.3.618 10.1371/journal.pbio.1000313 10.1111/jen.12262 10.1111/evo.12716 10.1126/science.aaa4984 10.1111/j.1469-8137.2004.01296.x 10.1371/journal.pbio.1001605 10.1029/2012JD017859 10.1242/jeb.089698 10.3897/rio.2.e9580 https://riojournal.com/article/9580/ https://riojournal.com/article/9580/download/pdf/ https://riojournal.com/article/9580/download/xml/ 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. text/html en_US Pensoft Publishers bet-hedging stochastic polyphenism fluctuating natural selection phenotypic plasticity phenology photoperiodism circadian clocks aphids Acyrthosiphon pisum Rhopalosiphum padi Megoura viciae Benefits and costs of aphid phenological bet-hedging strategies PostDoc Project Plan

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

University of São Paulo, Faculty of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, São Paulo, Brazil author Dutra Molino, João Vitor University of São Paulo, São Paulo, Brazil author Lubiana, Tiago https://orcid.org/0000-0003-2473-2313 University of São Paulo, Faculty of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, São Paulo, Brazil author Seno Ferreira Camargo, Livia University of São Paulo, São Paulo, Brazil author Croce, Miguel University of São Paulo, Faculty of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, São Paulo, Brazil author Tanaka, Allan University of São Paulo, São Paulo, Brazil author Buson, Felipe University of São Paulo, São Paulo, Brazil author Ribeiro, Pedro University of São Paulo, Faculty of Pharmaceutical Sciences, Department of Department of Clinical and Toxicological Analyses, São Paulo, Brazil author Campos-Salazar, Antony Federal University of São Paulo, São Paulo, Brazil author Padilha Antonio, Eduardo University of São Paulo, São Paulo, Brazil author Maizel, André University of São Paulo, Faculty of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, São Paulo, Brazil author Siratuti, Viviane University of São Paulo, São Paulo, Brazil author Costa, Claudia University of São Paulo, Faculty of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, São Paulo, Brazil author Wlodarczyk, Samarina University of São Paulo, São Paulo, Brazil author de Souza Lima, Raquel University of São Paulo, São Paulo, Brazil author Mello, Fabio University of California, San Diego. Food and Fuel for the 21st Department, San Diego, United States of America author Mayfield, Stephen University of São Paulo, Faculty of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, São Paulo, Brazil author Carvalho, João 2016-06-23 2016-06-23 2016 Research Ideas and Outcomes 2367-7163 2 e9342 2016 10.1371/journal.pbio.1001921 10.1371/journal.pone.0000514 10.1002/adfm.201302100 10.3109/07388551.2014.990414 10.1038/nbt0802-777 10.1007/s00425-008-0879-x 10.1046/j.1365-313x.1999.00526.x 10.1186/1471-2148-10-243 10.1073/pnas.54.6.1665 10.1016/j.polymer.2008.08.006 10.2144/000112556 10.1186/1471-2180-13-53 10.3923/rjbsci.2010.565.575 10.1016/j.tibtech.2008.02.006 10.1016/j.jbiotec.2012.10.010 10.1016/j.tibtech.2003.11.003 10.1021/cr010194g 10.1039/c3cs35511j 10.1371/journal.pone.0056469 10.1046/j.1365-313x.1998.00145.x 10.1073/pnas.0237108100 10.1016/j.copbio.2007.02.001 10.1371/journal.pone.0004944 10.1002/app.39475 10.1128/jb.187.20.7161-7164.2005 10.1016/s0168-1656(99)00185-6 10.1002/cncr.25489 10.4161/bbug.2.1.13423 10.1371/journal.pone.0043349 10.1086/521305 10.1016/j.copbio.2008.07.008 10.1016/j.biotechadv.2011.09.003 10.1046/j.1365-313x.2000.00652.x 10.1039/c3cs60075k 10.1016/j.actbio.2013.08.020 10.1385/abab:121:1-3:0149 10.1038/nbt.3040 10.1016/j.copbio.2013.04.004 10.1099/jmm.0.46788-0 10.1016/j.procbio.2016.01.006 10.3897/rio.2.e9342 https://riojournal.com/article/9342/ https://riojournal.com/article/9342/download/pdf/ https://riojournal.com/article/9342/download/xml/ text/html en_US Pensoft Publishers Bionanomaterial Silk protein Recombinant protein Microalgae Enzybiotic Chimeric spider silk production in microalgae: a modular bionanomaterial Research Idea

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

Cardiothoracic Surgery, Taipei Tzuchi Hospital, Tzuchi University College of Medicine, New Taipei City, Taiwan author Chen, Robert https://orcid.org/0000-0001-6892-0602 Laboratory of Connective Tissue and Stem Cell Research, Department of Biochemistry & Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan author Yu, Wei-hsuan 2016-06-23 2016-06-23 2016 Research Ideas and Outcomes 2367-7163 2 e9551 2016 10.3897/rio.2.e9551 https://riojournal.com/article/9551/ https://riojournal.com/article/9551/download/pdf/ https://riojournal.com/article/9551/download/xml/ text/html en_US Pensoft Publishers mitochondria epidermal growth factor receptor tyrosine kinase inhibitor matrix metalloproteinase-7 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) Conference Abstract

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

Dokuz Eylul University, Izmir, author Sabuncu, Metin Vestel Electronics, Manisa, author Yilmazlar, İsmail 2016-06-24 2016-06-24 2016 Research Ideas and Outcomes 2367-7163 2 e9597 2016 10.1109/5.649649 10.1364/oe.14.004736 10.1007/s10955-007-9440-8 10.1117/12.2080064 10.1117/12.539282 10.1016/j.optcom.2008.05.004 Photonic Imaging with Optical Coherence Tomography for Quality Monitoring in the Poultry Industry: a Preliminary Study Metin Sabuncu author 2015 text BJPS 2015 17 3 319 10.1155/2014/205191 10.1080/00405000.2015.1114791 10.1007/978-3-642-24986-0_8 10.1016/j.optlastec.2015.06.020 10.1109/lpt.2016.2524064 10.1038/srep14105 10.1109/jphot.2015.2478697 10.1016/j.optlastec.2015.04.014 10.1109/jdt.2008.924163 10.3897/rio.2.e9597 https://riojournal.com/article/9597/ https://riojournal.com/article/9597/download/pdf/ https://riojournal.com/article/9597/download/xml/ text/html en_US Pensoft Publishers Vertical cavity surface emitting lasers visible VCSEL speckle Speckle Contrast Reduction with a Visible VCSEL Projector Research Idea

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

Cardiovascular Surgery, Taipei Tzuchi Hospital, New Taipei City, Taiwan author Chen, Robert https://orcid.org/0000-0001-6892-0602 Laboratory of connective tissue and stem cell research, Department of Biochemistry & Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan author Yu, Wei-hsuan 2016-06-27 2016-06-27 2016 Research Ideas and Outcomes 2367-7163 2 e9617 2016 10.1093/cvr/cvs275 10.1016/j.yjmcc.2015.04.007 Myocardial and interstitial matrix metalloproteinase activity after acute myocardial infarction in pigs. T Etoh author 2001 text American journal of physiology. Heart and circulatory physiology http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=11514263&retmode=ref&cmd=prlinks 2001 281 3 987 94 Deletion of extracellular matrix metalloproteinase inducer/CD147 induces altered cardiac extracellular matrix remodeling in aging mice. E Huet author 2015 text Journal of physiology and pharmacology : an official journal of the Polish Physiological Society http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=26084217&retmode=ref&cmd=prlinks 2015 66 3 355 366 Matrix metalloproteinases and collagen ultrastructure in moderate myocardial ischemia and reperfusion in vivo. L Lu author 2000 text American journal of physiology. Heart and circulatory physiology http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=10924059&retmode=ref&cmd=prlinks 2000 279 2 601 9 10.1021/acs.biochem.5b00653 10.1161/HYPERTENSIONAHA.110.159525 Evolution of matrix metalloprotease and tissue inhibitor expression during heart failure progression in the infarcted rat. J T Peterson author 2000 text Cardiovascular Research http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=10773235&retmode=ref&cmd=prlinks 2000 46 2 307 315 10.1161/HYPERTENSIONAHA.112.203158 10.1016/j.cardiores.2005.10.002 10.1161/CIRCULATIONAHA.108.835488 10.1161/CIRCHEARTFAILURE.110.958199 10.3897/rio.2.e9617 https://riojournal.com/article/9617/ https://riojournal.com/article/9617/download/pdf/ https://riojournal.com/article/9617/download/xml/ 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. text/html en_US Pensoft Publishers Cytoscape matrix proteins metalloproteinase network cardiac disease Matrix Proteins and Proteinases Network in Human Cardiovascular Diseases Explored By Cytoscape Single-figure Publication

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

University of Padova, Padova, Italy author Pezzani, Raffaele https://orcid.org/0000-0003-3156-2500 2016-06-28 2016-06-28 2016 Research Ideas and Outcomes 2367-7163 2 e9632 2016 10.1002/rcm.2789 10.1016/j.bmc.2007.10.072 Herbal remedies. D S Kiefer author 1999 text American family physician 1999 60 6 1665 6 10.1021/jf405486c 10.3389/fphar.2016.00016 10.1007/BF01234480 10.3109/13880209.2015.1055634 10.1038/nchem.1694 Sandro Pignatti author 1982 Flora d'Italia 1982 2324 Saxifraga Wikipedia author text https://en.wikipedia.org/wiki/Saxifraga Saxifraga_aizoides Wikipedia author text https://en.wikipedia.org/wiki/Saxifraga_aizoides ANTI-INFLAMMATORY AND ANTIPYRETIC ACTIVITIES OF INDOMETHACIN, 1-(P-CHLOROBENZOYL)-5-METHOXY-2-METHYLINDOLE-3-ACETIC ACID. C A Winter author 1963 text The Journal of pharmacology and experimental therapeutics 1963 141 369 76 10.5732/cjc.009.10598 10.3897/rio.2.e9632 https://riojournal.com/article/9632/ https://riojournal.com/article/9632/download/pdf/ https://riojournal.com/article/9632/download/xml/ text/html en_US Pensoft Publishers Saxifraga aizoides saxifragaceae cancer cells ethnopharmacology phytotherapy Saxifraga aizoides extract: novel potential effects on tumor cell models Research Idea

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

Cardiovascular Surgery, Taipei Tzuchi Hospital, Tzuchi University, New Taipei City, Taiwan author Chen, Robert https://orcid.org/0000-0001-6892-0602 Emergency Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan author Fang, Cheng-Chung Emergency Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan author Shih, Fuh-Yuan Graduate Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan author King, Chwan-Chuen 2016-06-29 2016-06-29 2016 Research Ideas and Outcomes 2367-7163 2 e9648 2016 10.3201/eid1302.060557 10.3897/rio.2.e9648 https://riojournal.com/article/9648/ https://riojournal.com/article/9648/download/pdf/ https://riojournal.com/article/9648/download/xml/ text/html en_US Pensoft Publishers Influenza-like illness comorbidity ICD-9 risk model A Scoring System for Identifying Severe Cases of Influenza-like Illness by Comorbidity and Age - A Nationwide Cohort Analysis Research Presentation

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

Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Faulwetter, Sarah https://orcid.org/0000-0003-4892-4440 Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Pafilis, Evangelos Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece Australian Museum Research Institute, Sydney, Australia author Fanini, Lucia Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Bailly, Nicolas https://orcid.org/0000-0003-4994-0653 www.plazi.org, Bern, Switzerland author Agosti, Donat https://orcid.org/0000-0001-9286-1200 Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Arvanitidis, Christos NIMRD "Grigore Antipa", Constanța, Romania author Boicenco, Laura https://orcid.org/0000-0002-2116-9791 www.plazi.org, New York, United States of America author Catapano, Terry Flanders Marine Institute (VLIZ), Ostende, Belgium author Claus, Simon Flanders Marine Institute (VLIZ), Ostende, Belgium author Dekeyzer, Stefanie Pensoft Publishers, Sofia, Bulgaria author Georgiev, Teodor University of Athens, Athens, Greece Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Legaki, Aglaia Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Mavraki, Dimitra https://orcid.org/0000-0001-6775-530X Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Oulas, Anastasis University of Crete, Heraklion, Crete, Greece Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Papastefanou, Gabriella Bulgarian Academy of Sciences, Sofia, Bulgaria Pensoft Publishers, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 KIT / Plazi, Karlsruhe, Germany author Sautter, Guido Global Biodiversity Information Facility - Secretariat, Copenhagen Ø, Denmark author Schigel, Dmitry https://orcid.org/0000-0002-2919-1168 Pensoft Publishers, Sofia, Bulgaria Bulgarian Academy of Sciences, Sofia, Bulgaria author Senderov, Viktor https://orcid.org/0000-0003-3340-5963 National Research and Development Institute for Marine Geology and Geoecology - NIRD GeoEcoMar, Bucharest, Romania author Teaca, Adrian Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), Anavyssos, Attiki, Greece author Tsompanou, Marilena 2016-07-06 2016-07-06 2016 Research Ideas and Outcomes 2367-7163 2 e9774 2016 project Life Watch LIFEWATCH 211372 funder European Commission 10.13039/501100000780 10.1186/1756-0500-2-53 10.2218/ijdc.v7i1.218 10.5281/ZENODO.14941 TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions Terry Capatano author Bethesda (MD): National Center for Biotechnology Information (US); 2010 author 2010 text Proceedings of the Journal Article Tag Suite Conference 2010 Proceedings of the Journal Article Tag Suite Conference 2010 2010 10.1186/1471-2105-12-s15-s2 10.1111/j.1096-3642.1873.tb00560.x 10.5091/plecevo.2015.1048 10.12705/632.11 10.1111/j.1096-3642.1883.tb02779.x Adriatische Tintinnodeen H. Laackmann author 1913 text Sitzungsberichte der Kaiserlichen Akademie der Wissenschaften. Mathematisch-Naturwissenschaftliche Klasse http://biodiversitylibrary.org/page/36050965 1913 122 123 163 10.3897/zookeys.550.9702 10.1017/s1477200003001129 BioCreative IV Interactive Task Sherri Matis-Mitchell author 2013 text Proceedings of the Fourth BioCreative Challenge Evaluation Workshop http://www.biocreative.org/media/store/files/2013/bc4_v1_27.pdf 2013 1 190-203 10.1111/j.1096-3642.1976.tb00244.x 10.3897/bdj.3.e5063 10.1186/1741-7007-10-87 10.1016/j.tree.2011.11.001 Pensoft Data Publishing Policies and Guidelines for Biodiversity Data L Penev author text http://community.gbif.org/mod/file/download.php?file_guid=13043 10.3897/zookeys.150.2213 10.1111/j.1472-4642.2008.00519.x Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor. Guido Sautter author 2007 text Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007 12 391 402 10.3897/zookeys.150.1766 10.1155/2012/391574 From XML to XML: The why and how of making the biodiversity literature accessible to researcher Alistair Willis author 2010 text Language Resources and Evaluation Conference (LREC) http://oro.open.ac.uk/20856/1/787_Paper.pdf 2010 May 2010, Malta 1237 1244 10.3897/rio.2.e9774 https://riojournal.com/article/9774/ https://riojournal.com/article/9774/download/pdf/ https://riojournal.com/article/9774/download/xml/ 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. text/html en_US Pensoft Publishers biodiversity data legacy literature data archaeology data rescue text mining biogeographic databases data management EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases Project Report

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

National Library of Sweden, Stockholm, Sweden author Philipson, Joakim https://orcid.org/0000-0001-5699-994X 2016-07-07 2016-07-07 2016 Research Ideas and Outcomes 2367-7163 2 e9651 2016 G. Bammer author 2015 Change! Combining Analytic Approaches with Street Wisdom 9781925022650 2015 332 10.1007/978-3-319-07443-6_39 10.1080/00461520.2012.696438 10.1002/asi.23256 E. Garfield author 1979 Citation indexing: its theory and application in science, technology, and humanities 0-471-02559-3 1979 274 10.1177/030631277700700112 10.1002/(sici)1097-4571(199510)46:93.0.co;2-1 10.1002/(sici)1097-4571(199510)46:93.0.co;2-3 10.1007/s11192-007-1682-3 10.1002/(sici)1097-4571(199310)44:93.0.co;2-f 10.1073/pnas.1424329112 10.1007/s11192-007-1927-1 10.1002/asi.5090160207 10.1108/eb026920 10.1126/science.184.4140.987 10.1175/1520-0469(1983)0402.0.co;2 10.1007/1-4020-3714-7 10.1038/249810a0 10.1001/jama.1996.03530270057032 The relevance of citations: a case study of stratospheric ozone monitoring. Joakim Philipson author 1996 text [Masters thesis, ISSN: 1401-5358] http://hdl.handle.net/2320/13707 1996 1996 47 1 95 10.1016/0098-8472(80)90224-5 CiTO, the Citation Typing Ontology David Shotton author 2015 text [Web site] http://purl.org/spar/cito/ 2015 v2.6.4 1 10.1177/030631277700700202 Medical literature as a potential source of new knowledge. D R Swanson author 1990 text Bulletin of the Medical Library Association 1990 78 1 29 37 10.3115/1610075.1610091 10.1080/00031305.1983.10483166 10.1007/bf02498877 10.1023/b:scie.0000018543.82441.f1 10.1136/bjo.59.12.730 10.3897/rio.2.e9651 https://riojournal.com/article/9651/ https://riojournal.com/article/9651/download/pdf/ https://riojournal.com/article/9651/download/xml/ text/html en_US Pensoft Publishers knowledge export relevance citation functions cross-disciplinarity CiTO Citation functions revisited: learning from the princes Research Idea

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

Faculty of Earth Sciences and Technology. Bandung Institute of Technology, Bandung, Indonesia author Irawan, Dasapta Erwin https://orcid.org/0000-0002-1526-0863 Civil Engineering and Port Innovation, Delft University, Delft, Netherlands author Priyambodho, Bambang Adhi University of Sydney, Sydney, Australia author Rachmi, Cut Groundwater Engineering Program, Bandung Institute of Technology, Bandung, Indonesia author Wibowo, Dimas Universitas Pendidikan Indonesia, Bandung, Indonesia author Fahmi, Andita 2016-07-18 2016-07-18 2016 Research Ideas and Outcomes 2367-7163 2 e9841 2016 Jakarta Flood Hazard Mapping Framework JanJaap Brinkman author text http://www.hkv.nl/upload/publication/Jakarta_Flood_Hazard_Mapping_Framework_MH.pdf 10.1016/j.scitotenv.2008.10.003 Yao-Chuen Fang author 2004 Scientific research impact and data mining applications in hydrogeology http://dl.acm.org/citation.cfm?id=1048351 2004 136 PaperMachines: Zotero plug-in for text mining and visualisation J. Guldi author 2011 text PaperMachines http://papermachines.org 2011 10.6084/M9.FIGSHARE.3405685 Bibliometrics: an overview Leeds_University_Library author text https://library.leeds.ac.uk/downloads/file/265/bibliometrics_an_overview 10.1007/s10040-008-0278-1 10.1016/j.jhydrol.2014.07.064 10.1002/asi.20526 10.1111/j.1745-6584.2001.tb02337.x WHITEPAPER USING BIBLIOMETRICS: A guide to evaluating research performance with citation data Thomson_Reuters author text http://ip-science.thomsonreuters.com/m/pdfs/325133_thomson.pdf 10.1007/s11192-009-0146-3 VOSviewer manual Nees Jan van Eck author 2013 text Leiden: Univeristeit Leiden www.vosviewer.com/documentation/Manual_VOSviewer_1.5.4.pdf 2013 1 1 Text mining and visualization using VOSviewer Nees Jan Van Eck author 2011 text arXiv preprint arXiv:1109.2058 http://arxiv.org/abs/1109.2058 2011 1 1 RIS (file format) Wikipedia author text https://en.wikipedia.org/wiki/RIS_(file_format) Thirty years (1984-2014) of groundwater science teaching and research in China: A dissertation-based bibliometric survey ZHAI Yuan-zheng author 2015 text Journal of Groundwater Science and Engineering http://gwse.iheg.org.cn/EN/abstract/abstract190.shtml 2015 3 3 1 10.6084/M9.FIGSHARE.1092521.V1 Methods for Bibliometric Analysis of Research: Renewable Energy Case Study B. Ziegler author text http://web.mit.edu/smadnick/www/wp/2009-10.pdf Zotero: An open source reference manager Zotero_Community author 2016 text Zotero Community http://zotero.org 2016 10.3897/rio.2.e9841 https://riojournal.com/article/9841/ https://riojournal.com/article/9841/download/pdf/ https://riojournal.com/article/9841/download/xml/ 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. text/html en_US Pensoft Publishers Bibliometric literature review groundwater Jakarta Bibliometric study to assist research topic selection: a case from research design on Jakarta’s groundwater (part 1) Single-figure Publication

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

Natural History Museum, London, United Kingdom author Koureas, Dimitris https://orcid.org/https://orcid.org/0000-0002-4842-6487 Hellenic Center for Marine Recearch (HCMR), Heraklion Crete, Greece author Arvanitidis, Christos The Atlas of Living Australia, Carlton, Australia author Belbin, Lee https://orcid.org/0000-0001-8900-6203 Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany author Berendsohn, Walter G. https://orcid.org/0000-0001-9945-7606 Aarhus University, Silkeborg, Denmark author Damgaard, Christian Agentschap Plantentuin Meise, Meise, Belgium author Groom, Quentin https://orcid.org/0000-0002-0596-5376 Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany author Güntsch, Anton https://orcid.org/0000-0002-4325-4030 Museum für Naturkunde Berlin, Berlin, Germany author Hagedorn, Gregor Cardiff University, Cardiff, United Kingdom author Hardisty, Alex https://orcid.org/0000-0002-0767-4310 GBIF, Copenhagen, Denmark author Hobern, Donald https://orcid.org/0000-0001-6492-4016 CREAF, Cerdanyola del Vallès, Spain author Marcer, Arnald https://orcid.org/0000-0002-6532-7712 EvoMRI Communications, Jena, Germany author Mietchen, Daniel https://orcid.org/0000-0001-9488-1870 School of Computing and Communications, The Open University, Milton Keynes, United Kingdom author Morse, David Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden author Obst, Matthias https://orcid.org/0000-0003-0264-9631 Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 Biodiversity Unit, Department of Biology, Lund University, Lund, Sweden author Pettersson, Lars B. https://orcid.org/https://orcid.org/0000-0001-5745-508X Naturalis Biodiversity Center, Leiden, Netherlands author Sierra, Soraya Natural History Museum, London, United Kingdom author Smith, Vincent https://orcid.org/0000-0001-5297-7452 Naturalis Biodiversity Center, Leiden, Netherlands author Vos, Rutger https://orcid.org/0000-0001-9254-7318 2016-07-20 2016-07-20 2016 Research Ideas and Outcomes 2367-7163 2 e9933 2016 VIBRANT: New virtual research communities to create and share data on biodiversity CORDIS author text http://cordis.europa.eu/result/rcn/150383_en.html White Paper e-Infrastructures Reflection Group author text 9. http://e-irg.eu/documents/10920/11274/e-irg-white-paper-2013-final.pdf/ce8a2253-aebd-4cbe-9a93-4709a1166214 Communication from the Commission to the European Parliament, the Council, the European Economic and Social Committee and the Committee of the Regions - A Digital Agenda for Europe European Commission author text http://eur-lex.europa.eu/legal-content/EN/ALL/?uri=CELEX:52010DC0245 Communication from the Commission to the European Parliament, the Council, the European Economic and Social Committee and the Committee of the Regions European Commission author text http://ec.europa.eu/research/era/pdf/era-communication/era-communication_en.pdf Validation of the results of the public consultation on Science 2.0: Science in Transition European Commission author text http://www.eesc.europa.eu/resources/docs/validation-of-the-results-of-the-public-consultation-on-science-20.pdf FP7 Research Infrastructures European Commission author text https://ec.europa.eu/research/fp7/index_en.cfm?pg=infra Discipline Metrics Report European Grid Infrastructure author 2015 text http://operations-portal.egi.eu/metrics/disciplineMetricsReports/discipline/2015-12?disciplineId=1 2015 10.1177/0038038509103208 The Data Harvest Report – sharing data for knowledge, jobs and growth RDA Europe author text https://rd-alliance.org/data-harvest-report-sharing-data-knowledge-jobs-and-growth.html 10.3897/rio.2.e9933 https://riojournal.com/article/9933/ https://riojournal.com/article/9933/download/pdf/ https://riojournal.com/article/9933/download/xml/ 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. text/html en_US Pensoft Publishers e-infrastructure Virtual Research Environment Open Science Cloud Europe user engagement research infrastructure Community engagement: The ‘last mile’ challenge for European research e-infrastructures Policy Brief

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

MCPHS University, Worcester, MA, United States of America author Smith, Chase The University of Sydney, Sydney, Australia author Todd, Matthew Ecole polytechnique fédérale de Lausanne, Lausanne, Switzerland author Patiny, Luc Cambridge MedChem Consulting, Cambridge, United Kingdom author Swain, Christopher IUPHAR/BPS Guide to PHARMACOLOGY, Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom author Southan, Christopher The University of Sydney, Sydney, Australia author Williamson, Alice Molecular Materials Informatics, Inc., Montréal, Canada author Clark, Alex 2016-07-27 2016-07-27 2016 Research Ideas and Outcomes 2367-7163 2 e9995 2016 Frans Johansson author 2006 Medici Effect: What Elephants and Epidemics Can Teach Us about Innovation 9781422102824 http://www.fransjohansson.com/the-medici-effect-by-frans-johansson/ 2006 224 OpenSourceMalaria:Triazolopyrazine (TP) Series Open Source Malaria author text http://openwetware.org/wiki/OpenSourceMalaria:Triazolopyrazine_%28TP%29_Series 10.1017/s0031182013001121 10.1186/1758-2946-5-10 World Health Organization author 2015 Global Technical Strategy for Malaria 2016–2030 978 92 4 156499 1 http://www.who.int/malaria/publications/atoz/9789241564991/en/ 2015 32 World Health Organization author 2015 World Malaria Report 2015. 978 92 4 156515 8 http://www.who.int/malaria/publications/world-malaria-report-2015/report/en/ 2015 280 10.3897/rio.2.e9995 https://riojournal.com/article/9995/ https://riojournal.com/article/9995/download/pdf/ https://riojournal.com/article/9995/download/xml/ 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). text/html en_US Pensoft Publishers Open Science Malaria Drug Discovery Electronic Laboratory Notebook Reaction Informatics Chemical Structure Alerts Collaboration SCINDR - The SCience INtroDuction Robot that will Connect Open Scientists Small Grant Proposal

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

Boston College, Chestnut Hill, MA, United States of America author Madan, Christopher https://orcid.org/0000-0003-3228-6501 2016-08-23 2016-08-23 2016 Research Ideas and Outcomes 2367-7163 2 e10266 2016 funder Canadian Institutes of Health Research 10.13039/501100000024 10.1006/nimg.1998.0395 10.1016/j.neuroimage.2012.01.021 10.1016/S0896-6273(02)00569-X 10.1093/cercor/bhs231 10.12688/f1000research.6838.1 10.1016/j.neuroimage.2016.04.029 10.1073/pnas.070039597 10.1007/s11682-013-9277-5 10.1007/s11065-015-9281-1 10.1097/WCO.0000000000000074 10.3897/rio.2.e10266 https://riojournal.com/article/10266/ https://riojournal.com/article/10266/download/pdf/ https://riojournal.com/article/10266/download/xml/ text/html en_US Pensoft Publishers brain morphology 3d printing structural MRI Improved understanding of brain morphology through 3D printing: A brief guide Methods

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

University of Colorado Boulder, Boulder, United States of America author Nichols, Harvey University of Colorado Boulder, Boulder, United States of America author Stolze, Susann 2016-08-25 2016-08-25 2016 Research Ideas and Outcomes 2367-7163 2 e10269 2016 10.3897/rio.2.e10269 https://riojournal.com/article/10269/ https://riojournal.com/article/10269/download/pdf/ https://riojournal.com/article/10269/download/xml/ text/html en_US Pensoft Publishers data management plan Canadian Arctic surface pollen data modern pollen traps baseline study vegetation climate Migration of legacy data to new media formats for long-time storage and maximum visibility: Modern pollen data from the Canadian Arctic (1972/1973) Data Management Plan (NSF Generic)

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

National Oceanography Centre, Southampton, United Kingdom author Durden, Jennifer https://orcid.org/0000-0002-6529-9109 National Oceanography Centre, Southampton, United Kingdom author Billett, David Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, United Kingdom author Brown, Alastair Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom author Dale, Andrew Environmental Resources Management Limited, Oxford, United Kingdom author Goulding, Laura Senkenberg am Meer, German Centre for Marine Biodiversity Research, Wilhelmshaven, Germany author Gollner, Sabine https://orcid.org/0000-0001-9322-9258 Environmental Resources Management Limited, Oxford, United Kingdom author Murphy, Kevin Marine Biology Research Group, Ghent University, Ghent, Belgium author Pape, Ellen https://orcid.org/0000-0003-2881-8341 Alfred Wegener Institute, Bremerhaven, Germany author Purser, Autun Ifremer, Plouzane, France author Rolin, Jean-Francois Duke University Marine Lab, Nicholas School of the Environment, Duke University, Beaufort, United States of America author Smith, Austin Fugro EMU Limited, Edinburgh, United Kingdom author Stewart, Ian Duke University Marine Lab, Nicholas School of the Environment, Duke University, Beaufort, United States of America author Turner, Phillip Global Sea Mineral Resources NV, Zwijndrecht, Belgium author de Wachter, Tom Seascape Consultants Limited, Romsey, United Kingdom author Weaver, Philip Duke University Marine Lab, Nicholas School of the Environment, Duke University, Beaufort, United States of America author van Dover, Cindy University of Hawai’i at Manoa, Honolulu, United States of America author Verlaan, Philomene National Oceanography Centre, Southampton, United Kingdom author Jones, Daniel https://orcid.org/0000-0001-5218-1649 2016-09-07 2016-09-07 2016 Research Ideas and Outcomes 2367-7163 2 e10292 2016 project Managing Impacts of Deep-seA reSource exploitation MIDAS 603418 funder European Commission 10.13039/501100000780 International Seabed Authority author 2011 Environmental Management Needs for Exploration and Exploitation of Deep Sea Minerals, ISA Technical Study: No. 10 2011 52 10.1016/j.marpol.2014.04.006 10.1016/S0967-0645(01)00052-2 C. R. Smith author N. Polunin author 2008 Aquatic Ecosystems: Trends and Global Prospects 2008 10.1016/0022-0981(92)90094-Q 10.1098/rspb.2013.1684 10.3897/rio.2.e10292 https://riojournal.com/article/10292/ https://riojournal.com/article/10292/download/pdf/ https://riojournal.com/article/10292/download/xml/ text/html en_US Pensoft Publishers Environmental management deep-sea mining environmental impact assessment marine policy environmental management plan MIDAS project sustainable management European Union Framework 7 deep-sea biology Report on the Managing Impacts of Deep-seA reSource exploitation (MIDAS) workshop on environmental management of deep-sea mining Workshop Report

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

Boston College, Chestnut Hill, MA, United States of America author Madan, Christopher https://orcid.org/0000-0003-3228-6501 2016-09-08 2016-09-08 2016 Research Ideas and Outcomes 2367-7163 2 e10398 2016 funder Canadian Institutes of Health Research 10.13039/501100000024 10.1006/nimg.1998.0395 10.1016/j.neuroimage.2012.01.021 10.1016/S0896-6273(02)00569-X 10.1093/cercor/bhs231 10.12688/f1000research.6838.1 10.1016/j.neuroimage.2016.04.029 10.1073/pnas.070039597 10.1007/s11682-013-9277-5 10.1007/s11065-015-9281-1 10.1097/WCO.0000000000000074 10.3897/rio.2.e10398 https://riojournal.com/article/10398/ https://riojournal.com/article/10398/download/pdf/ https://riojournal.com/article/10398/download/xml/ text/html en_US Pensoft Publishers brain morphology 3d printing structural MRI Improved understanding of brain morphology through 3D printing: A brief guide Methods

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

Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Faulwetter, Sarah https://orcid.org/0000-0003-4892-4440 Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Pafilis, Evangelos Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Fanini, Lucia Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Bailly, Nicolas https://orcid.org/0000-0003-4994-0653 www.plazi.org, Bern, Switzerland author Agosti, Donat https://orcid.org/0000-0001-9286-1200 Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Arvanitidis, Christos NIMRD "Grigore Antipa", Constanța, Romania author Boicenco, Laura https://orcid.org/0000-0002-2116-9791 www.plazi.org, New York, United States of America author Catapano, Terry Flanders Marine Institute (VLIZ), Ostende, Belgium author Claus, Simon Flanders Marine Institute (VLIZ), Ostende, Belgium author Dekeyzer, Stefanie Pensoft Publishers, Sofia, Bulgaria author Georgiev, Teodor https://orcid.org/0000-0001-8558-6845 Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Legaki, Aglaia Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Mavraki, Dimitra https://orcid.org/0000-0001-6775-530X Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Oulas, Anastasis Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Papastefanou, Gabriella Pensoft Publishers, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 KIT / Plazi, Karlsruhe, Germany author Sautter, Guido Global Biodiversity Information Facility - Secretariat, Copenhagen, Denmark author Schigel, Dmitry https://orcid.org/0000-0002-2919-1168 Pensoft Publishers, Sofia, Bulgaria author Senderov, Viktor https://orcid.org/0000-0003-3340-5963 National Research and Development Institute for Marine Geology and Geoecology - NIRD GeoEcoMar, Bucharest, Romania author Teaca, Adrian Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece author Tsompanou, Marilena 2016-09-12 2016-09-12 2016 Research Ideas and Outcomes 2367-7163 2 e10445 2016 project Life Watch LIFEWATCH 211372 funder European Commission 10.13039/501100000780 10.1186/1756-0500-2-53 10.2218/ijdc.v7i1.218 10.5281/ZENODO.14941 TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions Terry Catapano author Bethesda (MD): National Center for Biotechnology Information (US); 2010 author 2010 text Proceedings of the Journal Article Tag Suite Conference 2010 https://www.ncbi.nlm.nih.gov/books/NBK47081/ 2010 10.1186/1471-2105-12-s15-s2 10.1111/j.1096-3642.1873.tb00560.x 10.5091/plecevo.2015.1048 10.12705/632.11 10.1111/j.1096-3642.1883.tb02779.x Adriatische Tintinnodeen H. Laackmann author 1913 text Sitzungsberichte der Kaiserlichen Akademie der Wissenschaften. Mathematisch-Naturwissenschaftliche Klasse http://biodiversitylibrary.org/page/36050965 1913 122 123 163 10.3897/zookeys.550.9702 10.1017/s1477200003001129 BioCreative IV Interactive Task Sherri Matis-Mitchell author 2013 text Proceedings of the Fourth BioCreative Challenge Evaluation Workshop http://www.biocreative.org/media/store/files/2013/bc4_v1_27.pdf 2013 1 190-203 10.1111/j.1096-3642.1976.tb00244.x 10.3897/bdj.3.e5063 10.1016/j.tree.2011.11.001 Pensoft Data Publishing Policies and Guidelines for Biodiversity Data L Penev author text http://community.gbif.org/mod/file/download.php?file_guid=13043 10.3897/zookeys.150.2213 10.1111/j.1472-4642.2008.00519.x Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor. Guido Sautter author 2007 text Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007 12 391 402 10.3897/zookeys.150.1766 10.1155/2012/391574 From XML to XML: The why and how of making the biodiversity literature accessible to researcher Alistair Willis author 2010 text Language Resources and Evaluation Conference (LREC) http://oro.open.ac.uk/20856/1/787_Paper.pdf 2010 May 2010, Malta 1237 1244 10.3897/rio.2.e10445 https://riojournal.com/article/10445/ https://riojournal.com/article/10445/download/pdf/ https://riojournal.com/article/10445/download/xml/ 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. text/html en_US Pensoft Publishers biodiversity data legacy literature data archaeology data rescue text mining biogeographic databases data management EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases Project Report

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

Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece author Gerovasileiou, Vasilis https://orcid.org/0000-0002-9143-7480 Consiglio Nazionale delle Ricerche, Istituto per lo Studio degli Ecosistemi CNR-ISE, Verbania Pallanza, Italy author Martinez, Alejandro https://orcid.org/0000-0003-0073-3688 Colección Nacional de Crustáceos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico author Alvarez, Fernando Department of Life Sciences, Natural History Museum, London, United Kingdom author Boxshall, Geoff Department of Terrestrial Zoology, Western Australian Museum, Welshpool, Australia author Humphreys, William Frank IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, Esporles, Balearic Islands, Spain author Jaume, Damia Marine Animal Ecology, Animal Science Group, Wageningen University, Wageningen, Netherlands author Becking, Leontine E. Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil author Muricy, Guilherme Department of Marine Science, Texas A&M University at Galveston, Galveston, United States of America author van Hengstum, Peter J. Flanders Marine Institute/Vlaams Instituut voor de Zee (VLIZ), Oostende, Belgium author Dekeyzer, Stefanie Flanders Marine Institute/Vlaams Instituut voor de Zee (VLIZ), Oostende, Belgium author Decock, Wim Flanders Marine Institute/Vlaams Instituut voor de Zee (VLIZ), Oostende, Belgium author Vanhoorne, Bart https://orcid.org/0000-0002-6642-4725 Flanders Marine Institute/Vlaams Instituut voor de Zee (VLIZ), Oostende, Belgium author Vandepitte, Leen https://orcid.org/0000-0002-8160-7941 Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece author Bailly, Nicolas https://orcid.org/0000-0003-4994-0653 Department of Marine Biology, Texas A&M University at Galveston, Galveston, United States of America author Illife, Thomas https://orcid.org/0000-0002-4342-5960 2016-09-13 2016-09-13 2016 Research Ideas and Outcomes 2367-7163 2 e10451 2016 F. Álvarez author F. Álvarez author 2008 Crustáceos de México: Estado Actual de su Conocimiento 978-970-694-482-5 2008 522 p. 10.1651/c-2658.1 10.15560/11.1.1505 10.1007/978-1-4020-8259-7 10.1186/1471-2148-11-221 10.1007/s10750-011-0742-0 10.3354/meps10155 10.1007/s12526-014-0268-6 10.1007/s12526-009-0018-3 10.1163/1937240x-00002335 Taxonomic catalog of the Brazilian fauna W. A. Boeger author text http://fauna.jbrj.gov.br L. Botoșăneanu author 1986 Stygofauna Mundi. A faunistic, distributional, and ecological synthesis of the world fauna inhabiting subterranean waters (including the marine interstitial) 1986 740 L. Botoșăneanu author 1998 Studies in Crenobiology: The biology of springs and springbrooks 1998 261 10.2307/1548221 10.1111/j.1096-3642.1987.tb01510.x Preliminary investigations in anchialine caves of Cuba J. E. Bozanic author J. Heine author 1993 text Diving for Science. Proceedings of the 13th annual scientific diving symposium 1993 10.1111/zsc.12173 MarineRegions.org S. Claus author text http://www.marineregions.org D. Culver author 2012 Encyclopedia of Caves 2012 654 10.1080/00364827.1991.10413472 M. N. Dawson author R. Gillespie author 2009 Encyclopedia of islands 9780520256491 2009 1111 10.1073/pnas.0306212101 M. S. Field author 1999 A lexicon of cave and karst terminology with special reference to environmental karst hydrology 1999 214 Parhippolyte uveae Borradaile. 1899 (Crustacea: Decapoda: Hippolytidae) from Kakaban Island, Indonesia C. H.J.M., Fransen author 1996 text ZOOLOGISCHE MEDEDEELINGEN 1996 70 227 233 FishBase R. Froese author text www.fishbase.org 10.1371/journal.pone.0039873 Mediterranean marine caves as biodiversity reservoirs: a preliminary overview V. Gerovasileiou author H. Langar author 2014 text Proceedings of the first Mediterranean Symposium on the conservation of Dark Habitats 978-9938-9574-1-9 2014 84 10.1111/maec.12268 10.12681/mms.1069 World Register of marine Cave Species V. Gerovasileiou author text http://www.marinespecies.org/worcs World Register of Deep-Sea species A. G., Glover author text http://www.marinespecies.org/deepsea 10.1007/s10750-011-0932-9 La fauna aquàtica dels hàbitats anquihalins i dolçaquícoles de les cavitats balears F. Gràcia author 2011 text ENDINS 2011 17 257 268 10.1080/02723646.1998.10642647 Les grottes sous-marines obscures: un milieu extrême et un remarquable biotope refuge J. G. Harmelin author 1985 text Téthys 1985 11 214 229 Caridean shrimps found in land-locked saltwater pools at four Indo-West Pacific localities (Sinai Peninsula, Funafuti Atoll, Maui and Hawaii Islands): with the description of one new genus and four new species L. B. Holthuis author 1973 text ZOOLOGISCHE VERHANDELINGEN 1973 128 1 48 10.18195/issn.0313-122x.83.2013.145-158 10.1007/978-1-4899-0646-5_11 Worldwide diving discoveries of living fossil animals from the depths of anchialine and marine caves T. M. Iliffe author 2009 text Smithsonian Contribution to the Marine Sciences 2009 38 269 280 10.1038/302141a0 Coves amb hàbitats anquialins de les Balears i coves amb hàbitats dolçaquícoles no litorals: catàleg espeleològic i faunístic D. Jaume author 2006 text ENDINS 2006 30 71 82 10.1130/0091-7613(1994)0222.3.co;2 10.5479/si.00810282.475 10.5479/si.00810282.616 10.1016/j.marpolbul.2012.07.024 10.1111/zsc.12024 10.1111/cla.12089 A. Martínez author 2016 Guide of the anchialine ecosystems of Jameos del Agua and Túnel de la Atlántida (Lanzarote, Canary Islands) 2016 308 10.1007/s12526-009-0023-6 World List of Lophogastrida, Stygiomysida and Mysida J. Mees author text http://www.marinespecies.org/mysidacea/ 10.11646/%25x W. H. Monroe author 1970 A glossary of karst terminology 1970 29 10.1007/bf03175407 A. Núñez-Jiménez author 1984 Cuevas y carsos 1984 431 World Register of Introduced Marine Species (WRIMS) S. Pagad author text http://www.marinespecies.org/introduced 10.1130/0016-7606(1991)103<0001:OAMOLC>2.3.CO;2 10.1007/978-1-4684-8261-4_17 10.1007/s10750-011-0624-5 10.1007/978-3-642-70290-7_9 A. Romero author 2009 Cave biology: life in darkness 978-0-521-82846-8 2009 306 10.1093/mollus/eyv049 10.1016/j.jcz.2013.08.004 10.1016/0169-5347(96)20031-x 10.1016/j.marchem.2013.05.005 10.1007/bf00006900 The concept “anchialine” reconsidered J. H., Stock author 1986 text Stygologia 1986 2 90 92 10.1007/s12665-010-0463-0 10.3390/jmse3041448 10.1016/j.marmicro.2012.02.007 10.1016/j.margeo.2011.05.004 10.4319/lo.2009.54.1.0391 World Porifera database R. W.M Van Soest author text http://www.marinespecies.org/porifera 10.1093/molbev/msr270 Origin and age of the marine stygofauna of Lanzarote, Canary Islands H. Wilkens author 1986 text Mitteilungen aus dem Hamburgischen Zoologischer Museum und Institut 1986 83 223 230 La fauna de unos biotopos anquialinos en Lanzarote H. Wilkens author 1993 text Mémoires de Bióspéologie 1993 20 283 285 10.1007/s12526-009-0019-2 10.1007/s12526-016-0522-1 World Register of Marine Species WoRMS Editorial Board author text http://www.marinespecies.org Longipalpa saltatrix, a new genus and species of the meiofaunal family Nerillidae (Annelida: Polychaeta) from an anchihaline cave in Bermuda K. Worsaae author 2004 text Proceedings of the Biological Society of Washington 2004 117 3 346 362 10.2307/1547965 10.3897/rio.2.e10451 https://riojournal.com/article/10451/ https://riojournal.com/article/10451/download/pdf/ https://riojournal.com/article/10451/download/xml/ 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. text/html en_US Pensoft Publishers Marine caves anchialine ecosystems biodiversity global species databases biodiversity management World Register of marine Cave Species (WoRCS): a new Thematic Species Database for marine and anchialine cave biodiversity Project Report

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

Natural History Museum, London, United Kingdom author Glover, Adrian https://orcid.org/0000-0002-9489-074X Uni Research, Bergen, Norway author Dahlgren, Thomas https://orcid.org/0000-0001-6854-2031 Natural History Museum, London, United Kingdom author Taboada, Sergio Natural History Museum, London, United Kingdom author Paterson, Gordon Natural History Museum, London, United Kingdom author Wiklund, Helena https://orcid.org/0000-0002-8252-3504 Natural History Museum, London, United Kingdom author Waeschenbach, Andrea Natural History Museum, London, United Kingdom author Cobley, Amber https://orcid.org/0000-0003-2418-8127 Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Senckenberg am Meer, Germany author Martínez, Pedro Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Senckenberg am Meer, Germany author Kaiser, Stefanie Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Senckenberg am Meer, Germany author Schnurr, Sarah Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Senckenberg am Meer, Germany author Khodami, Sahar Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Senckenberg am Meer, Germany author Raschka, Uwe Senckenberg Research Institute and Nature Museum, Frankfurt am Main, Germany author Kersken, Daniel Senckenberg Museum, Dresden, Germany author Stuckas, Heiko Deep-sea Environment Laboratory, Ifremer, Plouzane, France author Menot, Lenaick Deep-sea Environment Laboratory, Ifremer, Plouzane, France author Bonifácio, Paulo https://orcid.org/0000-0001-9036-7145 Marine Biology, Ghent University, Ghent, Belgium author Vanreusel, Ann Marine Biology, Ghent University, Ghent, Belgium author Macheriotou, Lara https://orcid.org/0000-0002-5662-5689 Universidade de Aveiro, Aveiro, Portugal author Cunha, Marina R. https://orcid.org/0000-0001-8833-6980 Universidade de Aveiro, Aveiro, Portugal author Hilário, Ana Universidade de Aveiro, Aveiro, Portugal author Rodrigues, Clara https://orcid.org/0000-0002-3426-8342 IMAR-Institute of Marine Research, University of the Azores, Portugal author Colaço, Ana IMAR-Institute of Marine Research, University of the Azores, Portugal author Ribeiro, Pedro University of Łódź, Łódź, Poland author Blazewicz, Magdalena https://orcid.org/0000-0002-4753-3424 National Oceanography Centre, Southampton, United Kingdom author Gooday, Andrew National Oceanography Centre, Southampton, United Kingdom author Jones, Daniel https://orcid.org/0000-0001-5218-1649 National Oceanography Centre, Southampton, United Kingdom author Billett, David National Oceanography Centre, Southampton, United Kingdom author Goineau, Aurélie University of Hawaii at Manoa, Honolulu, United States of America author Amon, Diva University of Hawaii at Manoa, Honolulu, United States of America author Smith, Craig https://orcid.org/0000-0002-3976-0889 Royal Belgian Institute of Natural Sciences, Brussels, Belgium author Patel, Tasnim University of Plymouth, Plymouth, United Kingdom author McQuaid, Kirsty https://orcid.org/0000-0002-0395-8332 UK Seabed Resources Ltd, London, United Kingdom author Spickermann, Ralph International Seabed Authority, Kingston, Jamaica author Brager, Stefan 2016-09-16 2016-09-16 2016 Research Ideas and Outcomes 2367-7163 2 e10528 2016 project Managing Impacts of Deep-seA reSource exploitation MIDAS 603418 funder European Commission 10.13039/501100000780 10.1038/srep30492 10.2307/2407208 10.1016/s0967-0645(01)00069-8 10.4031/002533205787444015 PW Bretsky author 1969 Adaptive response to environmental stability: a unifying concept in paleoecology. Proceedings of the North American Palaeontological Convention 1969 550 S Culver author S Donovan author 1998 The Adequacy of the Fossil Record 1998 312 10.3897/bdj.4.e9277 10.1111/j.1365-294x.2010.04978.x 10.1186/s12862-015-0559-y Project ABYSSLINE Interim Progress Report 2015 - Benthic Biological Studies in the Clarion-Clipperton Zone: Megafaunal and Macrofaunal Biodiversity and Genetics AG Glover author 2015 text NHM Consulting 2015 SBU13002/15 10.1111/j.1439-0485.2005.00060.x 10.3390/jmse4010002 10.3897/bdj.4.e7251 10.1146/annurev-marine-120709-142737 10.1016/j.dsr2.2016.04.003 Environmental Management Plan for the Clarion-Clipperton Zone ISA author text https://www.isa.org.jm/documents/isba17ltc7 Workshop on taxonomic methods and standardization of megafauna in the Clarion-Clipperton Fracture Zone ISA author text https://www.isa.org.jm/documents/briefing-paper-0214 Workshop on taxonomic methods and standardization of macrofauna in the Clarion-Clipperton Fracture Zone ISA author text https://www.isa.org.jm/workshop/workshop-taxonomic-methods-and-standardization-macrofauna-clarion-clipperton-fracture-zone Workshop on taxonomic methods and standardization of meiofauna in the Clarion-Clipperton Fracture Zone ISA author text https://www.isa.org.jm/workshop/workshop-taxonomic-methods-and-standardization-meiofauna-clarion-clipperton-zone-dec-2015 ISA author https://www.isa.org.jm 10.1371/journal.pone.0117790 Short Cruise Report R.V Sonne Cruise SO-239 P. Martinez Arbizu author text https://www.ldf.uni-hamburg.de/sonne/wochenberichte/wochenberichte-sonne/so239/so239-scr.pdf Global biodiversity indices from the Ocean Biogeographic Information System. Intergovernmental Oceanographic Commission of UNESCO OBIS author text http://www.iobis.org C. Rühlemann author 2011 Proceedings of the Ninth (2011) ISOPE Ocean Mining Symposium: Maui, Hawaii, USA, June 19-24. Cupertino, Calif. : International Society of Offshore and Polar Engineers (ISOPE) 978-1-880653-95-1 2011 168-173 10.1016/j.mio.2016.04.002 Review of Implementation of the Environmental Management Plan for the Clarion-Clipperton Zone Seascape Consultants author 2014 text Seascape Consultants Report 2014 2014 Preservation Reference Areas for Nodule Mining in the Clarion-Clipperton Zone: Rationale and Recommendations to the International Seabed Authority. International Seabed Authority. CR Smith author text http://www.soest.hawaii.edu/oceanography/faculty/csmith/MPA_webpage/documents/Smith%20et%20al.%20-%20Recommendations%20to%20the%20ISA%20for%20design%20of%20PRAs%20in%20the%20CCZ%20-%202-2008.pdf. Biodiversity, species ranges, and gene flow in the abyssal Pacific nodule province: predicting and managing the impacts of deep seabed mining: report CR Smith author text http://www.isa.org.jm/files/documents/EN/Pubs/TechStudy3.pdf 10.1098/rspb.2013.1684 10.3897/rio.2.e10528 https://riojournal.com/article/10528/ https://riojournal.com/article/10528/download/pdf/ https://riojournal.com/article/10528/download/xml/ text/html en_US Pensoft Publishers Deep-sea biology deep-sea mining biodiversity phylogeography population genetics European Union Framework 7 discussion meeting The London Workshop on the Biogeography and Connectivity of the Clarion-Clipperton Zone Workshop Report

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

Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria author Senderov, Viktor https://orcid.org/0000-0003-3340-5963 Pensoft Publishers, Sofia, Bulgaria author Georgiev, Teodor https://orcid.org/0000-0001-8558-6845 Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 2016-09-23 2016-09-23 2016 Research Ideas and Outcomes 2367-7163 2 e10617 2016 project EU BON: Building the European Biodiversity Observation Network EU BON 308454 project BIG4 - Biosystematics, Informatics and Genetics of the big 4 insect groups: training tomorrow's researchers and entrepreneurs BIG4 642241 funder European Commission 10.13039/501100000780 funder European Commission 10.13039/501100000780 Darwin-SW: Darwin Core-based terms for expressing biodiversity data as RDF Steven J. Baskauf author text http://www.semantic-web-journal.net/content/darwin-sw-darwin-core-based-terms-expressing-biodiversity-data-rdf-1 Terry Catapano author 2010 Journal Article Tag Suite Conference (JATS-Con) Proceedings 2010 2010 6 10.1186/1471-2105-12-s15-s2 10.1525/bio.2013.63.6.3 10.3897/zookeys.306.4898 10.3897/phytokeys.25.3100 10.1890/0012-9623(2005)86[158:mtvoed]2.0.co;2 R. T. Fielding author 2000 Architectural styles and the design of network-based software architectures. PhD Dissertation. 2000 180 10.1371/journal.pone.0114069 10.3897/natureconservation.4.4499 10.1007/978-1-4302-4978-8_2 10.1016/j.ecoinf.2005.08.004 10.5281/ZENODO.56660 10.3897/zookeys.204.3134 10.1371/journal.pone.0066213 10.3897/rio.2.e7757 10.3897/zookeys.198.3032 10.3897/bdj.4.e7599 10.1371/journal.pone.0029715 10.3897/rio.2.e10617 https://riojournal.com/article/10617/ https://riojournal.com/article/10617/download/pdf/ https://riojournal.com/article/10617/download/xml/ text/html en_US Pensoft Publishers 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 Online direct import of specimen records into manuscripts and automatic creation of data papers from biological databases Research Presentation

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

Lincoln University, Lincoln, New Zealand author Pannell, Jennifer 2016-09-27 2016-09-27 2016 Research Ideas and Outcomes 2367-7163 2 e10600 2016 Design and implementation of the Solar Analyst: an ArcView extension for modeling solar radiation at landscape scales P. Fu author 1999 text Proceedings of the Nineteenth Annual ESRI User Conference 1999 1 1 31 A spherical densiometer for estimating forest overstory density P. E. Lemmon author 1956 text Forest Science 1956 2 4 314 320 10.1111/2041-210x.12146 10.1111/2041-210x.12001 Montane outcrop vegetation of Banks Peninsula, South Island, New Zealand S. K. Wiser author 2009 text New Zealand Journal of Ecology 2009 33 2 164 176 10.3897/rio.2.e10600 https://riojournal.com/article/10600/ https://riojournal.com/article/10600/download/pdf/ https://riojournal.com/article/10600/download/xml/ text/html en_US Pensoft Publishers data management plan doctorate ecology Crassulaceae invasions Data Management Plan for PhD Thesis "Climatic Limitation of Alien Weeds in New Zealand: Enhancing Species Distribution Models with Field Data" Data Management Plan (NSF Generic)

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

Self, New Delhi, India author Abbey, Megha 2016-09-28 2016-09-28 2016 Research Ideas and Outcomes 2367-7163 2 e10593 2016 10.1016/j.ijdevneu.2015.02.004 10.1371/journal.pone.0058296 10.1016/j.biochi.2015.02.005 10.1093/nar/29.22.4751 10.1371/journal.pone.0018067 10.1523/ENEURO.0055-14.2014 10.3389/fnins.2013.00191 10.1093/nar/gks1466 10.1016/j.neuroscience.2012.03.049 10.1371/journal.pgen.1000898 10.1261/rna.035634.112 10.1093/hmg/ddu586 10.1136/jmedgenet-2014-102593 10.1093/hmg/5.1.95 10.1093/nar/gkr100 10.1016/j.str.2007.06.022 10.1073/pnas.1515737112 10.1186/2040-2392-5-30 10.1186/1471-2105-15-S7-S4 10.3897/rio.2.e10593 https://riojournal.com/article/10593/ https://riojournal.com/article/10593/download/pdf/ https://riojournal.com/article/10593/download/xml/ text/html en_US Pensoft Publishers FMRP Fmr1 splice variant alternative splicing CGG repeats protein isoform Functional characterization of the several splice variants of Fmr1 Research Idea

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

Arizona State University, Tempe, United States of America author Franz, Nico https://orcid.org/0000-0001-7089-7018 Arizona State University, Symbiota, Tempe, United States of America author Gilbert, Edward https://orcid.org/0000-0002-5006-8092 University of Illinois Urbana-Champaign, Champaign, United States of America author Ludäscher, Bertram The University of North Carolina at Chapel Hill, Chapel Hill, United States of America author Weakley, Alan 2016-09-30 2016-09-30 2016 Research Ideas and Outcomes 2367-7163 2 e10610 2016 funder National Science Foundation 10.13039/100000001 10.5962/bhl.title.15433 10.2307/3558389 10.2179/10-018.1 10.2307/1222443 10.1201/9781439832547.ch3 10.1016/j.ppees.2015.05.003 10.1579/0044-7447(2008)37[114:ecitbs]2.0.co;2 10.1002/cpe.1226 10.1186/1471-2105-14-16 10.5962/bhl.title.105339 10.5962/bhl.part.27406 10.1561/1900000006 10.1007/978-3-319-09870-8_9 Euler/X: a toolkit for logic-based taxonomy integration; arXiv:1402.1992 [cs.LO] M. Chen author 2014 text arXiv http://arxiv.org/abs/1402.1992 2014 2014 1 8 10.1007/978-3-319-16462-5_27 10.5962/bhl.title.38223 10.3732/ajb.92.2.330 ProvenanceMatrix: a visualization tool for multi-taxonomy alignments T. N. Dang author 2015 text CEUR Workshop Proceedings http://ceur-ws.org/Vol-1456/paper2.pdf 2015 1456 13 24 M. Döring author 2013 i4Life - Indexing for Life. D6.1. Integrated access to CoL in GBIF, Workpackage 6, pp. 1-4 http://www.i4life.eu/i4lifewebsite/wp-content/uploads/2012/12/D6-1-Integrated-Access-to-CoL-in-GBIF_V4.pdf 2013 4 GBIF Checklist Bank and the Backbone Taxonomy M. Döring author text http://www.slideshare.net/mdoering/checklist-bank-and-backbone Updating the GBIF Backbone M. Döring author text http://gbif.blogspot.co.uk/2016/04/updating-gbif-backbone.html 10.12705/622.1 Proposed rules for the incorporation of nomina of higher-ranked zoological taxa in the International Code of Zoological Nomenclature. 1. Some general questions, concepts and terms of biological nomenclature A. Dubois author 2005 text Zoosystema http://sciencepress.mnhn.fr/sites/default/files/articles/pdf/z2005n2a8.pdf 2005 27 2 365 426 Changes in Galactia (Fabaceae) of the southeastern United States W. H. Duncan author 1979 text SIDA, Contributions to Botany http://www.jstor.org/stable/23909679 1979 8 2 170 180 10.1038/srep30531 10.1093/nar/gkr1178 Some orchids of the Manual range M. L. Fernald author 1946 text Rhodora http://www.jstor.org/stable/23304761 1946 48 572 184 197 Some orchids of the Manual range M. L. Fernald author 1946 text Rodora http://www.jstor.org/stable/i23303797 1946 48 571 161 162 M. L. Fernald author 1950 Gray's Manual of Botany, Eigth (Centennial) Edition 1950 1632 10.3767/000651904x486214 10.1007/s10592-006-9119-8 Flora of North America Editorial Committee, eds. 1993+. Flora of North America North of Mexico. 16+ vols. New York and Oxford. Vol. 1, 1993; vol. 2, 1993; vol. 3, 1997; vol. 4, 2003; vol. 5, 2005; vol. 7, 2010; vol. 8, 2009; vol. 19, 2006; vol. 20, 2006; vol. 21, 2006; vol. 22, 2000; vol. 23, 2002; vol. 24, 2007; vol. 25, 2003; vol. 26, 2002; vol. 27, 2007; vol 28, 2014; vol. 9, 2014; vol. 6, 2015. FNA author text http://floranorthamerica.org 10.1111/geb.12501 10.1017/s147720000800282x 10.1101/022145 10.17161/bi.v7i1.3927 10.1201/9781420008562.ch5 10.1371/journal.pone.0118247 10.3233/SW-160220 10.1093/sysbio/syw023 10.1002/1097-024x(200009)30:113.3.co;2-e Global Biodiversity Information Facility. Darwin Core Archives – How-To Guide, Version 1, Released on 1 March 2011 (contributed by Remsen, D., K. Braak, M. Döring & T. Robertson), Copenhagen GBIF author text http://links.gbif.org/gbif_dwca_how_to_guide_v1 The concept problem in taxonomy: importance, components, approaches M. Geoffroy author 2003 text Schriftenreihe für Vegetationskunde http://www.nhbs.com/series/64263/schriftenreihe-fur-vegetationskunde 2003 39 4 15 Assembling and navigating the potential taxon graph M. Geoffroy author 2003 text Schriftenreihe für Vegetationskunde http://www.nhbs.com/series/64263/schriftenreihe-fur-vegetationskunde 2003 39 71 82 10.1057/ivs.2009.29 10.1016/j.biocon.2005.09.044 10.3897/bdj.2.e1114 10.1073/pnas.1423041112 10.1017/s0030605313001427 D. Isely author 1998 Native and Naturalized Leguminosae (Fabaceae) of the United States (Exclusive of Alaska and Hawaii) 978-0842523967 1998 1007 10.3897/zookeys.528.6001 10.1186/2041-1480-2-7 10.3897/bdj.2.e1558 Floristic Synthesis of North America, Version 9-15-2010. Biota of North America Program (BONAP), Chapel Hill J. Kartesz author text http://www.bonap.org/ 10.2307/2446402 10.1007/11530084_8 10.2307/2419701 10.3732/ajb.0800319 Referenzliste der Moose Deutschlands M. Koperski author 2000 text Schriftenreihe für Vegetationskunde https://www.amazon.de/Referenzliste-Moose-Deutschlands-Schriftenreihe-Vegetationskunde/dp/3784335047 2000 35 1 519 10.3100/1043-4534-13.2.209 10.1016/j.forpol.2009.03.004 10.1007/s13752-012-0049-z 10.3897/zookeys.420.7089 10.5962/bhl.title.669 10.5962/bhl.title.542 10.2307/2997216 Euler Project – Reasoning Over Taxonomies B. Ludäscher author 2016 text https://github.com/EulerProject 2016 10.1111/geb.12326 The varieties of Liatris elegans (Asteraceae) M. H. Mayfield author 2002 text SIDA, Contributions to Botany http://www.jstor.org/stable/41968077 2002 20 2 597 603 10.1186/2041-1480-4-34 10.2307/2419420 Examination of species boundaries in Hexastylis contracta Blomquist and H. rhombiformis Gaddy. (Abstract.) Z. E. Murrell author 1998 text American Journal of Botany (Supplement) 1998 85 146 147 10.3732/apps.1500065 C. K. Ogden author 1923 The Meaning of Meaning: a Study of the Influence of Language upon Thought and of the Science of Symbolism. 1st Edition 978-0156584463 1923 396 10.1016/j.shpsc.2012.10.003 10.1186/1471-2105-6-208 10.1007/s12225-008-9047-5 A new genus for the North American Cleistes R. P. Pansarin author 2009 text North American Native Orchid Journal https://www.scribd.com/document/42865188/March-2009-North-American-Native-Orchid-Journal 2009 15 1 50 58 10.1017/s0960428600002122 10.3897/bdj.4.e8080 10.7809/b-e.00080 C. S. Peirce author 1998 The Essential Peirce, Volume 2. Peirce Edition Project (Editor) 978-0-253-21190-3 http://www.iupress.indiana.edu/product_info.php?products_id=21333 1998 624 10.1046/j.1523-1739.1999.013002427.x 10.1111/j.1749-4877.2007.00044.x A. E. Radford author 1968 Manual of the Vascular Flora of the Carolinas 978-0-8078-1087-3 http://uncpress.unc.edu/books/T-766.html 1968 1245 D. A. Randell author B. Nebel author 1992 Proceedings of the Third International Conference on the Principles of Knowledge Representation and Reasoning 1992 10.3897/zookeys.550.9546 10.1600/036364414x680762 10.1371/journal.pone.0101704 10.1002/evan.21387 Taxonomy of Lantana sect. Lantana (Verbenaceae): I. Correct application of Lantana camara and associated names R. W. Sanders author 2006 text SIDA, Contributions to Botany http://www.jstor.org/stable/41968588 2006 22 1 381 421 Taxonomy of Lantana sect. Lantana (Verbenaceae): II. Taxonomic revision R. W. Sanders author 2012 text Journal of the Botanical Research Institute of Texas http://www.jstor.org/stable/41972430 2012 6 2 403 441 Barcoding the Asteraceae of Tennessee, tribe Cichorieae E. E. Schilling author 2015 text Phytoneuron http://www.phytoneuron.net/2015Phytoneuron/19PhytoN-TennCichorieae.pdf 2015 2019 19 1 8 10.1098/rstb.2003.1456 SouthEast Regional Network of Expertise and Collections, On-Line Portal; Community website available at http://sernec.appstate.edu SERNEC author text http://sernecportal.org Y. -K. Sima author 2012 A new system for the family Magnoliaceae; pp. 55-71 9787560973494 2012 304 10.5962/bhl.title.696 10.1111/j.1095-8339.2003.00265.x 10.5962/bhl.title.63883 Angiosperm Phylogeny Website. Version 12, July 2012 [and more or less continuously updated since] P. F. Stevens author text http://www.mobot.org/MOBOT/research/APweb 10.1016/j.ecoinf.2007.07.005 10.1109/icdew.2010.5452756 10.1145/1458484.1458492 10.1007/978-3-642-05151-7_26 D. M. Thau author 2010 Reasoning About Taxonomies. Doctoral Dissertation 978-1-124-22390-2 2010 204 10.1525/bio.2012.62.5.3 Keys to the flora of Florida – 10, Galactia (Leguminosae) D. B. Ward author 2004 text Phytologia http://www.biodiversitylibrary.org/bibliography/12678 2004 86 2 65 74 A practioner's guide to concept mapping. Narrative for "Least Divisible Taxonomic Unit" approach to "concept mapping" A. S. Weakley author text http://sernec.appstate.edu/sernec-working-groups/how-map-taxonomic-concepts-alan-weakley Applying concept mapping to 7,100 vascular plants. Presentation given at BIGCB Workshop, University of California at Berkeley, November 7-9, 2014 A. S. Weakley author text http://taxonbytes.org/wp-content/uploads/2014/10/Weakley-2014-BIGCB-Applying-Concept-Mapping-to-7100-Vascular-Plants.pdf A. S. Weakley author 2015 Flora of the Southern and Mid-Atlantic States http://www.herbarium.unc.edu/flora.htm 2015 1320 New combinations, rank changes, and nomenclatural and taxonomic comments in the vascular flora of the southeastern United States A. S. Weakley author 2011 text Journal of the Botanical Research Institute of Texas http://www.jstor.org/stable/41972288 2011 5 2 437 455 10.1371/journal.pone.0029715 10.1016/j.shpsa.2013.11.007 10.1111/jvs.12419 10.1007/s10539-014-9459-6 10.1007/s10739-015-9410-y R. P. Wunderlin author 2011 Guide to the Vascular Plants of Florida, Third Edition 978-0-8130-3543-7 http://upf.com/book.asp?id=wunde004# 2011 800 10.2307/25065525 10.3897/rio.2.e10610 https://riojournal.com/article/10610/ https://riojournal.com/article/10610/download/pdf/ https://riojournal.com/article/10610/download/xml/ 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. text/html en_US Pensoft Publishers Aggregation concept taxonomy conflict flora herbarium logic reasoning Region Connection Calculus specimens synthesis Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal NSF Grant Proposal

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

Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, United States of America author White, Ethan https://orcid.org/0000-0001-6728-7745 2016-10-04 2016-10-04 2016 Research Ideas and Outcomes 2367-7163 2 e10708 2016 funder Gordon and Betty Moore Foundation 10.13039/100000936 10.6084/M9.FIGSHARE.1189330 10.3897/rio.2.e10708 https://riojournal.com/article/10708/ https://riojournal.com/article/10708/download/pdf/ https://riojournal.com/article/10708/download/xml/ text/html en_US Pensoft Publishers ecology data driven discovery data-intensive research quantitative ecology Data Management Plan for Moore Investigator in Data Driven Discovery Grant Data Management Plan (Biosciences)

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

Former graduate student at University of Florida, Gainesville, United States of America author Dasari, Sriswaroop 2016-10-12 2016-10-12 2016 Research Ideas and Outcomes 2367-7163 2 e10714 2016 Julia Hartman author http://bama.ua.edu/~jleeper/627/choosestat.html 10.7449/2004/superalloys_2004_35_43 James D. Leeper author http://www.ats.ucla.edu/stat/mult_pkg/whatstat/choosestat.html National Institute for Materials Science author 2006 Fourth generation nickel base single crystal superalloy TMS-138/138A http://sakimori.nims.go.jp/catalog/TMS-138-A.pdf 2006 1-6 10.1016/j.msea.2008.08.052 10.1016/j.scriptamat.2006.01.003 10.1016/j.msea.2011.07.075 10.1007/s11661-008-9744-6 10.7449/2004/superalloys_2004_859_866 10.3897/rio.2.e10714 https://riojournal.com/article/10714/ https://riojournal.com/article/10714/download/pdf/ https://riojournal.com/article/10714/download/xml/ 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. text/html en_US Pensoft Publishers Ruthenium superalloy mechanical properties thermomechanical processing creep proposal 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 PhD Project Plan

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

www.plazi.org, Bern, Switzerland author Agosti, Donat https://orcid.org/0000-0001-9286-1200 2016-11-03 2016-11-03 2016 Research Ideas and Outcomes 2367-7163 2 e11014 2016 10.3897/rio.2.e11014 https://riojournal.com/article/11014/ https://riojournal.com/article/11014/download/pdf/ https://riojournal.com/article/11014/download/xml/ 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. text/html en_US Pensoft Publishers fellowship applications Shuttleworth biodiversity open access linked open data TreatmentBank taxonomic treatment Shuttleworth Fellowship Application 2016 Small Grant Proposal

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

Texas A&M University, Corpus Christi, Corpus Christi, United States of America author Xu, Hong The University of British Columbia, Vancouver, Canada author Ishida, Mayu https://orcid.org/0000-0003-4697-2414 Rutgers University, New Jersey, United States of America author Wang, Minglu 2016-11-09 2016-11-09 2016 Research Ideas and Outcomes 2367-7163 2 e11065 2016 10.3897/rio.2.e11065 https://riojournal.com/article/11065/ https://riojournal.com/article/11065/download/pdf/ https://riojournal.com/article/11065/download/xml/ text/html en_US Pensoft Publishers data management plan mine wastes Mojave Desert Souther California NSF A Data Management Plan for Effects of particle size on physical and chemical properties of mine wastes Data Management Plan (NSF Generic)

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

University of Bern, Bern, Switzerland author Ahmedien, Diaa https://orcid.org/0000-0001-8768-6858 2016-11-25 2016-11-25 2016 Research Ideas and Outcomes 2367-7163 2 e11150 2016 funder Ministry of Higher Education, Egypt 10.13039/501100003008 10.1162/leon_a_01376 10.1088/1742-6596/415/1/012023 10.1242/dmm.004291 10.7748/nr.11.1.77.s7 10.1093/oxartj/kcl017 10.2307/1576454 10.2184/lsj.28.2 10.1088/1742-6596/415/1/012007 10.2307/1575783 10.1162/002409402760181259 10.1117/1.oe.54.11.111309 10.3886/ICPSR35590.V1 10.1162/002409403321921488 10.1111/j.1467-8357.2010.01137_15.x 10.3897/rio.2.e11150 https://riojournal.com/article/11150/ https://riojournal.com/article/11150/download/pdf/ https://riojournal.com/article/11150/download/xml/ 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. text/html en_US Pensoft Publishers Laser Art New-Media arts sciences of visual arts holographic art neural holography new aesthetics Physics of Laser in Contemporary Visual Arts: the research protocol PhD Project Plan

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

University of Duisburg-Essen, Essen, Germany author Leese, Florian https://orcid.org/0000-0002-5465-913X Eawag, Dubendorf, Switzerland author Altermatt, Florian https://orcid.org/0000-0002-4831-6958 INFRA, Thonon, France author Bouchez, Agnès https://orcid.org/0000-0001-8802-6966 NTNU University Museum, Trondheim, Norway author Ekrem, Torbjørn https://orcid.org/0000-0003-3469-9211 University of Duisburg-Essen, Essen, Germany author Hering, Daniel Finnish Environment Institute, Jyvaskyla, Finland author Meissner, Kristian https://orcid.org/https://orcid.org/0000-0001-6316-8554 Royal Museum for Central Africa, Tervuren, Belgium author Mergen, Patricia https://orcid.org/0000-0003-2848-8231 University of Geneva, Geneve, Switzerland author Pawlowski, Jan https://orcid.org/0000-0003-2421-388X University of Otago, Dunedin, New Zealand author Piggott, Jeremy INRA, Thonen-les-Bains cedex, France author Rimet, Frederic University of Guelph, Guelph, Canada author Steinke, Dirk https://orcid.org/0000-0002-8992-575X Université Joseph Fourier, Grenoble, France author Taberlet, Pierre https://orcid.org/0000-0002-3554-5954 University of Duisburg-Essen, Essen, Germany author Weigand, Alexander https://orcid.org/0000-0001-7587-6531 University of Tartu, Tartu, Estonia author Abarenkov, Kessy https://orcid.org/0000-0001-5526-4845 CIBIO - Centro de Investigacao em Biodiversidade e Recursos Geneticos, Lisboa, Portugal author Beja, Pedro https://orcid.org/0000-0001-8164-0760 University of Antwerp, Antwerp, Belgium author Bervoets, Lieven University of Iceland, Reykjavik, Iceland author Bjornsdottir, Snaedis Provincial Centre of Environmental Research, Ghent, Belgium author Boets, Pieter National Research Council - Institute of Ecosystem Study, Verbania Pallanza, Italy author Boggero, Angela https://orcid.org/0000-0002-7534-3126 Norwegian University of Science and Technology, Trondheim, Norway author Bones, Atle AZTI, Pasaia, Spain author Borja, Ángel https://orcid.org/0000-0003-1601-2025 Nature Metrics Ltd, Egham, United Kingdom author Bruce, Kat University of Novi Sad, Novi Sad, Serbia author Bursić, Vojislava University College Dublin, Dublin, Ireland author Carlsson, Jens https://orcid.org/0000-0002-9262-5627 Slovak Academy of Sciences, Bratislava, Slovakia author Čiampor Jr, Fedor https://orcid.org/0000-0001-6269-3592 Slovak Academy of Sciences, Bratislava, Slovakia author Čiamporová-Zaťovičová, Zuzana https://orcid.org/0000-0003-0506-6212 Universite Grenoble Alpes LECA, Grenoble, France author Coissac, Eric University of Minho, Braga, Portugal author Costa, Filipe https://orcid.org/0000-0001-5398-3942 University to Bucharest, Bucharest, Romania author Costache, Marieta Bangor University, Bangor, United Kingdom author Creer, Simon University of Pecs, Pecs, Hungary author Csabai, Zoltán https://orcid.org/0000-0003-1700-2574 University of Notre Dame, Notre Dame, United States of America author Deiner, Kristy https://orcid.org/0000-0001-9755-3223 University of Cadiz, Puero Real, Spain author DelValls, Ángel Swedish University of Agricultural Sciences, Uppsala, Sweden author Drakare, Stina https://orcid.org/0000-0002-7389-2105 University of Minho, Braga, Portugal author Duarte, Sofia https://orcid.org/0000-0002-0181-0676 National Institute of Biology, Ljubljana, Slovenia author Elersek, Tina Water Research Institute - National Research Council, Monterotondo-Roma, Italy author Fazi, Stefano University of Ljubljana, Ljubljana, Slovenia author Fišer, Cene https://orcid.org/0000-0003-1982-8724 Université libre de Bruxelles (ULB), Bruxelles, Belgium author Flot, Jean-François https://orcid.org/0000-0003-4091-7916 Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany author Fonseca, Vera National Research Council - Institute of Ecosystem Study, Verbania Pallanza, Italy author Fontaneto, Diego https://orcid.org/0000-0002-5770-0353 University of Lodz, Lodz, Poland author Grabowski, Michal https://orcid.org/0000-0002-4551-3454 University of Natural Resources and Life Sciences, Vienna, Austria author Graf, Wolfram Marine and Freshwater Research Institute, Reykjavik, Iceland author Guobrandsson, Jóhannes AquaBiota Water Research, Stockholm, Sweden author Hellström, Micaela Tel Aviv University, Tel Aviv, Israel author Hershkovitz, Yaron Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom author Hollingsworth, Peter Ilia State University, Tiflis, Georgia author Japoshvili, Bella https://orcid.org/0000-0003-0966-0622 River Communities Group, The River Laboratory, Wareham, United Kingdom author Jones, John Swedish University of Agricultural Sciences, Uppsala, Sweden author Kahlert, Maria https://orcid.org/0000-0001-9643-4281 University of Sarajevo, Sarajevo, Bosnia and Herzegovina author Kalamujić Stroil, Belma https://orcid.org/0000-0002-4539-1266 Hellenic Centre of Marine Research, Heraklion, Greece author Kasapidis, Panagiotis https://orcid.org/0000-0002-1538-0320 Bowburn Consultancy, Bowburn, United Kingdom author Kelly, Martyn University College Dublin, Dublin, Ireland author Kelly-Quinne, Mary Ankara University, Ankara, author Keskin, Emre University of Tartu, Tartu, Estonia author Kõljalg, Urmas University of Zagreb, Zagreb, Croatia author Ljubešić, Zrinka University of Ljubljana, Ljubljana, Slovenia author Macek, Irena Eawag, Dubendorf, Switzerland author Mächler, Elvira Central Michigan University, Mt Pleasant, United States of America author Mahon, Andrew Crop Research Institute, Praha, Czech Republic author Marečková, Marketa University of Zagreb, Zagreb, Croatia author Mejdandzic, Maja Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia author Mirceva, Georgina Universita degli Studi di Milano, Milano, Italy author Montagna, Matteo https://orcid.org/0000-0003-4465-7146 ARGE Limnologie GesmbH, Innsbruck, Austria author Moritz, Christian Estonian Research Council, Tallinn, Estonia author Mulk, Vallo Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia author Naumoski, Andreja Institutul National de Cercetare-Dezvoltare Delta Dunarii, Tulcea, Romania author Navodaru, Ion Institute of Environmental Science, Vesuprem, Hungary author Padisák, Judit University of Iceland, Reykjavik, Iceland author Pálsson, Snæbjörn Estonian University of Life Sciences, Tartu, Estonia author Panksep, Kristel Pensoft Publishers Ltd, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 Charles University, Prague, Czech Republic author Petrusek, Adam https://orcid.org/0000-0001-5150-4370 Ruder Broskovic Institute, Rovinj, Croatia author Pfannkuchen, Martin https://orcid.org/0000-0002-6253-4716 University of Turku, Turku, Finland author Primmer, Craig National Institute of Oceanography, Haifa, Israel author Rinkevich, Baruch https://orcid.org/0000-0002-2401-0145 National Institute of Biology, Marine Biology Station, Piran, Slovenia author Rotter, Ana University of Natural Resources and Life Sciences, Vienna, Austria author Schmidt-Kloiber, Astrid https://orcid.org/0000-0001-8839-5913 Universidade de Lisboa, Lisboa, Portugal author Segurado, Pedro Naturalis Biodiversity Center, Leiden, Netherlands author Speksnijder, Arjen National Museum of Natural History, Sofia, Bulgaria author Stoev, Pavel Swedish Species Information Centre, Uppsala, Sweden author Strand, Malin https://orcid.org/0000-0002-8144-9592 Nature Research Centre, Vilnius, Lithuania author Šulčius, Sigitas University of Gothenburg, Gothenburg, Sweden author Sundberg, Per University of Innsbruck, Innsbruck, Austria author Traugott, Michael Hellenic Centre of Marine Research, Heraklion, Greece author Tsigenopoulos, Costas Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain author Turon, Xavier https://orcid.org/0000-0002-9229-5541 Spygen, Cexed, France author Valentini, Alice https://orcid.org/0000-0001-5829-5479 Naturalis Biodiversity Center, Leiden, Netherlands author van der Hoorn, Berry MTA Centre for Ecological Research, Danube Research Institute, Budapest, Hungary author Varbiro, Gabor https://orcid.org/0000-0001-5907-3472 Cyprus University of Technology, Limassol, Cyprus author Vasquez, Marlen Ines https://orcid.org/0000-0002-9849-5616 University of Cantabria, Santander, Spain author Viguri, Javier Nature Research Centre, Vilnius, Lithuania author Vitonyte, Irma Imperial College London, London, United Kingdom author Vogler, Alfried https://orcid.org/0000-0002-2462-3718 Norwegian Veterinary Institute, Sentrum Oslo, Norway author Vralstad, Trude Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany author Wägele, Wolfgang Polish Academy of Sciences, Sopot, Poland author Wenne, Roman Aarhus University, Roskilde, Denmark author Winding, Anne Imperial College London, London, United Kingdom author Woodward, Guy National Institute of Biology, Ljubljana, Slovenia author Zegura, Bojana Botanic Garden and Botanical Museum, Berlin, Germany author Zimmermann, Jonas 2016-11-29 2016-11-29 2016 Research Ideas and Outcomes 2367-7163 2 e11321 2016 funder European Cooperation in Science and Technology 10.13039/501100000921 10.1016/j.ecolind.2011.10.009 10.1016/j.marpolbul.2013.05.042 10.1186/1742-9994-10-45 10.1016/j.envres.2011.02.001 10.1371/journal.pone.0088786 10.1098/rspb.2002.2218 10.13140/RG.2.1.4002.1208 10.1016/j.scitotenv.2010.05.031 10.1038/nmeth.2633 10.1371/journal.pone.0095525 10.1016/j.tig.2014.07.001 10.1126/science.1261605 10.1021/es506158m 10.3897/rio.2.e11321 https://riojournal.com/article/11321/ https://riojournal.com/article/11321/download/pdf/ https://riojournal.com/article/11321/download/xml/ 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. text/html en_US Pensoft Publishers DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe Grant Proposal

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

University of Tartu, Tartu, Estonia author Runnel, Veljo https://orcid.org/0000-0001-5198-8678 Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany author Wetzel, Florian Agentschap Plantentuin Meise, Meise, Belgium author Groom, Quentin https://orcid.org/0000-0002-0596-5376 Norwegian Biodiversity Information Centre, Trondheim, Norway author Koch, Wouter https://orcid.org/0000-0001-9025-9486 GlueCAD, Haifa, Israel author Pe’er, Israel Norwegian Biodiversity Information Centre, Trondheim, Norway author Valland, Nils Hellenic Centre for Marine Research (HCMR), Heraklion, Greece author Panteri, Emmanouela University of Tartu, Tartu, Estonia author Kõljalg, Urmas 2016-12-22 2016-12-22 2016 Research Ideas and Outcomes 2367-7163 2 e11563 2016 10.1068/c0872 Cross-cultural recommendations for operational approaches in participatory monitoring networks to assess the 2010 target Sandra Bell author text http://eumon.ckff.si/deliverables_public/D24e.pdf Citizen Science and Environmental Monitoring: Towards a Methodology for Evaluating Opportunities, Costs and Benefits. R. J.P. Blaney author text http://www.ukeof.org.uk/resources/citizen-science-resources/Costbenefitcitizenscience.pdf 10.1126/science.1251554 CBD author 2014 Global Biodiversity Outlook 4 92-9225-539-8) 2014 155 PPSR_CORE Metadata Standard Citizen Science Association author text http://citizenscience.org/2015/10/09/ppsr_core-metadata-standard/ CitSci Colorado State University author text http://citsci.org/ 10.1007/s10661-010-1582-5 Webpage of the European Citizen Science Association ECSA author text http://ecsa.citizen-science.net/about-us Directory of Citizen Science Data Providers EU BON author text http://beta.eubon.ebd.csic.es/web/citizen-science/directory-of-cs-data-providers EU BON - Building the European Biodiversity Observation Network EU BON consortium author text http://eubon.eu/show/project_2731/ Participatory Monitoring Networks in Europe EuMon author text http://eumon.ckff.si/wp1/ European Citizen Science Association European Citizen Science Association author text http://ecsa.citizen-science.net/ Biodiversity observation schemes using citizen science European Environmental Agency author text http://www.eea.europa.eu/data-and-maps/daviz/biodiversity-observation-schemes-using-citizen-science Participatory monitoring networks EU-wide monitoring methods and systems of surveillance for species and habitats of Community interest author text http://eumon.ckff.si/wp1/ Licensing milestone for data access in GBIF.org GBIF author text http://www.gbif.org/newsroom/news/data-licensing-milestone 10.1111/1365-2664.12417 H. Geoghegan author 2016 Understanding motivations for citizen science. Final report on behalf of UKEOF, University of Reading, Stockholm Environment Institute (University of York) and University of the West of England. 2016 120 10.1007/s00267-012-9924-4 10.1111/1365-2664.12767 10.1016/j.ecolind.2013.03.028 10.1016/j.jnc.2012.08.002 10.3897/natureconservation.6.6498 10.1111/ddi.12463 10.1007/s13280-015-0710-4 10.1371/journal.pone.0147152 Scistarter Science for Citizens LLC author text http://scistarter.com/ 10.1111/cobi.12222 Species Observation System NBIC author text https://artsobservasjoner.no/ 10.3897/rio.2.e8458 10.1111/1365-2664.12423 10.1371/journal.pone.0102623 Understanding Citizen Science and Environmental Monitoring. Final Report on behalf of UK Environmental Observation Framework. H. E. Roy author text https://www.ceh.ac.uk/sites/default/files/citizensciencereview.pdf 10.2788/539115 10.3897/natureconservation.2.3644 10.1111/j.1523-1739.2008.01125.x 10.1016/j.biocon.2010.11.010 White paper on Citizen Science for Europe Socientize consortium author text http://www.socientize.eu/sites/default/files/white-paper_0.pdf 10.1016/j.biocon.2014.10.021 10.1016/j.biocon.2013.05.025 10.3897/rio.2.e8622 Gap analysis and priorities for filling identified gaps in data coverage and quality. Deliverable 1.1. p.162, EU BON, Berlin. Florian Wetzel author text http://eubon.eu/documents/1/ 10.1080/14888386.2015.1075902 Darwin Core: An evolving community-developed biodiversity data standard. J Wieczorek author 2012 text PLoS ONE 2012 7 1 10.3897/rio.2.e11563 https://riojournal.com/article/11563/ https://riojournal.com/article/11563/download/pdf/ https://riojournal.com/article/11563/download/xml/ 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. text/html en_US Pensoft Publishers citizen science biodiversity observations volunteering motivation data data sharing policy Summary report and strategy recommendations for EU citizen science gateway for biodiversity data Policy Brief

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

University of Cambridge, Cambridge, United Kingdom author Gatto, Laurent 2017-01-05 2017-01-05 2017 Research Ideas and Outcomes 2367-7163 3 e11624 2017 funder Biotechnology and Biological Sciences Research Council 10.13039/501100000268 10.1093/bioinformatics/btr645 10.1093/bioinformatics/btu013 10.1074/mcp.o113.036681 10.1038/nmeth.3252 10.1038/nbt.2839 10.3897/rio.3.e11624 https://riojournal.com/article/11624/ https://riojournal.com/article/11624/download/pdf/ https://riojournal.com/article/11624/download/xml/ text/html en_US Pensoft Publishers Spatial proteomics Bioconductor machine learning mass spectrometry proteomics software Data Management Plan for a Biotechnology and Biological Sciences Research Council (BBSRC) Tools and Resources Development Fund (TRDF) Grant Data Management Plan (Biosciences)

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

Universidad de Valparaíso, Valparaíso, Chile author Chabert, Steren Universidad de Valparaíso, Valparaíso, Chile author Mardones, Tomás Universidad de Valparaíso, Valparaíso, Chile Hospital Carlos van Buren, Valparaíso, Chile author Riveros, Rodrigo Hospital Carlos van Buren, Valparaíso, Chile Universidad de Valparaíso, Valparaíso, Chile author Godoy, Maximiliano Universidad de Valparaíso, Valparaíso, Chile author Veloz, Alejandro Universidad de Valparaíso, Valparaíso, Chile author Salas, Rodrigo https://orcid.org/0000-0002-0350-6811 Hospital Carlos van Buren, Valparaíso, Chile author Cox, Pablo 2017-01-10 2017-01-10 2017 Research Ideas and Outcomes 2367-7163 3 e11731 2017 funder Fondo Nacional de Desarrollo Científico y Tecnológico 10.13039/501100002850 10.1007/978-3-642-23091-2_6 10.1108/03684920710743466 10.1109/access.2014.2325029 10.1016/j.media.2007.01.002 10.1287/educ.2015.0135 10.1038/nrurol.2013.9 Assessment of Aortic Aneurysm Rupture Risk R. Izbicki author 2011 text Carnegie Mellon University. Research Showcase @ CMU http://repository.cmu.edu/cgi/viewcontent.cgi?article=1068&context=statistics 2011 J. D. Kelleher author 2015 Fundamentals of Machine Learning for Predictive Data Analytics. Algorithms, Worked Examples, and Case Studies 9780262029445 2015 624 10.1115/1.2401187 10.1109/TMI.2007.901008 Ministerio de Salud author 2007 Guía clínica. 2007 10.3171/jns.2005.102.2.0355 10.1007/s10439-013-0800-z B. Schölkopf author 2001 Learning with Kernels. Support Vector Machines, Regularization, Optimization and Beyond 9780262194754 2001 648 10.1007/978-3-642-35428-1_8 V. N. Vapnik author 1998 Statistical Learning Theory 978-0-471-03003-4 1998 768 10.1098/rsfs.2010.0033 10.1109/MSP.2010.936730 10.3897/rio.3.e11731 https://riojournal.com/article/11731/ https://riojournal.com/article/11731/download/pdf/ https://riojournal.com/article/11731/download/xml/ 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. text/html en_US Pensoft Publishers Image feature extraction Machine Learning Cerebral Aneurysms Biomedical Engineering Radiology Applying machine learning and image feature extraction techniques to the problem of cerebral aneurysm rupture Grant Proposal

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

author ElSabry, ElHassan https://orcid.org/0000-0001-6135-0280 2017-01-13 2017-01-13 2017 Research Ideas and Outcomes 2367-7163 3 e11743 2017 10.3897/rio.3.e11743 https://riojournal.com/article/11743/ https://riojournal.com/article/11743/download/pdf/ https://riojournal.com/article/11743/download/xml/ 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. text/html en_US Pensoft Publishers open access societal impact of research altmetrics Mapping Open Access Societal Impact Small Grant Proposal

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

California Digital Library, University of California Curation Center, Oakland, United States of America author Chodacki, John https://orcid.org/0000-0002-7378-2408 EMBO, Heidelberg, Germany author Lemberger, Thomas Crossref, Oxford, United Kingdom author Lin, Jennifer Hypothes.is, San Francisco, United States of America author Martone, Maryann https://orcid.org/0000-0002-8406-3871 National Institutes of Health, Bethesda, United States of America author Mietchen, Daniel https://orcid.org/0000-0001-9488-1870 ASAPbio, Cambridge, Massachusetts, United States of America author Polka, Jessica Cold Spring Harbor Laboratory, Cold Spring Harbor, United States of America author Sever, Richard Gordon & Betty Moore Foundation, Palo Alto, United States of America author Strasser, Carly 2017-01-16 2017-01-16 2017 Research Ideas and Outcomes 2367-7163 3 e11825 2017 10.6084/M9.FIGSHARE.C.2185342 10.1126/science.aaf9133 10.1091/mbc.e13-04-0193 10.5281/zenodo.231087 10.3897/zookeys.414.7717 10.1021/acs.energyfuels.5b01787 10.5281/zenodo.158940 10.5281/ZENODO.176452 10.7717/peerj-cs.86 10.3897/rio.3.e11825 https://riojournal.com/article/11825/ https://riojournal.com/article/11825/download/pdf/ https://riojournal.com/article/11825/download/xml/ text/html en_US Pensoft Publishers Preprints ASAPbio Technical aspects of preprint services in the life sciences: a workshop report Workshop Report

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

Museum fuer Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany author Wetzel, Florian United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, United Kingdom author Despot-Belmonte, Katherine United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, United Kingdom author Bingham, Heather Institute for European Environmental Policy (IEEP), London, United Kingdom author Underwood, Evelyn Museum fuer Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany author Hoffmann, Anke Museum fuer Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany author Haüser, Christoph UNEP/GRID-Warsaw Centre, Warsaw, Poland author Mikolajczyk, Piotr Museum fuer Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany author Vohland, Katrin 2017-01-24 2017-01-24 2017 Research Ideas and Outcomes 2367-7163 3 e11875 2017 10.1016/j.biocon.2016.09.004 10.1111/1365-2664.12767 10.3897/natureconservation.6.6498 Xianliang Pan author 2015 Development of a business plan for EU BON – Building the European Biodiversity Observation Network 2015 65 10.1016/j.agsy.2016.09.009 10.3897/rio.2.e11563 Alexander Thalmann author 2016 Science driven Business Models 2016 37 10.3897/rio.2.e8616 10.3897/rio.2.e8622 10.3897/rio.2.e8600 10.1080/14888386.2015.1075902 10.3897/rio.3.e11875 https://riojournal.com/article/11875/ https://riojournal.com/article/11875/download/pdf/ https://riojournal.com/article/11875/download/xml/ text/html en_US Pensoft Publishers sustainability biodiversity infrastructure EU BON business plan products and tools biodiversity observation networks 4th European Biodiversity Observation Network (EU BON) Stakeholder Roundtable: Pathways to sustainability for EU BONs network of collaborators and technical infrastructure Workshop Report

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

University of the Aegean, Department of Marine Sciences, Mytilene, Greece author Katsanevakis, Stelios https://orcid.org/0000-0002-5137-7540 Blue World Institute of Marine Research and Conservation, Veli Lošinj, Croatia author Mackelworth, Peter Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain Ecopath International Initiative (EII) Research Association, Barcelona, Spain author Coll, Marta Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, CoNISMa, Lecce, Italy author Fraschetti, Simonetta Institute of marine biology, University of Montenegro, Kotor, Montenegro author Mačić, Vesna Université Côte d'Azur, CNRS, Nice, France author Giakoumi, Sylvaine Department of Geography, University College London, London, United Kingdom author Jones, Peter Department of Geography, The Hebrew University of Jerusalem , Jerusalem, Israel author Levin, Noam Department of Palaeontology, University of Vienna, Vienna, Austria author Albano, Paolo G. https://orcid.org/0000-0001-9876-1024 CNR-IAMC Laboratorio di Biologia Marina, Castellammare del Golfo, Italy author Badalamenti, Fabio Technion, Israel Institute of Technology, Haifa, Israel author Brennan, Ruth Laboratoire d’Excellence, CORAIL, France National Center for Scientific Research, CRIOBE, Perpignan, France author Claudet, Joachim Faculty of Technical Sciences, University of Novi Sad, , Serbia author Culibrk, Dubravko CNR-IAMC, Castellammare del Golfo, Italy author D'Anna, Giovanni https://orcid.org/0000-0002-8644-8222 Department of Geosciences, University of Malta, , Malta author Deidun, Alan https://orcid.org/0000-0002-6919-5374 University of the Aegean, Department of Marine Sciences, Mytilene, Greece author Evagelopoulos, Athanasios https://orcid.org/0000-0002-6044-1719 Department of Ecology and Hydrology, University of Murcia, Murcia, Spain author García-Charton, José Van Hall Larenstein, University of Applied Sciences, Leeuwarden, Netherlands author Goldsborough, David Blue World Institute of Marine Research and Conservation, Veli Lošinj, Croatia Croatian Natural History Museum, Zagreb, Croatia author Holcer, Draško Enalia Physis, Nicosia, Cyprus author Jimenez, Carlos NESP Threatened Species Recovery hub, Centre for Biodiversity & Conservation Science, The University of Queensland, Brisbane, Australia The Biodiversity Research Group, The School of Biological Sciences, ARC Centre of Excellence for Environmental Decisions (CEED), The University of Queensland, Brisbane, Australia author Kark, Salit National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund, Denmark author Sørensen, Thomas Marine Sciences Program, Juraj Dobrila University of Pula, Pula, Croatia Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia author Lazar, Bojan Estonian Marine Institute, University of Tartu, Tallinn, Estonia author Martin, Georg Department of Ecology, School of Biology, Aristotle University of, Thessaloniki, Greece author Mazaris, Antonios Hopkins Marine Station, Stanford University, , United States of America author Micheli, Fiorenza Department of Zoology, University of Oxford, Oxford, United Kingdom author Milner-Gulland, E.J. CNR-IAMC, Castellammare del Golfo, Italy author Pipitone, Carlo https://orcid.org/0000-0002-7632-1228 Technion - Israel Institute of Technology, Haifa, Israel author Portman, Michelle Environmental Sciences, Informatics and Statistics Dept, Ca’ Foscari University of Venice, , Italy author Pranovi, Fabio National Institute of Oceanography, Israel Oceanographic and Limnological Research , Haifa, Israel author Rilov, Gil Durrell Institute of Conservation and Ecology, University of Kent, Canterbury, United Kingdom author Smith, Robert https://orcid.org/0000-0003-1599-9171 Thünen-Institute of Sea Fisheries, Hamburg, Germany author Stelzenmüller, Vanessa School of Pure and Applied Sciences, Open University of Cyprus, Nicosia, Cyprus author Vogiatzakis, Ioannis https://orcid.org/0000-0001-7071-6950 The Dead Sea-Arava Science Center, Neve Zohar, Israel author Winters, Gidon 2017-01-25 2017-01-25 2017 Research Ideas and Outcomes 2367-7163 3 e11884 2017 funder European Cooperation in Science and Technology 10.13039/501100000921 10.1146/annurev-ecolsys-102209-144702 10.1016/j.biocon.2009.11.006 10.1016/j.tree.2011.03.023 10.1016/j.ecss.2016.08.049 10.3389/fmars.2016.00020 10.1111/conl.12158 10.1016/j.ecolmodel.2009.06.029 10.1007/s10021-014-9803-3 10.1016/j.marpol.2008.11.001 10.1111/j.1466-8238.2011.00697.x 10.1016/j.marpol.2008.03.021 10.1111/ddi.12002 10.1038/nature13022 10.1016/s0169-5347(03)00189-7 10.1016/j.marpol.2015.07.004 10.1007/s11160-012-9272-8 10.1111/ddi.12491 10.1111/cobi.12468 L. Gunderson author 2002 Panarchy: Understanding transformations in human and natural systems 2002 507 10.1038/ncomms8615 10.1111/j.1365-2664.2008.01600.x 10.4324/9780203126295 10.1016/j.marpol.2012.12.025 10.1016/j.marpol.2016.04.026 10.1038/nclimate1533 10.1111/cobi.12562 10.1016/j.cosust.2014.08.005 10.1111/ddi.12429 10.3389/fmars.2014.00032 10.3391/ai.2014.9.4.01 10.1016/j.ocecoaman.2011.09.002 H. Kirkman author P. Mackelworth author 2016 Marine Transboundary Conservation and Protected Areas 978-1-138-85113-9 2016 35–50 10.1890/11-1718.1 10.3389/fmars.2016.00153 10.1016/j.ecolind.2011.09.023 10.1016/j.apgeog.2015.01.016 10.1525/bio.2013.63.7.8 10.1111/j.1755-263x.2012.00223.x P. Mackelworth author P. Mackelworth author 2016 Marine Transboundary Conservation and Protected Areas 978-1-138-85113-9 2016 1–14 10.3389/fmars.2015.00056 10.1016/j.ocecoaman.2015.09.003 10.1016/j.marpolbul.2007.09.038 10.1111/1365-2664.12404 10.1371/journal.pone.0079889 10.5751/es-06507-190446 10.1111/cobi.12183 10.1093/icesjms/fsr157 10.1007/978-3-319-26971-9_1 10.1017/s0376892916000023 G. Rilov author 2009 Biological Invasions in Marine Ecosystems: Ecological, Management, and Geographic Perspectives 2009 640 10.3354/meps08345 10.2307/3868659 10.1371/journal.pone.0116335 10.1126/science.1257484 10.1098/rspb.2014.0846 10.3897/rio.3.e11884 https://riojournal.com/article/11884/ https://riojournal.com/article/11884/download/pdf/ https://riojournal.com/article/11884/download/xml/ 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. text/html en_US Pensoft Publishers Integrated conservation planning marine biodiversity cumulative impacts biological invasions marine governance maritime spatial planning Advancing marine conservation in European and contiguous seas with the MarCons Action Small Grant Proposal

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

The Pennsylvania State University, University Park, United States of America author bipspau@gmail.com, Bipana The Pennsylvania State University, University Park, United States of America author Mikó, István https://orcid.org/0000-0001-9719-0215 2017-01-31 2017-01-31 2017 Research Ideas and Outcomes 2367-7163 3 e11997 2017 Differential activity and degradation of plant volatile elicitors in regurgitant of tobacco hornworm (Manduca sexta) larvae H. T. Alborn author 2003 text Journal of Chemical Ecology http://doi.org/10.1023/A:1024209302628 2003 29 6 1357 1372 10.1126/science.276.5314.945 Plant defense against insect herbivores J. Fürstenberg-Hägg author 2013 text International Journal of Molecular Sciences http://doi.org/10.3390/ijms140510242 2013 14 5 10242 10297 10.1242/jeb.02335 What is fluorescing? István Mikó author 2013 text Haemuli http://www.hymenopterists.org/newsletters/hamuli/HamuliVol4Issue2.pdf 2013 4 2 19 23 10.1007/BF00192725 Do caterpillars secrete "oral secretions"? Michelle Peiffer author 2009 text Journal of Chemical Ecology http://doi.org/10.1007/s10886-009-9604-x 2009 35 3 326 335 10.1038/nmeth.2089 10.1007/s10886-012-0143-5 N-(18-Hydroxylinolenoyl)-l-Glutamine: A Newly Discovered Analog of Volicitin in Manduca sexta and its Elicitor Activity in Plants N. Yoshinaga author 2014 text Journal of Chemical Ecology http://doi.org/10.1007/s10886-014-0436-y 2014 40 5 484 490 10.3897/rio.3.e11997 https://riojournal.com/article/11997/ https://riojournal.com/article/11997/download/pdf/ https://riojournal.com/article/11997/download/xml/ text/html en_US Pensoft Publishers regurgitation herbivory elicitor molecules Know your insect: The structural backgrounds of regurgitation, a case study on Manduca sexta and Heliothis virescens (Lepidoptera: Sphingidae, Noctuidae) Case Study

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

Heinrich Heine University, Düsseldorf, Germany author Schmelling, Nicolas https://orcid.org/0000-0002-6981-397X 2017-02-01 2017-02-01 2017 Research Ideas and Outcomes 2367-7163 3 e12032 2017 10.3897/rio.3.e12032 https://riojournal.com/article/12032/ https://riojournal.com/article/12032/download/pdf/ https://riojournal.com/article/12032/download/xml/ 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. text/html en_US Pensoft Publishers OER Learning Open Data Data Management Open Science Reproducibility Data Analysis Python R Data Intensive Science Small Grant Proposal

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

Pennsylvania State University, University Park, United States of America author Rivera Vega, Loren https://orcid.org/0000-0002-6853-0273 Pennsylvania State University, University Park, United States of America author Mikó, István https://orcid.org/0000-0001-9719-0215 2017-02-01 2017-02-01 2017 Research Ideas and Outcomes 2367-7163 3 e11827 2017 10.1016/j.pbi.2015.05.029 10.1146/annurev-ento-112408-085512 10.1016/j.jinsphys.2005.10.007 10.1016/s1467-8039(01)00017-2 10.1371/journal.pntd.0002929 10.1016/j.pbi.2008.07.001 10.1093/aesa/31.2.167 10.1016/0022-1910(66)90109-0 10.1093/aesa/53.2.229 What is fluorescing? István Mikó author 2013 text Hamuli http://www.hymenopterists.org/newsletters/hamuli/HamuliVol4Issue2.pdf 2013 4 2 19 23 10.1242/jeb.128314 10.4172/2161-0983.1000122 10.1155/2011/767963 10.1098/rspb.2012.2391 10.1038/nmeth.2089 10.1002/bio.2850 10.1146/annurev-ento-112408-085401 10.1093/aesa/7.1.1 10.1007/s003440000026 10.1371/journal.pone.0075731 10.3897/rio.3.e11827 https://riojournal.com/article/11827/ https://riojournal.com/article/11827/download/pdf/ https://riojournal.com/article/11827/download/xml/ 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. text/html en_US Pensoft Publishers cabbage looper caterpillars urinary bladder uric acid Know your insect: Malpighian tubules in Trichoplusia ni (Lepidoptera: Noctuidae) Case Study

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

Queensland University of Technology at the Translational Research Institute (TRI) , Brisbane, Australia Mater Medical Research - University of Queensland, Brisbane, Australia author Doran, Mike School of Public Health and Social Work & Institute of Health and Biomedical Innovation (IHBI), Queensland University of Technology (QUT), Brisbane, Australia author Barnett, Adrian Australian National Centre for the Public Awareness of Science, Australian National University (ANU), Canberra, Australia author Leach, Joan School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Australia author Lott, Bill School of Public Health and Social Work & Institute of Health and Biomedical Innovation (IHBI), Queensland University of Technology (QUT), Brisbane, Australia author Page, Katie Australian National Centre for the Public Awareness of Science, Australian National University (ANU), Canberra, Australia author Grant, Will 2017-02-01 2017-02-01 2017 Research Ideas and Outcomes 2367-7163 3 e11931 2017 Outcomes of Funding NHMRC Australian Government author text https://www.nhmrc.gov.au/grants-funding/outcomes-funding-rounds? Discovery Projects Australian Research Council author text http://www.arc.gov.au/selection-report-discovery-projects-2016 TIBS Science & Society: Multimedia for grant applications MR Doran author 2014 text Trends in Biochemical Science 2014 39 4 151 153 10.1016/j.tibs.2014.01.004 10.1038/505291d 10.1016/j.edurev.2015.06.001 10.1136/bmj.d4797 10.1086/669862 10.1348/000711006x126600 10.1136/bmjopen-2013-002800 10.1097/00001888-200302000-00018 10.1371/journal.pone.0002761 10.4159/9780674054158 10.1016/j.jclinepi.2005.12.007 K. E. Mow author 2009 Inside the Black Box: Research Grant Funding and Peer Review in Australian Research Councils 2009 254 10.1002/neu.480140202 10.1186/1472-6939-13-10 10.1371/journal.pone.0130450 10.1258/jrsm.99.4.178 10.1186/s12961-015-0074-z 10.3897/rio.3.e11931 https://riojournal.com/article/11931/ https://riojournal.com/article/11931/download/pdf/ https://riojournal.com/article/11931/download/xml/ 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”. text/html en_US Pensoft Publishers research funding grant writing video grant review peer review meta-research research policy Can video improve grant review quality and lead to more reliable ranking? Small Grant Proposal

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

Fondazione Edmund Mach di San Michele all'Adige, San Michele all'Adige (TN), Italy author Rocchini, Duccio University of Picardie Jules Verne, Amiens, France author Garzon-Lopez, Carol X https://orcid.org/0000-0002-4099-2740 2017-02-06 2017-02-06 2017 Research Ideas and Outcomes 2367-7163 3 e12029 2017 10.1111/ddi.12100 10.1073/pnas.0400280101 10.3897/rio.3.e12029 https://riojournal.com/article/12029/ https://riojournal.com/article/12029/download/pdf/ https://riojournal.com/article/12029/download/xml/ 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. text/html en_US Pensoft Publishers Uncertainty species distribution models cartogram GBIF sampling effort Cartograms tool to represent spatial uncertainty in species distribution Policy Brief

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

Institute for Biomedical Engineering, ETH and University of Zürich, Zurich, Switzerland author Ioanas, Horea-Ioan Preclinical Laboratory for Translational Research into Affective Disorders, DPPP, Psychiatric Hospital, University of Zurich, Zurich, Switzerland author Saab, Bechara Institute for Biomedical Engineering, ETH and University of Zürich, Zurich, Switzerland author Rudin, Markus 2017-02-07 2017-02-07 2017 Research Ideas and Outcomes 2367-7163 3 e12095 2017 10.3389/fninf.2014.00014 Portage: Bringing Hackers' Wisdom to Science G Amadio author 2016 text arXiv https://arxiv.org/abs/1610.02742 2016 Package Manager Specification Stephen P. Bennett author text https://web.archive.org/web/20151006123755/http://dev.gentoo.org/~ulm/pms/head/pms.html 10.5281/zenodo.259741 10.3389/fninf.2014.00008 10.3389/fninf.2015.00012 10.5281/zenodo.50186 10.3389/fninf.2012.00022 DataLad – decentralized data distribution for consumption and sharing of scientific datasets Y. O. Halchenko author Organization of Human Brain Mapping author 2016 text Poster 2016 10.3389/fninf.2011.00008 10.1016/j.neuroimage.2011.09.015 Gentoo Science Overlay Project Justin Lecher author text https://web.archive.org/web/20150919074807/https://wiki.gentoo.org/wiki/Project:Science/Overlay Scikit-learn: Machine Learning in Python F Pedregosa author 2011 text Journal of Machine Learning Research http://jmlr.csail.mit.edu/papers/v12/pedregosa11a.html 2011 12 2825 2830 10.3389/neuro.11.010.2008 10.6084/M9.FIGSHARE.1164194 10.1088/1749-4699/8/1/014010 10.3897/rio.3.e12095 https://riojournal.com/article/12095/ https://riojournal.com/article/12095/download/pdf/ https://riojournal.com/article/12095/download/xml/ text/html en_US Pensoft Publishers gentoo portage linux software management repository dependency management dependency resolution neuroscience flexible scalable rolling-release live software versioning source-based gnu gnu/linux Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software Software Management Plan

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

University of Southern California, Los Angeles, United States of America author Ito, Kaori L https://orcid.org/0000-0001-6380-6755 University of Southern California, Los Angeles, United States of America author Anglin, Julia University of Southern California, Los Angeles, United States of America author Liew, Sook-Lei 2017-02-14 2017-02-14 2017 Research Ideas and Outcomes 2367-7163 3 e12259 2017 10.1016/s1361-8415(01)00036-6 10.1006/nimg.2002.1132 10.1016/j.neuroimage.2011.09.015 10.1161/strokeaha.110.599340 10.3897/rio.3.e12259 https://riojournal.com/article/12259/ https://riojournal.com/article/12259/download/pdf/ https://riojournal.com/article/12259/download/xml/ 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. text/html en_US Pensoft Publishers stroke neuroimaging software neuroanatomy robust MRI analysis Semi-automated Robust Quantification of Lesions (SRQL) Toolbox Project Report

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

Pennsylvania State University, University Park, United States of America author Pearsons, Kirsten Pennsylvania State University, University Park, United States of America author Mikó, István https://orcid.org/0000-0001-9719-0215 Associate Professor of Entomology, Extension Specialist, University Park, United States of America author Tooker, John https://orcid.org/0000-0002-9303-6699 2017-02-14 2017-02-14 2017 Research Ideas and Outcomes 2367-7163 3 e12249 2017 10.1046/j.1365-294X.2003.02014.x 10.1086/503443 10.1007/s10530-006-9024-6 10.1093/ee/6.1.9 10.1603/022.038.0418 10.2307/2421156 S. S. Duffey author 1981 Cyanide in Biology 1981 10.1007/bf00988137 10.1126/science.139.3560.1218 10.1111/j.1365-2818.2011.03534.x 10.1007/s10021-016-9977-y The Marek Lab. Cyanide gland dissections Paul Marek author text http://jointedlegs.org/?p=192 10.1073/pnas.1500014112 10.1163/9789004188273 Postembryonic development of the common myriapoda of Japan X. Life history of Oxidus gracilis (KOCH)(Diplopoda, Strongylosomidae) Yoshiteru Murakami author 1962 text Zoological Magazine 1962 71 A correction regarding the article of the life history of Oxidus gracilis Koch Yoshiteru Murakami author 1966 text Zoological Magazine 1966 75 10.1016/0022-2011(85)90013-8 10.1086/285880 10.1007/s10021-014-9814-0 10.1038/nmeth.2089 10.1016/j.bse.2015.04.033 10.1146/annurev.ento.52.111805.090210 10.1016/j.soilbio.2012.08.022 10.1046/j.1365-294x.2000.01006.x 10.1303/aez.2003.401 10.1890/13-1721.1 10.3897/rio.3.e12249 https://riojournal.com/article/12249/ https://riojournal.com/article/12249/download/pdf/ https://riojournal.com/article/12249/download/xml/ 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. text/html en_US Pensoft Publishers Oxidus gracilis cyanide gland Diplopoda Polydesmida CLSM The cyanide gland of the greenhouse millipede, Oxidus gracilis (Polydesmida: Paradoxosomatidae) Case Study

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

UNEP World Conservation Monitoring Centre, Cambridge, United Kingdom author Despot-Belmonte, Katherine UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany author Neßhöver, Carsten University of Eastern Finland, Joensuu, Finland author Saarenmaa, Hannu The Biodiversity Consultancy, Cambridge, United Kingdom author Regan, Eugenie German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany author Meyer, Carsten National Centre for Flora Conservation/Rio de Janeiro Botanical Garden, Rio de Janeiro, Brazil author Martins, Eline Botanic Garden Meise, Meise, Belgium author Groom, Quentin https://orcid.org/0000-0002-0596-5376 Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany author Hoffmann, Anke Commonland, Amsterdam, Netherlands author Caine, Alessandra UNEP World Conservation Monitoring Centre, Cambridge, United Kingdom author Bowles-Newark, Nadine National Institute of Ecology, Choongnam, Seocheon-gun, Maseo-Myeon, Geumgang-ro, Korea, South author Bae, Haejin Centro de Referência em Informação Ambiental, Barão Geraldo, Campinas/SP, Brazil author Canhos, Dora Ann Lange https://orcid.org/0000-0001-8615-6652 Federal Agency for Nature Conservation (BfN), Bonn, Germany author Stenzel, Stefanie Senckenberg Biodiversität und Klima- Forschungszentrum (BiK-F), Frankfurt am Main, Germany author Bowler, Diana Martin Luther University of Halle-Wittenberg, Halle, Germany author Schneider, Aline UNEP World Conservation Monitoring Centre, Cambridge, United Kingdom author Weatherdon, Lauren https://orcid.org/0000-0002-3989-027X UNEP World Conservation Monitoring Centre, Cambridge, United Kingdom author Martin, Corinne https://orcid.org/0000-0002-5428-2766 2017-02-14 2017-02-14 2017 Research Ideas and Outcomes 2367-7163 3 e12165 2017 10.1016/j.biocon.2016.09.006 10.1111/1365-2664.12417 Vision and goals GEO BON author text http://geobon.org/about/vision-goals/ 10.3897/natureconservation.6.6498 10.1007/s10531-016-1143-5 G. Martinelli author 2013 Livro Vermelho da Flora do Brasil http://dspace.jbrj.gov.br/jspui/handle/doc/26 2013 10.1007/s10531-016-1127-5 10.1126/science.1229931 10.1080/14888386.2015.1075902 10.3897/rio.3.e12165 https://riojournal.com/article/12165/ https://riojournal.com/article/12165/download/pdf/ https://riojournal.com/article/12165/download/xml/ 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. text/html en_US Pensoft Publishers biodiversity data knowledge products science-policy interface GEO BON EU BON EBVs EKLIPSE mechanism Biodiversity data provision and decision-making - addressing the challenges Workshop Report

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

UCSF Department of Neurology, San Francisco, CA, United States of America author Keshavan, Anisha https://orcid.org/0000-0003-3554-043X Boston College, Chestnut Hill, MA, United States of America author Madan, Christopher https://orcid.org/0000-0003-3228-6501 UCSF Department of Neurology, San Francisco, CA, United States of America author Datta, Esha The University of Alabama, Tuscaloosa, AL, United States of America author McDonough, Ian 2017-02-15 2017-02-15 2017 Research Ideas and Outcomes 2367-7163 3 e12276 2017 10.1038/mp.2013.78 10.1101/090431 10.3389/fninf.2014.00089 10.1038/sdata.2014.49 10.3897/rio.3.e12276 https://riojournal.com/article/12276/ https://riojournal.com/article/12276/download/pdf/ https://riojournal.com/article/12276/download/xml/ 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. text/html en_US Pensoft Publishers Brain Interactive Visualization Curation Segmentation Mindcontrol: Organize, quality control, annotate, edit, and collaborate on neuroimaging processing results Project Report

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

Pensoft Publishers & Bulgarian Academy of Sciences, Sofia, Bulgaria author Penev, Lyubomir https://orcid.org/0000-0002-2186-5033 2017-02-15 2017-02-15 2017 Research Ideas and Outcomes 2367-7163 3 e12265 2017 10.1038/439392a 10.5281/ZENODO.165979 TaxPub: An extension of the NLM/NCBI Journal Publishing DTD for taxonomic descriptions T. Catapano author 2010 text Proceedings. http://www.ncbi.nlm.nih.gov/books/NBK47081/ 2010 H2020 Programme Guidelines on FAIR Data Management in Horizon 2020 European Commission author text http://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020-hi-oa-data-mgt_en.pdf Draft European Open Science Agenda European Commission author text http://ec.europa.eu/research/openscience/pdf/draft_european_open_science_agenda.pdf#view=fit&pagemode=none 10.3897/rio.1.e7547 Michael Nielsen author 2011 Reinventing Discovery: The New Era of Networked Science 978-0-691-14890-8 2011 Implementation of TaxPub, an NLM DTD extension for domain-specific markup in taxonomy, from the experience of a biodiversity publisher L. Penev author 2012 text Proceedings http://www.ncbi.nlm.nih.gov/books/NBK100351/ 2012 10.3897/zookeys.50.538 10.1145/2809563.2809571 Open Biodiversity Knowledge Management System (OBKMS). pro-iBiosphere author text http://adm.pro-ibiosphere.eu/getatt.php?filename=oo_4749.pdf. 10.3897/rio.2.e7757 10.3897/bdj.1.e995 Peter Suber author 2012 Open access (The MIT Press Essential Knowledge Series ed.) ISBN 9780262517638 2012 10.3897/rio.3.e12265 https://riojournal.com/article/12265/ https://riojournal.com/article/12265/download/pdf/ https://riojournal.com/article/12265/download/xml/ text/html en_US Pensoft Publishers open access open data open science scholarly publishing semantic publishing XML tagging data re-use science communication From Open Access to Open Science from the viewpoint of a scholarly publisher Research Presentation

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

University of California, San Francisco, San Francisco, CA, United States of America author Keshavan, Anisha https://orcid.org/0000-0003-3554-043X author Klein, Arno https://orcid.org/0000-0002-0707-2889 author Cipollini, Ben 2017-02-23 2017-02-23 2017 Research Ideas and Outcomes 2367-7163 3 e12358 2017 B Cipollini author 2015 45th Annual Meeting of the Society for Neuroscience} 2015 akeshavan/roygbiv: Initial Release Ben Cipollini author 2017 text Zenodo http://doi.org/10.5281/zenodo.268541 2017 10.1016/j.neuroimage.2004.09.016 10.3389/fnins.2012.00171 10.1371/journal.pcbi.1005350 10.3897/rio.3.e12358 https://riojournal.com/article/12358/ https://riojournal.com/article/12358/download/pdf/ https://riojournal.com/article/12358/download/xml/ 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. text/html en_US Pensoft Publishers three.js VTK morphometry d3.js Interactive online brain shape visualization Project Report cGFnZT0xJnNldD1yaW8mZnJvbT0mdW50aWw9Jm1ldGFkYXRhX3ByZWZpeD1tb2Rz